Update (pfmephisto#1)

* Polygonal Surface reconstruction
using CGAL

* Initial methods to convert point clouds to Speckle objects.
Untested

* Added Gurobi Solver

* Initial clustering

* Changed progress bar

* Working Embree-based ray tracing.

* Implementation of Markov Clustering in C++ using Eigen.

* Added ray visualisation
Changed plane origin

* Removing Python dependency in clustering

* Reenabeling OpenMP
Update MC params
Flipping of normal vectors
Clamped point cloud

* Renaming files to use C++ file extension

* Updating file references

* Adding PCL to CMake

* Adding HDF5 and H5pp as well as downgrading to C++17

* Fixing Eigen3 dependency inclusion.

* Dataset class added

* Intermediate Image projection

* Added Normal construction

* Custom depth to 3d function

* Initial registration pipeline

* Registering point cloud

* Updates to IPC

* Updated Progress bar

* Updated Display Function

* Fixed Transformation Inversion

* Added Size method to Dataset class

* Fixed inverse transformation

* Setting height, width and dense fields

* Updated interface

* Initial neural net support

* Yolo v8 Implementation

* Yolo v8 Model export file

* Viewer, Progressbar

* Added simple path constructor to Dataset class for use in Python

* Restructured Yolo in to pre-, main and post-process

* Updated refine and fit plane methods

* Downsampling, Regin growing, restructured Yolo pipeline

* Added Surface Mesh class and display method

* Custom accumulators

* Octree-based merging of point clouds

* Save and load methods

* Region growing

* Updated Total time formatting

* Filter method

* Updated crop plate with Surface Mesh support

* Surfacemesh reconstruction

* Added functions

* Added new PointCloud class and methods

* Changed PCL path

* updated test file

.gitignore

@@ -52,4 +52,10 @@ imgui.ini
 *.png
 .polyscope.ini
 **/__pycache__/**/*
-**/*.lp
+**/*.lp
+
+
+# Ignore machine learning data
+*.onnx
+*.pt
+*.pcd

.gitmodules

@@ -55,3 +55,9 @@
 [submodule "extern/pcl"]
 	path = extern/pcl
 	url = [email protected]:PointCloudLibrary/pcl.git
+[submodule "extern/fmt"]
+	path = extern/fmt
+	url = [email protected]:fmtlib/fmt.git
+[submodule "extern/nexus"]
+	path = extern/nexus
+	url = [email protected]:project-arcana/nexus.git

CMakeLists.txt

@@ -3,15 +3,29 @@ project(linkml)
 
 set(LIB_PROJECT_NAME "${PROJECT_NAME}_lib")
 set(PYBIND_PROJECT_NAME "${PROJECT_NAME}_py")
+set(TEST_PROJECT_NAME "${PROJECT_NAME}_test")
+
 
 # ===============================================
 # global settings
 
+if(NOT CMAKE_BUILD_TYPE)
+  set(CMAKE_BUILD_TYPE "Release")
+endif()
+message("CMAKE_BUILD_TYPE: ${CMAKE_BUILD_TYPE}")
 
-set(CMAKE_CXX_STANDARD 20)
+set(CMAKE_CXX_STANDARD 17)
 set(CMAKE_CXX_STANDARD_REQUIRED ON)
 set_property(GLOBAL PROPERTY USE_FOLDERS ON)
 
+option(CXX "enable C++ compilation" ON)
+
+if(CXX)
+  enable_language(CXX)
+endif()
+
+list(APPEND CMAKE_MODULE_PATH ${PROJECT_SOURCE_DIR}/cmake)
+
 # ===============================================
 # options
 
@@ -30,6 +44,11 @@ endif()
 
 option(LIN_ENABLE_WERROR "if true, enables -Werror, /WX" OFF)
 
+# enable tests
+option(LINKML_SAMPLES_TESTS "if true, builds linkml tests" ON)
+
+
+
 
 # ===============================================
 # compiler and linker flags
@@ -101,8 +120,13 @@ set(CMAKE_RUNTIME_OUTPUT_DIRECTORY ${BIN_DIR})
 set(CMAKE_RUNTIME_OUTPUT_DIRECTORY_RELEASE ${BIN_DIR})
 set(CMAKE_RUNTIME_OUTPUT_DIRECTORY_RELWITHDEBINFO ${BIN_DIR})
 set(CMAKE_RUNTIME_OUTPUT_DIRECTORY_DEBUG ${BIN_DIR})
+# Set CMAKE_POSITION_INDEPENDENT_CODE to ON
+set(CMAKE_POSITION_INDEPENDENT_CODE ON)
 #set(GLOW_BIN_DIR ${CMAKE_SOURCE_DIR}/bin)
 
