Complete rewrite

Update the API, and make the tests more robust.

Closes #75, #73.

Author: gadomski

.clang-format

@@ -1,57 +1,95 @@
 ---
 Language:        Cpp
-# BasedOnStyle:  LLVM
+# BasedOnStyle:  Mozilla
 AccessModifierOffset: -4
-ConstructorInitializerIndentWidth: 4
+AlignAfterOpenBracket: Align
+AlignConsecutiveAssignments: false
+AlignConsecutiveDeclarations: false
 AlignEscapedNewlinesLeft: false
+AlignOperands:   true
 AlignTrailingComments: true
-AllowAllParametersOfDeclarationOnNextLine: true
+AllowAllParametersOfDeclarationOnNextLine: false
 AllowShortBlocksOnASingleLine: false
+AllowShortCaseLabelsOnASingleLine: false
+AllowShortFunctionsOnASingleLine: Inline
 AllowShortIfStatementsOnASingleLine: false
 AllowShortLoopsOnASingleLine: false
-AllowShortFunctionsOnASingleLine: All
-AlwaysBreakTemplateDeclarations: true
+AlwaysBreakAfterDefinitionReturnType: None
+AlwaysBreakAfterReturnType: None
 AlwaysBreakBeforeMultilineStrings: false
-BreakBeforeBinaryOperators: false
-BreakBeforeTernaryOperators: true
-BreakConstructorInitializersBeforeComma: false
+AlwaysBreakTemplateDeclarations: true
+BinPackArguments: true
 BinPackParameters: true
+BraceWrapping:   
+  AfterClass:      true
+  AfterControlStatement: false
+  AfterEnum:       true
+  AfterFunction:   true
+  AfterNamespace:  false
+  AfterObjCDeclaration: false
+  AfterStruct:     true
+  AfterUnion:      true
+  BeforeCatch:     false
+  BeforeElse:      false
+  IndentBraces:    false
+BreakBeforeBinaryOperators: None
+BreakBeforeBraces: Attach
+BreakBeforeTernaryOperators: true
+BreakConstructorInitializersBeforeComma: true
+BreakAfterJavaFieldAnnotations: false
+BreakStringLiterals: true
 ColumnLimit:     80
-ConstructorInitializerAllOnOneLineOrOnePerLine: true
+CommentPragmas:  '^ IWYU pragma:'
+ConstructorInitializerAllOnOneLineOrOnePerLine: false
+ConstructorInitializerIndentWidth: 2
+ContinuationIndentWidth: 4
+Cpp11BracedListStyle: false
 DerivePointerAlignment: false
+DisableFormat:   false
 ExperimentalAutoDetectBinPacking: false
-IndentCaseLabels: false
+ForEachMacros:   [ foreach, Q_FOREACH, BOOST_FOREACH ]
+IncludeCategories: 
+  - Regex:           '^"(llvm|llvm-c|clang|clang-c)/'
+    Priority:        2
+  - Regex:           '^(<|"(gtest|isl|json)/)'
+    Priority:        3
+  - Regex:           '.*'
+    Priority:        1
+IncludeIsMainRegex: '$'
+IndentCaseLabels: true
+IndentWidth:     4
 IndentWrappedFunctionNames: false
-IndentFunctionDeclarationAfterType: false
-MaxEmptyLinesToKeep: 2
+JavaScriptQuotes: Leave
+JavaScriptWrapImports: true
 KeepEmptyLinesAtTheStartOfBlocks: true
+MacroBlockBegin: ''
+MacroBlockEnd:   ''
+MaxEmptyLinesToKeep: 1
 NamespaceIndentation: None
-ObjCSpaceAfterProperty: false
-ObjCSpaceBeforeProtocolList: true
+ObjCBlockIndentWidth: 2
+ObjCSpaceAfterProperty: true
+ObjCSpaceBeforeProtocolList: false
 PenaltyBreakBeforeFirstCallParameter: 19
 PenaltyBreakComment: 300
-PenaltyBreakString: 1000
 PenaltyBreakFirstLessLess: 120
+PenaltyBreakString: 1000
 PenaltyExcessCharacter: 1000000
-PenaltyReturnTypeOnItsOwnLine: 60
+PenaltyReturnTypeOnItsOwnLine: 200
 PointerAlignment: Left
+ReflowComments:  true
+SortIncludes:    true
+SpaceAfterCStyleCast: false
+SpaceBeforeAssignmentOperators: true
+SpaceBeforeParens: ControlStatements
+SpaceInEmptyParentheses: false
 SpacesBeforeTrailingComments: 1
-Cpp11BracedListStyle: true
+SpacesInAngles:  false
+SpacesInContainerLiterals: true
+SpacesInCStyleCastParentheses: false
+SpacesInParentheses: false
+SpacesInSquareBrackets: false
 Standard:        Cpp11
-IndentWidth:     4
 TabWidth:        8
 UseTab:          Never
-BreakBeforeBraces: Attach
-SpacesInParentheses: false
-SpacesInAngles:  false
-SpaceInEmptyParentheses: false
-SpacesInCStyleCastParentheses: false
-SpacesInContainerLiterals: true
-SpaceBeforeAssignmentOperators: true
-ContinuationIndentWidth: 4
-CommentPragmas:  '^ IWYU pragma:'
-ForEachMacros:   [ foreach, Q_FOREACH, BOOST_FOREACH ]
-SpaceBeforeParens: ControlStatements
-DisableFormat:   false
 ...
 

