init clean branch

.gitignore

@@ -0,0 +1,5 @@
+out
+.vs
+CMakeSettings.json
+diplib/lib
+main_sources.cmake

.gitmodules

@@ -0,0 +1,14 @@
+[submodule "external/diplib"]
+	path = external/diplib
+	url = https://github.com/DIPlib/diplib
+[submodule "external/libigl"]
+	path = external/libigl
+	url = https://github.com/libigl/libigl.git
+	branch = dev
+[submodule "external/vcglib"]
+	path = external/vcglib
+	url = https://github.com/cnr-isti-vclab/vcglib
+	branch = devel
+[submodule "external/tbb"]
+	path = external/tbb
+	url = https://github.com/wjakob/tbb

.travis.yml

@@ -0,0 +1,39 @@
+language: cpp
+os: linux
+dist: xenial
+branches:
+  only:
+  - master
+  - dev
+jobs:
+  include:
+    - os: linux
+      addons:
+        apt:
+          sources:
+            - ubuntu-toolchain-r-test
+          packages:
+            - g++-7
+      env: COMPILER=g++-7 CPP_VER=11
+    - os: osx
+      osx_image: xcode10
+      env: COMPILER=g++-7 CPP_VER=11
+      before_install:
+        - brew update
+        - brew install gcc@7
+    - os: windows
+
+install:
+  - if [[ "${COMPILER}" != "" ]]; then export CXX=${COMPILER}; fi
+  - ${CXX} --version
+
+before_script:
+  - mkdir -p -v build
+  - cd build
+  - cmake ..
+
+script:
+  - cmake --build .
+
+notifications:
+  email: off

CMakeLists.txt

@@ -0,0 +1,60 @@
+cmake_minimum_required (VERSION 3.8)
+
+project ("Scaffolder")
+
+set(CGAL_DO_NOT_WARN_ABOUT_CMAKE_BUILD_TYPE ON)
+set(CMAKE_MODULE_PATH ${CMAKE_MODULE_PATH} ${CMAKE_CURRENT_SOURCE_DIR}/cmake)
+set(CMAKE_CXX_STANDARD 11)
+set(CMAKE_CXX_STANDARD_REQUIRED ON)
+set(CMAKE_CXX_EXTENSIONS OFF)
+
+# libigl
+option(LIBIGL_WITH_OPENGL            "Use OpenGL"         OFF)
+option(LIBIGL_WITH_OPENGL_GLFW       "Use GLFW"           OFF)
+
+message(STATUS "PROJECT_SOURCE_DIR=${PROJECT_SOURCE_DIR}")
+
+find_package(LIBIGL REQUIRED)
+find_package(TBB REQUIRED)
+find_package(VCG REQUIRED)
+find_package(DIPlib REQUIRED)
+
+# Add your project files
+file(GLOB MAIN_SOURCES
+	"${PROJECT_SOURCE_DIR}/include/*.c"
+	"${PROJECT_SOURCE_DIR}/include/*.cpp"
+	"${PROJECT_SOURCE_DIR}/include/*.tpp"
+	"${PROJECT_SOURCE_DIR}/include/*.h"
+	"${PROJECT_SOURCE_DIR}/include/*.hpp"
+	"${PROJECT_SOURCE_DIR}/include/*/*.c"
+	"${PROJECT_SOURCE_DIR}/include/*/*.cpp"
+	"${PROJECT_SOURCE_DIR}/include/*/*.tpp"
+	"${PROJECT_SOURCE_DIR}/include/*/*.h"
+	"${PROJECT_SOURCE_DIR}/include/*/*.hpp"
+	"${PROJECT_SOURCE_DIR}/include/vcglib/*.h"
+	"${PROJECT_SOURCE_DIR}/include/vcglib/*/*.h"
+	"${PROJECT_SOURCE_DIR}/include/vcglib/*/*/*.h"
+	"${PROJECT_SOURCE_DIR}/include/vcglib/*/*/*/*.h"
+	"${VCG_INCLUDE_DIR}/wrap/ply/plylib.cpp"
+)
+include(update_deps_file)
+update_deps_file("main_sources" "${MAIN_SOURCES}")
+
+if(MSVC)
+  # Enable parallel compilation for Visual Studio
+  add_compile_options(/MP /bigobj)
+  add_definitions(-DNOMINMAX -D_USE_MATH_DEFINES)
+endif()
+
+add_definitions(-DDIP__IS_STATIC -DDIP__ENABLE_ASSERT -DDIP__HAS_JPEG -DDIP__EXCEPTIONS_RECORD_STACK_TRACE)
+add_executable(${PROJECT_NAME} ${MAIN_SOURCES} ${PROJECT_SOURCE_DIR}/src/Main.cpp)
+target_include_directories(${PROJECT_NAME} PRIVATE "${PROJECT_SOURCE_DIR}/include" ${TBB_INCLUDE_DIR} ${VCG_INCLUDE_DIR} ${DIPlib_INCLUDE_DIR} ${EIGEN_INCLUDE_DIR})
+target_link_libraries(${PROJECT_NAME} PRIVATE igl::core DIP tbb_static)
+
+add_executable(SliceTest ${MAIN_SOURCES} ${PROJECT_SOURCE_DIR}/src/SliceTest.cpp)
+target_include_directories(SliceTest PRIVATE "${PROJECT_SOURCE_DIR}/include" ${TBB_INCLUDE_DIR} ${VCG_INCLUDE_DIR} ${EIGEN_INCLUDE_DIR})
+target_link_libraries(SliceTest PRIVATE tbb_static)
+
+add_executable(Fixer ${MAIN_SOURCES} ${PROJECT_SOURCE_DIR}/src/FixSelfIntersect.cpp)
+target_include_directories(Fixer PRIVATE "${PROJECT_SOURCE_DIR}/include" ${TBB_INCLUDE_DIR} ${VCG_INCLUDE_DIR} ${EIGEN_INCLUDE_DIR})
+target_link_libraries(Fixer tbb_static)

