Add filter for converting Rice-corrupted images into Gaussian-corrupt…

…ed images

Anima/cmake/ANIMAConfig.cmake.in

@@ -24,6 +24,26 @@ set(NLOPT_INCLUDE_DIR "@NLOPT_INCLUDE_DIR@")
 set(NLOPT_LIBRARY_DIR "@NLOPT_LIBRARY_DIR@")
 set(NLOPT_LIBRARY "@NLOPT_LIBRARY@")
 
+set(USE_GMP "@USE_GMP@")
+set(GMP_INCLUDE_DIR "@GMP_INCLUDE_DIR@")
+set(GMP_LIBRARY_DIR "@GMP_LIBRARY_DIR@")
+set(GMP_LIBRARY "@GMP_LIBRARY@")
+
+set(USE_MPFR "@USE_MPFR@")
+set(MPFR_INCLUDE_DIR "@MPFR_INCLUDE_DIR@")
+set(MPFR_LIBRARY_DIR "@MPFR_LIBRARY_DIR@")
+set(MPFR_LIBRARY "@MPFR_LIBRARY@")
+
+set(USE_FLINT "@USE_FLINT@")
+set(FLINT_INCLUDE_DIR "@FLINT_INCLUDE_DIR@")
+set(FLINT_LIBRARY_DIR "@FLINT_LIBRARY_DIR@")
+set(FLINT_LIBRARY "@FLINT_LIBRARY@")
+
+set(USE_ARB "@USE_ARB@")
+set(ARB_INCLUDE_DIR "@ARB_INCLUDE_DIR@")
+set(ARB_LIBRARY_DIR "@ARB_LIBRARY_DIR@")
+set(ARB_LIBRARY "@ARB_LIBRARY@")
+
 set(TinyXML2_INCLUDE_DIR "@TinyXML2_INCLUDE_DIR@")
 set(TinyXML2_LIBRARY_DIR "@TinyXML2_LIBRARY_DIR@")
 set(TinyXML2_LIBRARY "@TinyXML2_LIBRARY@")

Anima/cmake/ANIMAExports.cmake.in

@@ -1,4 +1,5 @@
 include_directories(@ANIMA_BINARY_DIR@)
+include_directories(@ANIMA_BINARY_DIR@/math-tools/arb_special_functions)
 include_directories(@ANIMA_BINARY_DIR@/math-tools/data_io)
 include_directories(@ANIMA_BINARY_DIR@/math-tools/optimizers)
 include_directories(@ANIMA_BINARY_DIR@/math-tools/multi_compartment_base)

Anima/cmake/ANIMAUse.cmake.in

@@ -37,6 +37,42 @@ if(NOT ANIMA_USE_FILE_INCLUDED)
      set(NLOPT_FOUND 1)
    endif(USE_NLOPT)
 
+   set(USE_GMP ${USE_GMP})
+   if (USE_GMP)
+     set(GMP_INCLUDE_DIR ${GMP_INCLUDE_DIR})
+     include_directories(${GMP_INCLUDE_DIR})
+     set(GMP_LIBRARY_DIR ${GMP_LIBRARY_DIR})
+     set(GMP_LIBRARY ${GMP_LIBRARY})
+     set(GMP_FOUND 1)
+   endif(USE_GMP)
+
+   set(USE_MPFR ${USE_MPFR})
+   if (USE_MPFR)
+     set(MPFR_INCLUDE_DIR ${MPFR_INCLUDE_DIR})
+     include_directories(${MPFR_INCLUDE_DIR})
+     set(MPFR_LIBRARY_DIR ${MPFR_LIBRARY_DIR})
+     set(MPFR_LIBRARY ${MPFR_LIBRARY})
+     set(MPFR_FOUND 1)
+   endif(USE_MPFR)
+
+   set(USE_FLINT ${USE_FLINT})
+   if (USE_FLINT)
+     set(FLINT_INCLUDE_DIR ${FLINT_INCLUDE_DIR})
+     include_directories(${FLINT_INCLUDE_DIR})
+     set(FLINT_LIBRARY_DIR ${FLINT_LIBRARY_DIR})
+     set(FLINT_LIBRARY ${FLINT_LIBRARY})
+     set(FLINT_FOUND 1)
+   endif(USE_FLINT)
+
+   set(USE_ARB ${USE_ARB})
+   if (USE_ARB)
+     set(ARB_INCLUDE_DIR ${ARB_INCLUDE_DIR})
+     include_directories(${ARB_INCLUDE_DIR})
+     set(ARB_LIBRARY_DIR ${ARB_LIBRARY_DIR})
+     set(ARB_LIBRARY ${ARB_LIBRARY})
+     set(ARB_FOUND 1)
+   endif(USE_ARB)
+
    set(TinyXML2_INCLUDE_DIR ${TinyXML2_INCLUDE_DIR})
    include_directories(${TinyXML2_INCLUDE_DIR})
    set(TinyXML2_LIBRARY_DIR ${TinyXML2_LIBRARY_DIR})

