CMakeLists.txt

@@ -5,15 +5,16 @@
 ##-----------------------------------------------------------------------------
 project (plastimatch)
 
-## The version here should be equal to the "most recent release"
+# The version here should be equal to the "most recent release"
 set (PLM_VERSION_MAJOR "1")
-set (PLM_VERSION_MINOR "7")
-set (PLM_VERSION_PATCH "4")
+set (PLM_VERSION_MINOR "8")
+set (PLM_VERSION_PATCH "0")
 
 ##-----------------------------------------------------------------------------
 ##  Set up CMake defaults
 ##-----------------------------------------------------------------------------
-cmake_minimum_required (VERSION 2.8.12)
+# CMAKE_CXX_STANDARD was introduced in 3.1.3
+cmake_minimum_required (VERSION 3.1.3)
 
 # CMP0003: Libraries linked via full path no longer produce linker search
 #  paths.
@@ -35,9 +36,13 @@ endif ()
 if (POLICY CMP0054)
   cmake_policy (SET CMP0054 NEW)
 endif ()
+# Fix behavior of CMAKE_CXX_STANDARD when targeting macOS.
+if (POLICY CMP0025)
+  cmake_policy(SET CMP0025 NEW)
+endif ()
 
 ##-----------------------------------------------------------------------------
-##  CMake include files
+##  CMake path
 ##-----------------------------------------------------------------------------
 set (CMAKE_MODULE_PATH "${CMAKE_SOURCE_DIR}/cmake" ${CMAKE_MODULE_PATH})
 
@@ -47,11 +52,17 @@ set (CMAKE_MODULE_PATH "${CMAKE_SOURCE_DIR}/cmake" ${CMAKE_MODULE_PATH})
 include (PreventInSourceBuilds)
 
 ##-----------------------------------------------------------------------------
-##  Macros and functions used in this script
+##  Misc macros and functions used in this script
 ##-----------------------------------------------------------------------------
 include (PlmMacros)
 include (SuperbuildOptions)
 
+##-----------------------------------------------------------------------------
+##  Set C++ compiler standard
+##-----------------------------------------------------------------------------
+sb_set(CMAKE_CXX_STANDARD 11)
+sb_set(CMAKE_CXX_STANDARD_REQUIRED ON)
+
 ##-----------------------------------------------------------------------------
 ##  Define default build type as Release
 ##-----------------------------------------------------------------------------
@@ -96,6 +107,8 @@ sb_option (PLM_CONFIG_PREFER_PATCHED_ITK
   "Prefer to use the patched version of certain ITK files" ON)
 sb_option (PLM_CONFIG_VOL_LIST
   "Native support for volumes with irregular slice thicknesses" OFF)
+sb_option (PLM_CONFIG_HARDEN_XFORM_BY_DEFAULT
+  "By default, harden linear transforms rather than resample" OFF)
 
 # Plastimatch legacy options
 sb_option (PLM_CONFIG_LEGACY_BSPLINE_EXTEND
@@ -239,6 +252,13 @@ if (WIN32 AND NOT CYGWIN AND NOT MINGW)
     )
 endif ()
 
+##-----------------------------------------------------------------------------
+##  Disable spurious warnings on GCC
+##-----------------------------------------------------------------------------
+if (CMAKE_COMPILER_IS_GNUCC)
+  add_compile_options (-Wno-cpp)
+endif ()
+
 ##-----------------------------------------------------------------------------
 ##  Compile with -fPIC is needed for amd64 and other platforms
 ##-----------------------------------------------------------------------------
@@ -247,10 +267,10 @@ plm_set_pic_flags ()
 ##-----------------------------------------------------------------------------
 ##  Extra paths
 ##-----------------------------------------------------------------------------
-set (PLM_TESTING_SOURCE_DIR "${CMAKE_SOURCE_DIR}/Testing")
-set (PLM_TESTING_DATA_DIR "${CMAKE_SOURCE_DIR}/Testing/Data")
-set (PLM_TESTING_DOWNLOAD_DATA_DIR "${CMAKE_BINARY_DIR}/TestData")
-set (PLM_BUILD_TESTING_DIR "${CMAKE_BINARY_DIR}/Testing")
+set (PLM_TESTING_SOURCE_DIR "${PLM_SOURCE_DIR}/Testing")
+set (PLM_TESTING_DATA_DIR "${PLM_SOURCE_DIR}/Testing/Data")
+set (PLM_TESTING_DOWNLOAD_DATA_DIR "${PLM_BINARY_DIR}/TestData")
+set (PLM_BUILD_TESTING_DIR "${PLM_BINARY_DIR}/Testing")
 
 ##-----------------------------------------------------------------------------
 ##  Set the math library
@@ -342,7 +362,7 @@ find_package (wxWidgets)
 ##-----------------------------------------------------------------------------
 if (NOT LIBLBFGS_FOUND)
   add_subdirectory (libs/liblbfgs-1.9)
-  sb_set (LIBLBFGS_INCLUDE_DIR "${CMAKE_SOURCE_DIR}/libs/liblbfgs-1.9/include")
+  sb_set (LIBLBFGS_INCLUDE_DIR "${PLM_SOURCE_DIR}/libs/liblbfgs-1.9/include")
   sb_set (LIBLBFGS_LIBRARIES lbfgs)
   link_directories (${CMAKE_CURRENT_BINARY_DIR}/libs/liblbfgs-1.9)
   sb_set (LIBLBFGS_FOUND TRUE)
@@ -353,7 +373,7 @@ endif ()
 ##-----------------------------------------------------------------------------
 if (NOT SQLITE_FOUND AND NOT PLM_CONFIG_DEBIAN_BUILD)
   add_subdirectory (libs/sqlite-3.6.21)
-  set (SQLITE_INCLUDE_DIR "${CMAKE_SOURCE_DIR}/libs/sqlite-3.6.21")
+  set (SQLITE_INCLUDE_DIR "${PLM_SOURCE_DIR}/libs/sqlite-3.6.21")
   set (SQLITE_LIBRARIES sqlite3)
   set (SQLITE_FOUND TRUE)
 endif ()
@@ -361,13 +381,13 @@ endif ()
 #-----------------------------------------------------------------------------
 ##  Only use local devillard
 ##-----------------------------------------------------------------------------
-sb_set (DEVILLARD_INCLUDE_DIR "${CMAKE_SOURCE_DIR}/libs/devillard")
+sb_set (DEVILLARD_INCLUDE_DIR "${PLM_SOURCE_DIR}/libs/devillard")
 add_subdirectory (libs/devillard)
 
