Merge pull request #3016 from dzenanz/updateMINC

MINC 2021-12-23 (728d19e8)
InsightSoftwareConsortium · Jan 3, 2022 · ec6849f · ec6849f
2 parents bf36ae4 + da25355
commit ec6849f
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Showing 15 changed files with 125 additions and 86 deletions.
diff --git a/Modules/ThirdParty/MINC/UpdateFromUpstream.sh b/Modules/ThirdParty/MINC/UpdateFromUpstream.sh
@@ -1,16 +1,15 @@
 #!/usr/bin/env bash
 
-thirdparty_module_name='MINC'
+set -e
+set -x
+shopt -s dotglob
 
-upstream_git_url='https://github.com/BIC-MNI/libminc.git'
-upstream_git_branch='develop'
-
-snapshot_author_name='Vladimir S. FONOV'
-snapshot_author_email='vladimir.fonov@gmail.com'
-
-snapshot_redact_cmd='chmod u-x volume_io/Geometry/tensors.c'
-snapshot_relative_path='src/libminc'
-snapshot_paths='
+readonly name="MINC"
+readonly ownership="Vladimir S. FONOV <vladimir.fonov@gmail.com>"
+readonly subtree="Modules/ThirdParty/MINC/src/libminc"
+readonly repo="https://github.com/BIC-MNI/libminc.git"
+readonly tag="develop"
+readonly paths="
 ./ChangeLog
 ./volume_io
 ./libsrc
@@ -85,7 +84,16 @@ snapshot_paths='
 ./INSTALL
 ./config.h.cmake
 ./README
-./check_clock_gettime.c'
+./check_clock_gettime.c
+"
+
+
+extract_source () {
+    git_archive
+    pushd "${extractdir}/${name}-reduced"
+	git update-index --chmod=+x 'src/libminc/libsrc/Make.com'
+    # chmod u-x volume_io/Geometry/tensors.c
+    popd
+}
 
-source "${BASH_SOURCE%/*}/../../../Utilities/Maintenance/UpdateThirdPartyFromUpstream.sh"
-update_from_upstream
+. "${BASH_SOURCE%/*}/../../../Utilities/Maintenance/update-third-party.bash"
diff --git a/Modules/ThirdParty/MINC/src/libminc/CMakeLists.txt b/Modules/ThirdParty/MINC/src/libminc/CMakeLists.txt
@@ -22,7 +22,7 @@ INCLUDE(CTest)
 
 ENABLE_TESTING()
 
-CMAKE_MINIMUM_REQUIRED(VERSION 2.8.12)
+CMAKE_MINIMUM_REQUIRED(VERSION 3.6)
 
 IF( POLICY CMP0063 )
   CMAKE_POLICY(SET CMP0063 NEW)
@@ -49,7 +49,9 @@ IF(NOT LIBMINC_EXTERNALLY_CONFIGURED)
 
 
   OPTION(LIBMINC_MINC1_SUPPORT           "Support minc1 file format, requires NETCDF" OFF)
+  OPTION(LIBMINC_BUILD_EZMINC            "Build C++ EMINC library based on libminc1" OFF)
   OPTION(LIBMINC_BUILD_EZMINC_EXAMPLES   "Build EZminc examples" OFF)
+  OPTION(LIBMINC_USE_NIFTI               "Build with NIfTI support" OFF)
   OPTION(LIBMINC_USE_SYSTEM_NIFTI        "Use system NIfTI-1 library" OFF)
 
   SET (LIBMINC_EXPORTED_TARGETS "LIBMINC-targets")
@@ -67,13 +69,17 @@ IF(NOT LIBMINC_EXTERNALLY_CONFIGURED)
   SET(HDF5_NO_FIND_PACKAGE_CONFIG_FILE ON)
   FIND_PACKAGE(HDF5 REQUIRED COMPONENTS C )
 
+  IF(LIBMINC_USE_NIFTI)
   IF (LIBMINC_USE_SYSTEM_NIFTI)
     FIND_PACKAGE(NIFTI)
   ELSE(LIBMINC_USE_SYSTEM_NIFTI)
     INCLUDE(ExternalProject)
     INCLUDE(BuildNIFTI)
     build_nifti(${CMAKE_INSTALL_PREFIX} ${CMAKE_BINARY_DIR}/external)
   ENDIF(LIBMINC_USE_SYSTEM_NIFTI)
+  ELSE()
+  SET(NIFTI_FOUND OFF)
+  ENDIF()
 
