Merge pull request #322 from ukoethe/version-1-11-rc

Version 1.11.rc2
ukoethe · Mar 16, 2016 · a996189 · a996189
2 parents 641edae + 799e799
commit a996189
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diff --git a/.hgignore b/.hgignore
diff --git a/.hgtags b/.hgtags
diff --git a/.travis.yml b/.travis.yml
@@ -16,11 +16,11 @@ matrix:
     - os: osx
       osx_image: xcode7.3
       language: generic
-      env: TRAVIS_PYTHON_VERSION="2"
+      env: TRAVIS_PYTHON_VERSION="2" BREW_DEPS="cmake\nhdf5\nboost\nlibjpeg\nlibtiff\nlibpng\nfftw\nreadline\npython"
     - os: osx
       osx_image: xcode7.3
       language: generic
-      env: TRAVIS_PYTHON_VERSION="3"
+      env: TRAVIS_PYTHON_VERSION="3" BREW_DEPS="cmake\nhdf5\nboost\nlibjpeg\nlibtiff\nlibpng\nfftw\nreadline\npython3"
 
 
 addons:
@@ -43,29 +43,22 @@ addons:
 
 before_script:
   - if [[ "$TRAVIS_OS_NAME" == "osx" ]]; then export PATH="/usr/local/bin:${PATH}"                                                ; fi
-  - if [[ "$TRAVIS_OS_NAME" == "osx" ]]; then brew remove --force $(brew list); brew cleanup --force                              ; fi
-  - if [[ "$TRAVIS_OS_NAME" == "osx" ]]; then travis_retry brew update                                                            ; fi
   - if [[ "$TRAVIS_OS_NAME" == "osx" ]]; then brew tap homebrew/science                                                           ; fi
-  - if [[ "$TRAVIS_OS_NAME" == "osx" ]]; then brew install cmake                                                                  ; fi
-  - if [[ "$TRAVIS_OS_NAME" == "osx" ]]; then brew install hdf5                                                                   ; fi
-  - if [[ "$TRAVIS_OS_NAME" == "osx" ]]; then brew install boost                                                                  ; fi
-  - if [[ "$TRAVIS_OS_NAME" == "osx" ]]; then brew install libjpeg                                                                ; fi
-  - if [[ "$TRAVIS_OS_NAME" == "osx" ]]; then brew install libtiff                                                                ; fi
-  - if [[ "$TRAVIS_OS_NAME" == "osx" ]]; then brew install libpng                                                                 ; fi
-  - if [[ "$TRAVIS_OS_NAME" == "osx" ]]; then brew install fftw                                                                   ; fi
-  - if [[ "$TRAVIS_OS_NAME" == "osx" ]]; then brew install readline                                                               ; fi
-  - if [[ "$TRAVIS_OS_NAME" == "osx" ]] && [[ ${TRAVIS_PYTHON_VERSION:0:1} -eq 2 ]]; then brew install python                     ; fi
-  - if [[ "$TRAVIS_OS_NAME" == "osx" ]] && [[ ${TRAVIS_PYTHON_VERSION:0:1} -eq 3 ]]; then brew install python3                    ; fi
+  - if [[ "$TRAVIS_OS_NAME" == "osx" ]]; then brew remove --force $(grep -v -F -x -f <(cat <(brew deps --skip-optional --union $(echo -e $BREW_DEPS)) <(echo -e $BREW_DEPS))  <(cat <(brew leaves) <(brew deps --skip-optional --union $(brew leaves)))); brew cleanup --force ; fi
+  - if [[ "$TRAVIS_OS_NAME" == "osx" ]]; then brew install $(echo -e $BREW_DEPS) || true                                          ; fi
   - if [[ "$TRAVIS_OS_NAME" == "osx" ]] && [[ ${TRAVIS_PYTHON_VERSION:0:1} -eq 3 ]]; then sudo ln -s /usr/local/bin/pip3 /usr/local/bin/pip ; fi
   - if [[ "$TRAVIS_OS_NAME" == "osx" ]] && [[ ${TRAVIS_PYTHON_VERSION:0:1} -eq 3 ]]; then sudo ln -s /usr/local/bin/python3 /usr/local/bin/python ; fi
+  - if [[ "$TRAVIS_PYTHON_VERSION" == "3.2" ]]; then pip install --upgrade 'pip<8' 'setuptools<19'                                ; fi
+  - if [[ "$TRAVIS_PYTHON_VERSION" != "3.2" ]]; then pip install --upgrade pip setuptools                                         ; fi
   - pip install nose
   - pip install numpy
   - if [[ "$TRAVIS_OS_NAME" == "osx" ]] && [[ ${TRAVIS_PYTHON_VERSION:0:1} -eq 2 ]]; then brew install boost-python --with-python ; fi
-  - if [[ "$TRAVIS_OS_NAME" == "osx" ]] && [[ ${TRAVIS_PYTHON_VERSION:0:1} -eq 3 ]]; then brew install boost-python --without-python --with-python3 ; fi
+  - if [[ "$TRAVIS_OS_NAME" == "osx" ]] && [[ ${TRAVIS_PYTHON_VERSION:0:1} -eq 3 ]]; then curl -L -O https://bintray.com/artifact/download/casacore/homebrew-bottles/boost-python-1.60.0.el_capitan.bottle.1.tar.gz && brew install ./boost-python-1.60.0.el_capitan.bottle.1.tar.gz ; rm -f ./boost-python-1.60.0.el_capitan.bottle.1.tar.gz ; fi
   - if [[ "$TRAVIS_OS_NAME" == "osx" ]]; then brew cleanup --force -s; sudo rm -rf $(brew --cache)                                     ; fi
 