 ##-----------------------------------------------------------------------------
 ##  Only use local inih
 ##-----------------------------------------------------------------------------
-sb_set (INIH_INCLUDE_DIR "${CMAKE_SOURCE_DIR}/libs/inih-r29")
+sb_set (INIH_INCLUDE_DIR "${PLM_SOURCE_DIR}/libs/inih-r29")
 add_subdirectory (libs/inih-r29)
 
 ##-----------------------------------------------------------------------------
@@ -375,7 +395,7 @@ add_subdirectory (libs/inih-r29)
 ##-----------------------------------------------------------------------------
 # We can't use debian's lua 5.1 because it doesn't contain lobject.h
 #add_subdirectory (libs/lua-5.1.4)
-#set (LUA_INCLUDE_DIR "${CMAKE_SOURCE_DIR}/libs/lua-5.1.4/src")
+#set (LUA_INCLUDE_DIR "${PLM_SOURCE_DIR}/libs/lua-5.1.4/src")
 #link_directories (${CMAKE_CURRENT_BINARY_DIR}/libs/lua-5.1.4)
 
 # for history, etc in plastimatch tty mode
@@ -392,12 +412,12 @@ sb_set (SPECFUN_FOUND TRUE)
 ##-----------------------------------------------------------------------------
 ##  Only use local msinttypes
 ##-----------------------------------------------------------------------------
-sb_set (MSINTTYPES_INCLUDE_DIR "${CMAKE_SOURCE_DIR}/libs")
+sb_set (MSINTTYPES_INCLUDE_DIR "${PLM_SOURCE_DIR}/libs")
 
 ##-----------------------------------------------------------------------------
 ##  Only use local nkidecompress
 ##-----------------------------------------------------------------------------
-sb_set (NKIDECOMPRESS_INCLUDE_DIR "${CMAKE_SOURCE_DIR}/libs/nkidecompress")
+sb_set (NKIDECOMPRESS_INCLUDE_DIR "${PLM_SOURCE_DIR}/libs/nkidecompress")
 add_subdirectory (libs/nkidecompress)
 
 ##-----------------------------------------------------------------------------
@@ -513,7 +533,7 @@ set (PLM_BASIC_VERSION_STRING
   "${PLM_VERSION_MAJOR}.${PLM_VERSION_MINOR}.${PLM_VERSION_PATCH}")
 set (PLASTIMATCH_VERSION_STRING
   "${PLM_VERSION_MAJOR}.${PLM_VERSION_MINOR}.${PLM_VERSION_PATCH}")
-if (EXISTS "${CMAKE_SOURCE_DIR}/.git" AND GIT_FOUND)
+if (EXISTS "${PLM_SOURCE_DIR}/.git" AND GIT_FOUND)
   if (GIT_EXECUTABLE MATCHES "[wW][sS][lL].*")
     set (GIT_EXECUTABLE "wsl;git")
   endif ()
@@ -521,7 +541,7 @@ if (EXISTS "${CMAKE_SOURCE_DIR}/.git" AND GIT_FOUND)
     COMMAND
     #${GIT_EXECUTABLE} rev-list --first-parent --count HEAD
     ${GIT_EXECUTABLE} ${GIT_EXECUTABLE_EXTRA} describe --always
-    WORKING_DIRECTORY "${CMAKE_SOURCE_DIR}"
+    WORKING_DIRECTORY "${PLM_SOURCE_DIR}"
     RESULT_VARIABLE git_result
     OUTPUT_VARIABLE git_output
     ERROR_VARIABLE git_error
@@ -606,7 +626,7 @@ endif ()
 ##-----------------------------------------------------------------------------
 ##  Only use local rapidjson
 ##-----------------------------------------------------------------------------
-set (RAPIDJSON_DIR "${CMAKE_SOURCE_DIR}/libs/rapidjson-2015-03-22")
+set (RAPIDJSON_DIR "${PLM_SOURCE_DIR}/libs/rapidjson-2015-03-22")
 if (EXISTS "${RAPIDJSON_DIR}" AND IS_DIRECTORY "${RAPIDJSON_DIR}")
   set (RAPIDJSON_INCLUDE_DIR
     "${RAPIDJSON_DIR}/include"
@@ -694,7 +714,7 @@ endif ()
 
