Merge pull request #16 from InsightSoftwareConsortium/ITKv5_1rc2

Updates for ITKv5.2 code cleanups ... ROUND1

.clang-format

@@ -0,0 +1,151 @@
+## This config file is only relevant for clang-format version 8.0.0
+##
+## 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
+##
+## The clang-format binaries can be downloaded as part of the clang binary distributions
+## from http://releases.llvm.org/download.html
+##
+## Use the script Utilities/Maintenance/clang-format.bash to faciliate
+## 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
+## EXAMPLE apply code style enforcement after commit:
+#     Utilities/Maintenance/clang-format.bash --clang ${PATH_TO_CLANG_FORMAT_8.0.0} --last
+---
+# This configuration requires clang-format version 8.0.0 exactly.
+BasedOnStyle: Mozilla
+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
+AllowAllParametersOfDeclarationOnNextLine: false
+AllowShortBlocksOnASingleLine: false
+AllowShortCaseLabelsOnASingleLine: false
+AllowShortFunctionsOnASingleLine: Inline
+# clang 9.0 AllowShortLambdasOnASingleLine: All
+# clang 9.0 features AllowShortIfStatementsOnASingleLine: Never
+AllowShortIfStatementsOnASingleLine: false
+AllowShortLoopsOnASingleLine: false
+AlwaysBreakAfterDefinitionReturnType: None
+AlwaysBreakAfterReturnType: All
+AlwaysBreakBeforeMultilineStrings: false
+AlwaysBreakTemplateDeclarations: Yes
+BinPackArguments: false
+BinPackParameters: false
+BreakBeforeBraces: Custom
+BraceWrapping:
+  # clang 9.0 feature AfterCaseLabel:  false
+  AfterClass:      true
+  AfterControlStatement: true
+  AfterEnum:       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.
+  IndentBraces:    false
+  SplitEmptyFunction: false
+  SplitEmptyRecord: false
+  SplitEmptyNamespace: false
+BreakBeforeBinaryOperators: None
+#clang 6.0 BreakBeforeInheritanceComma: true
+BreakInheritanceList: BeforeComma
+BreakBeforeTernaryOperators: true
+#clang 6.0 BreakConstructorInitializersBeforeComma: true
+BreakConstructorInitializers: BeforeComma
+BreakAfterJavaFieldAnnotations: false
+BreakStringLiterals: true
+## 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
+ExperimentalAutoDetectBinPacking: false
+FixNamespaceComments: true
+ForEachMacros:
+  - foreach
+  - Q_FOREACH
+  - BOOST_FOREACH
+IncludeBlocks:   Preserve
+IncludeCategories:
+  - Regex:           '^"(llvm|llvm-c|clang|clang-c)/'
+    Priority:        2
+  - Regex:           '^(<|"(gtest|gmock|isl|json)/)'
+    Priority:        3
+  - Regex:           '.*'
+    Priority:        1
+IncludeIsMainRegex: '(Test)?$'
+IndentCaseLabels: true
+IndentPPDirectives: AfterHash
+IndentWidth:     2
+IndentWrappedFunctionNames: false
+JavaScriptQuotes: Leave
+JavaScriptWrapImports: true
+KeepEmptyLinesAtTheStartOfBlocks: true
+MacroBlockBegin: ''
+MacroBlockEnd:   ''
+MaxEmptyLinesToKeep: 2
+NamespaceIndentation: None
+ObjCBinPackProtocolList: Auto
+ObjCBlockIndentWidth: 2
+ObjCSpaceAfterProperty: true
+ObjCSpaceBeforeProtocolList: false
+PenaltyBreakAssignment: 2
+PenaltyBreakBeforeFirstCallParameter: 19
+PenaltyBreakComment: 300
+## The following line allows larger lines in non-documentation code
+PenaltyBreakFirstLessLess: 120
+PenaltyBreakString: 1000
+PenaltyBreakTemplateDeclaration: 10
+PenaltyExcessCharacter: 1000000
+PenaltyReturnTypeOnItsOwnLine: 200
+PointerAlignment: Middle
+ReflowComments:  true
+# We may want to sort the includes as a separate pass
+SortIncludes:    false
+# We may want to revisit this later
+SortUsingDeclarations: false
+SpaceAfterCStyleCast: false
+# SpaceAfterLogicalNot: false
+SpaceAfterTemplateKeyword: true
+SpaceBeforeAssignmentOperators: true
+SpaceBeforeCpp11BracedList: false
+SpaceBeforeCtorInitializerColon: true
+SpaceBeforeInheritanceColon: true
+SpaceBeforeParens: ControlStatements
+SpaceBeforeRangeBasedForLoopColon: true
+SpaceInEmptyParentheses: false
+SpacesBeforeTrailingComments: 1
+SpacesInAngles:  false
+SpacesInContainerLiterals: false
+SpacesInCStyleCastParentheses: false
+SpacesInParentheses: false
+SpacesInSquareBrackets: false
+Standard:        Cpp11
+StatementMacros:
+  - Q_UNUSED
+  - QT_REQUIRE_VERSION
+TabWidth:        2
+UseTab:          Never
+...

