.gitignore

+.project
+build
+src/config.h

.kdev4/beads.kdev4

+[Buildset]
+BuildItems=@Variant(\x00\x00\x00\t\x00\x00\x00\x00\x01\x00\x00\x00\x0b\x00\x00\x00\x00\x01\x00\x00\x00\n\x00b\x00e\x00a\x00d\x00s)
+
+[CMake]
+Build Directory Count=1
+Current Build Directory Index=0
+ProjectRootRelative=./
+
+[CMake][CMake Build Directory 0]
+Build Directory Path=file:///home/langella/developpement/git/beads/build
+Build Type=
+CMake Binary=file:///usr/bin/cmake
+Environment Profile=
+Extra Arguments=
+Install Directory=file:///usr/local
+
+[Defines And Includes][Compiler]
+Name=GCC
+Path=gcc
+Type=GCC
+
+[Project]
+VersionControlSupport=kdevgit

CMakeLists.txt

@@ -16,23 +16,21 @@ PROJECT(beads CXX C)
 
 #message ("compiler : ${CMAKE_CXX_COMPILER} ")
 
+SET(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -std=c++11")
 
-IF ( CMAKE_BASE_NAME MATCHES "cl")
-	message ("on est sous Windows")
-	SET( WIN32 "true")
-ENDIF(CMAKE_BASE_NAME MATCHES "cl")
-
+#IF ( CMAKE_BASE_NAME MATCHES "cl")
+#	message ("on est sous Windows")
+#	SET( WIN32 "true")
+#ENDIF(CMAKE_BASE_NAME MATCHES "cl")
 
+if (NOT CMAKE_BUILD_TYPE)
   SET( CMAKE_BUILD_TYPE "Release")
+ENDIF(NOT CMAKE_BUILD_TYPE)
+
 if (NOT CMAKE_INSTALL_PREFIX)
 	SET (CMAKE_INSTALL_PREFIX /usr/local)
 ENDIF(NOT CMAKE_INSTALL_PREFIX)
 
-IF (CMAKE_INSTALL_PREFIX MATCHES "/usr/local")
-	SET( CMAKE_BUILD_TYPE "Debug")
-	#SET( CMAKE_BUILD_TYPE "Release")
-ENDIF (CMAKE_INSTALL_PREFIX MATCHES "/usr/local")
-
 
 IF ( CMAKE_BUILD_TYPE MATCHES "Release")
 	MESSAGE("compiling as release version")
@@ -46,24 +44,15 @@ ENDIF( CMAKE_BUILD_TYPE MATCHES "Release" )
 #SET(WIN32 "true")
 #SET(MINGW "true")
 
-set(CMAKE_MODULE_PATH ${beads_SOURCE_DIR}/cmake_modules)
-#FIND_PACKAGE ( FindPTHREADS REQUIRED )
-#are we using pthreads ?
-#IF ( CMAKE_USE_PTHREADS_INIT )
-#	INCLUDE_DIRECTORIES ( ${EXPAT_INCLUDE_DIRS} )
-#ELSE ( CMAKE_USE_PTHREADS_INIT )
-#	MESSAGE( FATAL_ERROR "No pthread installed" )
-#ENDIF( CMAKE_USE_PTHREADS_INIT )
+#set(CMAKE_MODULE_PATH ${beads_SOURCE_DIR}/cmake_modules)
 
 #IF ( PTHREADS_FOUND )
-	INCLUDE_DIRECTORIES ( ${PTHREADS_INCLUDE_DIR} )
+#	INCLUDE_DIRECTORIES ( ${PTHREADS_INCLUDE_DIR} )
 #ELSE ( PTHREADS_FOUND )
 #	MESSAGE( FATAL_ERROR "No pthread installed" )
 #ENDIF( PTHREADS_FOUND )
 
 
-cmake_minimum_required(VERSION 2.6)
-
 
 SET ( EXTRA_CIMG_LIBRARY "")
 
@@ -75,18 +64,18 @@ IF(WIN32)
 	#SET(CMAKE_CXX_FLAGS_RELEASE "-O2 -DNDEBUG")
 #	FIND_PACKAGE(FindMagick REQUIRED)
 ELSE(WIN32)
-	FIND_PACKAGE(Pthreads REQUIRED)
-	SET(CMAKE_CXX_FLAGS_RELEASE "-O3 -DNDEBUG")
+	#FIND_PACKAGE(Pthreads REQUIRED)
+	SET(CMAKE_CXX_FLAGS_RELEASE "-s -O3 -DNDEBUG")
 	SET ( CIMG_OS 1)
 ENDIF(WIN32)
 
 #
 #CMAKE_CXX_FLAGS
-SET(CMAKE_CXX_FLAGS_DEBUG "-g")
+SET(CMAKE_CXX_FLAGS_DEBUG "-g -s")
 SET(CMAKE_CXX_FLAGS_MINSIZEREL "-Os -DNDEBUG")
 SET(CMAKE_CXX_FLAGS_RELWITHDEBINFO "-O2 -g")
 
-SET (BEADS_VERSION "1.1.13")
+SET (BEADS_VERSION "1.1.17")
 
 SET(CPACK_CMAKE_GENERATOR "Unix Makefiles")
 SET(CPACK_GENERATOR "STGZ;TGZ;TZ")
@@ -109,21 +98,23 @@ ENDIF( CMAKE_BUILD_TYPE MATCHES "Debug")
 SET(CPACK_PACKAGE_VERSION ${BEADS_VERSION})
 SET(CPACK_PACKAGE_VERSION_MAJOR "1")
 SET(CPACK_PACKAGE_VERSION_MINOR "1")
-SET(CPACK_PACKAGE_VERSION_PATCH "13")
+SET(CPACK_PACKAGE_VERSION_PATCH "15")
 SET(CPACK_RESOURCE_FILE_LICENSE ${beads_SOURCE_DIR}/COPYING)
 SET(CPACK_RESOURCE_FILE_README ${beads_SOURCE_DIR}/README)
 SET(CPACK_RESOURCE_FILE_WELCOME ${beads_SOURCE_DIR}/INSTALL)
 SET(CPACK_SOURCE_GENERATOR "TGZ;TZ")
 SET(CPACK_SOURCE_OUTPUT_CONFIG_FILE "./CPackSourceConfig.cmake")
-SET(CPACK_SOURCE_STRIP_FILES "")
-SET(CPACK_STRIP_FILES "bin/beads")
 SET(CPACK_SYSTEM_NAME "Linux-i686")
 SET(CPACK_TOPLEVEL_TAG "Linux-i686")
 
 SET(CPACK_SOURCE_IGNORE_FILES 
 	"moc_.*cxx"
 	"/devel_archives/"
+	"/build/"
+	"/cbuild/"
 	"/figures/"
+	".*\\\\.so"
+	".*\\\\.a"
 	"/Soumis/"
 	"/samples/"
 	"/win32/"
@@ -141,7 +132,7 @@ SET(CPACK_SOURCE_IGNORE_FILES
 	"/Debug/"
 	"/Release/"
 	"/\\\\.externalToolBuilders/"
-	"/\\\\.svn/"
+	"/\\\\.git/"
 	"/\\\\.settings/"
 	"Makefile"
 	"\\\\.cdtbuild"
@@ -165,6 +156,17 @@ SET(CPACK_SOURCE_IGNORE_FILES
 #  debuild -S -sa
 # dput -f olivier-langella *changes
 
+
+
+
+
+#dch -Djessie "message"
+#cmake ..
+#make deb
+# scp beads* proteus.moulon.inra.fr:/var/www/apt/incoming
+# reprepro -Vb /var/www/apt processincoming default
+
+
 configure_file (${beads_SOURCE_DIR}/src/config.h.cmake ${beads_SOURCE_DIR}/src/config.h)
 
 
@@ -177,16 +179,18 @@ INCLUDE(CPack)
 #INCLUDE(CPack)
 
 
-SET(CPACK_STRIP_FILES "src/beads;src/qtbeads/qtbeads")
 