 # Add sample directory/files to Install Only for windows users
 if (WIN32 OR WIN64)
-  set (PLM_WINDOWS_INSTALL_DIR "${CMAKE_SOURCE_DIR}/extra/windows-install")
+  set (PLM_WINDOWS_INSTALL_DIR "${PLM_SOURCE_DIR}/extra/windows-install")
   install (DIRECTORY "${PLM_WINDOWS_INSTALL_DIR}/sample" DESTINATION bin)
   install (FILES "${PLM_WINDOWS_INSTALL_DIR}/launch_cmd_prompt.bat" DESTINATION bin)
 endif ()
@@ -796,9 +816,9 @@ macro (PLM_ADD_TEST PLM_TEST_NAME PLM_TEST_COMMAND PARMS)
     -DPLM_BUILD_TESTING_DIR=${PLM_BUILD_TESTING_DIR}
     "-DPARMS=${TMP_PARMS}"
     ${EXTRA_PARMS}
-    -P ${CMAKE_SOURCE_DIR}/cmake/RUN_CTEST.cmake
+    -P ${PLM_SOURCE_DIR}/cmake/RUN_CTEST.cmake
     )
-# message (STATUS "${CMAKE_COMMAND} -DPLM_TEST_NAME=${PLM_TEST_NAME} ${PLM_ITK_LIBRARY_PATH_HACK} ${PLM_PLASTIMATCH_PATH_HACK} ${PLM_FFTW_PATH_HACK} -DPLM_TEST_COMMAND=${PLM_TEST_COMMAND} -DPLM_TESTING_SOURCE_DIR=${PLM_TESTING_SOURCE_DIR} -DPLM_BUILD_TESTING_DIR=${PLM_BUILD_TESTING_DIR} \"-DPARMS=${TMP_PARMS}\" ${EXTRA_PARMS} -P ${CMAKE_SOURCE_DIR}/cmake/RUN_CTEST.cmake")
+# message (STATUS "${CMAKE_COMMAND} -DPLM_TEST_NAME=${PLM_TEST_NAME} ${PLM_ITK_LIBRARY_PATH_HACK} ${PLM_PLASTIMATCH_PATH_HACK} ${PLM_FFTW_PATH_HACK} -DPLM_TEST_COMMAND=${PLM_TEST_COMMAND} -DPLM_TESTING_SOURCE_DIR=${PLM_TESTING_SOURCE_DIR} -DPLM_BUILD_TESTING_DIR=${PLM_BUILD_TESTING_DIR} \"-DPARMS=${TMP_PARMS}\" ${EXTRA_PARMS} -P ${PLM_SOURCE_DIR}/cmake/RUN_CTEST.cmake")
 endmacro ()
 
 # Figure out which tests to ignore
@@ -806,11 +826,11 @@ endmacro ()
 # in either directory.  MSVC uses the one in ${CMAKE_BINARY_DIR}.
 configure_file (
   ${PLM_TESTING_SOURCE_DIR}/CTestCustom.cmake.in
-  ${CMAKE_BINARY_DIR}/CTestCustom.cmake
+  ${PLM_BINARY_DIR}/CTestCustom.cmake
   @ONLY)
 configure_file (
   ${PLM_TESTING_SOURCE_DIR}/CTestCustom.cmake.in
-  ${CMAKE_BINARY_DIR}/Testing/CTestCustom.cmake
+  ${PLM_BINARY_DIR}/Testing/CTestCustom.cmake
   @ONLY)
 
 if (PLM_BUILD_TESTING)
@@ -818,10 +838,10 @@ if (PLM_BUILD_TESTING)
   add_subdirectory (Testing)
 
   # Copy the lconv script
-  if (EXISTS "${CMAKE_SOURCE_DIR}/extra/devtools/run_lcov.sh")
+  if (EXISTS "${PLM_SOURCE_DIR}/extra/devtools/run_lcov.sh")
     configure_file (
-      "${CMAKE_SOURCE_DIR}/extra/devtools/run_lcov.sh"
-      "${CMAKE_BINARY_DIR}/run_lcov.sh"
+      "${PLM_SOURCE_DIR}/extra/devtools/run_lcov.sh"
+      "${PLM_BINARY_DIR}/run_lcov.sh"
       COPYONLY)
   endif ()
 endif ()

Testing/Data/itk-affine-a.tfm

+#Insight Transform File V1.0
+#Transform 0
+Transform: AffineTransform_double_3_3
+Parameters: 0.925416578398323 0.1631759111665347 0.3420201433256686 0.018028311236297216 0.8825641192593854 -0.46984631039295405 -0.3785223063697923 0.4409696105298823 0.8137976813493736 2.257079707543866 31.926954809339303 -19.37976129358149
+FixedParameters: 0 0 0

cmake/FindDCMTK_wrap.cmake

@@ -8,16 +8,10 @@ if (DCMTK_wrap_FIND_REQUIRED)
   list (APPEND DCMTK_EXTRA_ARGS REQUIRED)
 endif ()
 
-# if (DCMTK_DIR AND EXISTS "${DCMTK_DIR}/DCMTKConfig.cmake")
-#   find_package (DCMTK NO_MODULE ${EXTRA_ARGS})
-# else ()
-#   find_package (DCMTK_legacy ${EXTRA_ARGS})
-# endif ()
-
-find_package (DCMTK NO_MODULE ${EXTRA_ARGS})
+find_package (DCMTK NO_MODULE ${DCMTK_EXTRA_ARGS})
 if (NOT DCMTK_FOUND)
   message (STATUS "Searching for DCMTK using legacy method")
-  find_package (DCMTK_legacy ${EXTRA_ARGS})
+  find_package (DCMTK_legacy ${DCMTK_EXTRA_ARGS})
 endif ()
 
 # The DCMTK 3.6.2 DCMTKConfig.cmake seems to be broken on windows

cmake/HandleITK.cmake

@@ -40,8 +40,8 @@ elseif (${ITK_VERSION_MAJOR} VERSION_EQUAL "4")
       "Fatal Error. ITK 4 must be 4.1 or greater")
   endif ()
 else ()
-  message (FATAL_ERROR 
-    "Fatal Error. ITK version should be either 3.X or 4.X")
+  message (AUTHOR_WARNING
+    "Warning. ITK version greater than 4.X is not tested")
 endif ()
 message (STATUS "ITK_VERSION = ${ITK_VERSION} found")
 

doc/STYLE_GUIDE_1.TXT

@@ -13,7 +13,7 @@ file is included in the distribution.
 