 script:
   - mkdir build && cd build
   - cmake -DCMAKE_BUILD_TYPE=Release -DTEST_VIGRANUMPY=1 -DDEPENDENCY_SEARCH_PREFIX=$VIRTUAL_ENV -DAUTOBUILD_TESTS=1 -DAUTOEXEC_TESTS=0 -DWITH_BOOST_THREAD=$WITH_BOOST_THREAD -DBoost_DEBUG=1 -DPYTHON_VERSION=${TRAVIS_PYTHON_VERSION:0:3} ..
   - make
+  - find . -name "*.o" | xargs rm -v
   - ctest --output-on-failure
diff --git a/CMakeLists.txt b/CMakeLists.txt
@@ -27,6 +27,10 @@ include(VigraSetDefaults)
 include(VigraCMakeUtils)
 INCLUDE_DIRECTORIES(${vigra_SOURCE_DIR}/include)
 
+if(SUPPRESS_3RD_PARTY_WARNINGS)
+    set(SUPPRESS_WARNINGS SYSTEM)
+endif()
+
 IF(VIGRA_STATIC_LIB)
     SET(LIBTYPE STATIC)
     ADD_DEFINITIONS(-DVIGRA_STATIC_LIB)
@@ -152,7 +156,7 @@ IF(WITH_BOOST)
 ENDIF()
 
 if(WITH_BOOST AND Boost_FOUND)
-    INCLUDE_DIRECTORIES(${Boost_INCLUDE_DIR})
+    INCLUDE_DIRECTORIES(${SUPPRESS_WARNINGS} ${Boost_INCLUDE_DIR})
     IF(WITH_BOOST_THREAD)
         ADD_DEFINITIONS(-DUSE_BOOST_THREAD)
     ENDIF()

diff --git a/config/FindOpenEXR.cmake b/config/FindOpenEXR.cmake
@@ -25,20 +25,43 @@
 
 FIND_PATH(OPENEXR_INCLUDE_DIR ImfRgbaFile.h PATH_SUFFIXES OpenEXR)
 
-FIND_LIBRARY(OPENEXR_ILMIMF_LIBRARY NAMES IlmImf)
-FIND_LIBRARY(OPENEXR_IMATH_LIBRARY NAMES Imath)
+FOREACH(V "" -2_2 -2_1 -2_0 -1_7)
+    if(NOT OPENEXR_ILMIMF_LIBRARY)
+        FIND_LIBRARY(OPENEXR_ILMIMF_LIBRARY NAMES IlmImf${V})
+        if(OPENEXR_ILMIMF_LIBRARY)
+            set(OPENEXR_VERSION ${V})
+        endif()
+    endif()
+ENDFOREACH(V)
+
+FIND_LIBRARY(OPENEXR_IMATH_LIBRARY NAMES Imath${OPENEXR_VERSION})
+FIND_LIBRARY(OPENEXR_IEX_LIBRARY NAMES Iex${OPENEXR_VERSION})
+FIND_LIBRARY(OPENEXR_ILMTHREAD_LIBRARY NAMES IlmThread${OPENEXR_VERSION})
 FIND_LIBRARY(OPENEXR_HALF_LIBRARY NAMES Half)
-FIND_LIBRARY(OPENEXR_IEX_LIBRARY NAMES Iex)
-FIND_LIBRARY(OPENEXR_ILMTHREAD_LIBRARY NAMES IlmThread)
 
 INCLUDE(FindPackageHandleStandardArgs)
-FIND_PACKAGE_HANDLE_STANDARD_ARGS(OPENEXR DEFAULT_MSG
+FIND_PACKAGE_HANDLE_STANDARD_ARGS(OpenEXR DEFAULT_MSG
     OPENEXR_HALF_LIBRARY OPENEXR_IEX_LIBRARY OPENEXR_IMATH_LIBRARY
     OPENEXR_ILMIMF_LIBRARY OPENEXR_INCLUDE_DIR
 )
 