+# REMOVED: this is not needed anymore
+set(CGAL_DO_NOT_WARN_ABOUT_CMAKE_BUILD_TYPE On)
+
 ## ===============================================
 ## disable glfw additionals
 #option(GLFW_BUILD_EXAMPLES  OFF)
@@ -114,7 +138,92 @@ set(CMAKE_RUNTIME_OUTPUT_DIRECTORY_DEBUG ${BIN_DIR})
 
 # set(ENV{CUDACXX} "/usr/local/cuda/bin/nvcc")
 
-# ===============================================s
+
+# ===============================================
+# find packages
+
+find_package( OpenCV REQUIRED )
+if (OpenCV_FOUND)
+    message(STATUS "Using OpenCV - ${OpenCV_VERSION} - ${OpenCV_INCLUDE_DIRS}")
+    set("OPENCV_LOG_LEVEL" "WARNING")
+    include_directories(${OpenCV_INCLUDE_DIRS})
+    link_directories(${OpenCV_LIBRARY_DIRS})
+    add_definitions(${OpenCV_DEFINITIONS})
+endif()
+# CGAL and its components
+find_package(CGAL REQUIRED)
+
+# Boost and its components
+find_package(Boost REQUIRED)
+if(NOT Boost_FOUND)
+
+  message(
+    STATUS
+      "NOTICE: This project requires the Boost library, and will not be compiled."
+  )
+
+  return()
+
+endif()
+
+find_package(Eigen3 3.3 REQUIRED) #(requires 3.1.0 or greater)
+include(CGAL_Eigen3_support)
+if(NOT TARGET CGAL::Eigen3_support)
+  message(
+    STATUS
+      "NOTICE: This project requires Eigen 3.1 (or greater) and will not be compiled."
+  )
+  return()
+endif()
+
+find_package( TBB REQUIRED )
+include(CGAL_TBB_support)
+
+find_package(SCIP REQUIRED)
+include(CGAL_SCIP_support)
+
+find_package(embree 3.12.2 REQUIRED)
+
+IF (EMBREE_ISPC_SUPPORT)
+
+  OPTION(ENABLE_ISPC_SUPPORT "Build ISPC version of find_embree tutorial." OFF)
+
+  # this configures the ADD_EMBREE_ISPC_EXECUTABLE from Embree
+  IF (ENABLE_ISPC_SUPPORT)
+    SET(ISPC_TARGETS "sse2;sse4;avx;avx2")
+    SET(CMAKE_MODULE_PATH "${CMAKE_CURRENT_SOURCE_DIR}/../../common/cmake" ${CMAKE_MODULE_PATH})
+    INCLUDE(ispc)
+
+    get_target_property(embree_include_dir embree INTERFACE_INCLUDE_DIRECTORIES)
+    INCLUDE_DIRECTORIES_ISPC(${embree_include_dir})
+    ADD_EMBREE_ISPC_EXECUTABLE(find_embree_ispc find_embree_ispc.cpp find_embree_ispc.ispc)
+    TARGET_LINK_LIBRARIES(find_embree_ispc embree)
+  ENDIF()
+ENDIF()
+
+
+find_package(GUROBI REQUIRED)
+if (GUROBI_FOUND)
+    message(STATUS "Using Gurobi Solver")
+    add_compile_definitions(CGAL_USE_GUROBI=1)
+    include_directories(${GUROBI_INCLUDE_DIRS})
+endif()
+
+find_package(PCL REQUIRED PATHS /usr/local NO_DEFAULT_PATH)
+if(PCL_FOUND)
+    message(STATUS "Using PCL - ${PCL_VERSION}")
+    include_directories(${PCL_INCLUDE_DIRS})
+    link_directories(${PCL_LIBRARY_DIRS})
+    add_definitions(${PCL_DEFINITIONS})
+endif()
+
+
+list(APPEND CMAKE_MODULE_PATH "./cmake/FindHDF5.cmake") # Replaces the bundled FindHDF5.cmake module
+find_package(HDF5 1.10 COMPONENTS C HL REQUIRED)
+
+
+
+# ===============================================
 # add submodules
 add_subdirectory(extern/clean-core)
 add_subdirectory(extern/typed-geometry)
@@ -128,20 +237,17 @@ add_subdirectory(extern/pybind11)
 add_subdirectory(extern/polyscope)
 add_subdirectory(extern/glpk)
 add_subdirectory(extern/lpsolve)
-add_subdirectory(extern/scip)
 add_subdirectory(extern/soplex)
+# add_subdirectory(extern/scip)
+# add_subdirectory(extern/cgal)
 # add_subdirectory(extern/pcl)
-
-
-
-
-
-#add_subdirectory(extern/glfw)
-#add_subdirectory(extern/glow)
-#add_subdirectory(extern/imgui)
-#add_subdirectory(extern/glow-extras)
-
-find_package( OpenCV REQUIRED )
+# add_subdirectory(extern/glfw)
+# add_subdirectory(extern/glow)
+# add_subdirectory(extern/imgui)
+# add_subdirectory(extern/glow-extras)
+add_subdirectory(extern/fmt)
+add_subdirectory(extern/nexus)
+# add_subdirectory(extern/Open3D)
 
