MINC 2019-10-02 (ebf6eee8)

Run the UpdateFromUpstream.sh script to extract upstream MINC
using the following shell commands.

$ git archive --prefix=upstream-minc/ ebf6eee8 -- 
./ChangeLog
./volume_io
./libsrc
./libsrc/minc_compat.h
./libcommon/minc_config.h
./libcommon/minc_config.c
./libsrc/minc_format_convert.c
./libsrc/value_conversion.c
./libsrc/hdf_convenience.c
./libcommon/read_file_names.c
./libsrc/minc_simple.c
./libcommon/time_stamp.h
./libsrc/hdf_convenience.h
./libsrc/type_limits.h
./libcommon/read_file_names.h
./libsrc/minc_varlists.h
./libcommon/restructure.h
./libsrc/nd_loop.h
./libcommon/restructure.c
./libsrc/minc_simple.h
./libsrc/strdup.c
./libsrc/minc_useful.h
./libsrc/minc_convenience.c
./libsrc/minc_basic.h
./libsrc/minc_compat.c
./libcommon/time_stamp.c
./libsrc/voxel_loop.h
./libsrc/minc_routines.h
./libsrc/minc_private.h
./libsrc/netcdf_convenience.c
./libsrc/voxel_loop.c
./libsrc/dim_conversion.c
./libsrc/minc_format_convert.h
./libsrc/nd_loop.c
./libcommon/ParseArgv.h
./libcommon/minc_error.c
./libcommon/minc_error.h
./libsrc/minc_structures.h
./libsrc/minc.h
./libsrc/image_conversion.c
./libcommon/ParseArgv.c
./libcommon/minc_common_defs.h
./COPYING
./UseLIBMINC.cmake.in
./NEWS
./AUTHORS
./libsrc2/m2util.c
./libsrc2/minc2_defs.h
./libsrc2/minc2_api.h
./libcommon/minc2_error.h
./libsrc2/grpattr.c
./libsrc2/hyper.c
./libsrc2/minc_compat2.h
./libcommon/minc2_error.c
./libsrc2/record.c
./libsrc2/volume.c
./libsrc2/datatype.c
./libsrc2/volprops.c
./libsrc2/valid.c
./libsrc2/convert.c
./libsrc2/free.c
./libsrc2/dimension.c
./libsrc2/label.c
./libsrc2/minc2.h
./libsrc2/minc2_private.h
./libsrc2/slice.c
./libsrc2/minc2_structs.h
./CMakeLists.txt
./nifti
./LIBMINCConfig.cmake.in
./README.release
./INSTALL
./config.h.cmake
./README
./check_clock_gettime.c | tar x
$ git shortlog --perl-regexp --author='^((?!Kitware Robot).*)$' --no-merges --abbrev=8 --format='%h %s' 44fae20d..ebf6eee8

Vladimir S. FONOV (6):
      d51d37b9 Updating passing MI2_ flags to netcdf, addresses InsightSoftwareConsortium#94
      799c1df7 Updated configuration for UseLIBMINC.cmake
      1d4565b0 Addresses compilation with newer Visual Studio, addresses InsightSoftwareConsortium#1115
      bd84a98d more fixes for compilation with newer Visual Studio, addresses InsightSoftwareConsortium#1115
      2404369b Ignoring VScode files
      ebf6eee8 Fixes InsightSoftwareConsortium#96

Change-Id: Ic62b1d1b8ffe648142e5c3bb809fce6da06aceb8

CMakeLists.txt

@@ -7,9 +7,9 @@ PROJECT(LIBMINC)
 
 SET(LIBMINC_PACKAGE_VERSION_MAJOR 2)
 SET(LIBMINC_PACKAGE_VERSION_MINOR 4)
-SET(LIBMINC_PACKAGE_VERSION_PATCH 04)
+SET(LIBMINC_PACKAGE_VERSION_PATCH 05)
 
-SET(LIBMINC_SOVERSION "5.2.0")
+SET(LIBMINC_SOVERSION "5.3.0")
 
 SET(LIBMINC_PACKAGE "libminc")
 SET(LIBMINC_PACKAGE_BUGREPORT "a.janke@gmail.com")
@@ -143,11 +143,27 @@ CHECK_FUNCTION_EXISTS(sleep     HAVE_SLEEP)
 CHECK_FUNCTION_EXISTS(gettimeofday  HAVE_GETTIMEOFDAY)
 
