Merge branch 'develop' of github.com:gofigure2/GoFigure2 into develop

.gitignore

@@ -15,3 +15,6 @@ qtcreator-build/
 
 #OSX specifics
 .DS_Store
+
+*.orig
+

CMake/ConfigBoost.cmake

@@ -3,5 +3,5 @@ FIND_PACKAGE( Boost REQUIRED )
 IF( Boost_FOUND )
   INCLUDE_DIRECTORIES( BEFORE ${Boost_INCLUDE_DIRS} )
 ELSE( Boost_FOUND )
-  MESSAGE( SEND_ERROR "BOOST NOT FOUND, CMAKE WILL STOP NOW")  
+  MESSAGE( SEND_ERROR "BOOST NOT FOUND, CMAKE WILL STOP NOW")
 ENDIF( Boost_FOUND )

CMake/ConfigITK.cmake

@@ -1,36 +1,66 @@
 #----------------------------------------------------------
 FIND_PACKAGE( ITK REQUIRED )
-IF( ITK_FOUND )
-
+  IF( ITK_FOUND )
   #----------------------------------------------------------
   INCLUDE( ${ITK_USE_FILE} )
 
   #----------------------------------------------------------
   # Check the version of ITK
-  IF( ( ${ITK_VERSION_MAJOR} LESS 3 ) OR
-    ( ( ${ITK_VERSION_MAJOR} EQUAL 3 ) AND
-      ( ${ITK_VERSION_MINOR} LESS 18 ) ) ) 
-    MESSAGE( SEND_ERROR
-      "GoFigure2 requires ITK 3.18 or newer version (your version of ITK is ${ITK_VERSION_MAJOR}.${ITK_VERSION_MINOR}.${ITK_VERSION_PATCH})" )
-  ENDIF( ( ${ITK_VERSION_MAJOR} LESS 3 ) OR
-       ( ( ${ITK_VERSION_MAJOR} EQUAL 3 ) AND
-         ( ${ITK_VERSION_MINOR} LESS 18 ) ) ) 
-
+  # ( by checking the existence of a variable
+  # can't check version: 4.0.0 is modularized and old style...)
   #----------------------------------------------------------
-  # Check if "REVIEW" is "ON"
-  IF( ${ITK_VERSION_MAJOR} EQUAL 3 ) 
-    IF( ( ${ITK_USE_REVIEW} MATCHES "OFF" ) OR 
-        ( ${ITK_USE_REVIEW_STATISTICS} MATCHES "OFF" ) )
-      MESSAGE( SEND_ERROR
-        "GoFigure2 requires ITK to be compiled with USE_REVIEW and USE_REVIEW_STATISTICS turned ON" )
-     ENDIF( ( ${ITK_USE_REVIEW} MATCHES "OFF" ) OR 
-      ( ${ITK_USE_REVIEW_STATISTICS} MATCHES "OFF" ) )
-  ELSE( ${ITK_VERSION_MAJOR} EQUAL 3 )
-    IF( ${ITK_USE_REVIEW} MATCHES "OFF" )
+  IF( ITK_VERSION_MAJOR EQUAL "4" )
+
+    ADD_DEFINITIONS( -DITKv4 )
+
+    IF( NOT DEFINED ITK_MODULES_ENABLED )
       MESSAGE( SEND_ERROR
-        "GoFigure2 requires ITK to be compiled with USE_REVIEW turned ON" )
-    ENDIF( ${ITK_USE_REVIEW} MATCHES "OFF" )
-  ENDIF( ${ITK_VERSION_MAJOR} EQUAL 3 ) 
+        "WRONG VERSION OF ITK, REQUIERES MODULARIZED ITK, CMAKE WILL STOP NOW")
+    ENDIF ( NOT DEFINED ITK_MODULES_ENABLED )
+
+    # check if requiered modules are enabled
+    # note that ITK-Review requires all modules to be turned ON...
+    list(FIND ITK_MODULES_ENABLED ITK-Review ITK-Review_FOUND)
+    IF( ITK-Review_FOUND LESS 0 )
+      MESSAGE( SEND_ERROR "GoFigure2 requires ITK to be compiled with ITK-Review turned ON")
+    ENDIF( ITK-Review_FOUND LESS 0 )
+
+  ELSE( ITK_VERSION_MAJOR EQUAL "4" )
+
+    REMOVE_DEFINITIONS( -DITKv4 )
+    # Make sure it is at least ITK 3
+    IF( ITK_VERSION_MAJOR EQUAL "3" )
+
+      # Make sure it is ITK 3.20
+      IF( ITK_VERSION_MINOR EQUAL "20" )
+
+        # Make sure it is ITK 3.20.1
+        IF( ITK_VERSION_PATCH EQUAL "1" )
+
+          IF( ( ${ITK_USE_REVIEW} MATCHES "OFF" ) OR
+              ( ${ITK_USE_REVIEW_STATISTICS} MATCHES "OFF" ) )
+            MESSAGE( SEND_ERROR
+              "GoFigure2 requires ITK to be compiled with USE_REVIEW"
+              " and USE_REVIEW_STATISTICS turned ON" )
+          ENDIF()
+
+        ELSE( ITK_VERSION_PATCH EQUAL "1" )
+          MESSAGE( SEND_ERROR "GoFigure2 requires at ITK 3.20.1" )
+        ENDIF( ITK_VERSION_PATCH EQUAL "1" )
+
+      ELSE( ITK_VERSION_MINOR EQUAL "20" )
+
+        MESSAGE( SEND_ERROR "GoFigure2 requires at ITK 3.20.1" )
+
+      ENDIF( ITK_VERSION_MINOR EQUAL "20" )
+
+    ELSE( ITK_VERSION_MAJOR EQUAL "3" )
+
+      MESSAGE( SEND_ERROR "GoFigure2 requires at ITK 3.20.1" )
+
+    ENDIF( ITK_VERSION_MAJOR EQUAL "3" )
+
+  ENDIF( ITK_VERSION_MAJOR EQUAL "4" )
 
