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Lee Newberg
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ENH: Updates required by updated ITK.
ENH: Add .clang-format style file. ENH: Use ITK_ prefix for macro names. ENH: Bump to C++14. ENH: Bump to CMake minimum 3.16.3. ENH: Update itk-git-tag in build-test-package.yml. ENH: Use ITK compliant template parameter names.
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‎.clang-format‎

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## This config file is only relevant for clang-format version 8.0.0
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##
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## Examples of each format style can be found on the in the clang-format documentation
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## See: https://clang.llvm.org/docs/ClangFormatStyleOptions.html for details of each option
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##
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## The clang-format binaries can be downloaded as part of the clang binary distributions
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## from http://releases.llvm.org/download.html
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##
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## Use the script Utilities/Maintenance/clang-format.bash to faciliate
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## maintaining a consistent code style.
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##
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## EXAMPLE apply code style enforcement before commit:
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# Utilities/Maintenance/clang-format.bash --clang ${PATH_TO_CLANG_FORMAT_8.0.0} --modified
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## EXAMPLE apply code style enforcement after commit:
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# Utilities/Maintenance/clang-format.bash --clang ${PATH_TO_CLANG_FORMAT_8.0.0} --last
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---
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# This configuration requires clang-format version 8.0.0 exactly.
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BasedOnStyle: Mozilla
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Language: Cpp
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AccessModifierOffset: -2
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AlignAfterOpenBracket: Align
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AlignConsecutiveAssignments: false
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AlignConsecutiveDeclarations: true
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AlignEscapedNewlines: Right
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AlignOperands: true
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AlignTrailingComments: true
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# clang 9.0 AllowAllArgumentsOnNextLine: true
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# clang 9.0 AllowAllConstructorInitializersOnNextLine: true
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AllowAllParametersOfDeclarationOnNextLine: false
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AllowShortBlocksOnASingleLine: false
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AllowShortCaseLabelsOnASingleLine: false
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AllowShortFunctionsOnASingleLine: Inline
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# clang 9.0 AllowShortLambdasOnASingleLine: All
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# clang 9.0 features AllowShortIfStatementsOnASingleLine: Never
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AllowShortIfStatementsOnASingleLine: false
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AllowShortLoopsOnASingleLine: false
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AlwaysBreakAfterDefinitionReturnType: None
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AlwaysBreakAfterReturnType: All
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AlwaysBreakBeforeMultilineStrings: false
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AlwaysBreakTemplateDeclarations: Yes
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BinPackArguments: false
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BinPackParameters: false
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BreakBeforeBraces: Custom
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BraceWrapping:
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# clang 9.0 feature AfterCaseLabel: false
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AfterClass: true
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AfterControlStatement: true
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AfterEnum: true
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AfterFunction: true
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AfterNamespace: true
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AfterObjCDeclaration: true
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AfterStruct: true
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AfterUnion: true
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AfterExternBlock: true
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BeforeCatch: true
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BeforeElse: true
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## This is the big change from historical ITK formatting!
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# Historically ITK used a style similar to https://en.wikipedia.org/wiki/Indentation_style#Whitesmiths_style
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# with indented braces, and not indented code. This style is very difficult to automatically
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# maintain with code beautification tools. Not indenting braces is more common among
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# formatting tools.
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IndentBraces: false
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SplitEmptyFunction: false
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SplitEmptyRecord: false
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SplitEmptyNamespace: false
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BreakBeforeBinaryOperators: None
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#clang 6.0 BreakBeforeInheritanceComma: true
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BreakInheritanceList: BeforeComma
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BreakBeforeTernaryOperators: true
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#clang 6.0 BreakConstructorInitializersBeforeComma: true
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BreakConstructorInitializers: BeforeComma
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BreakAfterJavaFieldAnnotations: false
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BreakStringLiterals: true
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## The following line allows larger lines in non-documentation code
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ColumnLimit: 120
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CommentPragmas: '^ IWYU pragma:'
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CompactNamespaces: false
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ConstructorInitializerAllOnOneLineOrOnePerLine: false
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ConstructorInitializerIndentWidth: 2
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ContinuationIndentWidth: 2
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Cpp11BracedListStyle: false
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DerivePointerAlignment: false
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DisableFormat: false
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ExperimentalAutoDetectBinPacking: false
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FixNamespaceComments: true
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ForEachMacros:
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- foreach
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- Q_FOREACH
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- BOOST_FOREACH
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IncludeBlocks: Preserve
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IncludeCategories:
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- Regex: '^"(llvm|llvm-c|clang|clang-c)/'
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Priority: 2
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- Regex: '^(<|"(gtest|gmock|isl|json)/)'
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Priority: 3
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- Regex: '.*'
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Priority: 1
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IncludeIsMainRegex: '(Test)?$'
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IndentCaseLabels: true
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IndentPPDirectives: AfterHash
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IndentWidth: 2
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IndentWrappedFunctionNames: false
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JavaScriptQuotes: Leave
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JavaScriptWrapImports: true
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KeepEmptyLinesAtTheStartOfBlocks: true
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MacroBlockBegin: ''
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MacroBlockEnd: ''
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MaxEmptyLinesToKeep: 2
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NamespaceIndentation: None
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ObjCBinPackProtocolList: Auto
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ObjCBlockIndentWidth: 2
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ObjCSpaceAfterProperty: true
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ObjCSpaceBeforeProtocolList: false
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PenaltyBreakAssignment: 2
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PenaltyBreakBeforeFirstCallParameter: 19
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PenaltyBreakComment: 300
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## The following line allows larger lines in non-documentation code
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PenaltyBreakFirstLessLess: 120
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PenaltyBreakString: 1000
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PenaltyBreakTemplateDeclaration: 10
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PenaltyExcessCharacter: 1000000
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PenaltyReturnTypeOnItsOwnLine: 200
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PointerAlignment: Middle
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ReflowComments: true
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# We may want to sort the includes as a separate pass
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SortIncludes: false
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# We may want to revisit this later
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SortUsingDeclarations: false
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SpaceAfterCStyleCast: false
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# SpaceAfterLogicalNot: false
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SpaceAfterTemplateKeyword: true
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SpaceBeforeAssignmentOperators: true
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SpaceBeforeCpp11BracedList: false
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SpaceBeforeCtorInitializerColon: true
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SpaceBeforeInheritanceColon: true
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SpaceBeforeParens: ControlStatements
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SpaceBeforeRangeBasedForLoopColon: true
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SpaceInEmptyParentheses: false
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SpacesBeforeTrailingComments: 1
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SpacesInAngles: false
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SpacesInContainerLiterals: false
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SpacesInCStyleCastParentheses: false
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SpacesInParentheses: false
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SpacesInSquareBrackets: false
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Standard: Cpp11
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StatementMacros:
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- Q_UNUSED
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- QT_REQUIRE_VERSION
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TabWidth: 2
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UseTab: Never
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...