   SET(HAVE_ZLIB ON)
 ELSE(NOT LIBMINC_EXTERNALLY_CONFIGURED)
@@ -132,6 +138,7 @@ set(CMAKE_REQUIRED_DEFINITIONS -D_GNU_SOURCE=1 )
 CHECK_SYMBOL_EXISTS(rint     "math.h"  HAVE_RINT)
 CHECK_SYMBOL_EXISTS(copysign "math.h" HAVE_COPYSIGN)
 CHECK_SYMBOL_EXISTS(round    "math.h" HAVE_ROUND)
+CHECK_SYMBOL_EXISTS(fabsf    "math.h" HAVE_FABSF)
 unset(CMAKE_REQUIRED_LIBRARIES)
 unset(CMAKE_REQUIRED_DEFINITIONS)
 
@@ -237,10 +244,13 @@ INCLUDE_DIRECTORIES(
    ${CMAKE_CURRENT_SOURCE_DIR}/libsrc2
    ${CMAKE_CURRENT_SOURCE_DIR}/libsrc
    ${CMAKE_CURRENT_SOURCE_DIR}/volume_io/Include
-   ${CMAKE_CURRENT_SOURCE_DIR}/ezminc
    ${HDF5_INCLUDE_DIRS}
    )
 
+IF(LIBMINC_BUILD_EZMINC AND LIBMINC_MINC1_SUPPORT)
+  INCLUDE_DIRECTORIES( ${CMAKE_CURRENT_SOURCE_DIR}/ezminc )
+ENDIF()
+
 IF(LIBMINC_NIFTI_SUPPORT)
     INCLUDE_DIRECTORIES(
         ${NIFTI_INCLUDE_DIR}
@@ -456,9 +466,9 @@ ELSE(LIBMINC_MINC1_SUPPORT)
   SET(NETCDF_LIBRARY_NAME )
 ENDIF(LIBMINC_MINC1_SUPPORT)
 
-IF(NOT LIBMINC_USE_SYSTEM_NIFTI AND NOT LIBMINC_EXTERNALLY_CONFIGURED)
+IF(NOT LIBMINC_USE_SYSTEM_NIFTI AND NOT LIBMINC_EXTERNALLY_CONFIGURED AND NIFTI_FOUND)
   ADD_DEPENDENCIES(minc2 NIFTI)
-ENDIF(NOT LIBMINC_USE_SYSTEM_NIFTI  AND NOT LIBMINC_EXTERNALLY_CONFIGURED)
+ENDIF()
 
 #EXPORT(TARGETS ${LIBMINC_LIBRARY} FILE "${LIBMINC_EXPORTED_TARGETS}.cmake")
 
@@ -507,12 +517,15 @@ IF(LIBMINC_INSTALL_INCLUDE_DIR AND NOT LIBMINC_INSTALL_NO_DEVELOPMENT)
   INSTALL(FILES   ${volume_io_HEADERS} DESTINATION  ${LIBMINC_INSTALL_INCLUDE_DIR}/volume_io COMPONENT headers)
 ENDIF(LIBMINC_INSTALL_INCLUDE_DIR AND NOT LIBMINC_INSTALL_NO_DEVELOPMENT)
 
-IF(LIBMINC_MINC1_SUPPORT)
+IF(LIBMINC_BUILD_EZMINC AND LIBMINC_MINC1_SUPPORT)
   ADD_SUBDIRECTORY( ezminc )
-ENDIF(LIBMINC_MINC1_SUPPORT)
+  SET(EZMINC_LIBRARIES                   minc_io ${LIBMINC_LIBRARIES})
+  SET(EZMINC_LIBRARIES_CONFIG            minc_io ${LIBMINC_LIBRARIES_CONFIG})
+ELSE()
+  SET(EZMINC_LIBRARIES                   "")
+  SET(EZMINC_LIBRARIES_CONFIG            "")
+ENDIF()
 
-SET(EZMINC_LIBRARIES                   minc_io ${LIBMINC_LIBRARIES})
-SET(EZMINC_LIBRARIES_CONFIG            minc_io ${LIBMINC_LIBRARIES_CONFIG})
 