 ELSE( ITK_FOUND )
     MESSAGE( SEND_ERROR "ITK NOT FOUND, CMAKE WILL STOP NOW")

CMake/SuperBuild/External-Boost.cmake

@@ -2,10 +2,10 @@
 # Get and build boost
 
 set( proj Boost )
-set( version 1.45.0 )
+set( version 1.46.1 )
 
 ExternalProject_Add(${proj}
-  GIT_REPOSITORY "${git_protocol}://github.com/boost-lib/boost-cmake.git"
+  GIT_REPOSITORY "${git_protocol}://github.com/pocb/boost.git"
   GIT_TAG "origin/cmake-${version}"
   SOURCE_DIR ${proj}
   BINARY_DIR ${proj}-build

CMake/SuperBuild/External-FFMPEG.cmake

@@ -9,21 +9,34 @@ IF( SUPER_SHARED_LIBS )
   set( SHARED_FFMPEG --enable-shared )
 ENDIF( SUPER_SHARED_LIBS )
 
+OPTION( FFMPEG_GPL "Use a GPL version of FFMPEG" OFF )
+
+SET(FFMPEG_GPL_FLAG "")
+
+IF( FFMPEG_GPL )
+  SET(FFMPEG_GPL_FLAG "--enable-gpl")
+  SET(msg "ATTENTION: You have enabled the use of GPL components of FFMPEG.")
+  SET(msg "${msg} By enabling this option, the binary of GoFigure2")
+  SET(msg "${msg} that you are going to build will be covered by a GPL license.")
+  MESSAGE("${msg}")
+ENDIF( FFMPEG_GPL )
+
 SET(FFMPEG_INSTALL_DIR  ${CMAKE_BINARY_DIR}/${proj}-install)
 
 ExternalProject_Add(${proj}
   # Set up dirs
   SOURCE_DIR ${CMAKE_BINARY_DIR}/${proj}
   INSTALL_DIR ${FFMPEG_INSTALL_DIR}
   # get the project
-  GIT_REPOSITORY "${git_protocol}://git.ffmpeg.org/ffmpeg.git"
+  GIT_REPOSITORY "${git_protocol}://git.videolan.org/ffmpeg.git"
+  GIT_TAG "ffmpeg-0.6.3"
 
   # Build the project
   BUILD_IN_SOURCE 1
-  
+
   # Configure step
   # DO STH FOR THE ARCHITECTURE...
-  CONFIGURE_COMMAND <SOURCE_DIR>/configure --prefix=${FFMPEG_INSTALL_DIR} ${SHARED_FFMPEG} --enable-gpl --enable-avfilter --disable-yasm --disable-decoders --disable-zlib --disable-demuxer=matroska
+  CONFIGURE_COMMAND <SOURCE_DIR>/configure --prefix=${FFMPEG_INSTALL_DIR} ${SHARED_FFMPEG} ${FFMPEG_GPL_FLAG} --enable-avfilter --disable-yasm --disable-decoders --disable-zlib --disable-demuxer=matroska
 )
 
