diff --git a/.clang-format b/.clang-format index 411b009..2fd9142 100644 --- a/.clang-format +++ b/.clang-format @@ -1,4 +1,4 @@ -## This config file is only relevant for clang-format version 8.0.0 +## This config file is only relevant for clang-format version 19.1.7 ## ## Examples of each format style can be found on the in the clang-format documentation ## See: https://clang.llvm.org/docs/ClangFormatStyleOptions.html for details of each option @@ -10,142 +10,310 @@ ## maintaining a consistent code style. ## ## EXAMPLE apply code style enforcement before commit: -# Utilities/Maintenance/clang-format.bash --clang ${PATH_TO_CLANG_FORMAT_8.0.0} --modified +# Utilities/Maintenance/clang-format.bash --clang ${PATH_TO_CLANG_FORMAT_19.1.7} --modified ## EXAMPLE apply code style enforcement after commit: -# Utilities/Maintenance/clang-format.bash --clang ${PATH_TO_CLANG_FORMAT_8.0.0} --last +# Utilities/Maintenance/clang-format.bash --clang ${PATH_TO_CLANG_FORMAT_19.1.7} --last --- -# This configuration requires clang-format version 8.0.0 exactly. -BasedOnStyle: Mozilla +# This configuration requires clang-format version 19.1.7 exactly. Language: Cpp AccessModifierOffset: -2 AlignAfterOpenBracket: Align -AlignConsecutiveAssignments: false -AlignConsecutiveDeclarations: true -AlignEscapedNewlines: Right -AlignOperands: true -AlignTrailingComments: true -# clang 9.0 AllowAllArgumentsOnNextLine: true -# clang 9.0 AllowAllConstructorInitializersOnNextLine: true +AlignArrayOfStructures: None +AlignConsecutiveAssignments: + Enabled: false + AcrossEmptyLines: false + AcrossComments: false + AlignCompound: false + AlignFunctionPointers: false + PadOperators: true +AlignConsecutiveBitFields: + Enabled: false + AcrossEmptyLines: false + AcrossComments: false + AlignCompound: false + AlignFunctionPointers: false + PadOperators: false +AlignConsecutiveDeclarations: + Enabled: true + AcrossEmptyLines: false + AcrossComments: false + AlignCompound: false + AlignFunctionPointers: false + PadOperators: true +AlignConsecutiveMacros: + Enabled: false + AcrossEmptyLines: false + AcrossComments: false + AlignCompound: false + AlignFunctionPointers: false + PadOperators: false +AlignConsecutiveShortCaseStatements: + Enabled: false + AcrossEmptyLines: false + AcrossComments: false + AlignCaseArrows: false + AlignCaseColons: false +AlignConsecutiveTableGenBreakingDAGArgColons: + Enabled: false + AcrossEmptyLines: false + AcrossComments: false + AlignCompound: false + AlignFunctionPointers: false + PadOperators: false +AlignConsecutiveTableGenCondOperatorColons: + Enabled: false + AcrossEmptyLines: false + AcrossComments: false + AlignCompound: false + AlignFunctionPointers: false + PadOperators: false +AlignConsecutiveTableGenDefinitionColons: + Enabled: false + AcrossEmptyLines: false + AcrossComments: false + AlignCompound: false + AlignFunctionPointers: false + PadOperators: false +AlignEscapedNewlines: Left +AlignOperands: Align +AlignTrailingComments: + Kind: Always + OverEmptyLines: 0 +AllowAllArgumentsOnNextLine: true AllowAllParametersOfDeclarationOnNextLine: false -AllowShortBlocksOnASingleLine: false +AllowBreakBeforeNoexceptSpecifier: Never +AllowShortBlocksOnASingleLine: Never +AllowShortCaseExpressionOnASingleLine: true AllowShortCaseLabelsOnASingleLine: false -AllowShortFunctionsOnASingleLine: Inline -# clang 9.0 AllowShortLambdasOnASingleLine: All -# clang 9.0 features AllowShortIfStatementsOnASingleLine: Never -AllowShortIfStatementsOnASingleLine: false +AllowShortCompoundRequirementOnASingleLine: true +AllowShortEnumsOnASingleLine: true +#AllowShortFunctionsOnASingleLine: Inline Only merge functions defined inside a class. Implies empty. +#AllowShortFunctionsOnASingleLine: None (in configuration: None) Never merge functions into a single