Anima/cmake/AnimaDependencies.cmake

@@ -30,6 +30,46 @@ if(USE_NLOPT)
   find_package(NLOPT REQUIRED)
 endif()
 
+# GMP
+option(USE_GMP 
+  "Use GMP external library (necessary for some special functions)" 
+  OFF
+  )
+
+if(USE_GMP)
+  find_package(GMP REQUIRED)
+endif()
+
+# MPFR
+option(USE_MPFR 
+  "Use MPFR external library (necessary for some special functions)" 
+  OFF
+  )
+
+if(USE_MPFR)
+  find_package(MPFR REQUIRED)
+endif()
+
+# FLINT
+option(USE_FLINT 
+  "Use FLINT external library (necessary for some special functions)" 
+  OFF
+  )
+
+if(USE_FLINT)
+  find_package(FLINT REQUIRED)
+endif()
+
+# ARB
+option(USE_ARB 
+  "Use ARB external library (necessary for some special functions)" 
+  OFF
+  )
+
+if(USE_ARB)
+  find_package(ARB REQUIRED)
+endif()
+
 # TinyXML2
 if (BUILD_MODULE_REGISTRATION OR BUILD_MODULE_DIFFUSION)
 	find_package(TinyXML2 REQUIRED)

Anima/cmake/AnimaModulesSetup.cmake

@@ -30,6 +30,10 @@ set(${PROJECT_NAME}_INCLUDE_DIRS
   "${Boost_INCLUDE_DIR}"
   "${TCLAP_INCLUDE_DIR}"
   "${NLOPT_INCLUDE_DIR}"
+  "${GMP_INCLUDE_DIR}"
+  "${MPFR_INCLUDE_DIR}"
+  "${FLINT_INCLUDE_DIR}"
+  "${ARB_INCLUDE_DIR}"
   "${TinyXML2_INCLUDE_DIR}"
 )
 

Anima/cmake/FindARB.cmake

@@ -0,0 +1,29 @@
+# Try to find the arb library
+# Once done this will define
+#
+# ARB_FOUND         - system has arb and it can be used
+# ARB_INCLUDE_DIR   - directory where the header file can be found
+# ARB_LIBRARY       - Path where arb library file can be found
+#
+
+SET (ARB_FOUND FALSE)
+
+FIND_PATH(ARB_INCLUDE_DIR arb.h
+  /usr/include
+  /usr/local/include
+)
+
+set(ARB_LIBRARY_DIR "" CACHE PATH "ARB library folder")
+
+FIND_LIBRARY(ARB_LIBRARY NAMES arb libarb
+  HINTS "${ARB_LIBRARY_DIR}"
+)
+
+mark_as_advanced(ARB_LIBRARY)
+
+IF( EXISTS "${ARB_INCLUDE_DIR}" AND EXISTS "${ARB_LIBRARY}" )
+  set(ARB_FOUND TRUE)
+else()
+  message(FATAL_ERROR "ARB not found")
+endif()
+

Anima/cmake/FindFLINT.cmake

@@ -0,0 +1,29 @@
+# Try to find the flint library
+# Once done this will define
+#
+# FLINT_FOUND         - system has flint and it can be used
+# FLINT_INCLUDE_DIR   - directory where the header file can be found
+# FLINT_LIBRARY       - Path where flint library file can be found
+#
+
+SET (FLINT_FOUND FALSE)
+
+FIND_PATH(FLINT_INCLUDE_DIR flint/flint.h
+  /usr/include
+  /usr/local/include
+)
+
+set(FLINT_LIBRARY_DIR "" CACHE PATH "FLINT library folder")
+
+FIND_LIBRARY(FLINT_LIBRARY NAMES flint libflint
+  HINTS "${FLINT_LIBRARY_DIR}"
+)
+
+mark_as_advanced(FLINT_LIBRARY)
+
+IF( EXISTS "${FLINT_INCLUDE_DIR}" AND EXISTS "${FLINT_LIBRARY}" )
+  set(FLINT_FOUND TRUE)
+else()
+  message(FATAL_ERROR "FLINT not found")
+endif()
+

Anima/cmake/FindGMP.cmake

@@ -0,0 +1,29 @@
+# Try to find the gmp library
+# Once done this will define
+#
+# GMP_FOUND         - system has gmp and it can be used
+# GMP_INCLUDE_DIR   - directory where the header file can be found
+# GMP_LIBRARY       - Path where gmp library file can be found
+#
+
+SET (GMP_FOUND FALSE)
+
+FIND_PATH(GMP_INCLUDE_DIR gmp.h
+  /usr/include
+  /usr/local/include
+)
+
+set(GMP_LIBRARY_DIR "" CACHE PATH "GMP library folder")
+
+FIND_LIBRARY(GMP_LIBRARY NAMES gmp libgmp
+  HINTS "${GMP_LIBRARY_DIR}"
+)
+
+mark_as_advanced(GMP_LIBRARY)
+
+IF( EXISTS "${GMP_INCLUDE_DIR}" AND EXISTS "${GMP_LIBRARY}" )
+  set(GMP_FOUND TRUE)
+else()
+  message(FATAL_ERROR "GMP not found")
+endif()
+