 # define the library suffix

CMake/SuperBuild/External-ITK.cmake

@@ -3,17 +3,24 @@
 
 set(proj ITK)
 
+if( WIN32 )
+  set( ITK_TAG "release" )
+else()
+  set( ITK_TAG "2260c095f5809045a10d76cca0acee326502ac53" )
+endif()
+
 ExternalProject_Add(${proj}
   GIT_REPOSITORY "${git_protocol}://itk.org/ITK.git"
-  GIT_TAG "v4.0a06"
+  GIT_TAG "${ITK_TAG}"
   UPDATE_COMMAND ""
   SOURCE_DIR ${proj}
   BINARY_DIR ${proj}-build
   CMAKE_GENERATOR ${gen}
   CMAKE_ARGS
     ${ep_common_args}
     -DITK_INSTALL_LIB_DIR:PATH=${GOFIGURE2_INSTALL_LIB_DIR}
-    -DITK_USE_REVIEW:BOOL=ON
+     # should change soon
+    -DITK_USE_REVIEW:INTERNAL=ON
   INSTALL_COMMAND ""
   DEPENDS
     ${ITK_DEPENDENCIES}

CMakeLists.txt

@@ -167,7 +167,6 @@ ELSE( SUPERBUILD )
   #----------------------------------------------------------
   # Then find ITK
   #### ITK ####
-
   INCLUDE( "${GOFIGURE2_SOURCE_DIR}/CMake/ConfigITK.cmake" )
 
   #----------------------------------------------------------
@@ -203,8 +202,15 @@ ELSE( SUPERBUILD )
     ${GOFIGURE2_BINARY_DIR}/Code/
     ${GOFIGURE2_SOURCE_DIR}/Code/IO/
     ${GOFIGURE2_BINARY_DIR}/Code/IO/
+    ${GOFIGURE2_SOURCE_DIR}/Code/IO/GoImage/
+    ${GOFIGURE2_BINARY_DIR}/Code/IO/GoImage/
     ${GOFIGURE2_SOURCE_DIR}/Code/Filters/
     ${GOFIGURE2_BINARY_DIR}/Code/Filters/
+    ${GOFIGURE2_SOURCE_DIR}/Code/Filters/Contour/
+    ${GOFIGURE2_SOURCE_DIR}/Code/Filters/Mesh/
+    ${GOFIGURE2_SOURCE_DIR}/Code/Filters/Mesh/Attributes/
+    ${GOFIGURE2_SOURCE_DIR}/Code/Filters/Mesh/Split/
+    ${GOFIGURE2_SOURCE_DIR}/Code/Filters/Mesh/Merge/
     ${GOFIGURE2_SOURCE_DIR}/Code/GUI/
     ${GOFIGURE2_BINARY_DIR}/Code/GUI/
     ${GOFIGURE2_SOURCE_DIR}/Code/GUI/lib/
@@ -218,6 +224,10 @@ ELSE( SUPERBUILD )
     ${GOFIGURE2_BINARY_DIR}/Code/GUI/lib/Video/
     ${GOFIGURE2_SOURCE_DIR}/Code/GUI/lib/Wizard/
     ${GOFIGURE2_BINARY_DIR}/Code/GUI/lib/Wizard/
+    ${GOFIGURE2_SOURCE_DIR}/Code/GUI/lib/TraceEditing/
+    ${GOFIGURE2_BINARY_DIR}/Code/GUI/lib/TraceEditing/
+    ${GOFIGURE2_SOURCE_DIR}/Code/GUI/lib/TransferFunctionEditor/
+    ${GOFIGURE2_BINARY_DIR}/Code/GUI/lib/TransferFunctionEditor/
     ${GOFIGURE2_SOURCE_DIR}/Interfaces/
     ${GOFIGURE2_BINARY_DIR}/Interfaces/
     ${GOFIGURE2_SOURCE_DIR}/Code/GUI/src/
@@ -323,6 +333,4 @@ ELSE( SUPERBUILD )
     "${CMAKE_COMMAND}" -P "${CMAKE_CURRENT_BINARY_DIR}/GOFIGURE2Uninstall.cmake"
     )
 
-  INCLUDE( GOFIGURE2CPack.cmake )
-
 ENDIF( SUPERBUILD )

Code/CMakeLists.txt

@@ -1,8 +1,10 @@
+# add subdirectories
 ADD_SUBDIRECTORY( ExternalCode )
 ADD_SUBDIRECTORY( Database )
 ADD_SUBDIRECTORY( IO )
-ADD_SUBDIRECTORY( GUI )
 ADD_SUBDIRECTORY( Filters )
+ADD_SUBDIRECTORY( GUI )
+
 
