Merge branch 'master' of https://github.com/copyme/DGtal into ParDirC…

…ollapse

.travis.yml

@@ -26,7 +26,7 @@ notifications:
 ########
 env:
   - CONFIG="Debug,Magick,GMP,ITK,FFTW3"
-  - CONFIG="Debug,Cairo,QGLviewer,HDF5"
+  - CONFIG="Debug,Cairo,QGLviewer,HDF5,EIGEN"
   - CONFIG="Documentation"
   - CONFIG="DGtalTools"
 
@@ -45,6 +45,7 @@ matrix:
     - os: osx
       compiler: gcc
 
+
 addons:
   apt:
    sources:
@@ -68,52 +69,40 @@ addons:
     - gcc-4.8
     - libfftw3-dev
 
-
 before_install:
-  - if [ $CXX == "g++" ]; then CCOMPILER="gcc-4.8"; CXXCOMPILER="g++-4.8"; fi
-  - BUILD_DOC="false"
-  - UPLOAD_DOC="false"
-  - NEEDCORE="true";
-  - NEEDEXAMPLESANDTESTS="true";
-  - if [ $CONFIG == "Documentation" ]; then NEEDEXAMPLESANDTESTS="false"; NEEDCORE="false"; BUILD_DOC="true"; if [ $OriginalRepo == "true" ];  then if [ $TRAVIS_PULL_REQUEST == "false" ]; then UPLOAD_DOC="true"; fi; fi; fi
-  - if [ $CONFIG == "Debug,Magick,GMP,ITK,FFTW3" ]; then BTYPE="-DCMAKE_BUILD_TYPE=Debug  -DWITH_MAGICK=true -DWITH_GMP=true -DWITH_FFTW3=true -DBUILD_TESTING=ON  -DWARNING_AS_ERROR=ON";  fi
-  - if [ $CONFIG == "Debug,Cairo,QGLviewer,HDF5" ]; then BTYPE="-DCMAKE_BUILD_TYPE=Debug -DWITH_HDF5=true -DWITH_CAIRO=true -DWITH_QGLVIEWER=true -DBUILD_TESTING=ON -DWARNING_AS_ERROR=OFF";   fi
-  - if [ $CONFIG == "DGtalTools" ]; then NEEDEXAMPLESANDTESTS="false"; BTYPE="-DCMAKE_BUILD_TYPE=Debug  -DWITH_MAGICK=true -DWITH_GMP=true -DWITH_HDF5=true -DWITH_CAIRO=true -DWITH_QGLVIEWER=true -DBUILD_TESTING=OFF -DBUILD_EXAMPLES=off";  fi
+  - source .travis/before_global.sh
+  - echo "C++ ===> $CXXCOMPILER"
+  - if [ $CONFIG == "Debug,Cairo,QGLviewer,HDF5,EIGEN" ]; then source .travis/install_eigen.sh  ; cd $TRAVIS_BUILD_DIR; fi
+  - echo $EIGEN_ROOT
+  - if [ $CONFIG == "Documentation" ]; then export NEEDEXAMPLESANDTESTS="false"; export NEEDCORE="false"; export BUILD_DOC="true"; if [ $OriginalRepo == "true" ];  then if [ $TRAVIS_PULL_REQUEST == "false" ]; then export UPLOAD_DOC="true"; fi; fi; fi
+  - if [ $CONFIG == "Debug,Magick,GMP,ITK,FFTW3" ]; then export BTYPE="-DCMAKE_BUILD_TYPE=Debug  -DWITH_MAGICK=true -DWITH_GMP=true -DWITH_FFTW3=true -DBUILD_TESTING=ON  -DWARNING_AS_ERROR=ON";  fi
+  - if [ $CONFIG == "Debug,Cairo,QGLviewer,HDF5,EIGEN" ]; then export BTYPE="-DCMAKE_BUILD_TYPE=Debug -DWITH_HDF5=true -DWITH_CAIRO=true -DWITH_QGLVIEWER=true -DBUILD_TESTING=ON -DWITH_EIGEN=true  -DWARNING_AS_ERROR=OFF  -DEIGEN3_INCLUDE_DIR='$EIGEN_ROOT/include/eigen3'";   fi
+  - if [ $CONFIG == "DGtalTools" ]; then export NEEDEXAMPLESANDTESTS="false"; export BTYPE="-DCMAKE_BUILD_TYPE=Debug  -DWITH_MAGICK=true -DWITH_GMP=true -DWITH_HDF5=true -DWITH_CAIRO=true -DWITH_QGLVIEWER=true -DBUILD_TESTING=OFF -DBUILD_EXAMPLES=off";  fi
   - if [ $UPLOAD_DOC == "true" ]; then openssl aes-256-cbc -K $encrypted_47769ec71275_key -iv $encrypted_47769ec71275_iv -in .travis/dgtal_rsa.enc -out .travis/dgtal_rsa -d; chmod 600 .travis/dgtal_rsa; BUILD_DOC="true"; fi
   - if [ $BUILD_DOC == "true" ]; then wget http://dgtal.org/doc/tags/DGtalTools-tagfile; fi
-  - if [ $BUILD_DOC == "true" ]; then .travis/install_doxygen.sh;  BTYPE="-DDOXYGEN_EXECUTABLE=$HOME/doxygen/doxygen-1.8.10/bin/doxygen"; fi
+  - if [ $BUILD_DOC == "true" ]; then .travis/install_doxygen.sh;  export BTYPE="-DDOXYGEN_EXECUTABLE=$HOME/doxygen/doxygen-1.8.10/bin/doxygen"; fi
+
 
