diff --git a/.clang-format b/.clang-format index 411b009..45b9502 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 19.1.4 ## ## 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 +10,309 @@ ## 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_19.1.4} --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_19.1.4} --last --- -# This configuration requires clang-format version 8.0.0 exactly. -BasedOnStyle: Mozilla +# This configuration requires clang-format version 19.1.4 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 + - 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 71459ec..96b7a48 100644 --- a/.github/workflows/build-test-package.yml +++ b/.github/workflows/build-test-package.yml @@ -4,12 +4,12 @@ on: [push,pull_request] jobs: cxx-build-workflow: - uses: InsightSoftwareConsortium/ITKRemoteModuleBuildTestPackageAction/.github/workflows/build-test-cxx.yml@36e33ec40332bb8fd85bfcd3ee899f82aa108e79 + uses: InsightSoftwareConsortium/ITKRemoteModuleBuildTestPackageAction/.github/workflows/build-test-cxx.yml@v5.4.2 with: itk-module-deps: 'BoneEnhancement@e6935aa760c3fa4e247ca0f4924a4fe3e420bf91:IOScanco@10a73c1ab2de044c4dd73608f91cf52012aff5e4' python-build-workflow: - uses: InsightSoftwareConsortium/ITKRemoteModuleBuildTestPackageAction/.github/workflows/build-test-package-python.yml@36e33ec40332bb8fd85bfcd3ee899f82aa108e79 + uses: InsightSoftwareConsortium/ITKRemoteModuleBuildTestPackageAction/.github/workflows/build-test-package-python.yml@v5.4.2 with: itk-module-deps: 'InsightSoftwareConsortium/ITKBoneEnhancement@e6935aa760c3fa4e247ca0f4924a4fe3e420bf91' secrets: diff --git a/.github/workflows/clang-format-linter.yml b/.github/workflows/clang-format-linter.yml index 69166d9..c8e1681 100644 --- a/.github/workflows/clang-format-linter.yml +++ b/.github/workflows/clang-format-linter.yml @@ -7,7 +7,9 @@ jobs: runs-on: ubuntu-latest steps: - - uses: actions/checkout@v1 + - uses: actions/checkout@v4 with: fetch-depth: 1 - uses: InsightSoftwareConsortium/ITKClangFormatLinterAction@master + with: + itk-branch: master diff --git a/.github/workflows/test-python-hasi.yml b/.github/workflows/test-python-hasi.yml index ef3918f..70ef42f 100644 --- a/.github/workflows/test-python-hasi.yml +++ b/.github/workflows/test-python-hasi.yml @@ -18,10 +18,10 @@ jobs: - os: macos-10.15 steps: - - uses: actions/checkout@v1 + - uses: actions/checkout@v4 - name: Set up Python 3.7 - uses: actions/setup-python@v1 + uses: actions/setup-python@v5 with: python-version: 3.7 diff --git a/examples/normalizedPoseMesh.cxx b/examples/normalizedPoseMesh.cxx index fb5f393..6726287 100644 --- a/examples/normalizedPoseMesh.cxx +++ b/examples/normalizedPoseMesh.cxx @@ -80,8 +80,8 @@ readSlicerFiducials(std::string fileName) std::ifstream pointsFile(fileName.c_str()); std::string line; // ignore first 3 lines (comments of fiducials savefile) - std::getline(pointsFile, line); //# Markups fiducial file version = 4.10 - std::getline(pointsFile, line); //# CoordinateSystem = 0 + std::getline(pointsFile, line); // # Markups fiducial file version = 4.10 + std::getline(pointsFile, line); // # CoordinateSystem = 0 line = line.substr(line.length() - 3); bool ras = false; if (line == "RAS" || line[line.length() - 1] == '0') @@ -93,7 +93,7 @@ readSlicerFiducials(std::string fileName) __FILE__, __LINE__, "Fiducials file with IJK coordinates is not supported", __FUNCTION__); else throw itk::ExceptionObject(__FILE__, __LINE__, "Unrecognized coordinate system", __FUNCTION__); - std::getline(pointsFile, line); //# columns = id,x,y,z,ow,ox,oy,oz,vis,sel,lock,label,desc,associatedNodeID + std::getline(pointsFile, line); // # columns = id,x,y,z,ow,ox,oy,oz,vis,sel,lock,label,desc,associatedNodeID std::vector points; std::getline(pointsFile, line); diff --git a/include/itkLandmarkAtlasSegmentationFilter.h b/include/itkLandmarkAtlasSegmentationFilter.h index c66188d..ab702b0 100644 --- a/include/itkLandmarkAtlasSegmentationFilter.h +++ b/include/itkLandmarkAtlasSegmentationFilter.h @@ -41,7 +41,7 @@ template class LandmarkAtlasSegmentationFilter : public ImageToImageFilter { public: - ITK_DISALLOW_COPY_AND_ASSIGN(LandmarkAtlasSegmentationFilter); + ITK_DISALLOW_COPY_AND_MOVE(LandmarkAtlasSegmentationFilter); static constexpr unsigned Dimension = TInputImage::ImageDimension; @@ -57,7 +57,7 @@ class LandmarkAtlasSegmentationFilter : public ImageToImageFilter; /** Run-time type information. */ - itkTypeMacro(LandmarkAtlasSegmentationFilter, ImageToImageFilter); + itkOverrideGetNameOfClassMacro(LandmarkAtlasSegmentationFilter); /** Standard New macro. */ itkNewMacro(Self); @@ -139,7 +139,7 @@ class LandmarkAtlasSegmentationFilter : public ImageToImageFilter::GenerateData() { this->AllocateOutputs(); - OutputImageType * output = this->GetOutput(); + // OutputImageType * output = this->GetOutput(); const InputImageType * input = this->GetInput(); - const RegionType & outputRegion = output->GetRequestedRegion(); - RegionType inputRegion = RegionType(outputRegion.GetSize()); + // const RegionType & outputRegion = output->GetRequestedRegion(); + // RegionType inputRegion = RegionType(outputRegion.GetSize()); m_LandmarksTransform = RigidTransformType::New(); @@ -67,7 +67,7 @@ LandmarkAtlasSegmentationFilter::GenerateData() m_LandmarksTransform->SetTranslation(m_AtlasLandmarks.front() - m_InputLandmarks.front()); using InterpolatorType = itk::NearestNeighborInterpolateImageFunction; - typename InterpolatorType::Pointer interpolator = InterpolatorType::New(); + typename InterpolatorType::Pointer interpolator = InterpolatorType::New(); using ResampleFilterType = itk::ResampleImageFilter; typename ResampleFilterType::Pointer resampleFilter = ResampleFilterType::New(); diff --git a/include/itkSegmentBonesInMicroCTFilter.h b/include/itkSegmentBonesInMicroCTFilter.h index fb5e6e0..674d864 100644 --- a/include/itkSegmentBonesInMicroCTFilter.h +++ b/include/itkSegmentBonesInMicroCTFilter.h @@ -42,7 +42,7 @@ template class SegmentBonesInMicroCTFilter : public ImageToImageFilter { public: - ITK_DISALLOW_COPY_AND_ASSIGN(SegmentBonesInMicroCTFilter); + ITK_DISALLOW_COPY_AND_MOVE(SegmentBonesInMicroCTFilter); using InputImageType = TInputImage; using OutputImageType = TOutputImage; @@ -56,7 +56,7 @@ class SegmentBonesInMicroCTFilter : public ImageToImageFilter; /** Run-time type information. */ - itkTypeMacro(SegmentBonesInMicroCTFilter, ImageToImageFilter); + itkOverrideGetNameOfClassMacro(SegmentBonesInMicroCTFilter); /** Standard New macro. */ itkNewMacro(Self); diff --git a/include/itkSegmentBonesInMicroCTFilter.hxx b/include/itkSegmentBonesInMicroCTFilter.hxx index 2d219df..d55a7b1 100644 --- a/include/itkSegmentBonesInMicroCTFilter.hxx +++ b/include/itkSegmentBonesInMicroCTFilter.hxx @@ -285,7 +285,7 @@ SegmentBonesInMicroCTFilter::GenerateData() // per-bone processing - for (unsigned bone = 1; bone <= numBones; bone++) + for (typename TOutputImage::PixelType bone = 1; bone <= numBones; bone++) { float boneProgress = 0.3f / numBones; float beginProgress = 0.7 + boneProgress * (bone - 1); diff --git a/test/itkLandmarkAtlasSegmentationFilterTest.cxx b/test/itkLandmarkAtlasSegmentationFilterTest.cxx index d83911c..f315d29 100644 --- a/test/itkLandmarkAtlasSegmentationFilterTest.cxx +++ b/test/itkLandmarkAtlasSegmentationFilterTest.cxx @@ -63,8 +63,8 @@ readSlicerFiducials(std::string fileName) std::ifstream pointsFile(fileName.c_str()); std::string line; // ignore first 3 lines (comments of fiducials savefile) - std::getline(pointsFile, line); //# Markups fiducial file version = 4.10 - std::getline(pointsFile, line); //# CoordinateSystem = 0 + std::getline(pointsFile, line); // # Markups fiducial file version = 4.10 + std::getline(pointsFile, line); // # CoordinateSystem = 0 line = line.substr(line.length() - 3); bool ras = false; if (line == "RAS" || line[line.length() - 1] == '0') @@ -78,7 +78,7 @@ readSlicerFiducials(std::string fileName) { throw itk::ExceptionObject(__FILE__, __LINE__, "Unrecognized coordinate system", __FUNCTION__); } - std::getline(pointsFile, line); //# columns = id,x,y,z,ow,ox,oy,oz,vis,sel,lock,label,desc,associatedNodeID + std::getline(pointsFile, line); // # columns = id,x,y,z,ow,ox,oy,oz,vis,sel,lock,label,desc,associatedNodeID std::vector points; std::getline(pointsFile, line);