 
 # Recurse into the "src" subdirectories.  This does not actually
 # cause another cmake executable to run.  The same process will walk through
 # the project's entire directory structure.
-SUBDIRS (src)
+#ADD_DEFINITIONS( -lpthread)
+add_subdirectory (src)
+
+#SET(CPACK_STRIP_FILES "src/beads;src/qtbeads/qtbeads")
 
-INSTALL(PROGRAMS src/beads DESTINATION bin)
-INSTALL(PROGRAMS src/qtbeads/qtbeads DESTINATION bin)
+INSTALL(PROGRAMS ${CMAKE_BINARY_DIR}/src/beads DESTINATION bin)
+INSTALL(PROGRAMS ${CMAKE_BINARY_DIR}/src/qtbeads/qtbeads DESTINATION bin)
 #INSTALL(DIRECTORY doc/man1 DESTINATION share/man/man1)
 INSTALL(FILES doc/man1/beads.1 DESTINATION share/man/man1)
 INSTALL(FILES share/applications/beads.desktop DESTINATION share/applications)
@@ -195,3 +199,16 @@ INSTALL(FILES share/beads/beads_silver.conf DESTINATION share/beads)
 INSTALL(FILES share/beads/beads_silver_small.conf DESTINATION share/beads)
 INSTALL(FILES share/beads/beads_icon.svg DESTINATION share/beads)
 
+add_custom_target(targz
+	cpack -G TGZ --config CPackSourceConfig.cmake && tar xvfz beads-${BEADS_VERSION}.tar.gz
+	WORKING_DIRECTORY ${CMAKE_BINARY_DIR}
+	COMMENT "Creating .tar.gz" VERBATIM
+)
+
+
+add_custom_target(deb
+	cd beads-${BEADS_VERSION} && dpkg-buildpackage 
+	DEPENDS targz
+	WORKING_DIRECTORY ${CMAKE_BINARY_DIR}
+	COMMENT "Creating Debian package" VERBATIM
+)