 ########
 # Deps.
 ########
 before_script:
   - if [ $TRAVIS_OS_NAME == linux ]; then echo "All done.";   fi
-  - if [ $TRAVIS_OS_NAME == osx ]; then brew update; brew install boost doxygen homebrew/science/hdf5 graphviz graphicsmagick  gmp libqglviewer fftw; echo "done";fi
+  - if [ $TRAVIS_OS_NAME == osx ]; then source .travis/install_deps_macos.sh; fi
 
 
 ############
 # Main rules
 ############
 script:
-  - cmake . $BTYPE -DCMAKE_CXX_COMPILER=$CXXCOMPILER -DCMAKE_C_COMPILER=$CCOMPILER
-  - echo $BUILD_DOC
-  - echo $UPLOAD_DOC
-  - echo $BTYPE
-  - if [ $NEEDCORE == "true" ]; then  make -j 3 DGtal && make -j 3 DGtalIO; fi
-  - if [ $NEEDEXAMPLESANDTESTS == "true" ]; then  cd examples && make  -j 3 ; fi
-  - if [ $NEEDEXAMPLESANDTESTS == "true" ]; then  cd ../tests &&  make -j 3 &&  cd .. ; fi
-  - if [ $NEEDEXAMPLESANDTESTS == "true" ]; then  make test ARGS=--output-on-failure ; fi
-  - if [ $CONFIG == "DGtalTools" ]; then pwd ; .travis/getAndCheckDGtalTools.sh ; fi
-  - if [ $BUILD_DOC == "true" ]; then make doc; fi
-  - if [ $CONFIG == "Documentation" ]; then ./.travis/checkDoxygenDocumentation.sh; fi
+  - echo "---- $BTYPE ---$BUILD_DOC---$UPLOAD_DOC"
+  - .travis/main_build.sh
+  - if [ $CONFIG == "DGtalTools" ]; then  .travis/getAndCheckDGtalTools.sh ; fi
+  - if [ $CONFIG == "Documentation" ]; then .travis/checkDoxygenDocumentation.sh; fi
 