-IF(OPENEXR_FOUND)
+IF(OpenEXR_FOUND)
     SET(OPENEXR_LIBRARIES ${OPENEXR_ILMIMF_LIBRARY}
         ${OPENEXR_IMATH_LIBRARY} ${OPENEXR_HALF_LIBRARY}
         ${OPENEXR_IEX_LIBRARY} ${OPENEXR_ILMTHREAD_LIBRARY} )
-ENDIF(OPENEXR_FOUND)
+
+    if(MSVC)
+        execute_process(
+            COMMAND lib /list "${OPENEXR_HALF_LIBRARY}"
+            OUTPUT_VARIABLE OPENEXR_HALF_CONTENTS)
+        if(OPENEXR_HALF_CONTENTS MATCHES "Half.dll")
+            SET(OPENEXR_CPPFLAGS -DOPENEXR_DLL)
+        endif()
+    endif()
+ELSE()
+    SET(OPENEXR_ILMIMF_LIBRARY      OPENEXR_ILMIMF_LIBRARY-NOTFOUND)
+    SET(OPENEXR_IMATH_LIBRARY       OPENEXR_IMATH_LIBRARY-NOTFOUND)
+    SET(OPENEXR_IEX_LIBRARY         OPENEXR_IEX_LIBRARY-NOTFOUND)
+    SET(OPENEXR_ILMTHREAD_LIBRARY   OPENEXR_ILMTHREAD_LIBRARY-NOTFOUND)
+    SET(OPENEXR_HALF_LIBRARY        OPENEXR_HALF_LIBRARY-NOTFOUND)
+ENDIF()
diff --git a/config/VigraSetDefaults.cmake b/config/VigraSetDefaults.cmake
@@ -43,6 +43,8 @@ OPTION(WITH_BOOST_THREAD "Use boost::thread instead of std::thread" OFF)
 
 OPTION(TEST_VIGRANUMPY "Consider lack of vigranumpy or failed vigranumpy test an error?" OFF)
 
+OPTION(SUPPRESS_3RD_PARTY_WARNINGS "Switch-off compiler warnings originating from dependencies?" ON)
+
 IF(TEST_VIGRANUMPY OR NOT DEFINED WITH_VIGRANUMPY)
     SET(WITH_VIGRANUMPY "ON")
 ENDIF()
@@ -116,11 +118,7 @@ IF(NOT VIGRA_DEFAULTS_INIT)
     # executed once in the first configure run.
     IF(CMAKE_COMPILER_IS_GNUCXX OR CMAKE_COMPILER_IS_CLANGXX)
         IF(NOT CMAKE_CXX_FLAGS)
-            if(NOT MINGW AND NOT MACOSX)
-                SET(CMAKE_CXX_FLAGS "-W -Wall -Wextra -Wno-unused-parameter -Wno-sign-compare -Wno-unused-variable -Wno-type-limits")
-            elseif(MACOSX)
-                SET(CMAKE_CXX_FLAGS "-W -Wall -Wextra -Wno-unused-parameter -Wno-sign-compare -Wno-unused-variable")
-            endif()
+            SET(CMAKE_CXX_FLAGS "-W -Wall -Wextra")
         ENDIF()
         IF(NOT CMAKE_C_FLAGS)
             SET(CMAKE_C_FLAGS "-W -Wall -Wextra -pedantic -std=c99 -Wno-sign-compare")

diff --git a/docsrc/Doxyfile.in b/docsrc/Doxyfile.in
@@ -532,8 +532,8 @@ WARN_LOGFILE           =
 # directories like "/usr/src/myproject". Separate the files or directories
 # with spaces.
 
-INPUT                  = @PROJECT_SOURCE_DIR@/include \
-                         @PROJECT_SOURCE_DIR@/docsrc
+INPUT                  = @PROJECT_SOURCE_DIR@/docsrc \
+                         @PROJECT_SOURCE_DIR@/include
 
 # This tag can be used to specify the character encoding of the source files
 # that doxygen parses. Internally doxygen uses the UTF-8 encoding, which is
@@ -556,6 +556,7 @@ FILE_PATTERNS          = index.dxx \
                          installation.dxx \
                          tutorial.dxx \
                          image_processing.dxx \
+                         parallel_processing.dxx \
                          *.hxx \
                          viff.h
 
@@ -617,7 +618,8 @@ EXAMPLE_RECURSIVE      = NO
 # directories that contain image that are included in the documentation (see
 # the \image command).
 