LICENSE

@@ -0,0 +1,21 @@
+MIT License
+
+Copyright (c) 2019 Jirawat I.
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

README.md

@@ -0,0 +1,78 @@
+# Scaffolder 
+[![Build Status](https://travis-ci.org/nodtem66/Scaffolder.svg?branch=master)](https://travis-ci.org/nodtem66/Scaffolder) [![Build Status](https://travis-ci.org/nodtem66/Scaffolder.svg?branch=dev)](https://travis-ci.org/nodtem66/Scaffolder) [![Build Status](https://dev.azure.com/n66/Public%20CI/_apis/build/status/nodtem66.Scaffolder?branchName=master)](https://dev.azure.com/n66/Public%20CI/_build/latest?definitionId=1&branchName=master) [![Build Status](https://dev.azure.com/n66/Public%20CI/_apis/build/status/nodtem66.Scaffolder?branchName=dev)](https://dev.azure.com/n66/Public%20CI/_build/latest?definitionId=1&branchName=dev)
+
+Generate scaffold from STL file with implicit function (Schwarz P/ Gyroid).
+
+```
+Scaffolder - generate 3D scaffold from STL file
+Usage:
+  Scaffolder [OPTION...] [option args]
+
+  -h, --help                    Print help
+  -q, --quiet                   Disable verbose output [default: false]
+  -m, --microstructure          Analysis microstructure ( [default: false]
+      --m1                      Export and analysis microstructure 1 (Image
+                                processing technique) [default: false]
+      --m2                      Export and analysis microstructure 2 (Slice
+                                coutour technique) [default: false]
+  -f, --format arg              Output format (OFF,PLY,STL,OBJ) [default:
+                                ply]
+  -i, --input FILE              Input file (STL)
+  -o, --output FILENAME         Output filename without extension [default:
+                                out]
+  -c, --coff DOUBLE             default:4*PI
+  -s, --shell INT               [default:0]
+  -n, --surface NAME            rectlinear, schwarzp, schwarzd, gyroid,
+                                double-p, double-d, double-gyroiod, lidinoid,
+                                schoen_iwp, neovius, bcc, tubular_g_ab, tubular_g_c
+                                [default: schwarzp]
+  -t, --thickness DOUBLE        Thickness [default: 0]
+  -g, --grid_size INT           Grid size [default: 100]
+      --grid_offset INT         [default:3]
+      --smooth_step INT         Smooth with laplacian (default: 5)
+      --method 0,1              Method of microstructure analysis: 0 (Image
+                                processing technique) or 1 (Slice contour
+                                technique) [default: 0]
+      --output_inverse          additional output inverse scaffold
+      --inverse                 Enable build inverse 3D scaffold (for pore
+                                connectivity analysis)
+      --dirty                   Disable autoclean
+      --fix_self_intersect	    Enable experimental fixing for self-intersect problems (default: false)
+      --qsim DOUBLE (0-1)       % Quadric simplification for reducing the resolution of 3D mesh (default: false)
+      --minimum_diameter DOUBLE
+                                used for removing small orphaned (between
+                                0-1) [default: 0.25]
+```
+
+## Screenshots
+
+** The figure of patterns implemented in this program
+
+![TPMS Patterns](https://github.com/nodtem66/Scaffolder/raw/master/images/patterns.jpg)
+
+** The examples of generated porous scaffold
+
+![Examples porous scaffold](https://github.com/nodtem66/Scaffolder/raw/master/images/examples.jpg)
+
+## Dependencies
+- [libigl](https://libigl.github.io/)
+- [vcglib](https://github.com/cnr-isti-vclab/vcglib)
+- [diplib](https://github.com/DIPlib/diplib)
+
+## How it works
+- Read STL file and finding the boundary box
+- Generate the grid and calculate the winding number with STL mesh
+- Use winding number to determine the condition for [implicit isosurface function](https://wewanttolearn.wordpress.com/2019/02/03/triply-periodic-minimal-surfaces/)
+- Generate the isosurface field in the same-size grid
+- Perform [Dual marching cube](https://github.com/dominikwodniok/dualmc) to construct the manifold
+- Clean up the duplicated vertices or faces, and abandon the group of connected faces having the diameter below the setting
+- Export to the target 3D format
+
+## Reference 
+- [dualmc](https://github.com/dominikwodniok/dualmc)
+- [cxxopts](https://github.com/jarro2783/cxxopts)
+- [ProgressBar](https://github.com/prakhar1989/progress-cpp)
+- [Minimal surface Blog](https://minimalsurfaces.blog/)
+
+## Citation
+