 # config for install dir
 SET(LIBMINC_USE_FILE_CONFIG     "\${LIBMINC_INSTALL_PREFIX}/lib/cmake/Use${LIBMINC_EXTERNAL_LIB_PREFIX}LIBMINC.cmake" )
@@ -540,8 +553,12 @@ IF(LIBMINC_MINC1_SUPPORT)
   SET(LIBMINC_INCLUDE_DIRS_CONFIG
     ${LIBMINC_INCLUDE_DIRS_CONFIG}
     ${CMAKE_CURRENT_SOURCE_DIR}/libsrc
-    ${CMAKE_CURRENT_SOURCE_DIR}/ezminc
   )
+
+  IF(LIBMINC_BUILD_EZMINC)
+    SET(LIBMINC_INCLUDE_DIRS_CONFIG ${LIBMINC_INCLUDE_DIRS_CONFIG}
+      ${CMAKE_CURRENT_SOURCE_DIR}/ezminc )
+  ENDIF()
 ENDIF(LIBMINC_MINC1_SUPPORT)
 
 SET(LIBMINC_LIBRARY_DIRS_CONFIG        ${CMAKE_CURRENT_BINARY_DIR})

diff --git a/Modules/ThirdParty/MINC/src/libminc/libcommon/restructure.c b/Modules/ThirdParty/MINC/src/libminc/libcommon/restructure.c
@@ -186,9 +186,9 @@ void restructure_array(size_t ndims,    /* Dimension count */
 #ifdef _DEBUG
         if (offset_next >= total) {
           printf("Fatal - offset %ld out of bounds!\n", offset_next);
-          printf("lengths %lld,%lld,%lld\n",
+          printf("lengths %zu,%zu,%zu\n",
                  lengths[0],lengths[1],lengths[2]);
-          printf("index %lld,%lld,%lld\n",
+          printf("index %zu,%zu,%zu\n",
                  index_perm[0], index_perm[0], index_perm[2]);
           //TODO: report MEMORY error somehow
           exit(-1);

diff --git a/Modules/ThirdParty/MINC/src/libminc/libsrc2/convert.c b/Modules/ThirdParty/MINC/src/libminc/libsrc2/convert.c
@@ -98,6 +98,14 @@ int miconvert_voxel_to_real(mihandle_t volume,
     double voxel_range, voxel_offset;
     double real_range, real_offset;
 
+    if( volume->volume_type==MI_TYPE_FLOAT    || volume->volume_type==MI_TYPE_DOUBLE ||
+      volume->volume_type==MI_TYPE_FCOMPLEX || volume->volume_type==MI_TYPE_DCOMPLEX ){
+      // If floating values voxel_value is the real value
+      *real_value_ptr = voxel_value;
+      return 0;
+    }
+
+
     /* get valid min/max, image min/max 
      */
     miget_volume_valid_range(volume, &valid_max, &valid_min);

diff --git a/Modules/ThirdParty/MINC/src/libminc/libsrc2/hyper.c b/Modules/ThirdParty/MINC/src/libminc/libsrc2/hyper.c
@@ -585,7 +585,7 @@ static int mirw_hyperslab_icv(int opcode,
     scaling_needed=0;
   } 
 #ifdef _DEBUG  
-  printf("mirw_hyperslab_icv:Slice_ndim:%d total_number_of_slices:%d image_slice_length:%d scaling_needed:%d\n",slice_ndims,total_number_of_slices,image_slice_length,scaling_needed);
+  printf("mirw_hyperslab_icv:Slice_ndim:%zu total_number_of_slices:%zu image_slice_length:%zu scaling_needed:%zu\n",(size_t)slice_ndims,(size_t)total_number_of_slices,(size_t)image_slice_length,(size_t)scaling_needed);
 #endif
 
   if (opcode == MIRW_OP_READ) 
@@ -952,7 +952,7 @@ static int mirw_hyperslab_normalized(int opcode,
   miget_volume_valid_range( volume, &volume_valid_max, &volume_valid_min);
 
 #ifdef _DEBUG
-  printf("mirw_hyperslab_normalized:Volume:%x valid_max:%f valid_min:%f scaling:%d\n",volume,volume_valid_max,volume_valid_min,volume->has_slice_scaling);
+  printf("mirw_hyperslab_normalized:Volume:%p valid_max:%f valid_min:%f scaling:%d\n",volume,volume_valid_max,volume_valid_min,volume->has_slice_scaling);
 #endif  
 
   if(volume->has_slice_scaling && 
@@ -1047,7 +1047,7 @@ static int mirw_hyperslab_normalized(int opcode,
   }
 
