Fixes for file format plugins on Linux

CMakeLists.txt

@@ -20,6 +20,8 @@ IF(NOT WIN32)
 SET(CMAKE_INSTALL_RPATH "\$ORIGIN/../lib:$ORIGIN/")
 ENDIF(NOT WIN32)
 
+set (CMAKE_CXX_STANDARD 11)
+
 # Set compile definitions to ignore some warnings
 if (WIN32)
     set(DEFAULT_COMPILE_DEFINITIONS ${DEFAULT_COMPILE_DEFINITIONS}
@@ -146,4 +148,4 @@ set(CPACK_DEBIAN_PACKAGE_DESCRIPTION "ASAP - Automated Slide Analysis Platform")
 set(CPACK_PACKAGING_INSTALL_PREFIX /opt/ASAP)
 ENDIF(WIN32)
 INCLUDE(CPack)
-ENDIF(PACKAGE_ON_INSTALL)
+ENDIF(PACKAGE_ON_INSTALL)

cmakemodules/FindOPENSLIDE.cmake

@@ -6,7 +6,7 @@
 #  OPENSLIDE_FOUND, If false, do not try to use OPENSLIDE.
 
 find_path(OPENSLIDE_INCLUDE_DIR openslide.h)
-find_library(OPENSLIDE_LIBRARY NAMES OPENSLIDE)
+find_library(OPENSLIDE_LIBRARY NAMES openslide)
 
 # handle the QUIETLY and REQUIRED arguments and set TIFF_FOUND to TRUE if
 # all listed variables are TRUE

cmakemodules/FindUNITTEST.cmake

@@ -9,12 +9,13 @@
 
 find_path(UNITTEST_INCLUDE_DIR UnitTest++.h)
 find_library(UNITTEST_LIBRARY NAMES UNITTEST)
+find_library(UNITTEST_LIBRARY_DEBUG NAMES UNITTEST)
 
 # handle the QUIETLY and REQUIRED arguments and set TIFF_FOUND to TRUE if
 # all listed variables are TRUE
 include(${CMAKE_ROOT}/Modules/FindPackageHandleStandardArgs.cmake)
 FIND_PACKAGE_HANDLE_STANDARD_ARGS(UNITTEST
-                                  REQUIRED_VARS UNITTEST_LIBRARY UNITTEST_INCLUDE_DIR)
+                                  REQUIRED_VARS UNITTEST_LIBRARY UNITTEST_LIBRARY_DEBUG UNITTEST_INCLUDE_DIR)
 
 if(UNITTEST_FOUND)
   set( UNITTEST_LIBRARIES ${UNITTEST_LIBRARY} )

config/ASAPMacros.h.in

@@ -9,9 +9,9 @@
 #ifndef __ASAPMACROS_H__
 #define __ASAPMACROS_H__
 
-#define ASAP_MAJOR_VERSION = @CURRENT_MAJOR_VERSION@
-#define ASAP_MINOR_VERSION = @CURRENT_MINOR_VERSION@
-#define ASAP_PATCH_VERSION = @CURRENT_PATCH_VERSION@
+#define ASAP_MAJOR_VERSION @CURRENT_MAJOR_VERSION@
+#define ASAP_MINOR_VERSION @CURRENT_MINOR_VERSION@
+#define ASAP_PATCH_VERSION @CURRENT_PATCH_VERSION@
 static const char* ASAP_VERSION_STRING = "@CURRENT_MAJOR_VERSION@.@CURRENT_MINOR_VERSION@.@CURRENT_PATCH_VERSION@";
 
 #ifdef __WIN32__

imgproc/NucleiSegmentation/CMakeLists.txt

@@ -33,4 +33,4 @@ INSTALL(TARGETS NucleiSegmentation
 )
 
 INSTALL(FILES FRST.h DESTINATION include/imgproc/NucleiSegmentation)
-INSTALL(FILES ${CMAKE_CURRENT_BINARY_DIR}/NucleiSegmentation_export.h DESTINATION include/imgproc/NucleiSegmentation)
+INSTALL(FILES ${CMAKE_CURRENT_BINARY_DIR}/nucleisegmentation_export.h DESTINATION include/imgproc/NucleiSegmentation)

imgproc/wholeslide/CMakeLists.txt

@@ -73,7 +73,7 @@ IF(WRAP_WHOLESLIDEFILTERS_PYTHON)
 
