Backend cpp for model-based semantic segmentation

.gitignore

@@ -85,7 +85,7 @@ temp/
 ## Python
 #######################################
 # Byte-compiled / optimized / DLL files
-__pycache__/
+**/__pycache__/
 *.py[cod]
 *$py.class
 
@@ -243,4 +243,7 @@ cython_debug/
 #  be found at https://github.com/github/gitignore/blob/main/Global/JetBrains.gitignore
 #  and can be added to the global gitignore or merged into this file.  For a more nuclear
 #  option (not recommended) you can uncomment the following to ignore the entire idea folder.
-#.idea/
+#.idea/
+
+# egg-info
+*.egg-info/

.vscode/settings.json

@@ -104,6 +104,7 @@
         "cwctype": "cpp",
         "memory_resource": "cpp",
         "scoped_allocator": "cpp",
-        "strstream": "cpp"
+        "strstream": "cpp",
+        "core": "cpp"
     }
 }

CMakeLists.txt

@@ -119,15 +119,6 @@ target_include_directories(${APP_NAME_EXE}
     PUBLIC ${CMAKE_CURRENT_SOURCE_DIR}/src
     )
 
-#--------------------------------------------------------------------------
-# Tests
-#--------------------------------------------------------------------------
-
-# include(CTest)
-# enable_testing()
-
-# add_subdirectory(${CMAKE_CURRENT_SOURCE_DIR}/tests/global_registrations)
-
 #--------------------------------------------------------------------------
 # pybind11
 #--------------------------------------------------------------------------
@@ -171,4 +162,42 @@ if (BUILD_PYTHON_MODULE)
             )
     endforeach()
 
-endif()
+endif()
+
+#--------------------------------------------------------------------------
+# Tests
+#--------------------------------------------------------------------------
+
+# include(CTest)
+# enable_testing()
+# add_subdirectory(${CMAKE_CURRENT_SOURCE_DIR}/deps/googletest)
+# set(TESTS_OUT_DIR ${CMAKE_BINARY_DIR}/tests/)
+
+
+# # Unit testing ------------------------------------------------------------
+# set(UNIT_TESTS unit_tests)
+# add_executable(${UNIT_TESTS} tests/unit_tests/DFPointCloudTest.cc)
+# set_target_properties(${UNIT_TESTS} PROPERTIES
+#     RUNTIME_OUTPUT_DIRECTORY ${TESTS_OUT_DIR}
+#     )
+
+# target_link_libraries(${UNIT_TESTS} gtest gtest_main)
+# target_link_libraries(${UNIT_TESTS} ${SHARED_LIB_NAME})
+
+# add_test(NAME ${UNIT_TESTS} COMMAND ${UNIT_TESTS})
+
+# Integration testing -----------------------------------------------------
+# Component testing -------------------------------------------------------
+# etc ---------------------------------------------------------------------
+
+# # TODO: a better way to copy the dlls to the tests directory for the tests
+# # get all the files -dlls in the bin directory and copy them one by one to tests dir
+# file(GLOB files ${CMAKE_BINARY_DIR}/bin/Release/*.dll)
+# foreach(file ${files})
+#     message(STATUS "Copying ${file} to ${TESTS_OUT_DIR}")
+#     add_custom_command(TARGET ${UNIT_TESTS} POST_BUILD
+#         COMMAND ${CMAKE_COMMAND} -E copy
+#         ${file}
+#         ${TESTS_OUT_DIR}/Release
+#         )
+# endforeach()