CMakeLists.txt

@@ -1,98 +1,72 @@
-project(cpd CXX)
 cmake_minimum_required(VERSION 2.8.12)
+set(CPD_LANGUAGES CXX C)
+set(CPD_VERSION 0.4.0)
+set(CPD_SOVERSION 0)
 
-if(POLICY CMP0042)
-    cmake_policy(SET CMP0042 NEW)
+# Policies
+if(POLICY CMP0048) # Project version
+    cmake_policy(SET CMP0048 NEW)
+    project(cpd LANGUAGES ${CPD_LANGUAGES} VERSION ${CPD_VERSION})
+else()
+    project(cpd ${CPD_LANGUAGES})
 endif()
-if(POLICY CMP0054)
-    cmake_policy(SET CMP0054 NEW) # Quoted variables in IF statements
+
+if(POLICY CMP0042) # MACOSX_RPATH
+    cmake_policy(SET CMP0042 NEW)
 endif()
 
-set(CPD_VERSION 0.3.3)
-configure_file(
-    src/version.cpp.in
-    ${PROJECT_BINARY_DIR}/src/version.cpp
-    )
-set(CPD_SOVERSION 0)
-message(STATUS "[cpd] Version: ${CPD_VERSION}")
+# Depdencies
+find_package(Fgt REQUIRED)
 
-set(GTEST_SOURCE_DIR "${PROJECT_SOURCE_DIR}/vendor/gtest-1.7.0")
+# Configuration
+option(BUILD_SHARED_LIBS "Build shared libraries" ON)
 
-option(WITH_TESTS "Build unit tests" ON)
+include(CMakePackageConfigHelpers)
+write_basic_package_version_file("${PROJECT_BINARY_DIR}/cmake/cpd-config-version.cmake" VERSION ${CPD_VERSION} COMPATIBILITY AnyNewerVersion)
+install(FILES cmake/cpd-config.cmake "${PROJECT_BINARY_DIR}/cmake/cpd-config-version.cmake" DESTINATION lib/cmake/cpd)
+configure_file(src/version.cpp.in "${PROJECT_BINARY_DIR}/src/version.cpp")
 
-set(FGT_MINIMUM_VERSION 0.4)
-find_package(Fgt ${FGT_MINIMUM_VERSION} REQUIRED)
-message(STATUS "[cpd] Fgt version: ${Fgt_VERSION}")
+option(WITH_STRICT_WARNINGS "Build with stricter warnings" ON)
+if(WITH_STRICT_WARNINGS)
+    if("${CMAKE_CXX_COMPILER_ID}" MATCHES "Clang")
+        set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -Wall -pedantic -Wno-gnu-zero-variadic-macro-arguments")
+    endif()
+endif()
 
