Merge pull request #15 from crvs/no_pcl

Removed dependency on PCL and CGAL

.gitignore

@@ -1,6 +1,9 @@
 # ignore all files
 *
 
+# tags file
+tags
+
 # unignore directories
 !*/
 

.gitmodules

@@ -0,0 +1,9 @@
+[submodule "KDTree"]
+	path = KDTree
+	url = [email protected]:crvs/KDTree.git
+[submodule "tinyply"]
+	path = tinyply
+	url = https://github.com/ddiakopoulos/tinyply
+[submodule "tinyobjloader"]
+	path = tinyobjloader
+	url = https://github.com/syoyo/tinyobjloader

CMakeLists.txt

@@ -1,22 +1,18 @@
-cmake_minimum_required(VERSION 2.8)
+cmake_minimum_required(VERSION 3.0)
 project(coefficient-flow CXX)
 
 # requirements:
 #   * Gudhi under /usr/include/gudhi
 #   * Eigen3 under /usr/include/eigen3
 #   * boost under /usr/include/boost
-#   * CGAL under /usr/include/CGAL
 #   * libyaml under /usr/local/include/libyaml
-#   * pcl 1.8 under /usr/include/pcl-1.8
 #
 
-# in case Eigen, and/or CGAL, and/or GUDHI are not found by find_package
+# in case Eigen, and/or GUDHI are not found by find_package
 # try setting the paths to them manually
 #
 # set(EIGEN3_INCLUDE_DIR "/usr/local/include/eigen3")
 # include_directories(${EIGEN3_INCLUDE_DIR})
-# set(CGAL_INCLUDE_DIR "/usr/local/include/eigen3")
-# include_directories(${CGAL_INCLUDE_DIR})
 #
 
 # GUDHI version should be 1.3 or higher, provided they don't break the
@@ -25,33 +21,32 @@ project(coefficient-flow CXX)
 # libyaml-cpp this should actually be found in "/usr/include" so there is no
 # real need for the find_package, but it's always nice to make sure
 #
-# pcl-1.8 version 1.7 doesn't let one read ply files into meshes which is
-# rather strange, but it is a thing.
-#
 
-find_package(Boost REQUIRED QUIET)
-message(STATUS "Boost version: ${BOOST_VERSION}")
-message(STATUS "Boost directory: ${BOOST_INCLUDE_DIRS}")
+# TODO remove
+add_subdirectory(KDTree)
+
+
+add_subdirectory(tinyply)
+include_directories("./tinyply/source/")
+
+add_subdirectory(tinyobjloader)
+include_directories("./tinyobjloader")
+
+find_package(Boost REQUIRED)
+message(STATUS "Boost version: ${Boost_VERSION}")
+message(STATUS "Boost directory: ${Boost_INCLUDE_DIRS}")
+message(STATUS "boost libraries: ${Boost_LIBRARIES}")
 
 find_package(Eigen3 3.1.2 REQUIRED QUIET)
 message(STATUS "Eigen3 version: ${EIGEN3_VERSION}")
 message(STATUS "Eigen3 directory: ${EIGEN3_INCLUDE_DIR}")
 include_directories(${EIGEN3_INCLUDE_DIR})
 
-find_package(CGAL REQUIRED QUIET)
-message(STATUS "CGAL version: ${CGAL_VERSION}")
-message(STATUS "CGAL directory: ${CGAL_INCLUDE_DIRS}")
-
 find_package(yaml-cpp REQUIRED QUIET)
 message(STATUS "yaml-cpp version: ${YAML_CPP_VERSION}")
 message(STATUS "yaml-cpp directory: ${YAML_CPP_INCLUDE_DIR}")
 include_directories(${YAML_CPP_INCLUDE_DIR})
 