 Conformance
 -----------
-Plastimatch 1.X series must conform to the C++03 standard.
+Plastimatch <= 1.7 series must conform to the C++03 standard.
 
 Supported hosts:
   Microsoft Windows 7 SP1           Visual Studio 2015 (for CUDA 8)
@@ -23,7 +23,7 @@ Supported hosts:
   Arch linux                        (varies)
   OSX 10.11 El Capitan              Xcode 8.2.1; clang-800; llvm 3.9.0svn
 
-Plastimatch 2.X series (planned) must conform to a restricted
+Plastimatch >= 1.8 series must conform to a restricted
 subset of the C++11 standard.  This subset is restricted to 
 features available in the stock compilers provided on
 a fully-updated install of the supported platforms.

doc/man/drr.1

 .\" Man page generated from reStructuredText.
 .
-.TH "DRR" "1" "Jan 08, 2019" "Plastimatch 1.7.4" "Plastimatch"
+.TH "DRR" "1" "Apr 30, 2019" "Plastimatch 1.8.0" "Plastimatch"
 .SH NAME
 drr \- create a digitally reconstructed radiograph
 .
@@ -178,6 +178,6 @@ as follows:
 .SH AUTHOR
 Plastimatch is a collaborative project.  For additional documentation, please visit http://plastimatch.org.  For questions, comments, and bug reports, please visit http://groups.google.com/group/plastimatch.
 .SH COPYRIGHT
-Plastimatch development team (C) 2010-2015.  You are free to use, modify, and distribute plastimatch according to a BSD-style license.  Please see LICENSE.TXT for details.
+Plastimatch development team (C) 2010-2019.  You are free to use, modify, and distribute plastimatch according to a BSD-style license.  Please see LICENSE.TXT for details.
 .\" Generated by docutils manpage writer.
 .

doc/man/fdk.1

 .\" Man page generated from reStructuredText.
 .
-.TH "FDK" "1" "Jan 08, 2019" "Plastimatch 1.7.4" "Plastimatch"
+.TH "FDK" "1" "Apr 30, 2019" "Plastimatch 1.8.0" "Plastimatch"
 .SH NAME
 fdk \- cone-beam reconstruction from projections using the FDK algorithm
 .
@@ -148,6 +148,6 @@ Geometry of Varian HND files.UNINDENT
 .SH AUTHOR
 Plastimatch is a collaborative project.  For additional documentation, please visit http://plastimatch.org.  For questions, comments, and bug reports, please visit http://groups.google.com/group/plastimatch.
 .SH COPYRIGHT
-Plastimatch development team (C) 2010-2015.  You are free to use, modify, and distribute plastimatch according to a BSD-style license.  Please see LICENSE.TXT for details.
+Plastimatch development team (C) 2010-2019.  You are free to use, modify, and distribute plastimatch according to a BSD-style license.  Please see LICENSE.TXT for details.
 .\" Generated by docutils manpage writer.
 .

doc/man/landmark_warp.1

 .\" Man page generated from reStructuredText.
 .
-.TH "LANDMARK_WARP" "1" "Jan 08, 2019" "Plastimatch 1.7.4" "Plastimatch"
+.TH "LANDMARK_WARP" "1" "Apr 30, 2019" "Plastimatch 1.8.0" "Plastimatch"
 .SH NAME
 landmark_warp \- warp an image using point landmarks
 .
@@ -123,6 +123,6 @@ Regularization of vector field is available for "gauss"  and "wendland" algorith
 .SH AUTHOR
 Plastimatch is a collaborative project.  For additional documentation, please visit http://plastimatch.org.  For questions, comments, and bug reports, please visit http://groups.google.com/group/plastimatch.
 .SH COPYRIGHT
-Plastimatch development team (C) 2010-2015.  You are free to use, modify, and distribute plastimatch according to a BSD-style license.  Please see LICENSE.TXT for details.
+Plastimatch development team (C) 2010-2019.  You are free to use, modify, and distribute plastimatch according to a BSD-style license.  Please see LICENSE.TXT for details.
 .\" Generated by docutils manpage writer.
 .

libs/demons_itk_insight/LOGDomainDemons/itkLogDomainDeformableRegistrationFilter.hxx

@@ -12,6 +12,9 @@
 #include "itkVectorNeighborhoodOperatorImageFilter.h"
 
 #include "vnl/vnl_math.h"
+#if ITK_VERSION_MAJOR >= 5
+#include "vcl_legacy_aliases.h"
+#endif
 
 namespace itk
 {

libs/demons_itk_insight/itkESMDemonsRegistrationWithMaskFunction.h

@@ -338,7 +338,11 @@ private:
   mutable double m_SumOfSquaredChange;
 