beads.kdev4

+[Project]
+CreatedFrom=beads
+Manager=KDevCMakeManager
+Name=beads

cmake_modules/FindCImg.cmake

+# - Try to find CImg lib
+#
+# The following variables are defined
+#
+#  CImg_FOUND - system has CImg lib
+#  CImg_INCLUDE_DIRS - the CImg include directory
+#  CImg_SYSTEM_LIBS - external libraries that CImg uses
+#  CImg_SYSTEM_LIBS_DIR - external library directories
+#  CImg_CFLAGS - compilation flags
+
+
+if (CImg_INCLUDE_DIR)
+  set(CImg_FOUND TRUE)
+else (CImg_INCLUDE_DIR)
+  find_path(CImg_INCLUDE_DIR
+    NAMES CImg.h
+    PATHS
+      ${CMAKE_INSTALL_PREFIX}/include
+      /usr/include
+  )
+  mark_as_advanced(CImg_INCLUDE_DIR)
+endif(CImg_INCLUDE_DIR)
+list(APPEND CImg_INCLUDE_DIRS
+  ${CImg_INCLUDE_DIR}
+)
+
+# To use PKG_CHECK_MODULES to find some optional packages
+find_package(PkgConfig)
+
+
+# ### CIMG related stuff
+# Flags to enable fast image display, using the XSHM library.
+#SET(CIMG_XSHM_CCFLAGS  -Dcimg_use_xshm)
+
+# Flags to enable screen mode switching, using the XRandr library.
+#SET(CIMG_XRANDR_CCFLAGS  -Dcimg_use_xrandr)
+
+# Flags to enable native support for JPEG image files, using the JPEG library.
+# ( http://www.ijg.org/ )
+SET(CIMG_JPEG_CCFLAGS  -Dcimg_use_jpeg)
+
+# Flags to enable native support for TIFF image files, using the TIFF library.
+# ( http://www.libtiff.org/ )
+SET(CIMG_TIFF_CCFLAGS  -Dcimg_use_tiff)
+
+# Flags to enable native support for PNG image files, using the PNG library.
+# ( http://www.libpng.org/ )
+SET(CIMG_PNG_CCFLAGS  -Dcimg_use_png)
+
+#Flags to enable OPENCV support (Camera)
+# ( http://www.opencv.org/ )
+#SET(CIMG_OPENCV_CCFLAGS -Dcimg_use_opencv)
+
+# Flags to enable native support for EXR image files, using the OpenEXR library.
+# ( http://www.openexr.com/ )
+#SET(CIMG_OPENEXR_CCFLAGS  -Dcimg_use_openexr)
+
+# Flags to enable native support for various video files, using the FFMPEG library.
+# ( http://www.ffmpeg.org/ )
+#SET(CIMG_FFMPEG_CCFLAGS  -Dcimg_use_ffmpeg)
+
+# Flags to enable native support of most classical image file formats, using the Magick++ library.
+# ( http://www.imagemagick.org/Magick++/ )
+#SET(CIMG_MAGICK_CCFLAGS -Dcimg_use_magick)
+
+# Flags to enable faster Discrete Fourier Transform computation, using the FFTW3 library
+# ( http://www.fftw.org/ )
+#SET(CIMG_FFTW3_CCFLAGS  -Dcimg_use_fftw3)
+
+# Flags to enable zlib.
+# ( http://www.zlib.net/ )
+SET(CIMG_ZLIB_CCFLAGS  -Dcimg_use_zlib)
+
+# ### Search Additional Libraries ##########
+#FIND_PACKAGE(OpenCV)
+FIND_PACKAGE(JPEG REQUIRED)
+FIND_PACKAGE(TIFF REQUIRED)
+FIND_PACKAGE(PNG REQUIRED)
+FIND_PACKAGE(ZLIB REQUIRED)
+#FIND_PACKAGE(LAPACK)
+#FIND_PACKAGE(BLAS)
+
+#PKG_CHECK_MODULES(FFTW3 fftw3)
+#PKG_CHECK_MODULES(OPENEXR OpenEXR)
+#PKG_CHECK_MODULES(MAGICK Magick++)
+
+# PKG_CHECK_MODULES(LIBAVCODEC libavcodec)
+# PKG_CHECK_MODULES(LIBAVFORMAT libavformat)
+# PKG_CHECK_MODULES(LIBSWSCALE libswscale)
+# PKG_CHECK_MODULES(LIBAVUTIL libavutil)
+
+if(NOT WIN32)
+  FIND_PACKAGE(X11)
+  FIND_PACKAGE(Threads REQUIRED)
+endif()
+
+# #### End of additional libraries search ##########
+
+### Configure Paths according to detected packages
+if(TIFF_FOUND)
+  get_filename_component(TIFF_LIB_DIRS ${TIFF_LIBRARIES} PATH)
+  SET(CIMG_CFLAGS "${CIMG_CFLAGS} ${CIMG_TIFF_CCFLAGS}")
+#  link_directories(${TIFF_LIB_DIRS})
+#  include_directories(${TIFF_INCLUDE_DIR})
+#  SET(CImg_SYSTEM_LIBS ${CImg_SYSTEM_LIBS} ${TIFF_LIBRARIES})
+  list(APPEND CImg_INCLUDE_DIRS
+    ${TIFF_INCLUDE_DIR}
+  )
+  list(APPEND CImg_SYSTEM_LIBS_DIR
+    ${TIFF_LIB_DIRS}
+  )
+  list(APPEND CImg_SYSTEM_LIBS
+    ${TIFF_LIBRARIES}
+  )
+endif()
+
+if(JPEG_FOUND)
+  get_filename_component(JPEG_LIB_DIRS ${JPEG_LIBRARIES} PATH)
+  SET(CIMG_CFLAGS "${CIMG_CFLAGS} ${CIMG_JPEG_CCFLAGS}")
+#  link_directories(${JPEG_LIB_DIRS})
+#  include_directories(${JPEG_INCLUDE_DIR})
+#  SET(CImg_SYSTEM_LIBS ${CImg_SYSTEM_LIBS} ${JPEG_LIBRARIES})
+  list(APPEND CImg_INCLUDE_DIRS
+    ${JPEG_INCLUDE_DIR}
+  )
+  list(APPEND CImg_SYSTEM_LIBS_DIR
+    ${JPEG_LIB_DIRS}
+  )
+  list(APPEND CImg_SYSTEM_LIBS
+    ${JPEG_LIBRARIES}
+  )
+endif()
+
+if (ZLIB_FOUND)
+  SET(CIMG_CFLAGS "${CIMG_CFLAGS} ${CIMG_ZLIB_CCFLAGS}")
+#  link_directories(${ZLIB_LIB_DIRS})
+#  include_directories(${ZLIB_INCLUDE_DIR})
+#  SET(CImg_SYSTEM_LIBS ${CImg_SYSTEM_LIBS} ${ZLIB_LIBRARIES})
+  list(APPEND CImg_INCLUDE_DIRS
+    ${ZLIB_INCLUDE_DIR}
+  )
+  list(APPEND CImg_SYSTEM_LIBS_DIR
+    ${ZLIB_LIB_DIRS}
+  )
+  list(APPEND CImg_SYSTEM_LIBS
+    ${ZLIB_LIBRARIES}
+  )
+  # PNG requires ZLIB
+  if(PNG_FOUND)
+    SET(CIMG_CFLAGS "${CIMG_CFLAGS} ${CIMG_PNG_CCFLAGS}")
+ #   link_directories(${PNG_LIB_DIRS})
+ #   include_directories(${PNG_INCLUDE_DIR} )
+ #   SET( CImg_SYSTEM_LIBS ${CImg_SYSTEM_LIBS} ${PNG_LIBRARIES} )
+  list(APPEND CImg_INCLUDE_DIRS
+    ${PNG_INCLUDE_DIR}
+  )
+  list(APPEND CImg_SYSTEM_LIBS_DIR
+    ${PNG_LIB_DIRS}
+  )
+  list(APPEND CImg_SYSTEM_LIBS
+    ${PNG_LIBRARIES}
+  )
+  endif()
+endif()
+
+if(FFTW3_FOUND)
+  SET(CIMG_CFLAGS "${CIMG_CFLAGS} ${CIMG_FFTW3_CCFLAGS}")
+  #link_directories( ${FFTW3_LIBRARY_DIRS} )
+  #include_directories( ${FFTW3_INCLUDE_DIRS} )
+  #SET( CImg_SYSTEM_LIBS ${CImg_SYSTEM_LIBS} ${FFTW3_LIBRARIES} )
+  list(APPEND CImg_INCLUDE_DIRS
+    ${FFTW3_INCLUDE_DIRS}
+  )
+  list(APPEND CImg_SYSTEM_LIBS_DIR
+    ${FFTW3_LIBRARY_DIRS}
+  )
+  list(APPEND CImg_SYSTEM_LIBS
+    ${FFTW3_LIBRARIES}
+  )
+endif()
+
+if(OPENEXR_FOUND)
+  SET(CIMG_CFLAGS "${CIMG_CFLAGS} ${CIMG_OPENEXR_CCFLAGS}")
+  #link_directories( ${OPENEXR_LIBRARY_DIRS} )
+  #include_directories( ${OPENEXR_INCLUDE_DIRS} )
+  #SET( CImg_SYSTEM_LIBS ${CImg_SYSTEM_LIBS} ${OPENEXR_LIBRARIES} )
+  list(APPEND CImg_INCLUDE_DIRS
+    ${OPENEXR_INCLUDE_DIRS}
+  )
+  list(APPEND CImg_SYSTEM_LIBS_DIR
+    ${OPENEXR_LIBRARY_DIRS}
+  )
+  list(APPEND CImg_SYSTEM_LIBS
+    ${OPENEXR_LIBRARIES}
+  )
+endif()
+
+if(MAGICK_FOUND)
+  SET(CIMG_CFLAGS "${CIMG_CFLAGS} ${CIMG_MAGICK_CCFLAGS}")
+  #link_directories( ${MAGICK_LIBRARY_DIRS} )
+  #include_directories( ${MAGICK_INCLUDE_DIRS} )
+  #SET( CImg_SYSTEM_LIBS ${CImg_SYSTEM_LIBS} ${MAGICK_LIBRARIES} )
+  list(APPEND CImg_INCLUDE_DIRS
+    ${MAGICK_INCLUDE_DIRS}
+  )
+  list(APPEND CImg_SYSTEM_LIBS_DIR
+    ${MAGICK_LIBRARY_DIRS}
+  )
+  list(APPEND CImg_SYSTEM_LIBS
+    ${MAGICK_LIBRARIES}
+  )
+endif()
+
+if( LIBAVCODEC_FOUND  AND LIBAVFORMAT_FOUND AND LIBSWSCALE_FOUND AND LIBAVUTIL_FOUND )
+  SET(CIMG_CFLAGS "${CIMG_CFLAGS} ${CIMG_FFMPEG_CCFLAGS}")
+  #link_directories( ${LIBAVFORMAT_LIBRARY_DIRS} )
+  #link_directories( ${LIBAVCODEC_LIBRARY_DIRS} )
+  #link_directories( ${LIBSWSCALE_LIBRARY_DIRS} )
+  #link_directories( ${LIBAVUTIL_LIBRARY_DIRS} )
+  #include_directories( ${LIBAVFORMAT_INCLUDE_DIRS} ${LIBAVFORMAT_INCLUDE_DIRS}/libavformat)
+  #include_directories( ${LIBAVCODEC_INCLUDE_DIRS} ${LIBAVCODEC_INCLUDE_DIRS}/libavcodec )
+  #include_directories( ${LIBSWSCALE_INCLUDE_DIRS} ${LIBSWSCALE_INCLUDE_DIRS}/libswscale)
+  #include_directories( ${LIBAVUTIL_INCLUDE_DIRS} ${LIBAVUTIL_INCLUDE_DIRS}/libavutil )
+  #SET( CImg_SYSTEM_LIBS ${CImg_SYSTEM_LIBS} ${LIBAVFORMAT_LIBRARIES} )
+  #SET( CImg_SYSTEM_LIBS ${CImg_SYSTEM_LIBS} ${LIBAVCODEC_LIBRARIES} )
+  #SET( CImg_SYSTEM_LIBS ${CImg_SYSTEM_LIBS} ${LIBSWSCALE_LIBRARIES} )
+  #SET( CImg_SYSTEM_LIBS ${CImg_SYSTEM_LIBS} ${LIBAVUTIL_LIBRARIES} )
+  list(APPEND CImg_INCLUDE_DIRS
+    ${LIBAVFORMAT_INCLUDE_DIRS} ${LIBAVFORMAT_INCLUDE_DIRS}/libavformat
+    ${LIBAVCODEC_INCLUDE_DIRS} ${LIBAVCODEC_INCLUDE_DIRS}/libavcodec 
+    ${LIBSWSCALE_INCLUDE_DIRS} ${LIBSWSCALE_INCLUDE_DIRS}/libswscale
+    ${LIBAVUTIL_INCLUDE_DIRS} ${LIBAVUTIL_INCLUDE_DIRS}/libavutil 
+  )
+  list(APPEND CImg_SYSTEM_LIBS_DIR
+    ${LIBAVFORMAT_LIBRARY_DIRS}
+    ${LIBAVCODEC_LIBRARY_DIRS}
+    ${LIBSWSCALE_LIBRARY_DIRS}
+    ${LIBAVUTIL_LIBRARY_DIRS}
+  )
+  list(APPEND CImg_SYSTEM_LIBS
+    ${LIBAVFORMAT_LIBRARIES}
+    ${LIBAVCODEC_LIBRARIES}
+    ${LIBSWSCALE_LIBRARIES}
+    ${LIBAVUTIL_LIBRARIES}
+  )
+endif()
+
+if(NOT APPLE)
+  if(NOT WIN32)
+    if(X11_FOUND)
+      SET(CIMG_CFLAGS "${CIMG_CFLAGS} ${CIMG_XSHM_CCFLAGS} ${CIMG_XRANDR_CCFLAGS}")
+      SET(CImg_SYSTEM_LIBS ${CImg_SYSTEM_LIBS} Xext Xrandr)
+    endif()
+  endif(NOT WIN32)
+endif(NOT APPLE)
+
+if(X11_FOUND)
+  #link_directories(${X11_LIB_DIRS})
+  #include_directories(${X11_INCLUDE_DIR})
+  #SET( CImg_SYSTEM_LIBS ${CImg_SYSTEM_LIBS} ${X11_LIBRARIES} )
+  list(APPEND CImg_INCLUDE_DIRS
+    ${X11_INCLUDE_DIR}
+  )
+  list(APPEND CImg_SYSTEM_LIBS_DIR
+    ${X11_LIB_DIRS}
+  )
+  list(APPEND CImg_SYSTEM_LIBS
+    ${X11_LIBRARIES}
+  )
+endif()
+
+if (NOT WIN32)
+  #SET( CImg_SYSTEM_LIBS ${CImg_SYSTEM_LIBS} ${CMAKE_THREAD_LIBS_INIT} )
+  list(APPEND CImg_SYSTEM_LIBS
+    ${CMAKE_THREAD_LIBS_INIT} 
+  )
+endif()
+
+if( WIN32)
+  #SET( CImg_SYSTEM_LIBS  ${CImg_SYSTEM_LIBS}  gdi32 )
+  list(APPEND CImg_SYSTEM_LIBS
+    gdi32
+  )
+endif()
+
+if (OpenCV_FOUND)
+  message("OpenCV Found")
+  SET(CIMG_CFLAGS "${CIMG_CFLAGS} ${CIMG_OPENCV_CCFLAGS}")
+  #include_directories(${OpenCV_INCLUDE_DIRS})
+  #link_directories(${OpenCV_LIB_DIRS})
+  #SET( CImg_SYSTEM_LIBS  ${CImg_SYSTEM_LIBS}  ${OpenCV_LIBS} )
+  list(APPEND CImg_INCLUDE_DIRS
+    ${OpenCV_INCLUDE_DIRS}
+  )
+  list(APPEND CImg_SYSTEM_LIBS_DIR
+    ${OpenCV_LIB_DIRS}
+  )
+  list(APPEND CImg_SYSTEM_LIBS
+    ${OpenCV_LIBS}
+  )
+endif()
+
+if(LAPACK_FOUND)
+  SET(CIMG_CFLAGS "${CIMG_CFLAGS} ${CIMG_LAPACK_CCFLAGS}")
+  #link_directories( ${LAPACK_LIBRARY_DIRS} )
+  #include_directories( ${LAPACK_INCLUDE_DIRS} )
+  #SET( CImg_SYSTEM_LIBS ${CImg_SYSTEM_LIBS} ${LAPACK_LIBRARIES} )
+  list(APPEND CImg_INCLUDE_DIRS
+    ${LAPACK_INCLUDE_DIRS}
+  )
+  list(APPEND CImg_SYSTEM_LIBS_DIR
+    ${LAPACK_LIBRARY_DIRS}
+  )
+  list(APPEND CImg_SYSTEM_LIBS
+    ${LAPACK_LIBRARIES}
+  )
+endif()
+
+if(BLAS_FOUND)
+  SET(CIMG_CFLAGS "${CIMG_CFLAGS} ${CIMG_BLAS_CCFLAGS}")
+  #link_directories( ${BLAS_LIBRARY_DIRS} )
+  #include_directories( ${BLAS_INCLUDE_DIRS} )
+  #SET( CImg_SYSTEM_LIBS ${CImg_SYSTEM_LIBS} ${BLAS_LIBRARIES} )
+  list(APPEND CImg_INCLUDE_DIRS
+    ${BLAS_INCLUDE_DIRS}
+  )
+  list(APPEND CImg_SYSTEM_LIBS_DIR
+    ${BLAS_LIBRARY_DIRS}
+  )
+  list(APPEND CImg_SYSTEM_LIBS
+    ${BLAS_LIBRARIES}
+  )
+endif()
+
+# Add CIMG Flags to Compilation Flags
+SET(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} ${CIMG_CFLAGS}")
+
+foreach(program ${CIMG_FILES})
+  add_executable(${program} ${program}.cpp)
+  target_link_libraries(${program} ${CImg_SYSTEM_LIBS} )
+endforeach(program)
+