-add_library(Library-C++
-    src/affine.cpp
-    src/matrix.cpp
+# Targets
+set(library_src
+    src/affinity_matrix.cpp
     src/nonrigid.cpp
-    src/normalization.cpp
+    src/normalize.cpp
     src/rigid.cpp
+    src/probabilities.cpp
     src/utils.cpp
-    ${PROJECT_BINARY_DIR}/src/version.cpp
-    )
-target_include_directories(Library-C++
-    INTERFACE
-    ${CMAKE_INSTALL_PREFIX}/include
-    PRIVATE
-    include
-    )
-target_link_libraries(Library-C++
-    PUBLIC
-    Fgt::Library-C++
-    )
-target_compile_definitions(Library-C++
-    PRIVATE
-    _USE_MATH_DEFINES
+    "${PROJECT_BINARY_DIR}/src/version.cpp"
     )
-if("${CMAKE_CXX_COMPILER_ID}" MATCHES "Clang" OR "${CMAKE_CXX_COMPILER_ID}" MATCHES "GNU")
-    target_compile_options(Library-C++
-        PRIVATE
-        -pedantic -Wall
-        )
-endif()
+add_library(Library-C++ ${library_src})
 set_target_properties(Library-C++ PROPERTIES
     OUTPUT_NAME cpd
     VERSION ${CPD_VERSION}
     SOVERSION ${CPD_SOVERSION}
     )
+target_link_libraries(Library-C++ PUBLIC Fgt::Library-C++)
+target_include_directories(Library-C++
+    INTERFACE $<INSTALL_INTERFACE:include> $<INSTALL_INTERFACE:include/cpd/vendor>
+    PRIVATE include include/cpd/vendor)
+install(TARGETS Library-C++ DESTINATION lib EXPORT cpd-targets)
 install(DIRECTORY include/cpd DESTINATION include)
-install(TARGETS Library-C++
-    DESTINATION lib
-    EXPORT cpd-targets
-    )
-
-configure_file(Doxyfile.in ${PROJECT_BINARY_DIR}/Doxyfile)
-add_custom_target(docs
-    COMMAND doxygen ${PROJECT_BINARY_DIR}/Doxyfile
-    )
+install(EXPORT cpd-targets NAMESPACE Cpd:: DESTINATION lib/cmake/cpd)
 
+# Optional targets
+option(WITH_TESTS "Build test suite" ON)
 if(WITH_TESTS)
     enable_testing()
-    add_subdirectory(${GTEST_SOURCE_DIR})
-    set_target_properties(gtest PROPERTIES MACOSX_RPATH ON)
-    set_target_properties(gtest_main PROPERTIES MACOSX_RPATH ON)
+    set(GOOGLETEST_DIR "${PROJECT_SOURCE_DIR}/vendor/googletest-release-1.8.0/googletest")
     add_subdirectory(test)
 endif()
 
-include(CMakePackageConfigHelpers)
-configure_file(cmake/cpd-config.cmake
-    ${PROJECT_BINARY_DIR}/cpd-config.cmake
-    @ONLY
-    )
-write_basic_package_version_file(
-    ${PROJECT_BINARY_DIR}/cpd-config-version.cmake
-    VERSION ${CPD_VERSION}
-    COMPATIBILITY AnyNewerVersion
-    )
-install(FILES
-    ${PROJECT_BINARY_DIR}/cpd-config.cmake
-    ${PROJECT_BINARY_DIR}/cpd-config-version.cmake
-    DESTINATION lib/cmake/cpd
-    )
-install(EXPORT cpd-targets
-    DESTINATION lib/cmake/cpd
-    NAMESPACE Cpd::
-    )
+option(WITH_DOCS "Build documentation" OFF)
+if(WITH_DOCS)
+    configure_file(Doxyfile.in "${PROJECT_BINARY_DIR}/Doxyfile")
+    add_custom_target(docs COMMAND doxygen "${PROJECT_BINARY_DIR}/Doxyfile")
+endif()

Doxyfile.in

@@ -58,7 +58,7 @@ PROJECT_LOGO           =
 # entered, it will be relative to the location where doxygen was started. If
 # left blank the current directory will be used.
 
-OUTPUT_DIRECTORY       = @PROJECT_BINARY_DIR@/doc
+OUTPUT_DIRECTORY       = @PROJECT_BINARY_DIR@/docs
 
 # If the CREATE_SUBDIRS tag is set to YES then doxygen will create 4096 sub-
 # directories (in 2 levels) under the output directory of each output format and
@@ -125,7 +125,7 @@ ABBREVIATE_BRIEF       =
 # description.
 # The default value is: NO.
 