‎.github/workflows/build-test-package.yml‎

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@@ -13,17 +13,17 @@ jobs:
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- os: ubuntu-18.04
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c-compiler: "gcc"
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cxx-compiler: "g++"
16-
itk-git-tag: "7548a390d71dc25b80e792703ee3cfea17853a99"
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itk-git-tag: "c693dbc830859ea10d573301f075e121a4c6c581"
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cmake-build-type: "MinSizeRel"
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- os: windows-2019
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c-compiler: "cl.exe"
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cxx-compiler: "cl.exe"
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itk-git-tag: "7548a390d71dc25b80e792703ee3cfea17853a99"
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itk-git-tag: "c693dbc830859ea10d573301f075e121a4c6c581"
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cmake-build-type: "Release"
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- os: macos-10.15
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c-compiler: "clang"
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cxx-compiler: "clang++"
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itk-git-tag: "7548a390d71dc25b80e792703ee3cfea17853a99"
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itk-git-tag: "c693dbc830859ea10d573301f075e121a4c6c581"
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cmake-build-type: "MinSizeRel"
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steps:

‎.github/workflows/clang-format-linter.yml‎

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steps:
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- uses: actions/checkout@v1
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with:
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fetch-depth: 1
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- uses: InsightSoftwareConsortium/ITKClangFormatLinterAction@master
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with:
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error-message: 'Code is inconsistent with ITK Coding Style. Add the *action:ApplyClangFormat* PR label to correct.'