cmake_modules/FindMagick.cmake

-# - Find Magick
-# This module finds if the Magick++ libraries and headers (distributed
-# with ImageMagick are installed.  If you are looking for the ImageMagick
-# programs please see FIND_PACKAGE(ImageMagick).
-#
-# This module sets the following variables:
-#
-# MAGICK_FOUND
-#    True if the Magick++ library was found
-# MAGICK_INCLUDE_DIR
-#    The include path of the Magick++.h header file
-# MAGICK_LIBRARY
-#    The location of the Magick library
-# MAGICK++_LIBRARY
-#    THe location of the Magick++ library
-#
-
-# Find the Magick++ include path
-FIND_PATH(MAGICK_INCLUDE_DIR Magick++.h
-    "[HKEY_LOCAL_MACHINE\\SOFTWARE\\ImageMagick\\Current;BinPath]/include"
-)
-
-FIND_LIBRARY(MAGICK_LIBRARY Magick CORE_RL_Magick_
-    PATHS 
-    "[HKEY_LOCAL_MACHINE\\SOFTWARE\\ImageMagick\\Current;BinPath]/lib"
-)
-
-FIND_LIBRARY(MAGICK++_LIBRARY Magick++ CORE_RL_Magick++_
-    PATHS
-    "[HKEY_LOCAL_MACHINE\\SOFTWARE\\ImageMagick\\Current;BinPath]/lib"
-)
-
-IF(MAGICK_INCLUDE_DIR AND MAGICK_LIBRARY AND MAGICK++_LIBRARY)
-    SET(MAGICK_FOUND true)
-    SET(MAGICK_INCLUDE_DIRS ${MAGICK_INCLUDE_DIR})
-    SET(MAGICK_LIBRARIES    ${MAGICK_LIBRARY} ${MAGICK++_LIBRARY})
-ENDIF(MAGICK_INCLUDE_DIR AND MAGICK_LIBRARY AND MAGICK++_LIBRARY)
-
-IF(MAGICK_FOUND)
-    IF(NOT MAGICK_FIND_QUIETLY)
-        MESSAGE(STATUS "Found Magick: ${MAGICK_LIBRARY}")
-        MESSAGE(STATUS "Found Magick++: ${MAGICK++_LIBRARY}")
-    ENDIF(NOT MAGICK_FIND_QUIETLY)
-ELSE(MAGICK_FOUND) 
-    IF(MAGICK_FIND_REQUIRED)
-        MESSAGE(FATAL_ERROR "Could not find the Magick library")
-    ENDIF(MAGICK_FIND_REQUIRED)
-ENDIF(MAGICK_FOUND)

cmake_modules/FindPTHREADSConfig.cmake

-# The following variables are set
-#  CMAKE_THREAD_LIBS_INIT     - the thread library
-#  CMAKE_USE_SPROC_INIT       - are we using sproc?
-#  CMAKE_USE_WIN32_THREADS_INIT - using WIN32 threads?
-#  CMAKE_USE_PTHREADS_INIT    - are we using pthreads
-#  CMAKE_HP_PTHREADS_INIT     - are we using hp pthreads
-
-IF( WIN32 )
-	FIND_PACKAGE(Threads REQUIRED)
-	
-	
-	#FIND_PATH(EXPAT_INCLUDE_DIR NAMES pthread.h /MinGW/include)
-	#MARK_AS_ADVANCED(EXPAT_INCLUDE_DIR)
-	#SET (EXPAT_INCLUDE_DIRS /MinGW/include)
-	# Look for the library.
-	
-	
-	#FIND_LIBRARY(CMAKE_THREAD_LIBS_INIT NAMES pthreadGCE2 PATHS /MinGW/lib)
-	#SET(CMAKE_USE_PTHREADS_INIT 1)
-	#MARK_AS_ADVANCED(CMAKE_USE_PTHREADS_INIT)
-	
-	
-	#ADD_LIBRARY(pthreadGCE2 STATIC)
-ELSE (WIN32)
-	FIND_PACKAGE(Threads REQUIRED)
-	#ADD_LIBRARY(pthread SHARED ${CMAKE_THREAD_LIBS_INIT})
-ENDIF( WIN32 )
\ No newline at end of file

