Merge pull request #38 from nilsbore/windows

Start of Windows library. Wohoo!!

.appveyor.yml

@@ -0,0 +1,39 @@
+version: 1.0.{build}
+os: Visual Studio 2017
+platform: x64
+clone_folder: C:\projects\auvlib
+#shallow_clone: true
+branches:
+  only:
+    - master
+environment:
+  matrix:
+  - CONFIG: Release
+    BOOST_ROOT: C:/Libraries/boost_1_65_1
+    OpenCV_DIR: C:/tools/opencv/build/x64/vc14/lib
+    PYTHON: 27
+install:
+  - cd C:\projects\auvlib
+  - git submodule update --init 
+  #- cinst python2 appveyor already has python
+  - cinst OpenCV --version 3.4.7
+build:
+  parallel: true
+build_script:
+  # Tutorials and tests
+  #- set PATH=C:\Python%PYTHON%-x64;C:\Python%PYTHON%-x64\Scripts;%PATH%
+  - mkdir build
+  - cd build
+  - cmake -DCMAKE_BUILD_TYPE=%CONFIG%
+      -G "Visual Studio 15 2017 Win64"
+      -DAUVLIB_WITH_GSF=OFF
+      -DAUVLIB_USE_LIBIGL_GLFW=ON
+      -DAUVLIB_USE_LIBIGL_TINYXML=ON
+      -DAUVLIB_EXPORT_BUILD=OFF
+      -DCMAKE_SKIP_INSTALL_RULES=true
+      ../
+      #-DCMAKE_INSTALL_PREFIX=../install
+  - set MSBuildLogger="C:\Program Files\AppVeyor\BuildAgent\Appveyor.MSBuildLogger.dll"
+  - set MSBuildOptions=/v:m /m /p:BuildInParallel=true /p:Configuration=%CONFIG% /logger:%MSBuildLogger%
+  #- msbuild %MSBuildOptions% INSTALL.vcxproj
+  - msbuild %MSBuildOptions% ALL_BUILD.vcxproj

.gitmodules

@@ -11,3 +11,6 @@
 [submodule "src/cxxopts"]
 	path = src/cxxopts
 	url = https://github.com/jarro2783/cxxopts.git
+[submodule "src/cereal"]
+	path = src/cereal
+	url = https://github.com/USCiLab/cereal.git

CMakeLists.txt

@@ -1,3 +1,4 @@
 cmake_minimum_required(VERSION 2.8)
+project(auvlib)
 
 add_subdirectory(src)

README.md

@@ -1,6 +1,7 @@
 # auvlib
 
 [![Build Status](https://travis-ci.org/nilsbore/auvlib.svg?branch=master)](https://travis-ci.org/nilsbore/auvlib)
+[![Build status](https://ci.appveyor.com/api/projects/status/kcfxp0jlpwqxt2fs/branch/master?svg=true)](https://ci.appveyor.com/project/nilsbore/auvlib/branch/master)
 [![license](https://img.shields.io/badge/License-BSD%203--Clause-blue.svg)](https://opensource.org/licenses/BSD-3-Clause)
 
 Tools for reading AUV deployment data files and for

src/CMakeLists.txt

@@ -11,11 +11,12 @@ set(CMAKE_MODULE_PATH ${CMAKE_MODULE_PATH} ${CMAKE_CURRENT_SOURCE_DIR}/cmake)
 # locations on all platforms.
 include(GNUInstallDirs)
 
-find_package(Eigen3 REQUIRED)
-find_package(OpenCV REQUIRED)
-find_package(OpenGL REQUIRED)
-find_package(glfw3 REQUIRED)
-find_package(Ceres REQUIRED)
+option(AUVLIB_WITH_GSF "Enable reading and processing gsf data"    ON)
+option(AUVLIB_USE_LIBIGL_EIGEN "Use libigl's version of Eigen"     ON)
+option(AUVLIB_USE_LIBIGL_GLFW "Use libigl's version of glfw"       OFF)
+option(AUVLIB_USE_LIBIGL_TINYXML "Use libigl's version of tinyxml" OFF)
+option(AUVLIB_USE_PYTHON3 "Use python3 instead of python2"         OFF)
+option(AUVLIB_EXPORT_BUILD "Export build dir configs"              ON)
 