 
 ###########
 ## Building the documentation
 ###########
 after_success:
-  - if [ $UPLOAD_DOC == "true" ]; then rsync -azv --delete --delete-after -e 'ssh -oStrictHostKeyChecking=no -i  .travis/dgtal_rsa' html/ dgtal@liris.cnrs.fr:/home/dgtal/public_html/doc/nightly/;  fi
-  - if [ $UPLOAD_DOC == "true" ]; then cd html; make ; wget http://dgtal.org/doc/docset/template.tgz ; tar zxvf template.tgz ; mv template/* org.dgtal.docset ; tar zcvf DGtal-devel.tgz org.dgtal.docset ; cd .. ;rsync  -azv --delete --delete-after -e 'ssh -oStrictHostKeyChecking=no -i  .travis/dgtal_rsa' html/DGtal-devel.tgz dgtal@liris.cnrs.fr:/home/dgtal/public_html/doc/docset ;   fi
-    ## We publish the DGtalTools tags
-  - if [ $UPLOAD_DOC == "true" ]; then scp -i  .travis/dgtal_rsa  DGtal-tagfile dgtal@liris.cnrs.fr:/home/dgtal/public_html/doc/tags/;scp -i  .travis/dgtal_rsa  Board-tagfile dgtal@liris.cnrs.fr:/home/dgtal/public_html/doc/tags/; fi
-  - echo "All done..."
+  - if [ $UPLOAD_DOC == "true" ]; then .travis/publish_doc.sh;  fi

.travis/before_global.sh

@@ -0,0 +1,22 @@
+#!/bin/bash
+
+export BUILD_DOC="false"
+export UPLOAD_DOC="false"
+export NEEDCORE="true"
+
+export NEEDEXAMPLESANDTESTS="true";
+export SRC_DIR="`pwd`"
+
+export CCOMPILER=$CC
+export CXXCOMPILER=$CXX
+
+##Forcing gcc-4.8
+if [ $CC = "gcc" ];
+then
+    export CCOMPILER="gcc-4.8"
+    export CXXCOMPILER="g++-4.8"
+fi
+
+##Preparing folders
+mkdir deps/
+mkdir deps/local

.travis/getAndCheckDGtalTools.sh

@@ -4,5 +4,5 @@ echo "DGtal path = $DGTALPATH"
 git clone --depth 1 git://github.com/DGtal-team/DGtalTools.git
 cd DGtalTools
 mkdir build ; cd build
-cmake .. -DDGtal_DIR=$DGTALPATH
+cmake .. -DDGtal_DIR=$DGTALPATH/build $BUILD
 make -j 2

.travis/install_deps_macos.sh

@@ -0,0 +1,13 @@
+#!/bin/bash
+
+
+## Temporary HDF5 build issue
+export BTYPE="$BTYPE -DWITH_HDF5=false" && echo "Disabling HDF5 on MacOS"; 
+
+#
+# Note: gmp and boost already installed
+#
+
+brew update
+brew install doxygen homebrew/science/hdf5 graphviz graphicsmagick fftw eigen homebrew/boneyard/libqglviewer
+

.travis/install_doxygen.sh

@@ -1,4 +1,8 @@
+#!/bin/bash
+
+#
+##Download and install 1.8.1
+#
 
 mkdir ~/doxygen && cd ~/doxygen
-wget http://ftp.stack.nl/pub/users/dimitri/doxygen-1.8.10.linux.bin.tar.gz
-tar xzf doxygen-1.8.10.linux.bin.tar.gz
+wget http://ftp.stack.nl/pub/users/dimitri/doxygen-1.8.10.linux.bin.tar.gz && tar xzf doxygen-1.8.10.linux.bin.tar.gz

.travis/install_eigen.sh

@@ -0,0 +1,24 @@
+#!/bin/bash
+
+
+#
+# Local install of Eigen on linux system
+#
+
+export EIGEN_ROOT="/usr/local/"
+
+if [ $TRAVIS_OS_NAME == linux ];
+then
+    cd deps
+    wget http://bitbucket.org/eigen/eigen/get/3.2.10.tar.bz2
+
+    bunzip2 3.2.10.tar.bz2
+    tar xvf 3.2.10.tar
+
+    cd eigen-eigen-b9cd8366d4e8
+    mkdir build ; cd build
+
+    cmake .. -DCMAKE_INSTALL_PREFIX="${SRC_DIR}/deps/local"
+    make && make install && cd ${SRC_DIR} && export EIGEN_ROOT="$SRC_DIR/deps/local"
+
+fi