cmake_modules/FindPthreads.cmake

-# - Find the Pthreads library
-# This module searches for the Pthreads library (including the
-# pthreads-win32 port).
-#
-# This module defines these variables:
-#
-#  PTHREADS_FOUND
-#      True if the Pthreads library was found
-#  PTHREADS_LIBRARY
-#      The location of the Pthreads library
-#  PTHREADS_INCLUDE_DIR
-#      The include path of the Pthreads library
-#  PTHREADS_DEFINITIONS
-#      Preprocessor definitions to define
-#
-# This module responds to the PTHREADS_EXCEPTION_SCHEME
-# variable on Win32 to allow the user to control the
-# library linked against.  The Pthreads-win32 port
-# provides the ability to link against a version of the
-# library with exception handling.  IT IS NOT RECOMMENDED
-# THAT YOU USE THIS because most POSIX thread implementations
-# do not support stack unwinding.
-#
-#  PTHREADS_EXCEPTION_SCHEME
-#      C  = no exceptions (default)
-#         (NOTE: This is the default scheme on most POSIX thread
-#          implementations and what you should probably be using)
-#      CE = C++ Exception Handling
-#      SE = Structure Exception Handling (MSVC only)
-#
-
-#
-# Define a default exception scheme to link against
-# and validate user choice.
-#
-IF(NOT DEFINED PTHREADS_EXCEPTION_SCHEME)
-    # Assign default if needed
-    SET(PTHREADS_EXCEPTION_SCHEME "C")
-ELSE(NOT DEFINED PTHREADS_EXCEPTION_SCHEME)
-    # Validate
-    IF(NOT PTHREADS_EXCEPTION_SCHEME STREQUAL "C" AND
-       NOT PTHREADS_EXCEPTION_SCHEME STREQUAL "CE" AND
-       NOT PTHREADS_EXCEPTION_SCHEME STREQUAL "SE")
-
-    MESSAGE(FATAL_ERROR "See documentation for FindPthreads.cmake, only C, CE, and SE modes are allowed")
-
-    ENDIF(NOT PTHREADS_EXCEPTION_SCHEME STREQUAL "C" AND
-          NOT PTHREADS_EXCEPTION_SCHEME STREQUAL "CE" AND
-          NOT PTHREADS_EXCEPTION_SCHEME STREQUAL "SE")
-
-     IF(NOT MSVC AND PTHREADS_EXCEPTION_SCHEME STREQUAL "SE")
-         MESSAGE(FATAL_ERROR "Structured Exception Handling is only allowed for MSVC")
-     ENDIF(NOT MSVC AND PTHREADS_EXCEPTION_SCHEME STREQUAL "SE")
-
-ENDIF(NOT DEFINED PTHREADS_EXCEPTION_SCHEME)
-
-#
-# Find the header file
-#
-FIND_PATH(PTHREADS_INCLUDE_DIR pthread.h)
-
-#
-# Find the library
-#
-SET(names)
-IF(MSVC)
-    SET(names
-            pthreadV${PTHREADS_EXCEPTION_SCHEME}2
-            pthread
-    )
-ELSEIF(MINGW)
-    SET(names
-            pthreadG${PTHREADS_EXCEPTION_SCHEME}2
-            pthread
-    )
-ELSE(MSVC) # Unix / Cygwin / Apple
-    SET(names pthread)
-ENDIF(MSVC)
-    
-FIND_LIBRARY(PTHREADS_LIBRARY ${names}
-    DOC "The Portable Threads Library")
-
-IF(PTHREADS_INCLUDE_DIR AND PTHREADS_LIBRARY)
-    SET(PTHREADS_FOUND true)
-    SET(PTHREADS_DEFINITIONS -DHAVE_PTHREAD_H)
-    SET(PTHREADS_INCLUDE_DIRS ${PTHREADS_INCLUDE_DIR})
-    SET(PTHREADS_LIBRARIES    ${PTHREADS_LIBRARY})
-ENDIF(PTHREADS_INCLUDE_DIR AND PTHREADS_LIBRARY)
-
-IF(PTHREADS_FOUND)
-    IF(NOT PTHREADS_FIND_QUIETLY)
-        MESSAGE(STATUS "Found Pthreads: ${PTHREADS_LIBRARY}")
-    ENDIF(NOT PTHREADS_FIND_QUIETLY)
-ELSE(PTHREADS_FOUND) 
-    IF(PTHREADS_FIND_REQUIRED)
-        MESSAGE(FATAL_ERROR "Could not find the Pthreads Library")
-    ENDIF(PTHREADS_FIND_REQUIRED)
-ENDIF(PTHREADS_FOUND)

debian/changelog

+beads (1.1.17+dfsg-1) UNRELEASED; urgency=medium
+
+  * New upstream version
+  * Watch file now reports new upstream URLs (not fit for proper download
+    yet since some more sophisticated name mangling is needed)
+  * Standards-Version: 4.1.3
+  * debhelper 11
+  * Build-Depends: libodsstream-qt5-dev
+
+ -- Andreas Tille <tille@debian.org>  Mon, 12 Feb 2018 10:22:39 +0100
+
 beads (1.1.13+dfsg-2) unstable; urgency=medium
 
   * replacing the build dependency on qttools5-dev-tools with qttools5-dev

debian/compat

-10
+11

debian/control

@@ -4,12 +4,13 @@ Uploaders: Andreas Tille <tille@debian.org>,
            Olivier Langella <olivier.langella@moulon.inra.fr>
 Section: science
 Priority: optional
-Build-Depends: debhelper (>= 10),
+Build-Depends: debhelper (>= 11),
                cmake,
                qtbase5-dev,
                qttools5-dev,
+               libodsstream-qt5-dev,
                cimg-dev
-Standards-Version: 4.1.1
+Standards-Version: 4.1.3
 Vcs-Browser: https://anonscm.debian.org/cgit/debian-med/beads.git
 Vcs-Git: https://anonscm.debian.org/git/debian-med/beads.git
 Homepage: http://moulon.inra.fr/beads/beads.html

debian/patches/installation.patch

-Author: Juhani Numminen <juhaninumminen0@gmail.com>
-Last-Update: 2017-10-21
-Description: CMakeFiles.txt assumed in-source build
- but we are using separate build directory.
-
---- a/CMakeLists.txt
-+++ b/CMakeLists.txt
-@@ -186,8 +186,8 @@ SET(CPACK_STRIP_FILES "src/beads;src/qtb
- # the project's entire directory structure.
- SUBDIRS (src)
- 
--INSTALL(PROGRAMS src/beads DESTINATION bin)
--INSTALL(PROGRAMS src/qtbeads/qtbeads DESTINATION bin)
-+INSTALL(PROGRAMS "${CMAKE_BINARY_DIR}/src/beads" DESTINATION bin)
-+INSTALL(PROGRAMS "${CMAKE_BINARY_DIR}/src/qtbeads/qtbeads" DESTINATION bin)
- #INSTALL(DIRECTORY doc/man1 DESTINATION share/man/man1)
- INSTALL(FILES doc/man1/beads.1 DESTINATION share/man/man1)
- INSTALL(FILES share/applications/beads.desktop DESTINATION share/applications)

debian/patches/qt5.patch

@@ -2,55 +2,9 @@ Author: Andreas Tille <tille@debian.org>
 Last-Update: Thu, 19 Oct 2017 14:58:04 +0200
 Description: Port from Qt4 to Qt5
 