   /** Mutex lock to protect modification to metric. */
+#if (ITK_VERSION_MAJOR >= 5)
+  mutable std::mutex m_MetricCalculationLock;
+#else
   mutable SimpleFastMutexLock m_MetricCalculationLock;
+#endif
   MaskPointer m_MovingMask;
   MaskPointer m_FixedMask;
   };

libs/demons_itk_insight/itkESMDemonsRegistrationWithMaskFunction.txx

@@ -21,6 +21,9 @@
 #include "itkESMDemonsRegistrationWithMaskFunction.h"
 #include "itkExceptionObject.h"
 #include "vnl/vnl_math.h"
+#if ITK_VERSION_MAJOR >= 5
+#include "vcl_legacy_aliases.h"
+#endif
 #include "itkImageMaskSpatialObject.h"
 
 namespace itk
@@ -546,7 +549,11 @@ ESMDemonsRegistrationWithMaskFunction<TFixedImage, TMovingImage,
 {
   GlobalDataStruct *globalData = (GlobalDataStruct *)gd;
 
+#if (ITK_VERSION_MAJOR >= 5)
+  m_MetricCalculationLock.lock();
+#else
   m_MetricCalculationLock.Lock();
+#endif
   m_SumOfSquaredDifference += globalData->m_SumOfSquaredDifference;
   m_NumberOfPixelsProcessed += globalData->m_NumberOfPixelsProcessed;
   m_SumOfSquaredChange += globalData->m_SumOfSquaredChange;
@@ -557,7 +564,11 @@ ESMDemonsRegistrationWithMaskFunction<TFixedImage, TMovingImage,
     m_RMSChange = vcl_sqrt( m_SumOfSquaredChange
       / static_cast<double>( m_NumberOfPixelsProcessed ) );
     }
+#if (ITK_VERSION_MAJOR >= 5)
+  m_MetricCalculationLock.unlock();
+#else
   m_MetricCalculationLock.Unlock();
+#endif
 
   delete globalData;
 }

libs/demons_itk_insight/itkPDEDeformableRegistrationWithMaskFilter.hxx

@@ -28,6 +28,9 @@
 #include "itkVectorNeighborhoodOperatorImageFilter.h"
 
 #include "vnl/vnl_math.h"
+#if ITK_VERSION_MAJOR >= 5
+#include "vcl_legacy_aliases.h"
+#endif
 
 namespace itk {
 

libs/ransac/RANSAC.h

@@ -8,8 +8,13 @@
 #include <time.h>
 #include <limits>
 #include "ParametersEstimator.h"
+#if ITK_VERSION_MAJOR >= 5
+#include <mutex>
+#include "itkPlatformMultiThreader.h"
+#else
 #include "itkMultiThreader.h"
 #include "itkSimpleFastMutexLock.h"
+#endif
 #include "itkExceptionObject.h"
 
 /**
@@ -168,8 +173,13 @@ private:
     std::vector<S> best_estimate;
 
     typename ParametersEstimator<T,S>::Pointer paramEstimator;
+#if ITK_VERSION_MAJOR >= 5
+    std::mutex hypothesisMutex;
+    std::mutex resultsMutex;
+#else
     itk::SimpleFastMutexLock hypothesisMutex;
     itk::SimpleFastMutexLock resultsMutex;
+#endif
 };
 
 } // end namespace itk

libs/ransac/RANSAC.txx

@@ -21,11 +21,17 @@ RANSAC<T,S>::~RANSAC( )
 template<class T, class S>
 void RANSAC<T,S>::SetNumberOfThreads( unsigned int numberOfThreads )
 {
+#if ITK_VERSION_MAJOR >= 5
+    if( numberOfThreads==0 || 
+	numberOfThreads>itk::PlatformMultiThreader::GetGlobalDefaultNumberOfThreads() )
+	throw ExceptionObject(__FILE__,__LINE__,
+	    "Invalid setting for number of threads.");
+#else
     if( numberOfThreads==0 || 
 	numberOfThreads>itk::MultiThreader::GetGlobalDefaultNumberOfThreads() )
 	throw ExceptionObject(__FILE__,__LINE__,
 	    "Invalid setting for number of threads.");
-
+#endif
     this->numberOfThreads = numberOfThreads;
 }
 
@@ -100,7 +106,11 @@ double RANSAC<T,S>::Compute( std::vector<S> &parameters,
 
     //STEP2: create the threads that generate hypotheses and test
 
+#if ITK_VERSION_MAJOR >= 5
+    itk::PlatformMultiThreader::Pointer threader = itk::PlatformMultiThreader::New();   
+#else
     itk::MultiThreader::Pointer threader = itk::MultiThreader::New();   
+#endif
     threader->SetNumberOfThreads( this->numberOfThreads );
     threader->SetSingleMethod( RANSAC<T,S>::RANSACThreadCallback, this );
     //runs all threads and blocks till they finish
@@ -139,9 +149,18 @@ double RANSAC<T,S>::Compute( std::vector<S> &parameters,
 
 
 template<class T, class S>
-ITK_THREAD_RETURN_TYPE RANSAC<T,S>::RANSACThreadCallback( void *arg )
+#if ITK_VERSION_MAJOR >= 5
+itk::ITK_THREAD_RETURN_TYPE
+#else
+ITK_THREAD_RETURN_TYPE
+#endif
+RANSAC<T,S>::RANSACThreadCallback( void *arg )
 {
+#if ITK_VERSION_MAJOR >= 5
+    typedef itk::PlatformMultiThreader::ThreadInfoStruct ThreadInfoType;
+#else
     typedef itk::MultiThreader::ThreadInfoStruct ThreadInfoType;
+#endif
     ThreadInfoType *infoStruct = static_cast<ThreadInfoType*>( arg );
     //dynamic_cast doesn't work with void *
     RANSAC<T,S> *caller = 
@@ -191,13 +210,20 @@ ITK_THREAD_RETURN_TYPE RANSAC<T,S>::RANSACThreadCallback( void *arg )
 		    l++;
 		}
 	    }
-
+#if ITK_VERSION_MAJOR >= 5
+	    caller->hypothesisMutex.lock();
+#else
 	    caller->hypothesisMutex.Lock();
+#endif
 