 # libigl
 option(LIBIGL_USE_STATIC_LIBRARY "Use libigl as static library" OFF)
@@ -35,13 +36,55 @@ option(LIBIGL_WITH_PYTHON            "Use Python"         OFF)
 option(LIBIGL_WITH_TETGEN            "Use Tetgen"         OFF)
 option(LIBIGL_WITH_TRIANGLE          "Use Triangle"       OFF)
 option(LIBIGL_WITH_VIEWER            "Use OpenGL viewer"  ON)
-option(LIBIGL_WITH_XML               "Use XML"            OFF)
+option(LIBIGL_WITH_XML               "Use XML"            ON)
 #option(LIBIGL_EXPORT_TARGETS         "Export libigl CMake targets" ON)
 
+find_package(OpenCV REQUIRED core highgui imgproc)
+find_package(OpenGL REQUIRED)
+if (AUVLIB_USE_LIBIGL_TINYXML)
+  set(TinyXML2_LIBRARIES tinyxml2)
+else()
+  #find_package(TinyXML2 REQUIRED)
+  set(TinyXML2_LIBRARIES -ltinyxml2)
+endif()
+
 set(ENV{LIBIGL_DIR} ${CMAKE_CURRENT_SOURCE_DIR}/libigl)
 find_package(LIBIGL REQUIRED QUIET)
 include(${CMAKE_CURRENT_BINARY_DIR}/embree/embree-config.cmake)
 
+if (AUVLIB_USE_LIBIGL_GLFW)
+  #add_subdirectory(${CMAKE_CURRENT_SOURCE_DIR}/libigl/external/glfw) # this might be needed on windows?
+  set(GLFW3_LIBRARY glfw)
+else()
+  find_package(glfw3 REQUIRED)
+endif()
+
+if (AUVLIB_USE_LIBIGL_EIGEN)
+  set(EIGEN3_INCLUDE_DIRS ${CMAKE_CURRENT_SOURCE_DIR}/libigl/external/eigen)
+else()
+  find_package(Eigen3 REQUIRED)
+endif()
+
+if(MSVC)
+  if (AUVLIB_USE_PYTHON3)
+    set(PYTHON_EXECUTABLE C:/Python35/python.exe)
+  else()
+    #set(PYTHON_EXECUTABLE C:/Python27/python.exe)
+    set(PYTHON_EXECUTABLE C:/Python27-x64/python.exe)
+  endif()
+else()
+  if (AUVLIB_USE_PYTHON3)
+    set(PYTHON_EXECUTABLE /usr/bin/python3.5)
+  else()
+    set(PYTHON_EXECUTABLE /usr/bin/python2.7)
+  endif()
+endif()
+
+if (MSVC)
+  set(Boost_USE_STATIC_LIBS ON CACHE BOOL "use static libraries from Boost")
+  set(Boost_USE_MULTITHREADED ON)
+  set(Boost_USE_DEBUG_RUNTIME OFF)
+endif()
 # For some reason it seems like we need to do this after libigl
 find_package(Boost COMPONENTS system filesystem date_time REQUIRED)
 
@@ -51,18 +94,21 @@ set(PYBIND11_CPP_STANDARD -std=c++11)
 #add_definitions(-DPYBIND11_PYTHON_VERSION=2.7)
 #set(PYBIND11_PYTHON_VERSION 2.7)
 #set(PYTHON_LIBRARIES /usr/lib/x86_64-linux-gnu/libpython2.7.so)
-set(PYTHON_EXECUTABLE /usr/bin/python2.7)
+
 add_subdirectory(pybind11)
 
 message("Pybind11: " ${PYBIND11_INCLUDE_DIR})
 
 add_subdirectory(cxxopts)
 
-include_directories(${PYBIND11_INCLUDE_DIR} ${CERES_INCLUDE_DIRS} ${EIGEN_INCLUDE_DIRS})
+include_directories(${PYBIND11_INCLUDE_DIR} ${EIGEN3_INCLUDE_DIRS} ${Boost_INCLUDE_DIRS} ${CMAKE_CURRENT_SOURCE_DIR}/cereal/include ${TinyXML2_INCLUDE_DIRS})
+link_directories(${Boost_LIBRARY_DIRS})
 #include_directories(eigen_cereal/include)
 
 include(cmake/glad.cmake)
-add_subdirectory(libgsf)
+if(AUVLIB_WITH_GSF)
+  add_subdirectory(libgsf)
+endif()
 add_subdirectory(libxtf)
 add_subdirectory(eigen_cereal)
 add_subdirectory(data_tools)

src/bathy_maps/CMakeLists.txt

@@ -44,7 +44,9 @@ add_library(sss_meas_data src/sss_meas_data.cpp)
 
 add_library(sss_gen_sim src/sss_gen_sim.cpp)
 