---- a/src/CMakeLists.txt
-+++ b/src/CMakeLists.txt
-@@ -1,12 +1,7 @@
- 
-- # this command finds Qt4 libraries and sets all required variables
--  # note that it's Qt4, not QT4 or qt4
--FIND_PACKAGE( Qt4 REQUIRED )
--
--  
--  # add some useful macros and variables
--  # (QT_USE_FILE is a variable defined by FIND_PACKAGE( Qt4 ) that contains a path to CMake script)
--INCLUDE( ${QT_USE_FILE} )
-+ # this command finds Qt5 libraries and sets all required variables
-+  # note that it's Qt5, not QT5 or qt5
-+FIND_PACKAGE( Qt5 REQUIRED COMPONENTS Widgets LinguistTools )
- 
- SET( BEADS_CPP
- 	beads.cpp
-@@ -62,7 +57,7 @@
- 	target_link_libraries (beads ${EXTRA_CIMG_LIBRARY} ${QT_LIBRARIES} )
- ELSE(WIN32)
- 	 # Link the executable to the Hello library.
--	target_link_libraries (beads ${X11_LIBRARIES} m ${PTHREADS_LIBRARY} ${EXTRA_CIMG_LIBRARY} ${QT_LIBRARIES} )
-+	target_link_libraries (beads ${X11_LIBRARIES} m ${PTHREADS_LIBRARY} ${EXTRA_CIMG_LIBRARY} Qt5::Widgets )
- ENDIF(WIN32)
- 
--SUBDIRS (qtbeads)
-\ No newline at end of file
-+SUBDIRS (qtbeads)
 --- a/src/qtbeads/CMakeLists.txt
 +++ b/src/qtbeads/CMakeLists.txt
-@@ -1,12 +1,9 @@
- 
-- # this command finds Qt4 libraries and sets all required variables
--  # note that it's Qt4, not QT4 or qt4
--FIND_PACKAGE( Qt4 REQUIRED )
-+ # this command finds Qt5 libraries and sets all required variables
-+  # note that it's Qt5, not QT5 or qt5
-+FIND_PACKAGE( Qt5 REQUIRED COMPONENTS Widgets PrintSupport LinguistTools )
- 
--  
--  # add some useful macros and variables
--  # (QT_USE_FILE is a variable defined by FIND_PACKAGE( Qt4 ) that contains a path to CMake script)
--INCLUDE( ${QT_USE_FILE} )
-+SET(CMAKE_AUTOMOC ON)
- 
- SET( BEADS_FOR_QT_CPP
- 	../ConfigFile/ConfigFile
-@@ -47,11 +44,6 @@
+@@ -16,11 +16,6 @@ SET( QTBEADS_SRCS
  	QCimg.cpp
  	q_gel_image.cpp
  	q_gel_image_scroll.cpp
@@ -62,48 +16,3 @@ Description: Port from Qt4 to Qt5
  	main_window.h
  	q_gel_image.h
  )  
-@@ -80,7 +72,7 @@
- # Translation files
- SET(GLOB TRANS translations/*.ts)
- # add translations ...
--QT4_ADD_TRANSLATION(QM ${TRANS})
-+QT5_ADD_TRANSLATION(QM ${TRANS})
- 
- 
- 
-@@ -90,25 +82,13 @@
- 
- #FIND_PACKAGE(Qwt5 REQUIRED) 
-   
--  
--  
--  # this command will generate rules that will run rcc on all files from SAMPLE_RCS
--  # in result SAMPLE_RC_SRCS variable will contain paths to files produced by rcc
--QT4_ADD_RESOURCES( QTBEADS_SRCS ${SAMPLE_RCS} )
--  
--  # this will run uic on .ui files:
--  #QT4_WRAP_UI( SAMPLE_UI_HDRS ${SAMPLE_UIS} )
--  
--  # and finally this will run moc:
--QT4_WRAP_CPP( QTBEADS_MOC_SRCS ${QTBEADS_MOC_HDRS} )
--  
-   # we need this to be able to include headers produced by uic in our code
-   # (CMAKE_BINARY_DIR holds a path to the build directory, while INCLUDE_DIRECTORIES() works just like INCLUDEPATH from qmake)
-   #INCLUDE_DIRECTORIES( ${CMAKE_BINARY_DIR} ${Qwt5_INCLUDE_DIR})
- INCLUDE_DIRECTORIES( ${CMAKE_BINARY_DIR})
-   
-   # here we instruct CMake to build "sample" executable from all of the source files
--ADD_EXECUTABLE( qtbeads ${BEADS_FOR_QT_CPP} ${QTBEADS_SRCS} ${QTBEADS_MOC_SRCS} ${SAMPLE_RC_SRCS} ${SAMPLE_UI_HDRS} ${QM} )
-+ADD_EXECUTABLE( qtbeads ${BEADS_FOR_QT_CPP} ${QTBEADS_SRCS} ${QM} )
- 
- 
-   # last thing we have to do is to tell CMake what libraries our executable needs,
-@@ -118,7 +98,7 @@
- IF(WIN32)
- 	TARGET_LINK_LIBRARIES( qtbeads ${QT_LIBRARIES} ${EXTRA_CIMG_LIBRARY})
- ELSE(WIN32)
--	TARGET_LINK_LIBRARIES( qtbeads ${QT_LIBRARIES} m ${PTHREADS_LIBRARY} ${EXTRA_CIMG_LIBRARY})
-+	TARGET_LINK_LIBRARIES( qtbeads Qt5::Widgets Qt5::PrintSupport m ${PTHREADS_LIBRARY} ${EXTRA_CIMG_LIBRARY})
- ENDIF(WIN32)
- 
-   

debian/patches/qt5_headers.patch

-Author: Andreas Tille <tille@debian.org>
-Last-Update: Thu, 19 Oct 2017 14:58:04 +0200
-Description: Add missing headers
-
---- a/src/qtbeads/main_window.cpp
-+++ b/src/qtbeads/main_window.cpp
-@@ -10,6 +10,12 @@
- #include <QMenu>
- #include <QMenuBar>
- #include <QFileDialog>
-+#include <QLineEdit>
-+#include <QMessageBox>
-+#include <QInputDialog>
-+#include <QStatusBar>
-+#include <QPrintDialog>
-+#include <QFontDialog>
- #include "main_window.h"
- #include "QCimg.h"
- #include "../config.h"

debian/patches/rpath.patch

-Author: Juhani Numminen <juhaninumminen0@gmail.com>
-Last-Update: 2017-10-21
-Description: Remove unusual statements, which gets rid of rpath.
- There is no directory with the literal name X11_INCLUDE_DIR.
- The other statement added -L/usr/include which is not correct.
-
---- a/src/CMakeLists.txt
-+++ b/src/CMakeLists.txt
-@@ -34,7 +34,6 @@ IF(WIN32)
- ELSE(WIN32)
- 	FIND_PACKAGE(X11 REQUIRED)
- 	
--	INCLUDE_DIRECTORIES(X11_INCLUDE_DIR)
- 	# X11_FOUND is true if X11 is available.
- 	#    * X11_INCLUDE_DIR contains the include directories to use X11.
- 	#    * X11_LIBRARIES points to the libraries to link against to use X11.
-@@ -44,8 +43,6 @@ ELSE(WIN32)
- 	ADD_DEFINITIONS(${PTHREADS_DEFINITIONS})
- 	# -m -pthread FindThreads
- 	
--	# Make sure the linker can find the Hello library once it is built.
--	link_directories (${X11_INCLUDE_DIR})
- ENDIF(WIN32)
- 
- 

debian/patches/series

-qt5.patch
-qt5_headers.patch
+# qt5.patch
 use_debian_packaged_cimg.h
-installation.patch
-rpath.patch
 spelling.patch

debian/patches/use_debian_packaged_cimg.h

@@ -4,46 +4,11 @@ Description: Use Debian packaged CImg.h from cimg-dev package since
  the code copy shipped together with upstream is outdated and does not
  build with recent gcc
 