.travis/main_build.sh

@@ -0,0 +1,32 @@
+#!/bin/bash
+
+set -e
+
+mkdir build
+cd build
+
+### Cmake
+echo "Using C++ = $CXXCOMPILER"
+cmake ..  $BTYPE -DCMAKE_CXX_COMPILER=$CXXCOMPILER -DCMAKE_C_COMPILER=$CCOMPILER 
+
+
+### DGtal Core build
+if [ $NEEDCORE = "true" ];
+then
+    make -j 3 DGtal && make -j 3 DGtalIO
+fi
+
+echo "NeedExample $NEEDEXAMPLESANDTESTS"
+### DGtal Examples and Examples
+if [ $NEEDEXAMPLESANDTESTS = "true" ];
+then
+    cd examples ; make  -j 3 ; echo "PWD"; pwd ; ls -l ..
+    cd ../tests ;  make -j 3
+    make test  ARGS=--output-on-failure
+fi
+
+### DGtal doc
+if [ $BUILD_DOC = "true" ];
+then
+    make doc
+fi

.travis/publish_doc.sh

@@ -0,0 +1,21 @@
+#!/bin/bash
+
+set -e
+
+rsync -azv --delete --delete-after -e 'ssh -oStrictHostKeyChecking=no -i  .travis/dgtal_rsa' html/ dgtal@liris.cnrs.fr:/home/dgtal/public_html/doc/nightly/
+
+
+##DOCSET build
+cd html
+make
+wget http://dgtal.org/doc/docset/template.tgz
+tar zxvf template.tgz ; mv template/* org.dgtal.docset
+tar zcvf DGtal-devel.tgz org.dgtal.docset
+
+cd ..
+
+rsync  -azv --delete --delete-after -e 'ssh -oStrictHostKeyChecking=no -i  .travis/dgtal_rsa' html/DGtal-devel.tgz dgtal@liris.cnrs.fr:/home/dgtal/public_html/doc/docset   
+
+
+###TAGS for DGtalTools
+scp -i  .travis/dgtal_rsa  DGtal-tagfile dgtal@liris.cnrs.fr:/home/dgtal/public_html/doc/tags/;scp -i  .travis/dgtal_rsa  Board-tagfile dgtal@liris.cnrs.fr:/home/dgtal/public_html/doc/tags/

ChangeLog.md

@@ -1,10 +1,33 @@
 # DGtal 0.9.3
 
+## New Features / Critical Changes
+
+- *Configuration/General*
+ - Set flag -std=c++11 only if needed. Modern compilers set compatible flags
+   by default (gnu++14, etc). (Pablo H Cerdan,
+   [#1222](https://github.com/DGtal-team/DGtal/pull/1222))
+
+- *Geometry Package*
+ - VoronoiMap, PowerMap, (Reverse)DistanceTransformation and ReducedMedialAxis
+   now work on toric domains (with per-dimension periodicity specification).
+   (David Coeurjolly, Roland Denis,
+   [#1206](https://github.com/DGtal-team/DGtal/pull/1206))
+
 ## Bug Fixes
 
 - *Configuration/General*
  - Fixing errors and warnings raised by g++ 4.7.x.
    (Roland Denis, [#1202](https://github.com/DGtal-team/DGtal/pull/1202))
+ - Explicit M_PI definition if needed.
+   (David Coeurjolly, [#1208](https://github.com/DGtal-team/DGtal/pull/1208))
+
+- *Geometry Package*
+ - ArithDSSIterator: fix missing postfix ++.
+   (I. Sivignon, [#1187](https://github.com/DGtal-team/DGtal/pull/1187))
+
+- *IO Package*
+ - Viewer3D: fix bad rendering when changing the scale.
+   (Bertrand Kerautret, [#1217](https://github.com/DGtal-team/DGtal/pull/1217))
 