-ALWAYS_DETAILED_SEC    = NO
+ALWAYS_DETAILED_SEC    = YES
 
 # If the INLINE_INHERITED_MEMB tag is set to YES, doxygen will show all
 # inherited members of a class in the documentation of that class as if those

README.md

@@ -8,13 +8,12 @@ While ICP minimizes point-to-point distances, CPD uses a [Gaussian Mixture Model
 If you're thinking that this is very computationally intensive, you're right — both the CPD algorithm and the underlying error calculations take a lot of time, which is why we've created [fgt](https://github.com/gadomski/fgt) to speed up those Gauss transforms.
 We hope this library provides a freer and more performant alternative to the original reference Matlab implementation.
 
-This library supports three variants of CPD:
+This library supports two variants of CPD:
 
 - **rigid**: Uses a rigid transformation (i.e. rotation and translation, with an optional scaling) to align the two datasets.
 - **nonrigid**: Uses a two-parameter non-rigid transformation function to align the two datasets.
-- **affine**: Uses an affine transformation (with an optional scaling) to align the two datasets.
 
-Andriy's reference implementation comes with one other type of registration, **nonrigid_lowrank**, which is not implemented in the latest version of this library (yet) (see [History](#history) for information on how to find and use a previous version of this library that has **nonrigid_lowrank**).
+Andriy's reference implementation comes with two other type of registrations, **affine** and **nonrigid_lowrank**, which are not implemented in the latest version of this library (yet) (see [History](#history) for information on how to find and use a previous version of this library that has **nonrigid_lowrank** and **affine**).
 
 This code lives [on Github](https://github.com/gadomski/cpd).
 It has some [Doxygen documentation](http://gadomski.github.io/cpd) and is tested [by Travis](https://travis-ci.org/gadomski/cpd) and [by AppVeyor](https:://ci.appveyor.com/project/gadomski/cpd/branch/master).
@@ -25,31 +24,42 @@ We also have a [gitter chatroom](https://gitter.im/gadomski/cpd).
 
 ## Usage
 
-**cpd** has a simple functional interface, which accepts [Eigen](http://eigen.tuxfamily.org/index.php?title=Main_Page) matrices and aligns them using some sensible default parameters:
+Basic, default usage can be accomplished via some namespace-level methods:
 
 ```cpp
 #include <cpd/rigid.hpp>
 
-cpd::RigidResult align_with_rigid(const Eigen::MatrixXd& X, const Eigen::MatrixXd& Y) {
-    return cpd::rigid(X, Y);
+int main(int argc, char** argv) {
+    cpd::Matrix fixed = load_points_from_somewhere();
+    cpd::Matrix moving = load_points_from_somewhere();
+    cpd::Rigid::Result result = cpd::rigid(fixed, moving);
 }
 ```
 
-If you want more control over the parameters, you can use the class-based interface:
+More advanced configuration can be accomplished by using a `Runner`:
 
 ```cpp
 #include <cpd/rigid.hpp>
-
-cpd::RigidResult align_with_rigid(const Eigen::MatrixXd& X, const Eigen::MatrixXd& Y) {
-    cpd::Rigid rigid;
-    rigid.allow_scaling(true).no_reflections(false);
-    return rigid.compute(X, Y);
+#include <cpd/runner.hpp>
+
+int main(int argc, char** argv) {
+    cpd::Matrix fixed = load_points_from_somewhere();
+    cpd::Matrix moving = load_points_from_somewhere();
+    cpd::Runner<cpd::Rigid, cpd::FgtProbabilityComputer> runner;
+    runner.correspondence(true).outliers(0.2);
+    cpd::Rigid::Result result = runner.run(fixed, moving);
 }
 ```
 
+See the code and the [documentation](http://gadomski.github.io/cpd) to discover all possible options, transformation methods, and probability calculation methods.
+
+## Examples
+
+See `examples/` in this code repository for some basic usage examples, including examples of how to set up a downstream CMake project that depends on cpd.
+
 ## Installation
 
-**cpd** depends on [fgt](https://github.com/gadomski/fgt) at runtime and [CMake](https://cmake.org/) and Eigen at build-time.
+**cpd** depends on [fgt](https://github.com/gadomski/fgt) at runtime and [CMake](https://cmake.org/) and [Eigen](http://eigen.tuxfamily.org/index.php?title=Main_Page) at build-time.
 
 ### On OSX