---- a/src/CMakeLists.txt
-+++ b/src/CMakeLists.txt
-@@ -29,7 +29,6 @@
- 	spot_document_gnumeric
- 	spotSvgDocument
- 	images/imageDeNovo
--	CImg
- )
- IF(WIN32)
- ELSE(WIN32)
---- a/src/qtbeads/CMakeLists.txt
-+++ b/src/qtbeads/CMakeLists.txt
-@@ -30,7 +30,6 @@
- 	../spot_document_gnumeric
- 	../spotSvgDocument
- 	../images/imageDeNovo
--	../CImg
- )
-   
- # with SET() command you can change variables or define new ones
---- a/src/images/imageCode.h
-+++ b/src/images/imageCode.h
-@@ -3,8 +3,10 @@
- 
- #include "../config.h"
- 
--#include "../CImg.h"
--//#include <CImg.h>
-+#include <CImg.h>
-+//CImg.h includes Xlib.h, which has evil "#define Bool int" that
-+//interferes with QMetaType::Bool in files generated by Qt MOC!
-+#undef Bool
- 
- //Images pour lesquelles les valeurs des pixels sont des codes et non des valeurs quantitatives
- //Sont des codes: l'image des directions, l'image des numeros
 --- a/CMakeLists.txt
 +++ b/CMakeLists.txt
-@@ -78,6 +78,7 @@
- 	FIND_PACKAGE(Pthreads REQUIRED)
- 	SET(CMAKE_CXX_FLAGS_RELEASE "-O3 -DNDEBUG")
+@@ -67,6 +67,7 @@ ELSE(WIN32)
+ 	#FIND_PACKAGE(Pthreads REQUIRED)
+ 	SET(CMAKE_CXX_FLAGS_RELEASE "-s -O3 -DNDEBUG")
  	SET ( CIMG_OS 1)
 +	SET(EXTRA_CIMG_LIBRARY "X11")
  ENDIF(WIN32)

debian/watch

 version=4
 
+# FIXME: this needs proper URL mangling
 opts="repacksuffix=+dfsg,dversionmangle=s/\+dfsg//g,repack,compression=xz" \
-  http://pappso.inra.fr/bioinfo/beads/index.php .*/downloads/beads-@ANY_VERSION@@ARCHIVE_EXT@
+  https://sourcesup.renater.fr/projects/beads/ .*/.*#beads-_@ANY_VERSION@-title-content

src/CMakeLists.txt

 
- # this command finds Qt4 libraries and sets all required variables
-  # note that it's Qt4, not QT4 or qt4
-FIND_PACKAGE( Qt4 REQUIRED )
+FIND_PACKAGE( Qt5 COMPONENTS Core Gui Xml REQUIRED )
 
+list( APPEND CMAKE_MODULE_PATH
+    ${PROJECT_SOURCE_DIR}/cmake_modules
+)
+
+set (CImg_INCLUDE_DIR "${CMAKE_SOURCE_DIR}/src/cimg")
+find_package( CImg REQUIRED )
+
+# Add CIMG Flags to Compilation Flags
+SET(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} ${CIMG_CFLAGS}")
+
+#INCLUDE_DIRECTORIES(${ODSSTREAM_INCLUDE_DIR})
+
+if (MINGW32)
+    INCLUDE_DIRECTORIES( ${QUAZIP_INCLUDE_DIR} )
+ELSE (MINGW32)
+    FIND_PACKAGE( Odsstream REQUIRED )
+ENDIF (MINGW32)
 
-  # add some useful macros and variables
-  # (QT_USE_FILE is a variable defined by FIND_PACKAGE( Qt4 ) that contains a path to CMake script)
-INCLUDE( ${QT_USE_FILE} )
 
-SET( BEADS_CPP
-	beads.cpp
+
+SET( BEADS_FOR_QT_CPP
 	ConfigFile/ConfigFile
 	parameters
 	encode/base64
@@ -31,38 +43,54 @@ SET( BEADS_CPP
 	spotPROTICdbDocument
 	spot
 	spotDocument
-	spot_document_gnumeric
 	spotSvgDocument
 	images/imageDeNovo
-	CImg
 )
+
 IF(WIN32)
 ELSE(WIN32)
-	FIND_PACKAGE(X11 REQUIRED)
+	#FIND_PACKAGE(X11 REQUIRED)
 	
-	INCLUDE_DIRECTORIES(X11_INCLUDE_DIR)
+	#INCLUDE_DIRECTORIES(X11_INCLUDE_DIR)
 	# X11_FOUND is true if X11 is available.
 	#    * X11_INCLUDE_DIR contains the include directories to use X11.
 	#    * X11_LIBRARIES points to the libraries to link against to use X11.
 	# Make sure the compiler can find include files from our Hello library.
-	include_directories (${X11_INCLUDE_DIR})
+	#include_directories (${X11_INCLUDE_DIR})
 	
-	ADD_DEFINITIONS(${PTHREADS_DEFINITIONS})
+	#ADD_DEFINITIONS(${PTHREADS_DEFINITIONS})
 	# -m -pthread FindThreads
 	
 	# Make sure the linker can find the Hello library once it is built.
-	link_directories (${X11_INCLUDE_DIR})
+	#link_directories (${X11_INCLUDE_DIR})
 ENDIF(WIN32)
 
 
-add_executable (beads ${BEADS_CPP})
+add_executable (beads beads.cpp )
+target_include_directories (beads PUBLIC ${ODSSTREAM_INCLUDE_DIR} ${CImg_INCLUDE_DIRS} ${CImg_SYSTEM_LIBS_DIR})
+SET_TARGET_PROPERTIES(beads
+      PROPERTIES OUTPUT_NAME beads
+      CLEAN_DIRECT_OUTPUT 1
+      CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} ${CImg_CFLAGS}"
+    )
+
+target_link_libraries (beads  cppbeads
+        ${ODSSTREAM_QT5_LIBRARY} ${CImg_SYSTEM_LIBS} Qt5::Core Qt5::Gui Qt5::Xml)
+
+
+add_library ( cppbeads STATIC
+		${BEADS_FOR_QT_CPP}
+)
+
+target_include_directories (cppbeads PUBLIC ${ODSSTREAM_INCLUDE_DIR}
+    ${CImg_INCLUDE_DIRS} ${CImg_SYSTEM_LIBS_DIR})
+SET_TARGET_PROPERTIES(cppbeads
+      PROPERTIES OUTPUT_NAME cppbeads-qt5
+      CLEAN_DIRECT_OUTPUT 1
+      CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} ${CImg_CFLAGS}"
+)
+target_link_libraries (cppbeads
+        ${ODSSTREAM_QT5_LIBRARY} ${CImg_SYSTEM_LIBS} Qt5::Core Qt5::Gui Qt5::Xml)
 
-IF(WIN32)
-	 # Link the executable to the Hello library.
-	target_link_libraries (beads ${EXTRA_CIMG_LIBRARY} ${QT_LIBRARIES} )
-ELSE(WIN32)
-	 # Link the executable to the Hello library.
-	target_link_libraries (beads ${X11_LIBRARIES} m ${PTHREADS_LIBRARY} ${EXTRA_CIMG_LIBRARY} ${QT_LIBRARIES} )
-ENDIF(WIN32)
     
 SUBDIRS (qtbeads)

src/beads.cpp

@@ -18,6 +18,8 @@
 #include "parameters.h"
 
 #include <QFileInfo>
+#include <odsstream/tsvoutputstream.h>
+#include <odsstream/odsdocwriter.h>
 
 using namespace std;
 