 #ifdef _DEBUG  
-  printf("mirw_hyperslab_normalized:Slice_ndim:%d total_number_of_slices:%d image_slice_length:%d\n",slice_ndims,total_number_of_slices,image_slice_length);
+  printf("mirw_hyperslab_normalized:Slice_ndim:%d total_number_of_slices:%zu image_slice_length:%zu\n",slice_ndims,(size_t)total_number_of_slices,(size_t)image_slice_length);
   printf("mirw_hyperslab_normalized:data min:%f data max:%f buffer_data_type:%d\n",data_min,data_max,buffer_data_type);
 #endif
 

diff --git a/Modules/ThirdParty/MINC/src/libminc/volume_io/Include/volume_io/alloc.h b/Modules/ThirdParty/MINC/src/libminc/volume_io/Include/volume_io/alloc.h
@@ -32,15 +32,15 @@
 #include  <volume_io/basic.h>
 #include  <stdlib.h>
 
-#define  _ALLOC_SOURCE_LINE
-#define  _ALLOC_SOURCE_LINE_ARG_DEF
-#define  _ALLOC_SOURCE_LINE_ARGUMENTS
+#define  ALLOC_SOURCE_LINE
+#define  ALLOC_SOURCE_LINE_ARG_DEF
+#define  ALLOC_SOURCE_LINE_ARGUMENTS
 #define  PRINT_ALLOC_SOURCE_LINE
 
 #if 0
-#define  _ALLOC_SOURCE_LINE    , __FILE__, __LINE__
-#define  _ALLOC_SOURCE_LINE_ARG_DEF   , char  filename[], int line_number
-#define  _ALLOC_SOURCE_LINE_ARGUMENTS   , filename, line_number
+#define  ALLOC_SOURCE_LINE    , __FILE__, __LINE__
+#define  ALLOC_SOURCE_LINE_ARG_DEF   , char  filename[], int line_number
+#define  ALLOC_SOURCE_LINE_ARGUMENTS   , filename, line_number
 #define  PRINT_ALLOC_SOURCE_LINE   print_alloc_source_line( filename, line_number );
 #endif
 
@@ -62,7 +62,7 @@
 #define  ALLOC( ptr, n_items )                                                \
              ASSIGN_PTR(ptr) =                                                \
                      alloc_memory_1d( (size_t) (n_items),                     \
-                                      sizeof(*(ptr)) _ALLOC_SOURCE_LINE )
+                                      sizeof(*(ptr)) ALLOC_SOURCE_LINE )
 
 /* ----------------------------- MNI Header -----------------------------------
 @NAME       : FREE
@@ -78,7 +78,7 @@
 ---------------------------------------------------------------------------- */
 
 #define  FREE( ptr )                                                          \
-         free_memory_1d( (void **) &(ptr) _ALLOC_SOURCE_LINE )
+         free_memory_1d( (void **) &(ptr) ALLOC_SOURCE_LINE )
 
 /* ----------------------------- MNI Header -----------------------------------
 @NAME       : REALLOC
@@ -97,7 +97,7 @@
 
 #define  REALLOC( ptr, n_items )                                              \
            realloc_memory( (void **) &(ptr), (size_t) (n_items),              \
-                           sizeof(*(ptr)) _ALLOC_SOURCE_LINE )
+                           sizeof(*(ptr)) ALLOC_SOURCE_LINE )
 
 /* ----------------------------- MNI Header -----------------------------------
 @NAME       : ALLOC_VAR_SIZED_STRUCT
@@ -139,7 +139,7 @@
 #define  ALLOC_VAR_SIZED_STRUCT( ptr, element_type, n_elements )              \
   ASSIGN_PTR(ptr) = alloc_memory_in_bytes(                                    \
   (size_t) (sizeof(*(ptr))+((size_t)(n_elements)-1) * sizeof(element_type))   \
-  _ALLOC_SOURCE_LINE )
+  ALLOC_SOURCE_LINE )
 
 /* ----------------------------- MNI Header -----------------------------------
 @NAME       : VIO_ALLOC2D
@@ -160,7 +160,7 @@
 
 #define  VIO_ALLOC2D( ptr, n1, n2 )                                               \
    ASSIGN_PTR(ptr) = alloc_memory_2d( (size_t) (n1), (size_t) (n2),           \
-                          sizeof(**(ptr)) _ALLOC_SOURCE_LINE )
+                          sizeof(**(ptr)) ALLOC_SOURCE_LINE )
 