‎CMakeLists.txt‎

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1-
cmake_minimum_required(VERSION 3.10.2)
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cmake_minimum_required(VERSION 3.16.3)
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project(StructurePreservingColorNormalization)
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set(CMAKE_CXX_STANDARD 11)
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set(CMAKE_CXX_STANDARD 14)
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if(NOT ITK_SOURCE_DIR)
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find_package(ITK REQUIRED)

‎include/itkStructurePreservingColorNormalizationFilter.h‎

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@@ -293,17 +293,21 @@ class StructurePreservingColorNormalizationFilter : public ImageToImageFilter< T
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// alternates.
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#define STRUCTUREPRESERVINGCOLORNORMALIZATIONFILTER_STRICT_EIGEN3_ITERATORS 0
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#if STRUCTUREPRESERVINGCOLORNORMALIZATIONFILTER_STRICT_EIGEN3_ITERATORS
296-
template< typename _Scalar, int _Rows, int _Cols, int _Options, int _MaxRows, int _MaxCols >
297-
static _Scalar *begin( Eigen::Matrix< _Scalar, _Rows, _Cols, _Options, _MaxRows, _MaxCols > &matrix );
296+
template <typename TScalar, int VRows, int VCols, int VOptions, int VMaxRows, int VMaxCols>
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static TScalar *
298+
begin(Eigen::Matrix<TScalar, VRows, VCols, VOptions, VMaxRows, VMaxCols> & matrix);
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299-
template< typename _Scalar, int _Rows, int _Cols, int _Options, int _MaxRows, int _MaxCols >
300-
static const _Scalar *cbegin( const Eigen::Matrix< _Scalar, _Rows, _Cols, _Options, _MaxRows, _MaxCols > &matrix );
300+
template <typename TScalar, int VRows, int VCols, int VOptions, int VMaxRows, int VMaxCols>
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static const TScalar *
302+
cbegin(const Eigen::Matrix<TScalar, VRows, VCols, VOptions, VMaxRows, VMaxCols> & matrix);
301303

302-
template< typename _Scalar, int _Rows, int _Cols, int _Options, int _MaxRows, int _MaxCols >
303-
static _Scalar *end( Eigen::Matrix< _Scalar, _Rows, _Cols, _Options, _MaxRows, _MaxCols > &matrix );
304+
template <typename TScalar, int VRows, int VCols, int VOptions, int VMaxRows, int VMaxCols>
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static TScalar *
306+
end(Eigen::Matrix<TScalar, VRows, VCols, VOptions, VMaxRows, VMaxCols> & matrix);
304307

305-
template< typename _Scalar, int _Rows, int _Cols, int _Options, int _MaxRows, int _MaxCols >
306-
static const _Scalar *cend( const Eigen::Matrix< _Scalar, _Rows, _Cols, _Options, _MaxRows, _MaxCols > &matrix );
308+
template <typename TScalar, int VRows, int VCols, int VOptions, int VMaxRows, int VMaxCols>
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static const TScalar *
310+
cend(const Eigen::Matrix<TScalar, VRows, VCols, VOptions, VMaxRows, VMaxCols> & matrix);
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308312
#else
309313
template< typename TMatrix >

‎include/itkStructurePreservingColorNormalizationFilter.hxx‎

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}
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771771
#if STRUCTUREPRESERVINGCOLORNORMALIZATIONFILTER_STRICT_EIGEN3_ITERATORS
772-
template< typename TImage >
773-
template< typename _Scalar, int _Rows, int _Cols, int _Options, int _MaxRows, int _MaxCols >
774-
_Scalar *
775-
StructurePreservingColorNormalizationFilter< TImage >
776-
::begin( Eigen::Matrix< _Scalar, _Rows, _Cols, _Options, _MaxRows, _MaxCols > &matrix )
772+
template <typename TImage>
773+
template <typename TScalar, int VRows, int VCols, int VOptions, int VMaxRows, int VMaxCols>
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TScalar *
775+
StructurePreservingColorNormalizationFilter<TImage>::begin(
776+
Eigen::Matrix<TScalar, VRows, VCols, VOptions, VMaxRows, VMaxCols> & matrix)
777777
{
778778
return matrix.data();
779779
}
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781-
template< typename TImage >
782-
template< typename _Scalar, int _Rows, int _Cols, int _Options, int _MaxRows, int _MaxCols >
783-
const _Scalar *
784-
StructurePreservingColorNormalizationFilter< TImage >
785-
::cbegin( const Eigen::Matrix< _Scalar, _Rows, _Cols, _Options, _MaxRows, _MaxCols > &matrix )
781+
template <typename TImage>
782+
template <typename TScalar, int VRows, int VCols, int VOptions, int VMaxRows, int VMaxCols>
783+
const TScalar *
784+
StructurePreservingColorNormalizationFilter<TImage>::cbegin(
785+
const Eigen::Matrix<TScalar, VRows, VCols, VOptions, VMaxRows, VMaxCols> & matrix)
786786
{
787787
return matrix.data();
788788
}
789789