@@ -95,13 +97,18 @@ bool exist(const string filename) {
 int main(int argc, char ** argv) {
 
     cout << "beads " << BEADS_VERSION << endl;
-
+    // no sub function : detect spots and write ouput
+    const std::string input_filename(cimg_option("-i","","input gel image file"));
+    const std::string output_filename(
+        cimg_option("-o","output.xml","output data file"));
+    QString outfile(output_filename.c_str());
+    QString infile(input_filename.c_str());
     const bool save_steps =
         cimg_option("--steps",false,"save each step of the beads process");
 
     //argument for parameter file :
     string parameter_filename =
-			cimg_option("--param","","configuration file for beads");
+        cimg_option("--param","beads.conf","configuration file for beads");
     if (parameter_filename == "") {
         parameter_filename
             = cimg_option("-p","beads.conf","configuration file for beads");
@@ -127,7 +134,9 @@ int main(int argc, char * * argv) {
     const std::string sub_function(
         cimg_option("-sub","nosub","function to apply"));
 
+    qDebug() << "command line parsed";
     if (sub_function == "total") {
+        qDebug() << "sub_function == total";
 #ifndef MINGW32 //deactivate the sub total for mingw32 version
         cimg_usage("Spot detection and quantification");
         const char * file_i1 =
@@ -326,10 +335,18 @@ int main(int argc, char * * argv) {
         // ecriture fichier de spots
         cout << "Writing text tabulated spot file" << endl;
 
-		spotDocument fspot;
-		fspot.open(source_filename);
+        QFile file(source_filename);
+        if (!file.open(QIODevice::WriteOnly | QIODevice::Text)) {
+            return 1;
+//             }
+
+            QTextStream flux(&file);
+            TsvOutputStream doc_writer(flux);
+            spotDocument fspot(&doc_writer);
+            fspot.open();
             fspot.write_detection(the_detection_from_prob);
             fspot.close();
+            file.close();
 
             if (svg_output) {
                 cout << "Computing SVG file" << endl;
@@ -376,22 +393,19 @@ int main(int argc, char * * argv) {
             //else {
             //	image.save(output_filename.c_str());
             //}
+        }
     } else {
-		// no sub function : detect spots and write ouput
-		QString input_filename = cimg_option("-i","","input gel image file");
-		QString output_filename =
-				cimg_option("-o","output.xml","output data file");
-
+        qDebug() << "no sub function";
         if (input_filename == "") {
             cerr << "please use argument -i to provide a gel image file."
                  << endl;
             return 1;
         }
 
-		QString source_filename(input_filename);
+        QString source_filename(infile);
         QFileInfo source_fileinfo(source_filename);
 
-		QFileInfo output_fileinfo(output_filename);
+        QFileInfo output_fileinfo(outfile);
 
         source_filename = source_fileinfo.baseName();
 
@@ -399,9 +413,9 @@ int main(int argc, char * * argv) {
 
         qDebug() << "main output_extension : " << output_extension;
 
-		cout << "Loading input image file " << input_filename.toStdString()
+        cout << "Loading input image file " << input_filename
              << endl;
-		imageIntensity gel_image_loaded(input_filename);
+        imageIntensity gel_image_loaded(infile);
 
         imageIntensity * p_gel_image;
         if (inverse) {
@@ -533,33 +547,60 @@ int main(int argc, char * * argv) {
             // the SVG output is a drawing of detected spots viewable with any SVG compatible software
             //  (example : http://www.inkscape.org)
             cout << "Writing PROTICdbML xml spot file "
-					<< output_filename.toStdString() << endl;
+                 << output_filename << endl;
             spotPROTICdbDocument proticdbml_file;
-			proticdbml_file.set_gel_image_file_name(input_filename);
-			proticdbml_file.open(output_filename);
+            proticdbml_file.set_gel_image_file_name(infile);
+            proticdbml_file.open(outfile);
             proticdbml_file.write_detection(the_detection_from_prob);
             proticdbml_file.close();
         }
+        if (output_extension == "ods") {
+            the_detection_from_prob.quantify_spots_with_image(*p_gel_image,
+                    numbers);
+            cout << "Writing ods spot file "
+                 << output_filename << endl;
+
+            OdsDocWriter doc_writer(outfile);
+
+            spotDocument fspot(&doc_writer);
+            fspot.open();
+            fspot.write_detection(the_detection_from_prob);
+            fspot.close();
+        }
         if (output_extension == "txt") {
             the_detection_from_prob.quantify_spots_with_image(*p_gel_image,
                     numbers);
             cout << "Writing text tabulated spot file "
-					<< output_filename.toStdString() << endl;
+                 << output_filename << endl;
 
-			spotDocument fspot;
-			fspot.open(output_filename);
+            QFile file(outfile);
+            if (!file.open(QIODevice::WriteOnly | QIODevice::Text)) {
+                return 1;
+            }
+
+            QTextStream flux(&file);
+            TsvOutputStream doc_writer(flux);
+            spotDocument fspot(&doc_writer);
+            fspot.open();
             fspot.write_detection(the_detection_from_prob);
             fspot.close();
+            file.close();
         }
         if (output_extension == "jpg") {
             imageContours contours;
             contours.compute_from_gel_image_and_numeros(*p_gel_image, numbers);
             contours.draw_contours(the_detection_from_prob, inverse);
-			cout << "Writing jpeg file of spot contours"
-					<< output_filename.toStdString() << endl;
-			cout << "Writing jpeg file " << output_filename.toStdString()
+            cout << "Writing jpeg file " << output_filename
                  << endl;
-			contours.save_inversed(output_filename);
+            contours.save_inversed(outfile);
+        }
+        if (output_extension == "png") {
+            imageContours contours;
+            contours.compute_from_gel_image_and_numeros(*p_gel_image, numbers);
+            contours.draw_contours(the_detection_from_prob, inverse);
+            cout << "Writing png file " << output_filename
+                 << endl;
+            contours.save_inversed(outfile);
         }
         if (output_extension == "jpg2") {
             //draw spot barycenters instead of detected spot centers
@@ -568,37 +609,31 @@ int main(int argc, char * * argv) {
             the_detection_from_prob.quantify_spots_with_image(*p_gel_image,
                     numbers);
             contours.draw_contours(the_detection_from_prob, inverse);
-			cout << "Writing jpeg file of spot contours"
-					<< output_filename.toStdString() << endl;
-			cout << "Writing jpeg file " << output_filename.toStdString()
+            cout << "Writing jpeg file " << output_filename
                  << endl;
-			contours.save_inversed(output_filename);
+            contours.save_inversed(outfile);
         }
         if ((output_extension == "tiff") || (output_extension == "tif")) {
             imageContours contours;
             contours.compute_from_gel_image_and_numeros(*p_gel_image, numbers);
             contours.draw_contours(the_detection_from_prob, inverse);
-			cout << "Write tiff file of spot contours"
-					<< output_filename.toStdString() << endl;
-			cout << "Writing tiff file " << output_filename.toStdString()
+            cout << "Writing tiff file " << output_filename
                  << endl;
-			contours.save_inversed(output_filename);
+            contours.save_inversed(outfile);
         }
         if (output_extension == "svg") {
             cout << "Writing SVG file of spot contours"
-					<< output_filename.toStdString() << endl;
+                 << output_filename << endl;
             the_detection_from_prob.store_spot_edges(numbers);
             spotSvgDocument svg_file;
-			svg_file.set_gel_image_file_name(input_filename);
+            svg_file.set_gel_image_file_name(infile);
             svg_file.set_css_class("detection",
                                    "fill:blue;fill-opacity:1;stroke:none");
             svg_file.set_css_class("contour",
                                    "stroke-linejoin:round;stroke:#000000;stroke-opacity:1;fill:none");
-
             svg_file.embed_gel_image(gel_image_loaded);
             //svg_file.embed_gel_image();
-
-			svg_file.open(output_filename);
+            svg_file.open(outfile);
             svg_file.write_detection(the_detection_from_prob, "detection");
             svg_file.draw_spot_numbers(the_detection_from_prob, "detection");
 
@@ -612,4 +647,3 @@ int main(int argc, char * * argv) {
     }
     return 0;
 }
-