-add_executable(test_mesh src/test_mesh.cpp)
+if(AUVLIB_WITH_GSF)
+  add_executable(test_mesh src/test_mesh.cpp)
+endif()
 
 # Define headers for this library. PUBLIC headers are used for
 # compiling the library, and will be added to consumers' build
@@ -110,14 +112,16 @@ target_include_directories(sss_gen_sim PUBLIC
 target_link_libraries(draw_map std_data ${OpenCV_LIBS})
 
 #target_link_libraries(mesh_map std_data igl::embree ${OpenCV_LIBS} glad ${GLFW3_LIBRARY} ${OPENGL_LIBRARY} ${OPENGL_glu_LIBRARY} -lpthread)
-target_link_libraries(mesh_map PRIVATE std_data ${OpenCV_LIBS} ${GLFW3_LIBRARY} auvlib_glad -lpthread -ltinyxml2) # ${TinyXML2_LIBRARIES})
+target_link_libraries(mesh_map std_data ${OpenCV_LIBS} ${GLFW3_LIBRARY} auvlib_glad -lpthread ${TinyXML2_LIBRARIES})
 
 target_link_libraries(align_map mesh_map std_data xyz_data ${GLFW3_LIBRARY} auvlib_glad -lpthread) # ${TinyXML2_LIBRARIES})
 
 
 target_link_libraries(drape_mesh snell_ray_tracing xtf_data ${GLFW3_LIBRARY} auvlib_glad)
 
-target_link_libraries(test_mesh std_data gsf_data xtf_data csv_data navi_data mesh_map draw_map patch_draper igl::embree ${OpenCV_LIBS} cxxopts)
+if(AUVLIB_WITH_GSF)
+  target_link_libraries(test_mesh std_data gsf_data xtf_data csv_data navi_data mesh_map draw_map patch_draper igl::embree ${OpenCV_LIBS} cxxopts)
+endif()
 
 target_link_libraries(patch_views eigen_cereal ${OpenCV_LIBS})
 
@@ -146,5 +150,7 @@ install(DIRECTORY include/ DESTINATION ${CMAKE_INSTALL_INCLUDEDIR})
 # just go into 'cmake'.
 install(EXPORT BathyMapsConfig DESTINATION share/BathyMaps/cmake)
 
-# This makes the project importable from the build directory
-export(TARGETS draw_map mesh_map align_map drape_mesh patch_draper base_draper map_draper patch_views sss_map_image sss_meas_data sss_gen_sim FILE BathyMapsConfig.cmake)
+if (AUVLIB_EXPORT_BUILD)
+  # This makes the project importable from the build directory
+  export(TARGETS draw_map mesh_map align_map drape_mesh patch_draper base_draper map_draper patch_views sss_map_image sss_meas_data sss_gen_sim FILE BathyMapsConfig.cmake)
+endif()

src/bathy_maps/include/bathy_maps/align_map.h

@@ -1,7 +1,7 @@
 #ifndef ALIGN_MAP_H
 #define ALIGN_MAP_H
 
-#include <eigen3/Eigen/Dense>
+#include <Eigen/Dense>
 #include <igl/AABB.h>
 #include <data_tools/xyz_data.h>
 

src/bathy_maps/include/bathy_maps/base_draper.h

@@ -15,7 +15,7 @@
 #include <igl/opengl/glfw/Viewer.h>
 #include <igl/opengl/gl.h>
 
-#include <eigen3/Eigen/Dense>
+#include <Eigen/Dense>
 #include <random>
 
 #include <data_tools/xtf_data.h>

src/bathy_maps/include/bathy_maps/drape_mesh.h

@@ -12,7 +12,7 @@
 #ifndef DRAPE_MESH_H
 #define DRAPE_MESH_H
 
-#include <eigen3/Eigen/Dense>
+#include <Eigen/Dense>
 #include <data_tools/xtf_data.h>
 #include <data_tools/csv_data.h>
 

src/bathy_maps/include/bathy_maps/mesh_map.h

@@ -12,7 +12,7 @@
 #ifndef MESH_MAP_H
 #define MESH_MAP_H
 
-#include <eigen3/Eigen/Dense>
+#include <Eigen/Dense>
 #include <data_tools/std_data.h>
 #include <data_tools/xtf_data.h>
 

