Merge branch 'master' of git.creatis.insa-lyon.fr:clitk

diff --git a/common/clitkEsrfHstImageIO.cxx b/common/clitkEsrfHstImageIO.cxx
index 8023ddd62d5aff56046c7fa26c9b4b2a45007ca6..e9b8fdf3ed6227a14670706c91bcf21f3b3fbe23 100644 (file)
--- a/common/clitkEsrfHstImageIO.cxx
+++ b/common/clitkEsrfHstImageIO.cxx
@@ -79,7 +79,7 @@ bool clitk::EsrfHstImageIO::CanReadFile(const char* FileNameToRead)
 
   std::string firstLine;
   std::getline(is, firstLine);
-  if(firstLine != std::string("<!-- PyHST VOLUME XML FILE -->") )
+  if(firstLine.find( std::string("<!-- PyHST VOLUME XML FILE -->") ) == std::string::npos)
     return false;
 
   return true;

diff --git a/registration/CMakeLists.txt b/registration/CMakeLists.txt
index 64b55dccfa0e71a6b33e3be2e333980bf52db9a9..1bf1bf5796824bcb03dda629fd1f898580f7a618 100644 (file)
--- a/registration/CMakeLists.txt
+++ b/registration/CMakeLists.txt
@@ -44,7 +44,6 @@ IF(CLITK_BUILD_REGISTRATION)
     TARGET_LINK_LIBRARIES(clitkConvertBSplineDeformableTransformToVF clitkCommon  ${ITK_LIBRARIES})
     SET(REGISTRATION_INSTALL ${REGISTRATION_INSTALL} clitkConvertBSplineDeformableTransformToVF)
 
-#    SET_TARGET_PROPERTIES(${REGISTRATION_INSTALL} PROPERTIES INSTALL_RPATH "${VTK_DIR}:${ITK_DIR}" )  
     INSTALL (TARGETS ${REGISTRATION_INSTALL} DESTINATION bin PERMISSIONS OWNER_READ OWNER_WRITE OWNER_EXECUTE GROUP_EXECUTE WORLD_EXECUTE)
 
 ENDIF(CLITK_BUILD_REGISTRATION)

diff --git a/segmentation/CMakeLists.txt b/segmentation/CMakeLists.txt
index 2e1ddac611cb2cf9ce1aef94770b71509641cd6d..64adbd9a1891ed995a7ffabd09fcd8643cf5dcdd 100644 (file)
--- a/segmentation/CMakeLists.txt
+++ b/segmentation/CMakeLists.txt
@@ -50,7 +50,6 @@ IF(CLITK_BUILD_SEGMENTATION)
     ADD_EXECUTABLE(clitkRegionGrowing clitkRegionGrowing.cxx ${clitkRegionGrowing_GGO_C} ${clitkRelativePosition_GGO_C})
     TARGET_LINK_LIBRARIES(clitkRegionGrowing clitkCommon ${ITK_LIBRARIES})
 
-#    SET_TARGET_PROPERTIES(${SEGMENTATION_INSTALL} PROPERTIES INSTALL_RPATH "${VTK_DIR}:${ITK_DIR}" )  
     INSTALL (TARGETS ${SEGMENTATION_INSTALL} DESTINATION bin PERMISSIONS OWNER_READ OWNER_WRITE OWNER_EXECUTE GROUP_EXECUTE WORLD_EXECUTE)
 