azure-pipelines.yml

@@ -0,0 +1,42 @@
+# Starter pipeline
+# Start with a minimal pipeline that you can customize to build and deploy your code.
+# Add steps that build, run tests, deploy, and more:
+# https://aka.ms/yaml
+
+trigger:
+- master
+- dev
+
+variables:
+  build_type: Debug
+  build_std: 11
+  CMAKE_BUILD_PARALLEL_LEVEL: 4
+
+strategy:
+  matrix:
+    Linux14:
+      vmImage: 'ubuntu-latest'
+    macOS17:
+      vmImage: 'macOS-latest'
+      build_std: 17
+    macOS11:
+      vmImage: 'macOS-latest'
+      build_std: 11
+    Windows17:
+      vmImage: 'vs2017-win2016'
+      build_std: 17
+    Windows11:
+      vmImage: 'vs2017-win2016'
+      build_std: 11
+pool:
+  vmImage: $(vmImage)
+steps:
+- checkout: self
+  submodules: true
+- task: CMake@1
+  inputs:
+    cmakeArgs: .. -DCMAKE_CXX_STANDARD=$(build_std) -DCMAKE_BUILD_TYPE=$(build_type)
+  displayName: 'Configure'
+- script: cmake --build .
+  displayName: 'Build'
+  workingDirectory: build

cmake/FindDIPlib.cmake

@@ -0,0 +1,42 @@
+# - Try to find the DIPlib library
+# Once done this will define
+#
+#  DIPlib_FOUND - system has DIPlib
+#  DIPlib_INCLUDE_DIR - **the** DIPlib include directory
+if(DIPlib_FOUND)
+    return()
+endif()
+
+find_path(DIPlib_INCLUDE_DIR diplib.h
+    HINTS
+        ${DIPlib_DIR}
+        ENV DIPlib_DIR
+    PATHS
+         ${PROJECT_SOURCE_DIR}/external/diplib
+         ${PROJECT_SOURCE_DIR}/../external/diplib
+         ${PROJECT_SOURCE_DIR}/../../external/diplib
+    PATH_SUFFIXES include
+    NO_DEFAULT_PATH
+)
+# TODO: Rewrite this cmake to add the source without compiled lib
+set(DIPlib_LIB_DIR ${DIPlib_INCLUDE_DIR}/../lib)
+set(DIPlib_ROOT_DIR ${DIPlib_INCLUDE_DIR}/../)
+
+include(FindPackageHandleStandardArgs)
+find_package_handle_standard_args(DIPlib
+    "\nDIPlib not found --- You can download it using:\n\tgit clone https://github.com/DIPlib/diplib ${CMAKE_SOURCE_DIR}/../diplib"
+    DIPlib_INCLUDE_DIR)
+mark_as_advanced(DIPlib_INCLUDE_DIR)
+
+set(DIP_BUILD_DIPIMAGE OFF CACHE INTERNAL "")
+set(DIP_BUILD_JAVAIO OFF CACHE INTERNAL "")
+set(DIP_BUILD_PYDIP OFF CACHE INTERNAL "")
+set(DIP_SHARED_LIBRARY OFF CACHE INTERNAL "")
+set(DIP_ENABLE_UNICODE OFF CACHE INTERNAL "")
+set(DIP_ENABLE_DOCTEST OFF CACHE INTERNAL "")
+set(DIP_ENABLE_STACK_TRACE OFF CACHE INTERNAL "")
+#set(DIP_ENABLE_MULTITHREADING ON CACHE INTERNAL "")
+
+list(APPEND CMAKE_MODULE_PATH "${DIPlib_ROOT_DIR}")
+message(STATUS "USE DIR: ${DIPlib_ROOT_DIR}")
+add_subdirectory(${DIPlib_ROOT_DIR})