.gitattributes

@@ -0,0 +1,14 @@
+# Custom attribute to mark sources as using our C++/C code style.
+[attr]our-c-style  whitespace=tab-in-indent,no-lf-at-eof  hooks.style=KWStyle,clangformat
+
+*.c              our-c-style
+*.h              our-c-style
+*.cxx            our-c-style
+*.hxx            our-c-style
+*.txx            our-c-style
+*.txt            whitespace=tab-in-indent,no-lf-at-eof
+*.cmake          whitespace=tab-in-indent,no-lf-at-eof
+
+# ExternalData content links must have LF newlines
+*.md5            crlf=input
+*.sha512         crlf=input

CTestConfig.cmake

@@ -1,7 +1,7 @@
 set(CTEST_PROJECT_NAME "ITK")
 set(CTEST_NIGHTLY_START_TIME "1:00:00 UTC")
 
-set(CTEST_DROP_METHOD "http")
+set(CTEST_DROP_METHOD "https")
 set(CTEST_DROP_SITE "open.cdash.org")
 set(CTEST_DROP_LOCATION "/submit.php?project=Insight")
 set(CTEST_DROP_SITE_CDASH TRUE)

examples/CellularSegmentation1.cxx

@@ -1,6 +1,6 @@
 /*=========================================================================
  *
- *  Copyright Insight Software Consortium
+ *  Copyright NumFOCUS
  *
  *  Licensed under the Apache License, Version 2.0 (the "License");
  *  you may not use this file except in compliance with the License.
@@ -39,15 +39,16 @@
 #include "itkVTKPolyDataWriter.h"
 
 
-int main( int argc, char *argv[] )
+int
+main(int argc, char * argv[])
 {
-  if( argc < 8 )
-    {
+  if (argc < 8)
+  {
     std::cerr << "Missing Parameters " << std::endl;
     std::cerr << "Usage: " << argv[0];
     std::cerr << " inputImage  seedX seedY lowThreshold highThreshold iterations outputMesh.vtk" << std::endl;
     return EXIT_FAILURE;
-    }
+  }
 
   //  Software Guide : BeginLatex
   //
@@ -60,7 +61,7 @@ int main( int argc, char *argv[] )
   // Software Guide : BeginCodeSnippet
   using InternalPixelType = float;
   constexpr unsigned int Dimension = 2;
-  using ImageType = itk::Image< InternalPixelType, Dimension >;
+  using ImageType = itk::Image<InternalPixelType, Dimension>;
   // Software Guide : EndCodeSnippet
 
   //  Software Guide : BeginLatex
@@ -71,7 +72,7 @@ int main( int argc, char *argv[] )
   //  Software Guide : EndLatex
 
   // Software Guide : BeginCodeSnippet
-  using CellularAggregateType = itk::bio::CellularAggregate< Dimension >;
+  using CellularAggregateType = itk::bio::CellularAggregate<Dimension>;
   using CellType = CellularAggregateType::BioCellType;
   // Software Guide : EndCodeSnippet
 
@@ -84,26 +85,25 @@ int main( int argc, char *argv[] )
   //  Software Guide : EndLatex
 
   // Software Guide : BeginCodeSnippet
-  CellularAggregateType::Pointer cellularAggregate
-                                               = CellularAggregateType::New();
+  CellularAggregateType::Pointer cellularAggregate = CellularAggregateType::New();
   // Software Guide : EndCodeSnippet
 