 ENDIF(CLITK_BUILD_SEGMENTATION)

diff --git a/superbuild/CMakeLists.txt b/superbuild/CMakeLists.txt
index e62c63030667614439e14b7fbe5b236b9385a3c3..df237735199d9f4b85e38aecd2708c94bdd79ea8 100644 (file)
--- a/superbuild/CMakeLists.txt
+++ b/superbuild/CMakeLists.txt
@@ -62,6 +62,7 @@ ExternalProject_Add(
                                                   -no-libtiff
                                                   -no-libjpeg
                                                   -no-libmng
+                                                  -no-glib
   INSTALL_COMMAND ""
 )
 SET(qmake_executable "${build_prefix}/QT/bin/qmake")

diff --git a/tools/CMakeLists.txt b/tools/CMakeLists.txt
index 71937728a25aea7f049db5e22bf1a9dbed95b14e..862148a10ee91817ef96abeae275f205147beb49 100644 (file)
--- a/tools/CMakeLists.txt
+++ b/tools/CMakeLists.txt
@@ -223,6 +223,11 @@ IF (CLITK_BUILD_TOOLS)
   TARGET_LINK_LIBRARIES(clitkTransformLandmarks clitkCommon ${ITK_LIBRARIES})
   SET(TOOLS_INSTALL ${TOOLS_INSTALL} clitkTransformLandmarks)
 
+  WRAP_GGO(clitkMaskLandmarks_GGO_C clitkMaskLandmarks.ggo)
+  ADD_EXECUTABLE(clitkMaskLandmarks clitkMaskLandmarks.cxx ${clitkMaskLandmarks_GGO_C})
+  TARGET_LINK_LIBRARIES(clitkMaskLandmarks clitkCommon ${ITK_LIBRARIES})
+  SET(TOOLS_INSTALL ${TOOLS_INSTALL} clitkMaskLandmarks)
+
   ADD_EXECUTABLE(clitkMakeSphereImage clitkMakeSphereImage.cxx) # clitkLineProfileGenericFilter.cxx ${clitkLineProfile_GGO_C})
   TARGET_LINK_LIBRARIES(clitkMakeSphereImage clitkCommon ${ITK_LIBRARIES})
   SET(TOOLS_INSTALL ${TOOLS_INSTALL} clitkMakeSphereImage)
@@ -268,7 +273,6 @@ IF (CLITK_BUILD_TOOLS)
     SET(TOOLS_INSTALL ${TOOLS_INSTALL} clitkDicomRTPlan2Gate)
   ENDIF(ITK_VERSION_MAJOR VERSION_LESS 4)
 
-#   SET_TARGET_PROPERTIES(${TOOLS_INSTALL} PROPERTIES INSTALL_RPATH "${VTK_DIR}:${ITK_DIR}" )  
   INSTALL (TARGETS ${TOOLS_INSTALL} DESTINATION bin PERMISSIONS OWNER_READ OWNER_WRITE OWNER_EXECUTE GROUP_READ GROUP_EXECUTE WORLD_READ WORLD_EXECUTE)
 
 ENDIF(CLITK_BUILD_TOOLS)

diff --git a/tools/clitkBinarizeImage.ggo b/tools/clitkBinarizeImage.ggo
index c99af0fa738f16337211088ed10da8cf5f74ea06..dfc37b8021555f843eb454afaa9c29e01b1f8ee2 100644 (file)
--- a/tools/clitkBinarizeImage.ggo
+++ b/tools/clitkBinarizeImage.ggo
@@ -14,6 +14,6 @@ option "upper"        u       "Upper intensity (default=max), fg is lower than this va
 
 option "fg"                    -       "Foreground (FG) or 'inside' value"               double        no      default="1"
 option "bg"                    -       "Background (BG) or 'ouside' value"               double        no      default="0"
-option "mode"          -       "Use FG and/or BG values (if FG, the BG is replaced by the input image values)" values="FG","BG","both"  default="both"
+option "mode"          -       "Use FG and/or BG values (if FG, the BG is replaced by the input image values)" values="FG","BG","both"  no default="both"
 
 

diff --git a/vv/CMakeLists.txt b/vv/CMakeLists.txt
index c37c3f606bebc1cc2d3386b0a6227b90d324eabb..0f95400ad18a431e9a45a4fd3c261999f02498ce 100644 (file)
--- a/vv/CMakeLists.txt
+++ b/vv/CMakeLists.txt
@@ -235,25 +235,8 @@ TARGET_LINK_LIBRARIES(vv vvLib)
 
