Merge pull request #1185 from rolanddenis/pr_RealFFT

Real-data in-place Fast Fourier Transform using FFTW3.

.travis.yml

@@ -20,12 +20,12 @@ notifications:
 #    - one build for the documentation on macosx (clang) and only for commits on
 #      DGtal-team repo (no pull request). Encrypted var. required.
 #    - No gcc on macos
-#    - clang build of dgtaltools in linux only. In this case, some dependencies are considerd in DGtal (GMP, QGLViewer, CAIRO, HDF5)
+#    - clang build of dgtaltools in linux only. In this case, some dependencies are considerd in DGtal (GMP, QGLViewer, CAIRO, HDF5, FFTW3)
 #    - Otherwise, 2 os x 2 configs
 #
 ########
 env:
-  - CONFIG="Debug,Magick,GMP,ITK"
+  - CONFIG="Debug,Magick,GMP,ITK,FFTW3"
   - CONFIG="Debug,Cairo,QGLviewer,HDF5"
   - CONFIG="Documentation"
   - CONFIG="DGtalTools"
@@ -66,6 +66,7 @@ addons:
     - libinsighttoolkit3-dev
     - g++-4.8
     - gcc-4.8
+    - libfftw3-dev
 
 
 before_install:
@@ -75,7 +76,7 @@ before_install:
   - 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" ]; then BTYPE="-DCMAKE_BUILD_TYPE=Debug  -DWITH_MAGICK=true -DWITH_GMP=true  -DBUILD_TESTING=ON  -DWARNING_AS_ERROR=ON";  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
   - 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
@@ -87,7 +88,7 @@ before_install:
 ########
 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; echo "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
 
 
 ############

ChangeLog.md

@@ -8,12 +8,16 @@
  - New "@seeDGtalTools" doxygen command to cite a DGtalTools tool in
    DGtal documentation (David Coeurjolly,
    [#1179](https://github.com/DGtal-team/DGtal/pull/1179))
- 
+
 - *Geometry Package*
  - New robust normal vector estimator using spherical accumulators and statistical
    voting (Boulc'h & Marlet, SGP 2012).
    (David Coeurjolly, [#1149](https://github.com/DGtal-team/DGtal/pull/1149))
 
+- *Math Package*
+ - New RealFFT class for in-place real-complex Fast Fourier Transform using
+   fftw3 library.
+   (Roland Denis, [#1185](https://github.com/DGtal-team/DGtal/pull/1185))
 - *Topology Package*
  - Adding periodic closure for KhalimskySpaceND and per-dimension closure
    specification.

cmake/CheckDGtalOptionalDependencies.cmake

@@ -24,6 +24,7 @@ OPTION(WITH_QGLVIEWER "With LibQGLViewer for 3D visualization (Qt4 required)." O
 OPTION(WITH_PATATE "With Patate library for geometry OFF (Eigen required)." processing)
 OPTION(WITH_QT5 "Using Qt5." OFF)
 OPTION(WITH_BENCHMARK "With Google Benchmark." OFF)
+OPTION(WITH_FFTW3 "With FFTW3 discrete Fourier Transform library." OFF)
 
 #----------------------------------
 # Removing -frounding-math compile flag for clang
@@ -113,6 +114,13 @@ else (WITH_QT5)
   message(STATUS "      WITH_QT5           false   (Using of Qt5 instead of Qt4)")
 endif (WITH_QT5)
 
+if (WITH_FFTW3)
+  set(LIST_OPTION ${LIST_OPTION} [FFTW3]\ )
+  message(STATUS "      WITH_FFTW3         true    (FFTW3 discrete Fourier transform library)")
+else (WITH_FFTW3)
+  message(STATUS "      WITH_FFTW3         false   (FFTW3 discrete Fourier transform library)")
+endif (WITH_FFTW3)
+
 message(STATUS "")
 message(STATUS "For Developpers:")
 IF(WITH_BENCHMARK)
@@ -455,5 +463,38 @@ IF(WITH_BENCHMARK)
  ENDIF(BENCHMARK_FOUND)
 ENDIF(WITH_BENCHMARK)
 