790-
template< typename TImage >
791-
template< typename _Scalar, int _Rows, int _Cols, int _Options, int _MaxRows, int _MaxCols >
792-
_Scalar *
793-
StructurePreservingColorNormalizationFilter< TImage >
794-
::end( Eigen::Matrix< _Scalar, _Rows, _Cols, _Options, _MaxRows, _MaxCols > &matrix )
790+
template <typename TImage>
791+
template <typename TScalar, int VRows, int VCols, int VOptions, int VMaxRows, int VMaxCols>
792+
TScalar *
793+
StructurePreservingColorNormalizationFilter<TImage>::end(
794+
Eigen::Matrix<TScalar, VRows, VCols, VOptions, VMaxRows, VMaxCols> & matrix)
795795
{
796796
itkAssertOrThrowMacro( std::distance( matrix.data(), &matrix( matrix.rows() - 1, matrix.cols() - 1 ) ) + 1 == matrix.size(), "Bad array stepping" )
797797
return matrix.data() + matrix.size();
798798
}
799799

800-
template< typename TImage >
801-
template< typename _Scalar, int _Rows, int _Cols, int _Options, int _MaxRows, int _MaxCols >
802-
const _Scalar *
803-
StructurePreservingColorNormalizationFilter< TImage >
804-
::cend( const Eigen::Matrix< _Scalar, _Rows, _Cols, _Options, _MaxRows, _MaxCols > &matrix )
800+
template <typename TImage>
801+
template <typename TScalar, int VRows, int VCols, int VOptions, int VMaxRows, int VMaxCols>
802+
const TScalar *
803+
StructurePreservingColorNormalizationFilter<TImage>::cend(
804+
const Eigen::Matrix<TScalar, VRows, VCols, VOptions, VMaxRows, VMaxCols> & matrix)
805805
{
806806
itkAssertOrThrowMacro( std::distance( matrix.data(), &matrix( matrix.rows() - 1, matrix.cols() - 1 ) ) + 1 == matrix.size(), "Bad array stepping" )
807807
return matrix.data() + matrix.size();

‎test/itkStructurePreservingColorNormalizationFilterTest.cxx‎

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@@ -109,7 +109,7 @@ int itkStructurePreservingColorNormalizationFilterTest( int argc, char * argv[]
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// filter->SetColorIndexSuppressedByHematoxylin( 0 );
110110
// filter->SetColorIndexSuppressedByEosin( 1 );
111111

112-
EXERCISE_BASIC_OBJECT_METHODS( filter, StructurePreservingColorNormalizationFilter, ImageToImageFilter );
112+
ITK_EXERCISE_BASIC_OBJECT_METHODS(filter, StructurePreservingColorNormalizationFilter, ImageToImageFilter);
113113

114114
ShowProgress::Pointer showProgress = ShowProgress::New();
115115
filter->AddObserver( itk::ProgressEvent(), showProgress );
@@ -206,7 +206,7 @@ int itkStructurePreservingColorNormalizationFilterTest( int argc, char * argv[]
206206
writer->SetInput( filter->GetOutput() );
207207
writer->SetUseCompression( true );
208208

209-
TRY_EXPECT_NO_EXCEPTION( writer->Update() );
209+
ITK_TRY_EXPECT_NO_EXCEPTION(writer->Update());
210210

211211

212212
std::cout << "Test finished." << std::endl;

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