 	    //check that the sub-set just chosen is unique
 	    std::pair< typename std::set<int *, SubSetIndexComparator >::iterator, bool> res = caller->chosenSubSets->insert( curSubSetIndexes );
 		 
+#if ITK_VERSION_MAJOR >= 5
+	    caller->hypothesisMutex.unlock();
+#else
 	    caller->hypothesisMutex.Unlock();
+#endif
 
 	    if(res.second == true) { //first time we chose this sub set        
 		//use the selected data for an exact model parameter fit
@@ -220,7 +246,11 @@ ITK_THREAD_RETURN_TYPE RANSAC<T,S>::RANSACThreadCallback( void *arg )
 		}
 
 		// Did we find a larger consensus set?
+#if ITK_VERSION_MAJOR >= 5
+		caller->resultsMutex.lock();
+#else
 		caller->resultsMutex.Lock();
+#endif
 		if( numVotesForCur > caller->numVotesForBest ) {
 		    caller->numVotesForBest = numVotesForCur;
 		    std::copy( curVotes, curVotes+numDataObjects, caller->bestVotes );
@@ -238,7 +268,11 @@ ITK_THREAD_RETURN_TYPE RANSAC<T,S>::RANSACThreadCallback( void *arg )
 			caller->numTries = caller->numTries<caller->allTries ? caller->numTries : caller->allTries;
 		    }
 		}
+#if ITK_VERSION_MAJOR >= 5
+		caller->resultsMutex.unlock();
+#else
 		caller->resultsMutex.Unlock();
+#endif
 	    }
 	    else {  //this sub set already appeared, release memory
 		delete [] curSubSetIndexes;			
@@ -247,7 +281,11 @@ ITK_THREAD_RETURN_TYPE RANSAC<T,S>::RANSACThreadCallback( void *arg )
 	delete [] curVotes;
 	delete [] notChosen;
     }
+#if ITK_VERSION_MAJOR >= 5
+    return itk::ITK_THREAD_RETURN_DEFAULT_VALUE;
+#else
     return ITK_THREAD_RETURN_VALUE;
+#endif
 }
 
 /*****************************************************************************/

src/plastimatch/CHANGELOG.TXT

-Version 1.7.4 (tag v1.7.4)
+Version 1.8.0 (tag 1.8.0)
+Tue Apr 30 09:18:59 EDT 2019
+* FDK, DRR and landmark-warp functionality is now included in the 
+  plastimatch program and no provided as a separate program
+* Change to C++11 as official standard
+* ITK 5 now supported
+* Many new options in the adjust command: linear, local linear, and histogram
+  matching are now supported
+* Registration and xf-convert can harden linear transforms instead of resampling
+* The xf-invert command can now use DICOM with the --fixed option
+
+Version 1.7.4 (tag 1.7.4)
 Tue Jan  8 12:28:02 EST 2019
 * Implement xf-invert for inverting linear transforms
 * Deformable DICOM SRO export

src/plastimatch/CMakeLists.txt

@@ -202,7 +202,7 @@ endif ()
 ##-----------------------------------------------------------------------------
 set (INCLUDE_THESE_TWICE false)
 
-include_directories (BEFORE ${CMAKE_BINARY_DIR})
+include_directories (BEFORE ${PLM_BINARY_DIR})
 include_directories (BEFORE ${CMAKE_CURRENT_SOURCE_DIR})
 include_directories (BEFORE ${CMAKE_CURRENT_SOURCE_DIR}/base)
 include_directories (BEFORE ${CMAKE_CURRENT_SOURCE_DIR}/cli)
@@ -288,9 +288,9 @@ endif ()
 ##  CONFIGURE INCLUDE FILES
 ##-----------------------------------------------------------------------------
 configure_file (${CMAKE_CURRENT_SOURCE_DIR}/sys/plm_config.h.in
-  ${CMAKE_BINARY_DIR}/plm_config.h)
+  ${PLM_BINARY_DIR}/plm_config.h)
 configure_file (${CMAKE_CURRENT_SOURCE_DIR}/sys/plm_version.h.in
-  ${CMAKE_BINARY_DIR}/plm_version.h)
+  ${PLM_BINARY_DIR}/plm_version.h)
 
 ##-----------------------------------------------------------------------------
 ## Option to generate .clang_complete for hip Vim users using clang_complete
@@ -363,7 +363,7 @@ if (NOT PLM_PACKAGE_LEGACY_CMAKE_CONFIG)
     $<INSTALL_INTERFACE:${PLM_INSTALL_INCLUDE_DIR}>
     )
   list (APPEND PLASTIMATCH_INCLUDE_DIRECTORIES
-    $<BUILD_INTERFACE:${CMAKE_BINARY_DIR}>
+    $<BUILD_INTERFACE:${PLM_BINARY_DIR}>
     $<BUILD_INTERFACE:${CMAKE_SOURCE_DIR}/src/plastimatch/sys>
     $<BUILD_INTERFACE:${CMAKE_SOURCE_DIR}/src/plastimatch/base>
     $<BUILD_INTERFACE:${CMAKE_SOURCE_DIR}/src/plastimatch/util>
@@ -470,7 +470,7 @@ if (PLM_PACKAGE_LEGACY_CMAKE_CONFIG)
 
   export (TARGETS
     ${EXPORT_TARGET_LIST}
-    FILE "${CMAKE_BINARY_DIR}/PlastimatchLibraryDepends.cmake")
+    FILE "${PLM_BINARY_DIR}/PlastimatchLibraryDepends.cmake")
 