+# -----------------------------------------------------------------------------
+# Look for FFTW3.
+# (They are not compulsory).
+# -----------------------------------------------------------------------------
+SET(FFTW3_FOUND_DGTAL 0)
+IF(WITH_FFTW3)
+  FIND_PACKAGE(FFTW3 REQUIRED)
+  IF(FFTW3_FOUND)
+    SET(FFTW3_FOUND_DGTAL 1)
+    ADD_DEFINITIONS("-DWITH_FFTW3 ")
+    INCLUDE_DIRECTORIES(${FFTW3_INCLUDES})
+    SET(DGtalLibDependencies ${DGtalLibDependencies} ${FFTW3_LIBRARIES} ${FFTW3_DEP_LIBRARIES} )
+    message(STATUS "FFTW3 is found : ${FFTW3_LIBRARIES}.")
+  ELSE(FFTW3_FOUND)
+    message(FATAL_ERROR "FFTW3 is not found.")
+  ENDIF(FFTW3_FOUND)
+
+  IF(FFTW3_FLOAT_FOUND)
+    SET(FFTW3_FLOAT_FOUND_DGTAL 1)
+    ADD_DEFINITIONS("-DWITH_FFTW3_FLOAT ")
+  ENDIF(FFTW3_FLOAT_FOUND)
+
+  IF(FFTW3_DOUBLE_FOUND)
+    SET(FFTW3_DOUBLE_FOUND_DGTAL 1)
+    ADD_DEFINITIONS("-DWITH_FFTW3_DOUBLE ")
+  ENDIF(FFTW3_DOUBLE_FOUND)
+
+  IF(FFTW3_LONG_FOUND)
+    SET(FFTW3_LONG_FOUND_DGTAL 1)
+    ADD_DEFINITIONS("-DWITH_FFTW3_LONG ")
+  ENDIF(FFTW3_LONG_FOUND)
+
+ENDIF(WITH_FFTW3)
 
 message(STATUS "-------------------------------------------------------------------------------")

cmake/DGtalConfig.cmake.in

@@ -157,6 +157,23 @@ IF(@CGAL_FOUND_DGTAL@)
   SET(WITH_CGAL 1)
 ENDIF(@CGAL_FOUND_DGTAL@)
 
+IF(@FFTW3_FOUND_DGTAL@)
+  ADD_DEFINITIONS("-DWITH_FFTW3 ")
+  SET(WITH_FFTW3 1)
+
+  IF(@FFTW3_FLOAT_FOUND_DGTAL@)
+    ADD_DEFINITIONS("-DWITH_FFTW3_FLOAT ")
+  ENDIF(@FFTW3_FLOAT_FOUND_DGTAL@)
+
+  IF(@FFTW3_DOUBLE_FOUND_DGTAL@)
+    ADD_DEFINITIONS("-DWITH_FFTW3_DOUBLE ")
+  ENDIF(@FFTW3_DOUBLE_FOUND_DGTAL@)
+
+  IF(@FFTW3_LONG_FOUND_DGTAL@)
+    ADD_DEFINITIONS("-DWITH_FFTW3_LONG ")
+  ENDIF(@FFTW3_LONG_FOUND_DGTAL@)
+
+ENDIF(@FFTW3_FOUND_DGTAL@)
 