 # DGtal 0.9.2
 

README.md

@@ -64,4 +64,6 @@ More Information
 * Release 0.9.1 [![DOI](https://zenodo.org/badge/doi/10.5281/zenodo.45125.svg)](http://dx.doi.org/10.5281/zenodo.45125)
 * Release 0.9 [![DOI](https://zenodo.org/badge/doi/10.5281/zenodo.31884.svg)](http://dx.doi.org/10.5281/zenodo.31884)
 * Release 0.8 [![DOI](https://zenodo.org/badge/doi/10.5281/zenodo.11586.png)](http://dx.doi.org/10.5281/zenodo.11586)
-* Continuous Integration [![Build Status](https://travis-ci.org/DGtal-team/DGtal.svg?branch=master)](https://travis-ci.org/DGtal-team/DGtal)
+* Continuous Integration (Linux/MacOS) [![Build Status](https://travis-ci.org/DGtal-team/DGtal.svg?branch=master)](https://travis-ci.org/DGtal-team/DGtal)
+*  Continuous Integration (Windows) [![Build status](https://ci.appveyor.com/api/projects/status/7labe8ft0jf30ng7/branch/master?svg=true)](https://ci.appveyor.com/project/kerautret/dgtal-8op01/branch/master)
+

cmake/CheckCPP11.cmake

@@ -2,10 +2,25 @@
 # Test some c++11 functionalities
 # -----------------------------------------------------------------------------
 
-try_compile( CPP11_COMPATIBLE 
+try_compile( CPP11_COMPATIBLE_FLAG_SET_BY_USER
   ${CMAKE_BINARY_DIR}/CMakeTmp
   ${CMAKE_SOURCE_DIR}/cmake/src/cpp11/cpp11_check.cpp
-  COMPILE_DEFINITIONS "-std=c++11"
+  CMAKE_FLAGS "-DCMAKE_CXX_FLAGS=${CMAKE_CXX_FLAGS}"
   OUTPUT_VARIABLE OUTPUT
   )
 
+IF (CPP11_COMPATIBLE_FLAG_SET_BY_USER)
+  MESSAGE(STATUS "  CPP11 enabled compiler by default.") 
+ENDIF()
+
+IF (NOT CPP11_COMPATIBLE_FLAG_SET_BY_USER)
+  try_compile( CPP11_COMPATIBLE_FLAG_SET_BY_DGTAL
+    ${CMAKE_BINARY_DIR}/CMakeTmp
+    ${CMAKE_SOURCE_DIR}/cmake/src/cpp11/cpp11_check.cpp
+    COMPILE_DEFINITIONS "-std=c++11"
+    OUTPUT_VARIABLE OUTPUT
+    )
+ENDIF()
+
+SET(CPP11_COMPATIBLE CPP11_COMPATIBLE_FLAG_SET_BY_USER OR CPP11_COMPATIBLE_FLAG_SET_BY_DGTAL)
+

cmake/CheckDGtalDependencies.cmake

@@ -25,8 +25,11 @@ endif( Boost_FOUND )
 MESSAGE(STATUS "Checking C++11 compatibility:")
 INCLUDE(CheckCPP11)
 IF (CPP11_COMPATIBLE)
-  IF (NOT MSVC)
-    set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -std=c++11 ")
+  IF (NOT CPP11_COMPATIBLE_FLAG_SET_BY_USER)
+    IF (NOT MSVC)
+      set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -std=c++11 ")
+      MESSAGE(STATUS "  -std=c++11 added to CMAKE_CXX_FLAGS. ")
+    ENDIF()
   ENDIF()
   MESSAGE(STATUS "OK.")
 ELSE()