 #=========================================================
 # Install options (also used by CPack)
-IF(UNIX OR APPLE)
-#   SET_TARGET_PROPERTIES(vv
-#     PROPERTIES INSTALL_RPATH "${VTK_DIR}:${ITK_DIR}")
-  INSTALL (TARGETS vv DESTINATION bin PERMISSIONS OWNER_READ OWNER_WRITE OWNER_EXECUTE GROUP_EXECUTE WORLD_EXECUTE)
-  #  INSTALL (FILES ${CMAKE_CURRENT_SOURCE_DIR}/icons/ducky.png DESTINATION .)
+INSTALL (TARGETS vv DESTINATION bin PERMISSIONS OWNER_READ OWNER_WRITE OWNER_EXECUTE GROUP_EXECUTE WORLD_EXECUTE)
 
-  #QT
-  #FOREACH(LIB QtCore QtGui QtOpenGL QtNetwork QtSql)
-  #  INSTALL(FILES "${QT_LIBRARY_DIR}/lib${LIB}.so.${QT_VERSION_MAJOR}.${QT_VERSION_MINOR}.${QT_VERSION_PATCH}"
-  #          RENAME "lib${LIB}.so.${QT_VERSION_MAJOR}"
-  #          DESTINATION .)
-  #ENDFOREACH(LIB)
-ENDIF(UNIX OR APPLE)
-
-IF(WIN32)
-  #INCLUDE(InstallRequiredSystemLibraries)
-  INSTALL(TARGETS vv DESTINATION bin)
-  #INSTALL(FILES ${CMAKE_CURRENT_SOURCE_DIR}/icons/ducky.png DESTINATION .)
-ENDIF(WIN32)
 #=========================================================
 
 #=========================================================
@@ -267,7 +250,11 @@ SET(CPACK_RESOURCE_FILE_LICENSE "${CMAKE_CURRENT_SOURCE_DIR}/License.txt")
 SET(CPACK_PACKAGE_VERSION_MAJOR "1")
 SET(CPACK_PACKAGE_VERSION_MINOR "3")
 SET(CPACK_PACKAGE_VERSION_PATCH "0")
-SET(CPACK_PACKAGE_INSTALL_DIRECTORY "vv")
+IF(NIGHTLY)
+  SET(CPACK_PACKAGE_INSTALL_DIRECTORY "vv-nightly")
+ELSE(NIGHTLY)
+  SET(CPACK_PACKAGE_INSTALL_DIRECTORY "vv")
+ENDIF(NIGHTLY)
 SET(CPACK_STRIP_FILES TRUE)
 
 IF(WIN32)
@@ -275,11 +262,15 @@ IF(WIN32)
   # sure there is at least one set of four (4) backlasshes.
   SET(CPACK_NSIS_MUI_ICON "${CMAKE_CURRENT_SOURCE_DIR}\\\\icons\\\\ducky.ico")
   SET(CPACK_NSIS_INSTALLED_ICON_NAME "vv.exe")
+IF(NIGHTLY)
+  SET(CPACK_NSIS_DISPLAY_NAME "vv - The 4D slicer (nightly)")
+ELSE(NIGHTLY)
   SET(CPACK_NSIS_DISPLAY_NAME "vv - The 4D slicer")
+ENDIF(NIGHTLY)
   SET(CPACK_NSIS_HELP_LINK "http://www.creatis.insa-lyon.fr/rio/vv")
   SET(CPACK_NSIS_URL_INFO_ABOUT "http://www.creatis.insa-lyon.fr/rio")
   SET(CPACK_NSIS_CONTACT "vv@creatis.insa-lyon.fr")
-  SET(CPACK_NSIS_CREATE_ICONS_EXTRA "CreateShortCut \\\"$SMPROGRAMS\\\\$STARTMENU_FOLDER\\\\vv.lnk\\\" \\\"$INSTDIR\\\\vv.exe\\\" ")
+  SET(CPACK_NSIS_CREATE_ICONS_EXTRA "CreateShortCut \\\"$SMPROGRAMS\\\\$STARTMENU_FOLDER\\\\vv.lnk\\\" \\\"$INSTDIR\\\\bin\\\\vv.exe\\\" ")
   SET(CPACK_NSIS_DELETE_ICONS_EXTRA "Delete \\\"$SMPROGRAMS\\\\$MUI_TEMP\\\\vv.lnk\\\" ")
   #SET(CPACK_NSIS_MODIFY_PATH ON) SR: buggy, wait for cmake updates for a fix
   #SET(CPACK_BINARY_ZIP ON)