 # ===============================================
 # configure executable
@@ -152,7 +258,6 @@ file(GLOB_RECURSE LIB_SOURCES
 
 file(GLOB_RECURSE LIB_HEADERS
     "src/*.hh"
-    "src/*.h"
 )
 
 list(FILTER LIB_SOURCES EXCLUDE REGEX ".*py.cpp")
@@ -169,7 +274,13 @@ include_directories( ${OpenCV_INCLUDE_DIRS} )
 
 add_library(${LIB_PROJECT_NAME} STATIC ${LIB_SOURCES} ${LIB_HEADERS})
 set_target_properties(${LIB_PROJECT_NAME} PROPERTIES POSITION_INDEPENDENT_CODE TRUE)
-target_link_libraries(${LIB_PROJECT_NAME} PRIVATE pybind11::embed)
+target_link_libraries(${LIB_PROJECT_NAME} 
+    PRIVATE 
+    pybind11::embed 
+    optimized ${GUROBI_CXX_LIBRARY}
+    debug ${GUROBI_CXX_DEBUG_LIBRARY}
+    HDF5::HDF5
+    )
 target_link_libraries(${LIB_PROJECT_NAME} PUBLIC
     clean-core
     typed-geometry
@@ -178,29 +289,36 @@ target_link_libraries(${LIB_PROJECT_NAME} PUBLIC
     task-dispatcher
     rich-log
     polymesh
-    nanoflann
     polyscope
     glpk
     lpsolve
-    scip
+    nanoflann
+    # scip
+    embree
     soplex
+    Eigen3::Eigen3
+    CGAL::Eigen3_support
+    CGAL::SCIP_support
+    CGAL::TBB_support
+    ${GUROBI_LIBRARY}
+    # CGAL::GLPK_support
     # pcl
+    ${PCL_LIBRARIES}
+    ${PCL_COMMON_LIBRARIES}
+    # ${PCL_IO_LIBRARIES}
 #    glfw
 #    glow
 #    imgui
 #    glow-extras
+    fmt
+    nexus
 
     ${OpenCV_LIBS}
 
     ${COMMON_LINKER_FLAGS}
 )
 
 
-
-target_include_directories(${LIB_PROJECT_NAME} PUBLIC "src")
-target_compile_options(${LIB_PROJECT_NAME} PUBLIC ${COMMON_COMPILER_FLAGS})
-
-
 # dependency grouping in the IDE
 foreach(TARGET_NAME
     clean-core
@@ -214,20 +332,55 @@ foreach(TARGET_NAME
     polyscope
     glpk
     lpsolve
-    scip
+    # scip
+    # glfw
+    # glow
+    # imgui
+    # glow-extras
     soplex
-#    glfw
-#    glow
-#    imgui
-#    glow-extras
 
 )
 set_property(TARGET ${TARGET_NAME} PROPERTY FOLDER "Extern")
 endforeach()
 
 
+# ===============================================
+# main libary
+target_include_directories(${LIB_PROJECT_NAME} PUBLIC "src")
+target_compile_options(${LIB_PROJECT_NAME} PUBLIC ${COMMON_COMPILER_FLAGS})
+
+
 # ===============================================
 # pyind11
 pybind11_add_module("${PYBIND_PROJECT_NAME}" src/linkmlpy.cpp)
 target_link_libraries("${PYBIND_PROJECT_NAME}" PRIVATE ${LIB_PROJECT_NAME})
 
+
+# ===============================================
+# tests
+if (LINKML_SAMPLES_TESTS)
+
+    file(GLOB_RECURSE TEST_SOURCES
+        "tests/*.cc"
+        "tests/*.hh"
+    )
+
+    source_group(TREE ${CMAKE_CURRENT_SOURCE_DIR} FILES ${TEST_SOURCES})
+
+    add_executable("${TEST_PROJECT_NAME}" ${TEST_SOURCES})
+
+    target_link_libraries("${TEST_PROJECT_NAME}" PUBLIC
+        ${LIB_PROJECT_NAME}
+        nexus
+    )
+
+    target_include_directories("${TEST_PROJECT_NAME}" PUBLIC "tests")
+
+    if(MSVC)
+        target_compile_options("${TEST_PROJECT_NAME}" PUBLIC /MP /FC)
+    else()
+        target_compile_options("${TEST_PROJECT_NAME}" PUBLIC -Wall)
+    endif()
+
+endif()
+