cmake/CheckDGtalOptionalDependencies.cmake

@@ -384,7 +384,7 @@ ENDIF(WITH_OPENMP)
 # -----------------------------------------------------------------------------
 SET(EIGEN_FOUND_DGTAL 0)
 IF(WITH_EIGEN)
-  FIND_PACKAGE(Eigen3 3.2 REQUIRED)
+  FIND_PACKAGE(Eigen3 REQUIRED)
   IF(EIGEN3_FOUND)
     SET(EIGEN_FOUND_DGTAL 1)
     ADD_DEFINITIONS("-DWITH_EIGEN ")

cmake/DGtalConfig.cmake.in

@@ -71,12 +71,22 @@ IF (@COLOR_WITH_ALPHA_ARITH_DGTAL@)
   ADD_DEFINITIONS(-DCOLOR_WITH_ALPHA_ARITH)
 ENDIF(@COLOR_WITH_ALPHA_ARITH_DGTAL@)
 
-
-IF(NOT MSVC)
-  set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -std=c++11")
+# Set c++11 flag only if needed.
+# When user or compiler have not set any std flag.
+try_compile( CPP11_COMPATIBLE_FLAG_SET_BY_USER
+  ${CMAKE_BINARY_DIR}/CMakeTmp
+  @DGTAL_CMAKE_DIR@/cpp11_check.cpp
+  CMAKE_FLAGS "-DCMAKE_CXX_FLAGS=${CMAKE_CXX_FLAGS}"
+  OUTPUT_VARIABLE OUTPUT
+  )
+
+IF (NOT CPP11_COMPATIBLE_FLAG_SET_BY_USER)
+   IF (NOT MSVC)
+     set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -std=c++11 ")
+     MESSAGE(STATUS "-std=c++11 added to CMAKE_CXX_FLAGS. ")
+   ENDIF()
 ENDIF()
 
-
 IF(@GMP_FOUND_DGTAL@)
   ADD_DEFINITIONS("-DWITH_GMP ")
   SET(WITH_GMP 1)

cmake/DGtalConfigGenerator.cmake

@@ -21,6 +21,9 @@ configure_file(${PROJECT_SOURCE_DIR}/cmake/DGtalConfig.cmake.in
 
 configure_file(${PROJECT_SOURCE_DIR}/cmake/DGtalConfigVersion.cmake.in
   "${PROJECT_BINARY_DIR}/DGtalConfigVersion.cmake" @ONLY)
+# Copy also the cpp11_check.cpp for the build tree.
+file(COPY ${PROJECT_SOURCE_DIR}/cmake/src/cpp11/cpp11_check.cpp
+     DESTINATION ${PROJECT_BINARY_DIR})
 
 # Install the export set for use with the install-tree
 install(EXPORT DGtalLibraryDepends DESTINATION
@@ -40,4 +43,5 @@ configure_file(${PROJECT_SOURCE_DIR}/cmake/DGtalConfigVersion.cmake.in
 install(FILES
   "${PROJECT_BINARY_DIR}/InstallFiles/DGtalConfig.cmake"
   "${PROJECT_BINARY_DIR}/InstallFiles/DGtalConfigVersion.cmake"
+  "${PROJECT_SOURCE_DIR}/cmake/src/cpp11/cpp11_check.cpp"
   DESTINATION "${DGTAL_CMAKE_DIR}" COMPONENT dev)

examples/geometry/curves/CMakeLists.txt

@@ -16,6 +16,7 @@ SET(DGTAL_EXAMPLES_SRC
   exampleDSLSubsegment
   exampleArithmeticalDSL
   exampleNaive3DDSSComputer
+  exampleArithDSSIterator
 )
 
 

examples/geometry/curves/exampleArithDSSIterator.cpp

@@ -43,7 +43,7 @@ using namespace DGtal;
 
 ///////////////////////////////////////////////////////////////////////////////
 
-int main( int UNUSED(argc), char** UNUSED(argv) )
+int main()
 {
   trace.beginBlock ( "Example exampleArithDSSIterator" );
 

examples/geometry/volumes/distance/CMakeLists.txt

@@ -1,4 +1,5 @@
 SET(DGTAL_EXAMPLES_SRC
+  toricdomainvolumetric
   distancetransform2D
   exampleFMM2D
   voronoimap2D