-find_package(PCL 1.8 REQUIRED QUIET COMPONENTS io)
-message(STATUS "PCL version: ${PCL_VERSION}")
-message(STATUS "PCL directory: ${PCL_INCLUDE_DIRS}")
-include_directories(${PCL_INCLUDE_DIRS})
-
 find_package(GUDHI 1.3 REQUIRED QUIET)
 message(STATUS "Gudhi version: ${GUDHI_VERSION}")
 string(REGEX MATCH "^/home/" LOCAL_INSTALLED "${GUDHI_DIR}")
@@ -79,16 +74,22 @@ set(CMAKE_OBJDUMP "/usr/bin/llvm-objdump")
 set(CMAKE_RANLIB  "/usr/bin/llvm-ranlib")
 
 set(CMAKE_BUILD_TYPE Release)
+# set(CMAKE_BUILD_TYPE Debug)
+
+include_directories(
+    "./lib" # where all the library files are
+    "KDTree" # for the KDTree library
+    )
 
-include_directories("./lib") # where all the library files are
 
 add_library(scomplex SHARED "./lib/scomplex/simplicial_complex.cpp")
 add_library(pathsnap SHARED "./lib/scomplex/path_snapper.cpp")
+target_link_libraries(pathsnap KDTree)
 
 add_executable(qhull2ply "src/make_mesh.cpp")
 
 add_executable(yamltest "src/testing_facility.cpp")
-target_link_libraries(yamltest yaml-cpp scomplex pathsnap ${PCL_LIBRARIES})
+target_link_libraries(yamltest yaml-cpp scomplex pathsnap tinyply tinyobjloader)
 
 message(INFO ${CMAKE_CURRENT_SOURCE_DIR})
 message(INFO ${CMAKE_CURRENT_BINARY_DIR})
@@ -98,3 +99,4 @@ add_custom_target(timing_test
     COMMAND "cp" "${CMAKE_CURRENT_SOURCE_DIR}/test/dumbexample.yaml" "${CMAKE_CURRENT_BINARY_DIR}"
     COMMAND "${CMAKE_CURRENT_BINARY_DIR}/run_dumb_tests.sh" "1"
     DEPENDS yamltest qhull2ply "test/run_dumb_tests.sh" "test/dumbexample.yaml")
+

README.md

@@ -14,14 +14,11 @@ In order to compile this repository you will need the following packages:
 - `clang (v == 3.8)`
 - `Eigen (v == 3.3.2)`
 - `Boost (v >= 1.54.0)`
-- `CGAL  (v >= 4.9.1)`
 - `Gudhi (v >= 1.3.1)`
-- `pcl   (v >= 1.8.0)`
 - `libyaml`
 
 **Note:**
 - In case you are using a different version of `clang`, everything should still compile without problems, but you will need to change the appropriate lines in `CMakeLists.txt`.
-- pcl needs to be version 1.8 or higher because 1.7 does not support reading ply files into `pcl::PolygonMesh` elements.
 
 ## Running
 

lib/scomplex/chain_calc.hpp

@@ -41,13 +41,13 @@ bounding_chain::bounding_chain(std::shared_ptr<simplicial_complex> sc) {
 }
 
 bounding_chain::bounding_chain(simplicial_complex& sc) {
-    s_comp.reset(new simplicial_complex(sc));
+    s_comp = std::make_shared<simplicial_complex>(sc);
     populate_matrices();
 }
 
 bounding_chain::bounding_chain(std::vector<point_t>& points,
                                std::vector<cell_t>& tris) {
-    s_comp.reset(new simplicial_complex(points, tris));
+    s_comp = std::make_shared<simplicial_complex>(points,tris);
     populate_matrices();
 }
 

lib/scomplex/graph_utils.hpp

@@ -110,7 +110,7 @@ std::vector<vertex_t> shortest_path(graph_t& g, vertex_t s, vertex_t t) {
 
 std::vector<vertex_t> complete_path(graph_t& g,
                                     std::vector<vertex_t> vec) {
-    std::vector<vertex_t>::iterator s{vec.begin()};
+    std::vector<vertex_t>::iterator s = vec.begin();
     std::vector<vertex_t>::iterator t = std::next(s);
 
     // start calculatinng the full path