Anima/cmake/FindMPFR.cmake

@@ -0,0 +1,29 @@
+# Try to find the mpfr library
+# Once done this will define
+#
+# MPFR_FOUND         - system has mpfr and it can be used
+# MPFR_INCLUDE_DIR   - directory where the header file can be found
+# MPFR_LIBRARY       - Path where mpfr library file can be found
+#
+
+SET (MPFR_FOUND FALSE)
+
+FIND_PATH(MPFR_INCLUDE_DIR mpfr.h
+  /usr/include
+  /usr/local/include
+)
+
+set(MPFR_LIBRARY_DIR "" CACHE PATH "MPFR library folder")
+
+FIND_LIBRARY(MPFR_LIBRARY NAMES mpfr libmpfr
+  HINTS "${MPFR_LIBRARY_DIR}"
+)
+
+mark_as_advanced(MPFR_LIBRARY)
+
+IF( EXISTS "${MPFR_INCLUDE_DIR}" AND EXISTS "${MPFR_LIBRARY}" )
+  set(MPFR_FOUND TRUE)
+else()
+  message(FATAL_ERROR "MPFR not found")
+endif()
+

Anima/diffusion/dti_estimator/animaDTIEstimationImageFilter.hxx

@@ -214,14 +214,12 @@ DTIEstimationImageFilter<InputPixelScalarType, OutputPixelScalarType>
         for (unsigned int i = 0;i < numInputs;++i)
         {
             dwi[i] = inIterators[i].Get();
-            lnDwi[i] = std::log(std::max(1.0e-6,dwi[i]));
+            lnDwi[i] = (dwi[i] <= 0) ? 0 : std::log(dwi[i]);
         }
 
         for (unsigned int i = 0;i < m_NumberOfComponents;++i)
-        {
             for (unsigned int j = 0;j < numInputs;++j)
                 resVec[i] += m_InitialMatrixSolver(i+1,j) * lnDwi[j];
-        }
 
         anima::GetTensorFromVectorRepresentation(resVec,data.workTensor);
 

Anima/diffusion/mcm_estimator/animaMCMEstimatorImageFilter.hxx

@@ -479,7 +479,7 @@ MCMEstimatorImageFilter<InputPixelType, OutputPixelType>
         // Load DWI
         for (unsigned int i = 0;i < m_NumberOfImages;++i)
             observedSignals[i] = inIterators[i].Get();
-
+        
         int moseValue = -1;
         bool estimateNonIsoCompartments = false;
         if (m_ExternalMoseVolume)
@@ -818,7 +818,7 @@ MCMEstimatorImageFilter<InputPixelType, OutputPixelType>
     workVec = mcmUpdateValue->GetParametersAsVector();
     for (unsigned int i = 0;i < dimension;++i)
         p[i] = workVec[i];
-
+    
     double costValue = this->PerformSingleOptimization(p,cost,lowerBounds,upperBounds);
     this->GetProfiledInformation(cost,mcmUpdateValue,b0Value,sigmaSqValue);
 
@@ -832,7 +832,7 @@ MCMEstimatorImageFilter<InputPixelType, OutputPixelType>
 
     if (m_CompartmentType == Stick)
         return;
-
+    
     // We're done with ball and stick, next up is ball and zeppelin
     // - First create model
     mcmCreator->SetCompartmentType(Zeppelin);

Anima/filtering/CMakeLists.txt

@@ -7,6 +7,11 @@ project(ANIMA-FILTERING)
 add_subdirectory(bias_correction)
 add_subdirectory(denoising)
 add_subdirectory(dti_tools)
+
+if (USE_GMP AND GMP_FOUND AND USE_MPFR AND MPFR_FOUND AND USE_FLINT AND FLINT_FOUND AND USE_ARB AND ARB_FOUND) 
+  add_subdirectory(gaussianizer)
+endif()
+
 add_subdirectory(noise_generator)
 add_subdirectory(nyul_standardization)
 add_subdirectory(regularization)

Anima/filtering/gaussianizer/CMakeLists.txt

@@ -0,0 +1,37 @@
+if(BUILD_TOOLS)
+
+project(animaGaussianizer)
+
+## #############################################################################
+## List Sources
+## #############################################################################
+
+list_source_files(${PROJECT_NAME}
+  ${CMAKE_CURRENT_SOURCE_DIR}
+  )
+
+## #############################################################################
+## add executable
+## #############################################################################
+
+add_executable(${PROJECT_NAME}
+  ${${PROJECT_NAME}_CFILES}
+  )
+
+
+## #############################################################################
+## Link
+## #############################################################################
+
+target_link_libraries(${PROJECT_NAME}
+  ${ITKIO_LIBRARIES}
+  AnimaArbSpecialFunctions
+  )
+
+## #############################################################################
+## install
+## #############################################################################
+
+set_exe_install_rules(${PROJECT_NAME})
+
+endif()