   // We instantiate reader and writer types
-  using ReaderType = itk::ImageFileReader< ImageType >;
+  using ReaderType = itk::ImageFileReader<ImageType>;
   ReaderType::Pointer reader = ReaderType::New();
-  reader->SetFileName( argv[1] );
+  reader->SetFileName(argv[1]);
   std::cout << "Filename = " << argv[1] << std::endl;
 
   try
-    {
+  {
     reader->Update();
-    }
-  catch( itk::ExceptionObject & excep )
-    {
+  }
+  catch (itk::ExceptionObject & excep)
+  {
     std::cerr << "Exception caught !" << std::endl;
     std::cerr << excep << std::endl;
     return EXIT_FAILURE;
-    }
+  }
 
   //  Software Guide : BeginLatex
   //
@@ -119,7 +119,7 @@ int main( int argc, char *argv[] )
   //  Software Guide : EndLatex
 
   // Software Guide : BeginCodeSnippet
-  cellularAggregate->AddSubstrate( reader->GetOutput() );
+  cellularAggregate->AddSubstrate(reader->GetOutput());
   // Software Guide : EndCodeSnippet
 
   //  Software Guide : BeginLatex
@@ -137,16 +137,16 @@ int main( int argc, char *argv[] )
   //
   //  Software Guide : EndLatex
 
-  ImageType::IndexType  index;
+  ImageType::IndexType index;
 
-  index[0] = atoi( argv[2] );
-  index[1] = atoi( argv[3] );
+  index[0] = atoi(argv[2]);
+  index[1] = atoi(argv[3]);
 
-  CellType::PointType  position;
+  CellType::PointType position;
 
-  reader->GetOutput()->TransformIndexToPhysicalPoint( index, position );
+  reader->GetOutput()->TransformIndexToPhysicalPoint(index, position);
 
-  std::cout << "Egg position index = " <<  index   << std::endl;
+  std::cout << "Egg position index = " << index << std::endl;
   std::cout << "Egg position point = " << position << std::endl;
 
   //  Software Guide : BeginLatex
@@ -186,8 +186,8 @@ int main( int argc, char *argv[] )
   //  Software Guide : EndLatex
 
   // Software Guide : BeginCodeSnippet
-  CellType::SetChemoAttractantLowThreshold(  atof( argv[4] ) );
-  CellType::SetChemoAttractantHighThreshold( atof( argv[5] ) );
+  CellType::SetChemoAttractantLowThreshold(atof(argv[4]));
+  CellType::SetChemoAttractantHighThreshold(atof(argv[5]));
   // Software Guide : EndCodeSnippet
 
 
@@ -201,7 +201,7 @@ int main( int argc, char *argv[] )
   //  Software Guide : EndLatex
 
   // Software Guide : BeginCodeSnippet
-  cellularAggregate->SetEgg( egg, position );
+  cellularAggregate->SetEgg(egg, position);
   // Software Guide : EndCodeSnippet
 
 
@@ -219,14 +219,14 @@ int main( int argc, char *argv[] )
   //  Software Guide : EndLatex
 
   // Software Guide : BeginCodeSnippet
-  unsigned int numberOfIterations = atoi( argv[6] );
+  unsigned int numberOfIterations = atoi(argv[6]);
 
   std::cout << "numberOfIterations " << numberOfIterations << std::endl;
 
-  for(unsigned int i=0; i<numberOfIterations; i++)
-    {
+  for (unsigned int i = 0; i < numberOfIterations; i++)
+  {
     cellularAggregate->AdvanceTimeStep();
-    }
+  }
   // Software Guide : EndCodeSnippet
 
 
@@ -235,25 +235,24 @@ int main( int argc, char *argv[] )
 
   //  Write the mesh to a file
   //
-  using WriterType = itk::VTKPolyDataWriter< CellularAggregateType::MeshType >;
+  using WriterType = itk::VTKPolyDataWriter<CellularAggregateType::MeshType>;
 
   WriterType::Pointer writer = WriterType::New();
 
-  writer->SetInput( cellularAggregate->GetMesh() );
-  writer->SetFileName( argv[7] );
+  writer->SetInput(cellularAggregate->GetMesh());
+  writer->SetFileName(argv[7]);
 
   try
-    {
+  {
     writer->Update();
-    }
-  catch( itk::ExceptionObject & excep )
-    {
+  }
+  catch (itk::ExceptionObject & excep)
+  {
     std::cerr << "Exception caught !" << std::endl;
     std::cerr << excep << std::endl;
     return EXIT_FAILURE;
-    }
+  }
 
 
   return EXIT_SUCCESS;
-
-  }
+}