-IMAGE_PATH             = @PROJECT_SOURCE_DIR@/src/images
+IMAGE_PATH             = @PROJECT_SOURCE_DIR@/src/images \
+                         @PROJECT_SOURCE_DIR@/docsrc/documents
 
 # The INPUT_FILTER tag can be used to specify a program that doxygen should
 # invoke to filter for each input file. Doxygen will invoke the filter program

diff --git a/docsrc/credits_changelog.dxx b/docsrc/credits_changelog.dxx
@@ -20,15 +20,15 @@
       <li> Gunnar Kedenburg
       (<a href="mailto:[email protected]">[email protected]</a>)
       completely rewrote the image import/export library and implemented
-      much of the \ref vigra::MultiArray functionality.
+      the initial version of the \ref vigra::MultiArray functionality.
 
       <li> Yevgen Reznichenko
       (<a href="mailto:[email protected]">[email protected]</a>)
       added a number of image processing algorithms.
 
       <li> Christian Dennis Rahn
       (<a href="mailto:[email protected]">[email protected]</a>)
-      implemented much of the \ref MultiArrayConvolutionFilters.
+      implemented initial versions of multi-dimensional convolution filters.
 
       <li> Kasim Terzic, Florian Heinrich and Benjamin Seppke
       implemented image analysis functionality for 3- and higher-dimensional data.
@@ -65,6 +65,8 @@
 
       <li> Benjamin Seppke contributed various \ref Registration "image registration" algorithms.
 
+      <li> John Kirkham figured out how to configure Travis to run tests for Python3 and on OS X.
+
       <li> Numerous people reported and fixed bugs and made suggestions.
 </ul>
 
@@ -88,7 +90,7 @@ Many thanks to all!
 
       <li> Added many \ref Registration "image registration" functions.
 
-      <li> Extended the collection of \ref MultiArrayDistanceTransform "multi-dimensional distance transform" algorithms by vectorial DT, boundary DT, and eccentricity transform.
+      <li> Extended the collection of \ref DistanceTransform "multi-dimensional distance transform" algorithms by vectorial DT, boundary DT, and eccentricity transform.
 
       <li> Added \ref skeletonizeImage(), nonLocalMean(), multi-dimensional integral images.
 
@@ -192,7 +194,7 @@ Many thanks to all!
 
       <li> Added \ref vigra::StridedScanOrderIterator and corresponding \ref vigra::MultiArrayView::begin().
 
-      <li> Extended \ref vigra::MultiArrayView. Added \ref vigra::Shape1 ... \ref vigra::Shape5 convenience typedefs.
+      <li> Extended \ref vigra::MultiArrayView. Added vigra::Shape1 ... vigra::Shape5 convenience typedefs.
 
       <li> Implemented \ref MultiMathModule (arithmetic and algebraic functions for multi-dimensional arrays).
 
@@ -290,7 +292,7 @@ Many thanks to all!
 <ul>
       <li> Added functions for arrays of arbitrary dimensions:
       <ul>
-          <li> \ref MultiArrayDistanceTransform "Euclidean distance transform"
+          <li> \ref DistanceTransform "Euclidean distance transform"
           <li> \ref MultiArrayMorphology "separable morphology"
           <li> \ref resizeMultiArraySplineInterpolation()
       </ul>
@@ -467,8 +469,8 @@ Many thanks to all!
 <b> Changes from Version 1.2.0 to 1.3.0</b>
 
 <ul>
-      <li> Added algorithms for \ref MultiDimensionalArrays :
-           \ref MultiPointoperators and \ref MultiArrayConvolutionFilters
+      <li> Added algorithms for multi-dimensional arrays: see
+           \ref MultiPointoperators and \ref ConvolutionFilters
            and the \link vigra::MultiArrayNavigator navigator utility\endlink.
 
       <li> Extended \ref convolveImage() (non-separable convolution)
@@ -543,7 +545,7 @@ Many thanks to all!
           "metaprogramming.hxx", "tuple.hxx". "utilities.hxx" now includes
           these other files.
 
-      <li> Added \ref MultiDimensionalArrays and \ref VolumeImpex
+      <li> Added multi-dimensional arrays and \ref VolumeImpex
 
       <li> Redesigned \ref vigra::TinyVector, added \ref vigra::TinyVectorView
 </ul>
@@ -589,7 +591,7 @@ Many thanks to all!
       <li> Added \ref FourierTransform "Fourier transform" support,
            and \ref vigra::FFTWComplex "FFTWComplex" complex number type.
 
-      <li> Added convolution convenience functions (see \ref CommonConvolutionFilters).
+      <li> Added convolution convenience functions (see \ref ConvolutionFilters).
 
       <li> Added \ref vigra::IteratorAdaptor template for quick and
            easy generation of iterator adaptors.