   # Help cmake find the PlastimatchConfig.cmake in the build directory
   if (NOT ${CMAKE_MAJOR_VERSION}.${CMAKE_MINOR_VERSION} VERSION_LESS 2.8)
@@ -482,15 +482,15 @@ if (PLM_PACKAGE_LEGACY_CMAKE_CONFIG)
     "${PLM_INSTALL_INCLUDE_DIR}")
   configure_file (
     "${PROJECT_SOURCE_DIR}/cmake/PlastimatchConfig-Legacy.cmake.in"
-    "${CMAKE_BINARY_DIR}/PlastimatchConfig.cmake"
+    "${PLM_BINARY_DIR}/PlastimatchConfig.cmake"
     @ONLY)
   configure_file (
     "${PROJECT_SOURCE_DIR}/cmake/PlastimatchBuildTreeSettings.cmake.in"
-    "${CMAKE_BINARY_DIR}/PlastimatchBuildTreeSettings.cmake" @ONLY)
+    "${PLM_BINARY_DIR}/PlastimatchBuildTreeSettings.cmake" @ONLY)
 
   # Install the PlastimatchConfig.cmake file
   install (FILES
-    "${CMAKE_BINARY_DIR}/PlastimatchConfig.cmake"
+    "${PLM_BINARY_DIR}/PlastimatchConfig.cmake"
     DESTINATION "${PLM_INSTALL_CMAKE_DIR}"
     # COMPONENT dev
     )
@@ -516,14 +516,14 @@ else (PLM_PACKAGE_LEGACY_CMAKE_CONFIG)
   # Make the targets file
   if (NOT ${CMAKE_MAJOR_VERSION}.${CMAKE_MINOR_VERSION} VERSION_LESS 3.0)
     export (EXPORT PlastimatchLibraryDepends
-      FILE "${CMAKE_BINARY_DIR}/PlastimatchLibraryDepends.cmake"
+      FILE "${PLM_BINARY_DIR}/PlastimatchLibraryDepends.cmake"
       )
   endif ()
 
   # Make the config file
   configure_file (
     "${PROJECT_SOURCE_DIR}/cmake/PlastimatchConfig.cmake.in"
-    "${CMAKE_BINARY_DIR}/PlastimatchConfig.cmake"
+    "${PLM_BINARY_DIR}/PlastimatchConfig.cmake"
     @ONLY)
 
   # Install the files
@@ -531,7 +531,7 @@ else (PLM_PACKAGE_LEGACY_CMAKE_CONFIG)
     DESTINATION "${PLM_INSTALL_CMAKE_DIR}"
     )
   install (FILES
-    "${CMAKE_BINARY_DIR}/PlastimatchConfig.cmake"
+    "${PLM_BINARY_DIR}/PlastimatchConfig.cmake"
     "${CMAKE_CURRENT_BINARY_DIR}/PlastimatchConfigVersion.cmake"
     DESTINATION "${PLM_INSTALL_CMAKE_DIR}"
     COMPONENT Devel
@@ -543,14 +543,14 @@ endif (PLM_PACKAGE_LEGACY_CMAKE_CONFIG)
 ##  DOXYGEN
 ##-----------------------------------------------------------------------------
 if (DOXYGEN_FOUND)
-  file (MAKE_DIRECTORY "${CMAKE_BINARY_DIR}/doc")
+  file (MAKE_DIRECTORY "${PLM_BINARY_DIR}/doc")
   configure_file (
     ${CMAKE_CURRENT_SOURCE_DIR}/Doxyfile.in
     ${CMAKE_CURRENT_BINARY_DIR}/Doxyfile
     @ONLY)
   add_custom_target (doc
     ${DOXYGEN_EXECUTABLE} ${CMAKE_CURRENT_BINARY_DIR}/Doxyfile
-    WORKING_DIRECTORY "${CMAKE_BINARY_DIR}/doc"
+    WORKING_DIRECTORY "${PLM_BINARY_DIR}/doc"
     COMMENT "Generating API documentation with Doxygen" VERBATIM
     )
 endif ()

src/plastimatch/base/CMakeLists.txt

@@ -5,7 +5,7 @@ project (src_plastimatch_base)
 
 configure_file (
     ${CMAKE_CURRENT_SOURCE_DIR}/plmbase_config.h.in
-    ${CMAKE_BINARY_DIR}/plmbase_config.h
+    ${PLM_BINARY_DIR}/plmbase_config.h
 )
 
 include_directories (BEFORE ${CMAKE_CURRENT_SOURCE_DIR})
@@ -62,7 +62,7 @@ set (PLMBASE_LIBRARY_SRC
   itk_image_origin.cxx itk_image_origin.h
   itk_image_region.cxx itk_image_region.h
   itk_image_save.cxx itk_image_save.h
-  itk_image_scale.cxx itk_image_scale.h
+  itk_image_shift_scale.cxx itk_image_shift_scale.h
   itk_image_stats.cxx itk_image_stats.h
   itk_image_type.h
   itk_metadata.cxx itk_metadata.h
@@ -189,7 +189,7 @@ else ()
 endif ()
 
 set (PLMBASE_LIBRARY_HEADERS
-  "${CMAKE_BINARY_DIR}/plmbase_config.h"
+  "${PLM_BINARY_DIR}/plmbase_config.h"
   )
 foreach (ARG ${PLMBASE_LIBRARY_SRC})
   string (REGEX MATCH ".*\\.h$" TMP "${ARG}")

src/plastimatch/base/dcmtk_image.cxx

@@ -69,6 +69,7 @@ Dcmtk_rt_study::image_load ()
             continue;
         }
         /* Else insert new element into group_list */
+        //printf ("Match not found.  :(\n");
         group_list.push_back (Dcmtk_file_list());
         group_list.back().push_back (df);
     }
@@ -209,15 +210,15 @@ Dcmtk_rt_study::image_load ()
        into a PLM_IMG_TYPE_GPUIT_LIST */
 #if (PLM_CONFIG_VOL_LIST)
 