 /* ----------------------------- MNI Header -----------------------------------
 @NAME       : VIO_FREE2D
@@ -176,7 +176,7 @@
 ---------------------------------------------------------------------------- */
 
 #define  VIO_FREE2D( ptr )                                                        \
-         free_memory_2d( (void ***) &(ptr) _ALLOC_SOURCE_LINE )
+         free_memory_2d( (void ***) &(ptr) ALLOC_SOURCE_LINE )
 
 /* ----------------------------- MNI Header -----------------------------------
 @NAME       : VIO_ALLOC3D
@@ -196,7 +196,7 @@
 
 #define  VIO_ALLOC3D( ptr, n1, n2, n3 )                                           \
          ASSIGN_PTR(ptr) = alloc_memory_3d( (size_t) (n1), (size_t) (n2),     \
-                          (size_t) (n3), sizeof(***(ptr)) _ALLOC_SOURCE_LINE )
+                          (size_t) (n3), sizeof(***(ptr)) ALLOC_SOURCE_LINE )
 
 /* ----------------------------- MNI Header -----------------------------------
 @NAME       : VIO_FREE3D
@@ -212,7 +212,7 @@
 ---------------------------------------------------------------------------- */
 
 #define  VIO_FREE3D( ptr )                                                        \
-         free_memory_3d( (void ****) &(ptr) _ALLOC_SOURCE_LINE )
+         free_memory_3d( (void ****) &(ptr) ALLOC_SOURCE_LINE )
 
 /* ----------------------------- MNI Header -----------------------------------
 @NAME       : ALLOC4D
@@ -234,7 +234,7 @@
 #define  VIO_ALLOC4D( ptr, n1, n2, n3, n4 )                                       \
        ASSIGN_PTR(ptr) = alloc_memory_4d( (size_t) (n1), (size_t) (n2),       \
                           (size_t) (n3), (size_t) (n4),                       \
-                          sizeof(****(ptr)) _ALLOC_SOURCE_LINE )
+                          sizeof(****(ptr)) ALLOC_SOURCE_LINE )
 
 /* ----------------------------- MNI Header -----------------------------------
 @NAME       : FREE4D
@@ -250,7 +250,7 @@
 ---------------------------------------------------------------------------- */
 
 #define  VIO_FREE4D( ptr )                                                        \
-         free_memory_4d( (void *****) &(ptr) _ALLOC_SOURCE_LINE )
+         free_memory_4d( (void *****) &(ptr) ALLOC_SOURCE_LINE )
 
 /* ----------------------------- MNI Header -----------------------------------
 @NAME       : ALLOC5D
@@ -274,7 +274,7 @@
 #define  VIO_ALLOC5D( ptr, n1, n2, n3, n4, n5 )                                   \
      ASSIGN_PTR(ptr) = alloc_memory_5d( (size_t) (n1), (size_t) (n2),         \
                           (size_t) (n3), (size_t) (n4), (size_t) (n5),        \
-                          sizeof(*****(ptr)) _ALLOC_SOURCE_LINE )
+                          sizeof(*****(ptr)) ALLOC_SOURCE_LINE )
 
 /* ----------------------------- MNI Header -----------------------------------
 @NAME       : FREE5D
@@ -290,6 +290,6 @@
 ---------------------------------------------------------------------------- */
 
 #define  VIO_FREE5D( ptr )                                                        \
-         free_memory_5d( (void ******) &(ptr) _ALLOC_SOURCE_LINE )
+         free_memory_5d( (void ******) &(ptr) ALLOC_SOURCE_LINE )
 
 #endif /*VOL_IO_ALLOC_H*/
diff --git a/Modules/ThirdParty/MINC/src/libminc/volume_io/Include/volume_io/arrays.h b/Modules/ThirdParty/MINC/src/libminc/volume_io/Include/volume_io/arrays.h
@@ -54,7 +54,7 @@
          set_array_size( (void **) (&(array)), sizeof(*(array)),              \
                          (size_t) (previous_n_elems),                         \
                          (size_t) (new_n_elems),                              \
-                         (size_t) (chunk_size) _ALLOC_SOURCE_LINE )
+                         (size_t) (chunk_size) ALLOC_SOURCE_LINE )
 
 /* ----------------------------- MNI Header -----------------------------------
 @NAME       : ADD_ELEMENT_TO_ARRAY