diff --git a/vv/qt_ui/vvMainWindow.ui b/vv/qt_ui/vvMainWindow.ui
index 67a467dd820c0f681cba79b8806956c7f61b6770..b80a782fc5bf38ab4ffc8a5d368be9db249eda0d 100644 (file)
--- a/vv/qt_ui/vvMainWindow.ui
+++ b/vv/qt_ui/vvMainWindow.ui
@@ -441,7 +441,7 @@
          </sizepolicy>
         </property>
         <property name="currentIndex">
-         <number>1</number>
+         <number>0</number>
         </property>
         <widget class="QWidget" name="DataTab">
          <attribute name="title">

diff --git a/vv/vvSlicer.cxx b/vv/vvSlicer.cxx
index 30a8f1034931e169815e884c2ada69129a72ae4c..ed53d2c83b138c600eeabf680da7edd775854cbc 100644 (file)
--- a/vv/vvSlicer.cxx
+++ b/vv/vvSlicer.cxx
@@ -155,6 +155,7 @@ vvSlicer::vvSlicer()
   mConcatenatedTransform = vtkSmartPointer<vtkTransform>::New();
   mConcatenatedFusionTransform = vtkSmartPointer<vtkTransform>::New();
   mConcatenatedOverlayTransform = vtkSmartPointer<vtkTransform>::New();
+  mFirstSetSliceOrientation = true;
 }
 //------------------------------------------------------------------------------
 
@@ -853,15 +854,17 @@ void vvSlicer::SetSliceOrientation(int orientation)
   // DDV(cursorPos, 3);
   // SetCurrentPosition(cursorPos[0],cursorPos[1],cursorPos[2],cursorPos[3]);
 
-  if (this->Renderer && this->GetInput()) {
+  if (mFirstSetSliceOrientation) {
+    int *range = this->GetSliceRange();
+    if (range)
+      this->Slice = static_cast<int>((range[0] + range[1]) * 0.5);
+    mFirstSetSliceOrientation = false;
+  }
+  else if (this->Renderer && this->GetInput()) {
     double s = mCursor[orientation];
     double sCursor = (s - this->GetInput()->GetOrigin()[orientation])/this->GetInput()->GetSpacing()[orientation];
     this->Slice = static_cast<int>(sCursor);
   }
-  
-//   int *range = this->GetSliceRange();
-//   if (range)
-//     this->Slice = static_cast<int>((range[0] + range[1]) * 0.5);
 
   this->UpdateOrientation();
   this->UpdateDisplayExtent();

diff --git a/vv/vvSlicer.h b/vv/vvSlicer.h
index 570c43ddcbd83b027fab6b7ac7f2a87f7e0c453a..0bffd1f36abcc46f92d5b43a3c51aab519685e59 100644 (file)
--- a/vv/vvSlicer.h
+++ b/vv/vvSlicer.h
@@ -297,5 +297,6 @@ private:
   bool mOverlayVisibility;
   bool mFusionVisibility;
   bool mVFVisibility;
+  bool mFirstSetSliceOrientation;
 };
 #endif