-    /* Get first slice of group */
+    /* Get first slice of first chunk */
     Dcmtk_file_list::iterator it = flist->begin();
     df = it->get();
 
-    /* Get next slice in group */
     float z_init, z_prev, z_diff, z_last;
     int slice_no = 0;
     float best_chunk_z_start = z_init = z_prev = df->get_z_position ();
 
+    /* Get second slice to form first chunk */
     ++it; ++slice_no;
     df = (*it).get();
     z_diff = df->get_z_position() - z_prev;
@@ -234,7 +235,6 @@ Dcmtk_rt_study::image_load ()
     while (++it != flist->end())
     {
         ++slice_no;
-        printf ("Slice no: %d\n", slice_no);
         df = (*it).get();
         z_diff = df->get_z_position() - z_prev;
         z_last = z_prev = df->get_z_position();
@@ -275,21 +275,23 @@ Dcmtk_rt_study::image_load ()
 #endif
 
 #else /* NOT VOL_LIST */
-    /* Get next slice in first chunk */
+
+    /* We want to find the largest chunk (most slices) with equal spacing.  
+       This will be used to resample in the case of irregular spacing. */
+
+    /* Get first slice of first chunk */
     float z_init, z_prev, z_diff, z_last;
     int slice_no = 0;
     float best_chunk_z_start = z_init = z_prev = df->get_z_position ();
     const Dcmtk_file* df_this_chunk_start = df;
     const Dcmtk_file* df_best_chunk_start = df;
 
+    /* Get second slice to form first chunk */
     std::list<Dcmtk_file::Pointer>::const_iterator it = flist->begin();
     ++it; ++slice_no;
     df = (*it).get();
     z_diff = df->get_z_position() - z_prev;
     z_last = z_prev = df->get_z_position();
-
-    /* We want to find the largest chunk with equal spacing.  This will 
-       be used to resample in the case of irregular spacing. */
     int this_chunk_start = 0, best_chunk_start = 0;
     float this_chunk_diff = z_diff, best_chunk_diff = z_diff;
     size_t this_chunk_len = 2, best_chunk_len = 2;
@@ -301,6 +303,7 @@ Dcmtk_rt_study::image_load ()
 	df = (*it).get();
 	z_diff = df->get_z_position() - z_prev;
 	z_last = z_prev = df->get_z_position();
+        // lprintf ("Slice %d, z_pos %f\n", slice_no, df->get_z_position());
 
 	if (fabs (this_chunk_diff - z_diff) > 0.11) {
 	    /* Start a new chunk if difference in thickness is 
@@ -308,7 +311,7 @@ Dcmtk_rt_study::image_load ()
 	    this_chunk_start = slice_no - 1;
 	    this_chunk_len = 2;
 	    this_chunk_diff = z_diff;
-            df_best_chunk_start = it->get();
+            df_this_chunk_start = std::prev(it)->get();
 	} else {
 	    /* Same thickness, increase size of this chunk */
 	    this_chunk_diff = ((this_chunk_len * this_chunk_diff) + z_diff)
@@ -351,22 +354,27 @@ Dcmtk_rt_study::image_load ()
 
     /* Create a Volume_header to hold the final, resampled, image geometry */
     Volume_header vh (df_best_chunk_start->get_volume_header());
-    printf ("--- *2 ----\n");
-    vh.print();
+    // vh.print();
     const float *dc = vh.get_direction_cosines();
     plm_long *dim = vh.get_dim();
     float *spacing = vh.get_spacing();
     float *origin = vh.get_origin();
     int slices_before = 
 	ROUND_INT ((best_chunk_z_start - z_init) / best_chunk_diff);
+    // printf ("bczs: %f, zi: %f, bcd: %f\n", best_chunk_z_start, z_init, best_chunk_diff);
+    // printf ("slices_before: %d\n", slices_before);
     int slices_after = 
 	ROUND_INT ((z_last - best_chunk_z_start 
 		- (best_chunk_len - 1) * best_chunk_diff) / best_chunk_diff);
+    // printf ("zl: %f, bczs: %f, bcl: %d, bcd: %d\n", z_last, best_chunk_z_start, best_chunk_len, best_chunk_diff);
+    // printf ("slices_after: %d\n", slices_after);
     dim[2] = slices_before + best_chunk_len + slices_after;
     spacing[2] = best_chunk_diff;
     float origin_diff[3] = {
-        slices_before * dc[2], slices_before * dc[5], slices_before * dc[8] };
-    vec3_add (origin, origin_diff);
+        slices_before * best_chunk_diff * dc[2],
+        slices_before * best_chunk_diff * dc[5],
+        slices_before * best_chunk_diff * dc[8] };
+    vec3_sub2 (origin, origin_diff);
 
     /* Store image header */
     if (d_ptr->rt_study_metadata) {
@@ -407,7 +415,6 @@ Dcmtk_rt_study::image_load ()
 		best_slice_it = it;
 	    }
 	}
-
 	/* Load the slice image data into volume */
 	df = (*best_slice_it).get();