line. +AllowShortFunctionsOnASingleLine: All +AllowShortIfStatementsOnASingleLine: Never +AllowShortLambdasOnASingleLine: All AllowShortLoopsOnASingleLine: false AlwaysBreakAfterDefinitionReturnType: None -AlwaysBreakAfterReturnType: All AlwaysBreakBeforeMultilineStrings: false -AlwaysBreakTemplateDeclarations: Yes +AttributeMacros: + - __capability BinPackArguments: false BinPackParameters: false -BreakBeforeBraces: Custom +BitFieldColonSpacing: Both BraceWrapping: - # clang 9.0 feature AfterCaseLabel: false + AfterCaseLabel: true AfterClass: true - AfterControlStatement: true + AfterControlStatement: Always AfterEnum: true + AfterExternBlock: true AfterFunction: true AfterNamespace: true AfterObjCDeclaration: true AfterStruct: true AfterUnion: true - AfterExternBlock: true BeforeCatch: true BeforeElse: true -## This is the big change from historical ITK formatting! -# Historically ITK used a style similar to https://en.wikipedia.org/wiki/Indentation_style#Whitesmiths_style -# with indented braces, and not indented code. This style is very difficult to automatically -# maintain with code beautification tools. Not indenting braces is more common among -# formatting tools. + BeforeLambdaBody: false + BeforeWhile: false IndentBraces: false SplitEmptyFunction: false SplitEmptyRecord: false SplitEmptyNamespace: false +BreakAdjacentStringLiterals: true +BreakAfterAttributes: Leave +BreakAfterJavaFieldAnnotations: false +BreakAfterReturnType: All +BreakArrays: true BreakBeforeBinaryOperators: None -#clang 6.0 BreakBeforeInheritanceComma: true -BreakInheritanceList: BeforeComma +BreakBeforeConceptDeclarations: Always +BreakBeforeBraces: Custom +BreakBeforeInlineASMColon: OnlyMultiline BreakBeforeTernaryOperators: true -#clang 6.0 BreakConstructorInitializersBeforeComma: true BreakConstructorInitializers: BeforeComma -BreakAfterJavaFieldAnnotations: false +BreakFunctionDefinitionParameters: false +BreakInheritanceList: BeforeComma BreakStringLiterals: true +BreakTemplateDeclarations: Yes ## The following line allows larger lines in non-documentation code ColumnLimit: 120 CommentPragmas: '^ IWYU pragma:' CompactNamespaces: false -ConstructorInitializerAllOnOneLineOrOnePerLine: false ConstructorInitializerIndentWidth: 2 ContinuationIndentWidth: 2 Cpp11BracedListStyle: false DerivePointerAlignment: false DisableFormat: false +EmptyLineAfterAccessModifier: Never +EmptyLineBeforeAccessModifier: LogicalBlock ExperimentalAutoDetectBinPacking: false FixNamespaceComments: true ForEachMacros: - foreach - Q_FOREACH - BOOST_FOREACH +IfMacros: + - KJ_IF_MAYBE IncludeBlocks: Preserve IncludeCategories: - Regex: '^"(llvm|llvm-c|clang|clang-c)/' Priority: 2 + SortPriority: 0 + CaseSensitive: false - Regex: '^(<|"(gtest|gmock|isl|json)/)' Priority: 3 + SortPriority: 0 + CaseSensitive: false - Regex: '.*' Priority: 1 + SortPriority: 0 + CaseSensitive: false IncludeIsMainRegex: '(Test)?$' +IncludeIsMainSourceRegex: '' +IndentAccessModifiers: false +IndentCaseBlocks: false IndentCaseLabels: true +IndentExternBlock: AfterExternBlock +IndentGotoLabels: true IndentPPDirectives: AfterHash +IndentRequiresClause: true IndentWidth: 2 IndentWrappedFunctionNames: false +InsertBraces: false +InsertNewlineAtEOF: false +InsertTrailingCommas: None +IntegerLiteralSeparator: + Binary: 0 + BinaryMinDigits: 0 + Decimal: 0 + DecimalMinDigits: 0 + Hex: 0 + HexMinDigits: 0 JavaScriptQuotes: Leave JavaScriptWrapImports: true -KeepEmptyLinesAtTheStartOfBlocks: true +KeepEmptyLines: + AtEndOfFile: false + AtStartOfBlock: true + AtStartOfFile: true +LambdaBodyIndentation: Signature +LineEnding: DeriveLF MacroBlockBegin: '' MacroBlockEnd: '' +MainIncludeChar: Quote MaxEmptyLinesToKeep: 2 NamespaceIndentation: None ObjCBinPackProtocolList: Auto ObjCBlockIndentWidth: 2 +ObjCBreakBeforeNestedBlockParam: true ObjCSpaceAfterProperty: true ObjCSpaceBeforeProtocolList: false +PackConstructorInitializers: BinPack PenaltyBreakAssignment: 2 PenaltyBreakBeforeFirstCallParameter: 19 PenaltyBreakComment: 300 ## The following line allows larger lines in non-documentation code PenaltyBreakFirstLessLess: 120 +PenaltyBreakOpenParenthesis: 0 +PenaltyBreakScopeResolution: 500 PenaltyBreakString: 1000 PenaltyBreakTemplateDeclaration: 10 PenaltyExcessCharacter: 1000000 +PenaltyIndentedWhitespace: 0 PenaltyReturnTypeOnItsOwnLine: 200 PointerAlignment: Middle +PPIndentWidth: -1 +QualifierAlignment: Custom +QualifierOrder: + - friend + - static + - inline + - constexpr + - const + - type +ReferenceAlignment: Pointer ReflowComments: true +RemoveBracesLLVM: false +RemoveParentheses: Leave +RemoveSemicolon: false +RequiresClausePosition: OwnLine +RequiresExpressionIndentation: OuterScope +SeparateDefinitionBlocks: Leave +ShortNamespaceLines: 1 +SkipMacroDefinitionBody: false # We may want to sort the includes as a separate pass -SortIncludes: false +SortIncludes: Never +SortJavaStaticImport: Before # We may want to revisit this later -SortUsingDeclarations: false +SortUsingDeclarations: Never SpaceAfterCStyleCast: false -# SpaceAfterLogicalNot: false +SpaceAfterLogicalNot: false SpaceAfterTemplateKeyword: true +SpaceAroundPointerQualifiers: Default SpaceBeforeAssignmentOperators: true +SpaceBeforeCaseColon: false SpaceBeforeCpp11BracedList: false SpaceBeforeCtorInitializerColon: true SpaceBeforeInheritanceColon: true +SpaceBeforeJsonColon: false SpaceBeforeParens: ControlStatements +SpaceBeforeParensOptions: + AfterControlStatements: true + AfterForeachMacros: true + AfterFunctionDefinitionName: false + AfterFunctionDeclarationName: false + AfterIfMacros: true + AfterOverloadedOperator: false + AfterPlacementOperator: true + AfterRequiresInClause: false + AfterRequiresInExpression: false + BeforeNonEmptyParentheses: false SpaceBeforeRangeBasedForLoopColon: true -SpaceInEmptyParentheses: false +SpaceBeforeSquareBrackets: false +SpaceInEmptyBlock: false SpacesBeforeTrailingComments: 1 -SpacesInAngles: false +SpacesInAngles: Never SpacesInContainerLiterals: false -SpacesInCStyleCastParentheses: false -SpacesInParentheses: false +SpacesInLineCommentPrefix: + Minimum: 1 + Maximum: -1 +SpacesInParens: Never +SpacesInParensOptions: + ExceptDoubleParentheses: false + InCStyleCasts: false + InConditionalStatements: false + InEmptyParentheses: false + Other: false SpacesInSquareBrackets: false -Standard: Cpp11 +Standard: Latest +StatementAttributeLikeMacros: + - Q_EMIT StatementMacros: - Q_UNUSED - QT_REQUIRE_VERSION + - ITK_GCC_PRAGMA_PUSH + - ITK_GCC_PRAGMA_POP + - ITK_GCC_SUPPRESS_Wfloat_equal + - ITK_GCC_SUPPRESS_Wformat_nonliteral + - ITK_GCC_SUPPRESS_Warray_bounds + - ITK_CLANG_PRAGMA_PUSH + - ITK_CLANG_PRAGMA_POP + - ITK_CLANG_SUPPRESS_Wzero_as_null_pointer_constant + - ITK_CLANG_SUPPRESS_Wduplicate_enum + - CLANG_PRAGMA_PUSH + - CLANG_PRAGMA_POP + - CLANG_SUPPRESS_Wfloat_equal + - INTEL_PRAGMA_WARN_PUSH + - INTEL_PRAGMA_WARN_POP + - INTEL_SUPPRESS_warning_1292 + - itkTemplateFloatingToIntegerMacro + - itkLegacyMacro +TableGenBreakInsideDAGArg: DontBreak TabWidth: 2 UseTab: Never +VerilogBreakBetweenInstancePorts: true +WhitespaceSensitiveMacros: + - BOOST_PP_STRINGIZE + - CF_SWIFT_NAME + - NS_SWIFT_NAME + - PP_STRINGIZE + - STRINGIZE ... diff --git a/.github/workflows/build-test-package.yml b/.github/workflows/build-test-package.yml index 19b97f5..18758d6 100644 --- a/.github/workflows/build-test-package.yml +++ b/.github/workflows/build-test-package.yml @@ -5,10 +5,10 @@ on: [push,pull_request] jobs: cxx-build-workflow: - uses: InsightSoftwareConsortium/ITKRemoteModuleBuildTestPackageAction/.github/workflows/build-test-cxx.yml@v5.4.0 + uses: InsightSoftwareConsortium/ITKRemoteModuleBuildTestPackageAction/.github/workflows/build-test-cxx.yml@v5.4.4 python-build-workflow: - uses: InsightSoftwareConsortium/ITKRemoteModuleBuildTestPackageAction/.github/workflows/build-test-package-python.yml@v5.4.0 + uses: InsightSoftwareConsortium/ITKRemoteModuleBuildTestPackageAction/.github/workflows/build-test-package-python.yml@v5.4.4 with: test-notebooks: false secrets: diff --git a/.github/workflows/clang-format-linter.yml b/.github/workflows/clang-format-linter.yml index 69166d9..7d1df4f 100644 --- a/.github/workflows/clang-format-linter.yml +++ b/.github/workflows/clang-format-linter.yml @@ -7,7 +7,8 @@ jobs: runs-on: ubuntu-latest steps: - - uses: actions/checkout@v1 + - uses: actions/checkout@v5 + + - uses: InsightSoftwareConsortium/ITKClangFormatLinterAction@main with: - fetch-depth: 1 - - uses: InsightSoftwareConsortium/ITKClangFormatLinterAction@master + itk-branch: main diff --git a/CMakeLists.txt b/CMakeLists.txt index 5d0c36f..bd3c86a 100644 --- a/CMakeLists.txt +++ b/CMakeLists.txt @@ -1,4 +1,4 @@ -cmake_minimum_required(VERSION 3.10.2) +cmake_minimum_required(VERSION 3.16.3) project(TwoProjectionRegistration) if(NOT ITK_SOURCE_DIR) diff --git a/README.rst b/README.rst index 6df7751..c45cbdb 100644 --- a/README.rst +++ b/README.rst @@ -8,7 +8,7 @@ ITKTwoProjectionRegistration :alt: PyPI Version .. image:: https://img.shields.io/badge/License-Apache%202.0-blue.svg - :target: https://github.com/InsightSoftwareConsortium/TwoProjectionRegistration/blob/master/LICENSE) + :target: https://github.com/InsightSoftwareConsortium/TwoProjectionRegistration/blob/main/LICENSE) :alt: License Overview diff --git a/include/itkNormalizedCorrelationTwoImageToOneImageMetric.h b/include/itkNormalizedCorrelationTwoImageToOneImageMetric.h index b650ca7..3b77bd3 100644 --- a/include/itkNormalizedCorrelationTwoImageToOneImageMetric.h +++ b/include/itkNormalizedCorrelationTwoImageToOneImageMetric.h @@ -57,7 +57,7 @@ class NormalizedCorrelationTwoImageToOneImageMetric : public TwoImageToOneImageM itkNewMacro(Self); /** Run-time type information (and related methods). */ - itkTypeMacro(NormalizedCorrelationTwoImageToOneImageMetric, Object); + itkOverrideGetNameOfClassMacro(NormalizedCorrelationTwoImageToOneImageMetric); /** Types transferred from the base class */ diff --git a/include/itkSiddonJacobsRayCastInterpolateImageFunction.h b/include/itkSiddonJacobsRayCastInterpolateImageFunction.h index b5f3d9c..4861943 100644 --- a/include/itkSiddonJacobsRayCastInterpolateImageFunction.h +++ b/include/itkSiddonJacobsRayCastInterpolateImageFunction.h @@ -90,7 +90,7 @@ class SiddonJacobsRayCastInterpolateImageFunction : public InterpolateImageFunct /** Run-time type information (and related methods). */ - itkTypeMacro(SiddonJacobsRayCastInterpolateImageFunction, InterpolateImageFunction); + itkOverrideGetNameOfClassMacro(SiddonJacobsRayCastInterpolateImageFunction); /** Method for creation through the object factory. */ itkNewMacro(Self); diff --git a/include/itkTwoImageToOneImageMetric.h b/include/itkTwoImageToOneImageMetric.h index de1f5ac..f16f3ff 100644 --- a/include/itkTwoImageToOneImageMetric.h +++ b/include/itkTwoImageToOneImageMetric.h @@ -64,7 +64,7 @@ class TwoImageToOneImageMetric : public SingleValuedCostFunction using CoordinateRepresentationType = Superclass::ParametersValueType; /** Run-time type information (and related methods). */ - itkTypeMacro(TwoImageToOneImageMetric, SingleValuedCostFunction); + itkOverrideGetNameOfClassMacro(TwoImageToOneImageMetric); /** Type of the moving Image. */ using MovingImageType = TMovingImage; @@ -81,9 +81,7 @@ class TwoImageToOneImageMetric : public SingleValuedCostFunction static constexpr unsigned int FixedImageDimension = TFixedImage::ImageDimension; /** Type of the Transform Base class */ - using TransformType = Transform; + using TransformType = Transform; using TransformPointer = typename TransformType::Pointer; using InputPointType = typename TransformType::InputPointType; @@ -97,8 +95,8 @@ class TwoImageToOneImageMetric : public SingleValuedCostFunction /** Gaussian filter to compute the gradient of the Moving Image */ using RealType = typename NumericTraits::RealType; - using GradientPixelType = CovariantVector; - using GradientImageType = Image; + using GradientPixelType = CovariantVector; + using GradientImageType = Image; using GradientImagePointer = SmartPointer; using GradientImageFilterType = GradientRecursiveGaussianImageFilter; using GradientImageFilterPointer = typename GradientImageFilterType::Pointer; @@ -106,12 +104,12 @@ class TwoImageToOneImageMetric : public SingleValuedCostFunction /** Type for the mask of the fixed image. Only pixels that are "inside" this mask will be considered for the computation of the metric */ - typedef SpatialObject FixedImageMaskType; + typedef SpatialObject FixedImageMaskType; using FixedImageMaskPointer = typename FixedImageMaskType::Pointer; /** Type for the mask of the moving image. Only pixels that are "inside" this mask will be considered for the computation of the metric */ - typedef SpatialObject MovingImageMaskType; + typedef SpatialObject MovingImageMaskType; using MovingImageMaskPointer = typename MovingImageMaskType::Pointer; diff --git a/include/itkTwoProjectionImageRegistrationMethod.h b/include/itkTwoProjectionImageRegistrationMethod.h index 1442c9a..5003720 100644 --- a/include/itkTwoProjectionImageRegistrationMethod.h +++ b/include/itkTwoProjectionImageRegistrationMethod.h @@ -77,7 +77,7 @@ class TwoProjectionImageRegistrationMethod : public ProcessObject itkNewMacro(Self); /** Run-time type information (and related methods). */ - itkTypeMacro(TwoProjectionImageRegistrationMethod, ProcessObject); + itkOverrideGetNameOfClassMacro(TwoProjectionImageRegistrationMethod); /** Type of the Fixed image. */ using FixedImageType = TFixedImage; diff --git a/pyproject.toml b/pyproject.toml index ff2e32c..47f40fa 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -4,7 +4,7 @@ build-backend = "scikit_build_core.build" [project] name = "itk-twoprojectionregistration" -version = "2.0.0" +version = "2.0.1" description = "ITK classes for two-projection 2D/3D registration" readme = "README.rst" license = {file = "LICENSE"} @@ -36,7 +36,7 @@ classifiers = [ "Topic :: Scientific/Engineering :: Medical Science Apps.", "Topic :: Software Development :: Libraries", ] -requires-python = ">=3.8" +requires-python = ">=3.9" dependencies = [ "itk == 5.4.*", ] @@ -49,7 +49,7 @@ Homepage = "https://github.com/InsightSoftwareConsortium/ITKTwoProjectionRegistr # The versions of CMake to allow. If CMake is not present on the system or does # not pass this specifier, it will be downloaded via PyPI if possible. An empty # string will disable this check. -cmake.version = ">=3.16.3" +cmake.version = ">=3.22.1" # A list of args to pass to CMake when configuring the project. Setting this in # config or envvar will override toml. See also ``cmake.define``. diff --git a/test/TwoProjection2D3DRegistration.cxx b/test/TwoProjection2D3DRegistration.cxx index 1cb1880..9f75878 100644 --- a/test/TwoProjection2D3DRegistration.cxx +++ b/test/TwoProjection2D3DRegistration.cxx @@ -46,7 +46,7 @@ // We have chosen to implement the registration using the normalized coorelation // similarity measure. -//#include "itkGradientDifferenceTwoImageToOneImageMetric.h" +// #include "itkGradientDifferenceTwoImageToOneImageMetric.h" #include "itkNormalizedCorrelationTwoImageToOneImageMetric.h" // This is an intensity based registration algorithm so ray casting is