 	  set_source_files_properties(wholeslidefilters.i PROPERTIES CPLUSPLUS ON)
 	  set_source_files_properties(wholeslidefilters.i PROPERTIES SWIG_FLAGS "-builtin")
-	  include_directories(. ${PYTHON_INCLUDE_DIR} ${DIAGPathology_BINARY_DIR})
+	  include_directories(. ${PYTHON_INCLUDE_DIR} ${DIAGPathology_BINARY_DIR} ${CMAKE_CURRENT_BINARY_DIR})
 	  SWIG_ADD_MODULE(wholeslidefilters python wholeslidefilters.i)
 	  SWIG_LINK_LIBRARIES(wholeslidefilters wholeslidefilters core) 
 	  SWIG_LINK_LIBRARIES(wholeslidefilters ${PYTHON_LIBRARIES} ${PYTHON_DEBUG_LIBRARIES})

io/multiresolutionimageinterface/CMakeLists.txt

@@ -139,6 +139,6 @@ INSTALL(TARGETS multiresolutionimageinterface
 INSTALL(TARGETS openslidefileformat
   EXPORT asap-targets
   RUNTIME DESTINATION bin/formats
-  LIBRARY DESTINATION lib
+  LIBRARY DESTINATION bin/formats
   ARCHIVE DESTINATION lib
 )

io/multiresolutionimageinterface/MultiResolutionImage.h

@@ -156,4 +156,4 @@ template <> void MULTIRESOLUTIONIMAGEINTERFACE_EXPORT MultiResolutionImage::getR
 template <> void MULTIRESOLUTIONIMAGEINTERFACE_EXPORT MultiResolutionImage::getRawRegion(const long long& startX, const long long& startY, const unsigned long long& width,
   const unsigned long long& height, const unsigned int& level, float*& data);
 
-#endif
+#endif

io/multiresolutionimageinterface/MultiResolutionImageFactory.cpp

@@ -65,13 +65,18 @@ void MultiResolutionImageFactory::registerExternalFileFormats() {
   pathStr = std::string(path);
 #else
   Dl_info dlInfo;
-  dladdr(&MultiResolutionImageFactory::registerExternalFileFormats, &dlInfo);
+  dladdr((void*)&MultiResolutionImageFactory::registerExternalFileFormats, &dlInfo);
   pathStr = std::string(dlInfo.dli_fname);
 #endif
   std::string rootDir = core::extractFilePath(pathStr);
-  std::string fileFormatPluginDir = core::completePath("formats", rootDir);
   std::vector<std::string> formatPlugins;
+#ifdef _WIN32
+  std::string fileFormatPluginDir = core::completePath("formats", rootDir);  
   core::getFiles(fileFormatPluginDir, "*.dll", formatPlugins);
+#else
+  std::string fileFormatPluginDir = core::completePath("bin/formats", core::upOneLevel(rootDir));  
+  core::getFiles(fileFormatPluginDir, "*.so", formatPlugins);
+#endif
   for (std::vector<std::string>::const_iterator it = formatPlugins.begin(); it != formatPlugins.end(); ++it) {
 #ifdef _WIN32
     SetDllDirectory(rootDir.c_str());
@@ -85,6 +90,14 @@ void MultiResolutionImageFactory::registerExternalFileFormats() {
     else {
       DWORD test = GetLastError();
     }
+#else
+    void *hndl = dlopen(core::completePath((*it), fileFormatPluginDir).c_str(), RTLD_NOW);
+    if(hndl != NULL){
+      FileFormatLoader loadfunction = (FileFormatLoader)dlsym(hndl, "filetypeLoad");
+      if (loadfunction) {
+        (*loadfunction)();
+      }
+    }
 #endif
   }
   MultiResolutionImageFactory::_externalFormatsRegistered = true;

io/multiresolutionimageinterface/VSIImage.cpp

@@ -2,6 +2,7 @@
 #include <iostream>
 #include <fstream>
 #include <string>
+#include <cstring>
 #include <math.h>
 #include "core/filetools.h"
 #include "core/Box.h"
@@ -300,7 +301,7 @@ void* VSIImage::readDataFromImage(const long long& startX, const long long& star
         for (int trow=0; trow<intersection.getSize()[1]; trow++) {
           int realRow = trow + intersection.getStart()[1] - tile.getStart()[1];
           int inputOffset = 3 * (realRow * width + intersectionX);
-          memcpy(data+outputOffset, tileBuf+inputOffset, rowLen);
+          std::memcpy(data+outputOffset, tileBuf+inputOffset, rowLen);
           outputOffset += outputRowLen;
         }