 FILE( GLOB __source_file_h "${CMAKE_CURRENT_SOURCE_DIR}/*.h" )
 

Code/ExternalCode/MegaVTK/vtkItk/itkImageToVTKImageFilter.txx

@@ -153,4 +153,4 @@ ImageToVTKImageFilter< TInputImage >
 
 } // end namespace itk
 
-#endif
+#endif

Code/ExternalCode/MegaVTK/vtkRenderingAddOn/vtkFillImageWithPolyData.cxx

@@ -133,22 +133,21 @@ void vtkFillImageWithPolyDataExecuteZ(vtkFillImageWithPolyData *self,
                                       unsigned char *outPtr,
                                       int id, int slice, double bbox[6])
 {
-  int           num0, num1, num2, numC, pixSize;
   int           idx0, idx1, idx2;
   vtkIdType     in1Inc0, in1Inc1, in1Inc2;
   vtkIdType     outInc0, outInc1, outInc2;
   unsigned long count = 0;
   unsigned long target;
 
-  numC = outData->GetNumberOfScalarComponents();
-  pixSize = numC * static_cast< int >( sizeof( T ) );
+//  numC = outData->GetNumberOfScalarComponents();
+//  pixSize = numC * static_cast< int >( sizeof( T ) );
 
   // Get information to march through data
   inData->GetContinuousIncrements(ext, in1Inc0, in1Inc1, in1Inc2);
   outData->GetContinuousIncrements(ext, outInc0, outInc1, outInc2);
-  num0 = ext[1] - ext[0] + 1;
-  num1 = ext[3] - ext[2] + 1;
-  num2 = ext[5] - ext[4] + 1;
+  int num0 = ext[1] - ext[0] + 1;
+  int num1 = ext[3] - ext[2] + 1;
+  int num2 = ext[5] - ext[4] + 1;
 
   double outVal = self->GetInsidePixelValue();
 
@@ -226,22 +225,21 @@ void vtkFillImageWithPolyDataExecuteY(vtkFillImageWithPolyData *self, int ext[6]
                                       vtkImageData *outData, unsigned char *outPtr,
                                       int id, int slice, double bbox[6])
 {
-  int           num0, num1, num2, numC;
   int           idx0, idx1, idx2;
   vtkIdType     in1Inc0, in1Inc1, in1Inc2;
   vtkIdType     outInc0, outInc1, outInc2;
   unsigned long count = 0;
   unsigned long target;
 
-  numC = outData->GetNumberOfScalarComponents();
+//  numC = outData->GetNumberOfScalarComponents();
 //   int pixSize = numC * static_cast<int>(sizeof(T));
 
   // Get information to march through data
   inData->GetContinuousIncrements(ext, in1Inc0, in1Inc1, in1Inc2);
   outData->GetContinuousIncrements(ext, outInc0, outInc1, outInc2);
-  num0 = ext[1] - ext[0] + 1;
-  num1 = ext[3] - ext[2] + 1;
-  num2 = ext[5] - ext[4] + 1;
+  int num0 = ext[1] - ext[0] + 1;
+  int num1 = ext[3] - ext[2] + 1;
+  int num2 = ext[5] - ext[4] + 1;
 
   vtkPoints *points = self->GetPolyData()->GetPoints();
   vtkIdType  numP = self->GetPolyData()->GetNumberOfPoints();
@@ -319,15 +317,15 @@ void vtkFillImageWithPolyDataExecuteX(vtkFillImageWithPolyData *self, int ext[6]
                                       vtkImageData *outData, unsigned char *outPtr,
                                       int id, int slice, double bbox[6])
 {
-  int           num0, num1, num2, numC, pixSize;
+  int           num0, num1, num2;
   int           idx0, idx1, idx2;
   vtkIdType     in1Inc0, in1Inc1, in1Inc2;
   vtkIdType     outInc0, outInc1, outInc2;
   unsigned long count = 0;
   unsigned long target;
 
-  numC = outData->GetNumberOfScalarComponents();
-  pixSize = numC * static_cast< int >( sizeof( T ) );
+//  numC = outData->GetNumberOfScalarComponents();
+//  pixSize = numC * static_cast< int >( sizeof( T ) );
 
   // Get information to march through data
   inData->GetContinuousIncrements(ext, in1Inc0, in1Inc1, in1Inc2);
@@ -520,4 +518,4 @@ double vtkFillImageWithPolyData::Angle2D(const double dp1[2], const double dp2[2
     }
 
   return dt;
-}
+}