src/bathy_maps/include/bathy_maps/patch_views.h

@@ -12,7 +12,7 @@
 #ifndef PATCH_VIEWS_H
 #define PATCH_VIEWS_H
 
-#include <eigen3/Eigen/Dense>
+#include <Eigen/Dense>
 #include <eigen_cereal/eigen_cereal.h>
 #include <cereal/archives/binary.hpp>
 #include <cereal/types/vector.hpp>

src/bathy_maps/include/bathy_maps/sss_map_image.h

@@ -12,7 +12,7 @@
 #ifndef SSS_MAP_IMAGE_H
 #define SSS_MAP_IMAGE_H
 
-#include <eigen3/Eigen/Dense>
+#include <Eigen/Dense>
 #include <eigen_cereal/eigen_cereal.h>
 #include <cereal/archives/binary.hpp>
 #include <cereal/types/vector.hpp>
@@ -27,7 +27,7 @@ struct sss_map_image {
 
     BoundsT bounds;
 
-    Eigen::MatrixXd sss_map_image;
+    Eigen::MatrixXd sss_map_image_;
 
     double sss_ping_duration; // max time in waterfall image
     Eigen::MatrixXf sss_waterfall_image;
@@ -40,7 +40,7 @@ struct sss_map_image {
 	template <class Archive>
     void serialize( Archive & ar )
     {
-        ar(CEREAL_NVP(bounds), CEREAL_NVP(sss_map_image), CEREAL_NVP(sss_ping_duration),
+        ar(CEREAL_NVP(bounds), CEREAL_NVP(sss_map_image_), CEREAL_NVP(sss_ping_duration),
            CEREAL_NVP(sss_waterfall_image), CEREAL_NVP(sss_waterfall_cross_track),
            CEREAL_NVP(sss_waterfall_depth), CEREAL_NVP(sss_waterfall_model), CEREAL_NVP(pos));
     }

src/bathy_maps/include/bathy_maps/sss_meas_data.h

@@ -12,7 +12,7 @@
 #ifndef SSS_MEAS_DATA_H
 #define SSS_MEAS_DATA_H
 
-#include <eigen3/Eigen/Dense>
+#include <Eigen/Dense>
 #include <eigen_cereal/eigen_cereal.h>
 #include <cereal/archives/binary.hpp>
 #include <cereal/types/vector.hpp>

src/bathy_maps/src/align_map.cpp

@@ -31,7 +31,7 @@ double compute_overlap_ratio(const Eigen::MatrixXd& P1, const Eigen::MatrixXd& P
     int overlapping_points = 0;
     for (int i = 0; i < P1.rows(); i += skip) {
         Eigen::MatrixXd::Index index;
-          // find nearest neighbour
+          // find near_est neighbour
         //(P2_sub.rowwise() - P1.row(i)).colwise().squaredNorm().minCoeff(&index);
         double dist = sqrt((P2_sub.rowwise() - P1.row(i)).colwise().squaredNorm().minCoeff(&index));
         //double dist = (P2_sub.row(index) - P1.row(i)).norm();
@@ -113,16 +113,16 @@ double points_to_mesh_rmse(const Eigen::MatrixXd& P, const Eigen::MatrixXd& V, c
     tree.squared_distance(V, F, P, sqrD, I, Q);
     //Eigen::ArrayXd temp = (P - Q).rowwise().squaredNorm().array();
     //cout << "Temp: " << temp.transpose() << endl;
-    Eigen::Array<bool, Eigen::Dynamic, 1> near = (P - Q).rowwise().squaredNorm().array() < assoc_threshold*assoc_threshold;
+    Eigen::Array<bool, Eigen::Dynamic, 1> near_ = (P - Q).rowwise().squaredNorm().array() < assoc_threshold*assoc_threshold;
 
-    int nbr_near = near.cast<int>().sum();
+    int nbr_near_ = near_.cast<int>().sum();
 
-    cout << "Number points near surface: " << nbr_near << endl;
+    cout << "Number points near_ surface: " << nbr_near_ << endl;
     cout << "Out of: " << P.rows() << endl;
     cout << "P rows: " << P.rows() << endl;
 
-    Eigen::MatrixXd goodP = igl::slice_mask(P, near, 1);
-    Eigen::MatrixXd goodQ = igl::slice_mask(Q, near, 1);
+    Eigen::MatrixXd goodP = igl::slice_mask(P, near_, 1);
+    Eigen::MatrixXd goodQ = igl::slice_mask(Q, near_, 1);
 
     cout << "GoodP rows: " << goodP.rows() << ", cols: " << goodP.cols() << endl;
 
