Minor changes in CMakeLists.txt

Author: krzysg

CMakeLists.txt

@@ -17,7 +17,7 @@ else()
     set(CMAKE_C_FLAGS "${CMAKE_C_FLAGS} -DHAVE_OPENMP ${OpenMP_C_FLAGS}")
     set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -DHAVE_OPENMP ${OpenMP_CXX_FLAGS}")
 endif()
-include_directories(${HDF5_INCLUDE_DIR} ${TIFF_INCLUDE_DIR} ${CMAKE_CURRENT_SOURCE_DIR})
+include_directories(${HDF5_INCLUDE_DIR} ${TIFF_INCLUDE_DIR} )
 add_subdirectory("external/c-blosc")
 set_target_properties(blosc_shared PROPERTIES RUNTIME_OUTPUT_DIRECTORY_DEBUG ${PROJECT_BINARY_DIR})
 set_target_properties(blosc_shared PROPERTIES RUNTIME_OUTPUT_DIRECTORY_RELEASE ${PROJECT_BINARY_DIR})
@@ -83,11 +83,11 @@ if(APR_BUILD_JAVA_WRAPPERS)
     find_package(SWIG 3.0 REQUIRED)
     find_package(JNI REQUIRED)
     set(CMAKE_LIBRARY_OUTPUT_DIRECTORY "${CMAKE_CURRENT_SOURCE_DIR}/src/natives")
-    include_directories(${JNI_INCLUDE_DIRS})
-    INCLUDE(${SWIG_USE_FILE})
+    include_directories(${JNI_INCLUDE_DIRS} ${CMAKE_CURRENT_SOURCE_DIR})
+    include(${SWIG_USE_FILE})
     set(CMAKE_SWIG_OUTDIR "${CMAKE_CURRENT_SOURCE_DIR}/src/main/java/de/mpicbg/mosaic/apr")
     set(CMAKE_SWIG_FLAGS -package de.mpicbg.mosaic.apr -Wall)
-    SET_SOURCE_FILES_PROPERTIES(libapr.i PROPERTIES CPLUSPLUS ON)
-    SWIG_ADD_LIBRARY(apr LANGUAGE java SOURCES libapr.i ${SOURCE_FILES})
-    SWIG_LINK_LIBRARIES(apr ${HDF5_LIBRARIES} blosc_static ${TIFF_LIBRARIES})
+    set_source_files_properties(libapr.i PROPERTIES CPLUSPLUS ON)
+    swig_add_library(apr LANGUAGE java SOURCES libapr.i ${SOURCE_FILES})
+    swig_link_libraries(apr ${HDF5_LIBRARIES} blosc_static ${TIFF_LIBRARIES})
 endif(APR_BUILD_JAVA_WRAPPERS)

src/algorithm/APRConverter.hpp

@@ -353,6 +353,7 @@ void APRConverter<ImageType>::init_apr(APR<ImageType>& aAPR,MeshData<T>& input_i
     int min_dim = std::min(std::min(aAPR.apr_access.org_dims[1], aAPR.apr_access.org_dims[0]), aAPR.apr_access.org_dims[2]);
 
     int levelMax = ceil(std::log2(max_dim));
+    // TODO: why minimum level is forced here to be 2?
     int levelMin = std::max( (int)(levelMax - floor(std::log2(min_dim))), 2);
 
     aAPR.apr_access.level_min = levelMin;
@@ -561,7 +562,6 @@ void APRConverter<ImageType>::auto_parameters(const MeshData<T>& input_img){
     //  Detecting background subtracted images, or no-noise, in these cases the above estimates do not work
     //
     if((proportion_flat > 1.0f) && (proportion_next > 0.00001f)){
-
         std::cout << "AUTOPARAMTERS:**Warning** Detected that there is likely noisy background, instead assuming background subtracted and minimum signal of 5 (absolute), if this is not the case please set parameters manually" << std::endl;
         this->par.Ip_th = 1;
         this->par.sigma_th = 5;
@@ -570,7 +570,6 @@ void APRConverter<ImageType>::auto_parameters(const MeshData<T>& input_img){
         this->par.rel_error = 0.125;
         this->par.min_signal = 5;
         this->par.SNR_min = 1;
-
     } else {
         std::cout << "AUTOPARAMTERS: **Assuming image has atleast 5% dark background" << std::endl;
     }

src/data_structures/APR/ExtraParticleData.hpp

@@ -6,6 +6,9 @@
 #define PARTPLAY_EXTRAPARTICLEDATA_HPP
 
 
+#include <algorithm>
+
+
 template<typename V> class APR;
 template<typename V> class APRIterator;