cmake/FindHighFive.cmake

@@ -0,0 +1,34 @@
+# - Try to find the HighFive library
+# Once done this will define
+#
+#  HighFive_FOUND - system has HighFive
+#  HighFive_INCLUDE_DIR - **the** HighFive include directory
+if(HighFive_FOUND)
+    return()
+endif()
+find_path(HighFive_INCLUDE_DIR H5Easy.hpp
+    HINTS
+        ${HighFive_DIR}
+        ENV HighFive_DIR
+    PATHS
+        ${CMAKE_SOURCE_DIR}/HighFive
+        ${CMAKE_SOURCE_DIR}/../HighFive
+        ${CMAKE_SOURCE_DIR}/../../HighFive
+        ${CMAKE_SOURCE_DIR}/../..
+        ${CMAKE_SOURCE_DIR}/..
+        ${CMAKE_SOURCE_DIR}
+        /usr
+        /usr/local
+        /usr/local/igl/HighFive
+    PATH_SUFFIXES include/highfive
+)
+
+# find_path(H5_INCLUDE_DIR H5Ppublic.h)
+# LIST(APPEND HighFive_INCLUDE_DIR ${H5_INCLUDE_DIR})
+
+include(FindPackageHandleStandardArgs)
+find_package_handle_standard_args(HighFive
+    "\nHighFive not found --- You can download it using:\n\tgit clone https://github.com/BlueBrain/HighFive ${CMAKE_SOURCE_DIR}/../HighFive"
+    HighFive_INCLUDE_DIR)
+mark_as_advanced(HighFive_INCLUDE_DIR)
+message(STATUS "USE DIR: ${HighFive_INCLUDE_DIR}/")

cmake/FindLIBIGL.cmake

@@ -0,0 +1,34 @@
+# - Try to find the LIBIGL library
+# Once done this will define
+#
+#  LIBIGL_FOUND - system has LIBIGL
+#  LIBIGL_INCLUDE_DIR - **the** LIBIGL include directory
+if(LIBIGL_FOUND)
+    return()
+endif()
+find_path(LIBIGL_INCLUDE_DIR igl/readOBJ.h
+    HINTS
+        ${LIBIGL_DIR}
+        ENV LIBIGL_DIR
+    PATHS
+        ${PROJECT_SOURCE_DIR}/external/libigl
+        ${PROJECT_SOURCE_DIR}/../external/libigl
+        ${PROJECT_SOURCE_DIR}/../../external/libigl
+    PATH_SUFFIXES include
+    NO_DEFAULT_PATH
+)
+
+include(FindPackageHandleStandardArgs)
+find_package_handle_standard_args(LIBIGL
+    "\nlibigl not found --- You can download it using:\n\tgit clone https://github.com/libigl/libigl.git ${CMAKE_SOURCE_DIR}/../libigl"
+    LIBIGL_INCLUDE_DIR)
+mark_as_advanced(LIBIGL_INCLUDE_DIR)
+
+set(LIBIGL_WITH_OPENGL OFF CACHE INTERNAL "turn off OPENGL in LIBIGL")
+set(LIBIGL_WITH_OPENGL_GLFW OFF CACHE INTERNAL "turn off OPENGL GLFW in LIBIGL")
+set(LIBIGL_USE_STATIC_LIBRARY OFF CACHE INTERNAL "prefer STATIC build")
+
+list(APPEND CMAKE_MODULE_PATH "${LIBIGL_INCLUDE_DIR}/../cmake")
+message(STATUS "USE DIR: ${LIBIGL_INCLUDE_DIR}")
+set(EIGEN_INCLUDE_DIR "${LIBIGL_INCLUDE_DIR}/../external/eigen")
+include(libigl)