@@ -142,13 +142,13 @@ Eigen::MatrixXd filter_points_mesh_offset(const Eigen::MatrixXd& P, const Eigen:
     cout << "Finding closes mesh points..." << endl;
 
     tree.squared_distance(V, F, P, sqrD, I, Q);
-    Eigen::Array<bool, Eigen::Dynamic, 1> near = sqrD.array() < offset*offset;
+    Eigen::Array<bool, Eigen::Dynamic, 1> near_ = sqrD.array() < offset*offset;
 
-    int nbr_near = near.cast<int>().sum();
+    int nbr_near_ = near_.cast<int>().sum();
 
-    cout << "Number points near surface: " << nbr_near << " out of: " << P.rows() << endl;
+    cout << "Number points near_ surface: " << nbr_near_ << " out of: " << P.rows() << endl;
 
-    Eigen::MatrixXd goodP = igl::slice_mask(P, near, 1);
+    Eigen::MatrixXd goodP = igl::slice_mask(P, near_, 1);
 
     cout << "GoodP rows: " << goodP.rows() << ", cols: " << goodP.cols() << endl;
 
@@ -304,26 +304,26 @@ tuple<Eigen::Matrix4d, double, bool> icp_iteration(const Eigen::MatrixXd& P, con
     Eigen::MatrixXd Q;
 
     tree.squared_distance(V, F, P, sqrD, I, Q);
-    //Eigen::Array<bool, Eigen::Dynamic, 1> near = (P - Q).rowwise().squaredNorm().array() < assoc_threshold*assoc_threshold;
+    //Eigen::Array<bool, Eigen::Dynamic, 1> near_ = (P - Q).rowwise().squaredNorm().array() < assoc_threshold*assoc_threshold;
     Eigen::Array<bool, Eigen::Dynamic, 1> close = (P - Q).leftCols<2>().rowwise().squaredNorm().array() < 0.1*0.1;
-    Eigen::Array<bool, Eigen::Dynamic, 1> near = sqrD.array() < assoc_threshold*assoc_threshold && close;
+    Eigen::Array<bool, Eigen::Dynamic, 1> near_ = sqrD.array() < assoc_threshold*assoc_threshold && close;
 
-    int nbr_near = near.cast<int>().sum();
-    cout << "Number points near surface: " << nbr_near << endl;
+    int nbr_near_ = near_.cast<int>().sum();
+    cout << "Number points near_ surface: " << nbr_near_ << endl;
     cout << "Out of: " << P.rows() << endl;
 
-    if (nbr_near < 100) {
+    if (nbr_near_ < 100) {
         cout << "Breaking since we do not have enough points!" << endl;
         return make_tuple(Eigen::Matrix4d::Identity(), 0., false);
     }
 
-    Eigen::MatrixXd goodP = igl::slice_mask(P, near, 1);
-    Eigen::MatrixXd goodQ = igl::slice_mask(Q, near, 1);
+    Eigen::MatrixXd goodP = igl::slice_mask(P, near_, 1);
+    Eigen::MatrixXd goodQ = igl::slice_mask(Q, near_, 1);
 
     Eigen::Vector3d meanP = goodP.rowwise().mean().transpose();
     Eigen::Vector3d meanQ = goodQ.rowwise().mean().transpose();
 
-    double mean_dist = igl::slice_mask(sqrD, near, 1).mean(); //(goodP - goodQ).rowwise().squaredNorm().mean();
+    double mean_dist = igl::slice_mask(sqrD, near_, 1).mean(); //(goodP - goodQ).rowwise().squaredNorm().mean();
 
     Eigen::Matrix3d covariance = 1./double(goodP.rows())*(goodQ.transpose().colwise() - meanQ)*(goodP.rowwise() - meanP.transpose());
 

src/bathy_maps/src/sss_gen_sim.cpp

@@ -489,7 +489,7 @@ bool SSSGenSim::callback_pre_draw(igl::opengl::glfw::Viewer& viewer)
         time_windows.tail(time_windows_right.rows()) = time_windows_right;
         time_windows.head(time_windows_left.rows()) = time_windows_left.reverse();
 
-        for (int i = 0; i < std::min(time_windows.rows(), long(waterfall_image.cols)); ++i) {
+        for (int i = 0; i < std::min(time_windows.rows(), int64_t(waterfall_image.cols)); ++i) {
             waterfall_image.at<uint8_t>(0, i) = uint8_t(255.*time_windows(i));
         }