README.md

@@ -36,19 +36,6 @@ gantt
     Data collection and evaluation      :dataeval, after fabrob, 4w
 ```
 
-```mermaid
-gantt
-    dateFormat  YYYY-MM-DD
-    title       diffCheck - backend dev
-    excludes    weekends
-
-    data i/o                                 :active, dataio, 2024-03-15, 3w
-    global registration                      :glbreg, 2024-03-29, 2w
-    semantic seg. from 3D model              :semseg, after glbreg, 1w
-    local registration                       :locreg, after semseg, 2w
-    error computation + results              :errcomp, after locreg, 1w
-```
-
 ## 3rd party libraries
 
 The project uses the following 3rd party libraries:
@@ -63,22 +50,22 @@ To build and test the project, follow the following steps:
 ```terminal
 cmake/config.bat
 cmake/build.bat
-./build/bin/Release/diffCheckApp.exe <-- for prototyping
+./build/bin/Release/diffCheckApp.exe <-- for prototyping in c++
 ```
 
 ## Prototype diffCheck in C++
 To prototype:
 1) add a header/source file in `src/diffCheck` and include the header in `diffCheck.hh` interface
-1) test it in `diffCheckApp` (the cmake will output an executable in bin)
+2) test it in `diffCheckApp` (the cmake will output an executable in bin)
 
 See the [CONTRIBUTING.md](https://github.com/diffCheckOrg/diffCheck/blob/main/CONTRIBUTING.md) for more information on how to prototype with diffCheck (code guidelines, visualizer, utilities, etc).
 
 ## Component roadmap
 From the 3/5/2024 meeting, the architecture of the different grasshopper components was discussed as following:
-- [ ] PLY loader point cloud: @eleni: loads the pointcloud ply files and converts it into rg.PointCloud (+ cvt submodule)
-- [ ] PLY loader mesh: @eleni: loads the mesh ply files and converts it into rg.Mesh (+ cvt submodule)
-- [ ] Global registration: @andrea: to align the scan to the reference model
-- [ ] Refined registration: @andrea: to refine the alignement
+- [x] PLY loader point cloud: @eleni: loads the pointcloud ply files and converts it into rg.PointCloud (+ cvt submodule)
+- [x] PLY loader mesh: @eleni: loads the mesh ply files and converts it into rg.Mesh (+ cvt submodule)
+- [x] Global registration: @andrea: to align the scan to the reference model
+- [x] Refined registration: @andrea: to refine the alignement
 - [ ] Semantic segmentation additive: to identify the pieces or joints in the point cloud
 - [ ] Semantic segmentation subtractive: to identify the pieces or joints in the point cloud
 - [ ] Per-joint refinement to refine the global registration to each joints (only in the "substractive" case)

ScreenCamera_2024-06-30-00-00-53.json

@@ -0,0 +1,41 @@
+{
+	"class_name" : "PinholeCameraParameters",
+	"extrinsic" : 
+	[
+		0.78518600604290978,
+		-0.4688467948733368,
+		0.4045560762754441,
+		0.0,
+		-0.61432912235314374,
+		-0.67201447960085037,
+		0.41351695084435719,
+		0.0,
+		0.077991444038432445,
+		-0.57321830234544802,
+		-0.81568260525341763,
+		0.0,
+		1416.8243739322577,
+		908.62300697364822,
+		1063.1264987715035,
+		1.0
+	],
+	"intrinsic" : 
+	{
+		"height" : 800,
+		"intrinsic_matrix" : 
+		[
+			692.82032302755101,
+			0.0,
+			0.0,
+			0.0,
+			692.82032302755101,
+			0.0,
+			499.5,
+			399.5,
+			1.0
+		],
+		"width" : 1000
+	},
+	"version_major" : 1,
+	"version_minor" : 0
+}

ScreenCamera_2024-06-30-11-58-46.json

@@ -0,0 +1,41 @@
+{
+	"class_name" : "PinholeCameraParameters",
+	"extrinsic" : 
+	[
+		0.76239913059926834,
+		-0.422274821893041,
+		0.49033818988192268,
+		0.0,
+		-0.54132130094127906,
+		-0.00099240450767756894,
+		0.8408152378974435,
+		0.0,
+		-0.35456849099817256,
+		-0.90646731321570218,
+		-0.22934296427574399,
+		0.0,
+		1550.6223360557265,
+		197.24908733414611,
+		336.92784140962624,
+		1.0
+	],
+	"intrinsic" : 
+	{
+		"height" : 800,
+		"intrinsic_matrix" : 
+		[
+			692.82032302755101,
+			0.0,
+			0.0,
+			0.0,
+			692.82032302755101,
+			0.0,
+			499.5,
+			399.5,
+			1.0
+		],
+		"width" : 1000
+	},
+	"version_major" : 1,
+	"version_minor" : 0
+}

cmake/build_run.bat

@@ -0,0 +1 @@
+.\cmake\build.bat ; if ($?) { .\build\bin\Release\diffCheckApp.exe }

src/diffCheck.hh

@@ -3,6 +3,8 @@
 #include <open3d/Open3D.h>
 #include <loguru.hpp>
 
+#include <cilantro/cilantro.hpp>
+
 // diffCheck includes
 #include "diffCheck/log.hh"
 const diffCheck::Log LOG = diffCheck::Log();

src/diffCheck/geometry/DFMesh.cc

@@ -71,6 +71,30 @@ namespace diffCheck::geometry
         this->Cvt2DFMesh(O3DTriangleMesh);
     }
 
+    std::vector<Eigen::Vector3d> DFMesh::GetTightBoundingBox()
+    {
+        auto O3DTriangleMesh = this->Cvt2O3DTriangleMesh();
+        open3d::geometry::OrientedBoundingBox tightOOBB = O3DTriangleMesh->GetMinimalOrientedBoundingBox();
+        std::vector<Eigen::Vector3d> bboxPts = tightOOBB.GetBoxPoints();
+        return bboxPts;
+    }
+
+    Eigen::Vector3d DFMesh::GetFirstNormal()
+    {
+        if (this->NormalsFace.size() == 0)
+        {
+            std::shared_ptr<open3d::geometry::TriangleMesh> O3DTriangleMesh = this->Cvt2O3DTriangleMesh();
+            O3DTriangleMesh->ComputeTriangleNormals();
+            this->NormalsFace.resize(O3DTriangleMesh->triangle_normals_.size());
+            for (size_t i = 0; i < O3DTriangleMesh->triangle_normals_.size(); i++)
+            {
+                this->NormalsFace[i] = O3DTriangleMesh->triangle_normals_[i];
+            }
+
+        }
+        return this->NormalsFace[0];
+    }
+
     void DFMesh::LoadFromPLY(const std::string &path)
     {
         std::shared_ptr<diffCheck::geometry::DFMesh> tempMesh_ptr = diffCheck::io::ReadPLYMeshFromFile(path);

src/diffCheck/geometry/DFMesh.hh

@@ -62,6 +62,22 @@ namespace diffCheck::geometry
          */
         void ApplyTransformation(const diffCheck::transformation::DFTransformation &transformation);
 
+    public:  ///< Utils
+        /**
+         * @brief Get the mesh tight bounding box
+         * 
+         * @return std::vector<Eigen::Vector3d> A vector of two Eigen::Vector3d, with the first one being the minimum
+         * point and the second one the maximum point of the bounding box.
+         */
+        std::vector<Eigen::Vector3d> GetTightBoundingBox();
+
+        /**
+         * @brief Get the first normal of the mesh. Meant for planar meshes
+         * 
+         * @return Eigen::Vector3d the normal
+         */
+        Eigen::Vector3d GetFirstNormal();
+
     public:  ///< I/O loader
         /**
          * @brief Read a mesh from a file