 # These are IMPORTED targets created by DGtalLibraryDepends.cmake
 set(DGTAL_LIBRARIES DGtal DGtalIO)

cmake/FindFFTW3.cmake

@@ -0,0 +1,45 @@
+# Try to find the FFTW3 librairies
+#  FFTW3_FOUND        - True if FFTW3 is found for at least one precision.
+#  FFTW3_FLOAT_FOUND  - True if FFTW3 is found for float precision.
+#  FFTW3_DOUBLE_FOUND - True if FFTW3 is found for double precicion.
+#  FFTW3_LONG_FOUND   - True if FFTW3 is found for long double precision.
+#  FFTW3_INCLUDE_DIR  - The FFTW3 include directory.
+#  FFTW3_LIBRARIES    - FFTW3 libraries.
+#  FFTW3_DEP_LIBRARIES - Libraries needed by FFTW3.
+
+if (FFTW3_INCLUDE_DIR AND FFTW3_LIBRARIES)
+  # Already in cache, be silent
+  set(FFTW3_FIND_QUIETLY TRUE)
+endif (FFTW3_INCLUDE_DIR AND FFTW3_LIBRARIES)
+
+# Searching for all supported FFT precisions.
+find_path    (FFTW3_INCLUDE_DIR NAMES fftw3.h )
+find_library (FFTW3_FLOAT_LIBRARIES  NAMES fftw3f )
+find_library (FFTW3_FLOAT_THREADS_LIBRARIES  NAMES fftw3f_threads )
+find_library (FFTW3_DOUBLE_LIBRARIES  NAMES fftw3 )
+find_library (FFTW3_DOUBLE_THREADS_LIBRARIES NAMES fftw3_threads  )
+find_library (FFTW3_LONG_LIBRARIES   NAMES fftw3l )
+find_library (FFTW3_LONG_THREADS_LIBRARIES   NAMES fftw3l_threads )
+
+# Gathering FFTW3 libraries
+set (FFTW3_LIBRARIES ${FFTW3_FLOAT_LIBRARIES} ${FFTW3_DOUBLE_LIBRARIES} ${FFTW3_LONG_LIBRARIES})
+set (FFTW3_THREADS_LIBRARIES ${FFTW3_FLOAT_THREADS_LIBRARIES} ${FFTW3_DOUBLE_THREADS_LIBRARIES} ${FFTW3_LONG_THREADS_LIBRARIES})
+set (FFTW3_DEP_LIBRARIES m)
+
+# Telling which FFT precisions are found.
+include(FindPackageHandleStandardArgs)
+FIND_PACKAGE_HANDLE_STANDARD_ARGS(FFTW3        DEFAULT_MSG FFTW3_INCLUDE_DIR FFTW3_LIBRARIES)
+FIND_PACKAGE_HANDLE_STANDARD_ARGS(FFTW3_FLOAT  DEFAULT_MSG FFTW3_INCLUDE_DIR FFTW3_FLOAT_LIBRARIES)
+FIND_PACKAGE_HANDLE_STANDARD_ARGS(FFTW3_DOUBLE DEFAULT_MSG FFTW3_INCLUDE_DIR FFTW3_DOUBLE_LIBRARIES)
+FIND_PACKAGE_HANDLE_STANDARD_ARGS(FFTW3_LONG   DEFAULT_MSG FFTW3_INCLUDE_DIR FFTW3_LONG_LIBRARIES)
+
+# Adding threaded version of FFTW3
+if (FFTW3_THREADS_LIBRARIES)
+  set (FFTW3_LIBRARIES ${FFTW3_LIBRARIES} ${FFTW3_THREADS_LIBRARIES})
+  set (FFTW3_DEP_LIBRARIES ${FFTW3_DEP_LIBRARIES} pthread)
+endif (FFTW3_THREADS_LIBRARIES)
+
+
+mark_as_advanced(FFTW3_INCLUDE_DIR FFTW3_LIBRARIES, FFTW3_DEP_LIBRARIES)
+mark_as_advanced(FFTW3_FLOAT_LIBRARIES FFTW3_DOUBLE_LIBRARIES FFTW3_LONG_LIBRARIES)
+mark_as_advanced(FFTW3_FLOAT_THREADS_LIBRARIES FFTW3_DOUBLE_THREADS_LIBRARIES FFTW3_LONG_THREADS_LIBRARIES)

doc/doxy.config.in

@@ -345,7 +345,7 @@ IDL_PROPERTY_SUPPORT   = YES
 # all members of a group must be documented explicitly.
 # The default value is: NO.
 
-DISTRIBUTE_GROUP_DOC   = NO
+DISTRIBUTE_GROUP_DOC   = YES
 
 # If one adds a struct or class to a group and this option is enabled, then also
 # any nested class or struct is added to the same group. By default this option
@@ -2054,8 +2054,8 @@ PREDEFINED             = "BOOST_FUSION_ADAPT_STRUCT(x,y)=" \
                          "WITH_ITK=" \
                          "WITH_MAGICK=" \
                          "WITH_PATATE=" \
-                         "WITH_QGLVIEWER="
-
+                         "WITH_QGLVIEWER=" \
+                         "WITH_FFTW3=" "WITH_FFTW3_FLOAT=" "WITH_FFTW3_DOUBLE" "WITH_FFTW3_LONG"
 
 # If the MACRO_EXPANSION and EXPAND_ONLY_PREDEF tags are set to YES then this
 # tag can be used to specify a list of macro names that should be expanded. The