 CHECK_LIBRARY_EXISTS(rt clock_gettime "time.h" HAVE_CLOCK_GETTIME_RT)
+
 IF(HAVE_CLOCK_GETTIME_RT)
   SET(RT_LIBRARY "rt")
   SET(HAVE_CLOCK_GETTIME ON)
 ELSE(HAVE_CLOCK_GETTIME_RT)
-  CHECK_SYMBOL_EXISTS(clock_gettime "time.h" HAVE_CLOCK_GETTIME)
+  # first check if the function is defined in header
+  CHECK_SYMBOL_EXISTS(clock_gettime "time.h" HAVE_CLOCK_GETTIME_SYMBOL)
+  # then check that it's available
+  IF(HAVE_CLOCK_GETTIME_SYMBOL)
+    TRY_RUN(HAVE_CLOCK_GETTIME_RUN HAVE_CLOCK_GETTIME_COMP 
+            ${CMAKE_CURRENT_BINARY_DIR}
+            ${CMAKE_CURRENT_SOURCE_DIR}/check_clock_gettime.c
+            )
+    IF(HAVE_CLOCK_GETTIME_RUN EQUAL 0 AND HAVE_CLOCK_GETTIME_COMP)
+      SET(HAVE_CLOCK_GETTIME ON)
+    ELSE()
+      SET(HAVE_CLOCK_GETTIME OFF)
+    ENDIF()
+  ENDIF()
+
+
 ENDIF(HAVE_CLOCK_GETTIME_RT)
 
 INCLUDE(CheckIncludeFiles)
@@ -495,7 +511,7 @@ 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/UseLIBMINC.cmake" )
+SET(LIBMINC_USE_FILE_CONFIG     "\${LIBMINC_INSTALL_PREFIX}/lib/cmake/Use${LIBMINC_EXTERNAL_LIB_PREFIX}LIBMINC.cmake" )
 SET(LIBMINC_INCLUDE_DIRS_CONFIG "\${LIBMINC_INSTALL_PREFIX}/include" )
 SET(LIBMINC_LIBRARY_DIRS_CONFIG "\${LIBMINC_INSTALL_PREFIX}/lib" )
 SET(LIBMINC_STATIC_LIBRARIES_CONFIG   "" )

check_clock_gettime.c

@@ -0,0 +1,15 @@
+#  if defined(__APPLE__)
+#    include <AvailabilityMacros.h>
+#    if MAC_OS_X_VERSION_MIN_REQUIRED < 101200
+#      error "clock_gettime not available on macOS < 10.12"
+#    endif
+#  endif
+
+#include <time.h>
+#include <stdio.h>
+
+int main(int argc, char **argv)
+{
+  struct timespec ts;
+  return clock_gettime(CLOCK_REALTIME, &ts);
+}

libcommon/minc_config.c

@@ -20,9 +20,12 @@
 
 #include "minc_config.h"
 
-#ifdef _MSC_VER
+#if defined(_MSC_VER) && _MSC_VER < 1900
 #define snprintf _snprintf 
 #define vsnprintf _vsnprintf 
+#endif
+
+#ifdef _MSC_VER
 #define strcasecmp _stricmp 
 #define strncasecmp _strnicmp 
 #endif

libcommon/time_stamp.c

@@ -67,9 +67,9 @@
 #endif
 #include <stdio.h>
 
-// MS Visual Studio 12 and below.
-// Defined after include of `stdio.h` in case it is already defined in that
-// header file.
+/* MS Visual Studio 12 and below.
+   Defined after include of `stdio.h` in case it is already defined in that
+   header file. */
 #if defined(_MSC_VER) && _MSC_VER <= 1800
 #ifndef snprintf
 #define snprintf _snprintf

libsrc/minc.h

@@ -603,8 +603,8 @@ extern int miget_file_type(const char *filename);
 
 #define MI2_GRPNAME "/minc-2.0"
 /* These must not interfere with any NC_ flags we might have to support. */
-#define MI2_CREATE_V2 0x1000    /* Force V2 format */
-#define MI2_CREATE_V1 0x2000    /* Force V1 format */
+#define MI2_CREATE_V2 0x10000    /* Force V2 format */
+#define MI2_CREATE_V1 0x20000    /* Force V1 format */
 
 /* Possible compression type values. */
 #define MI2_COMP_UNKNOWN (-1)

libsrc/netcdf_convenience.c

@@ -600,7 +600,7 @@ MNCAPI int micreatex(const char *path, int cmode, struct mi2opts *opts_ptr)
     MI_SAVE_ROUTINE_NAME("micreate");
 
     if ((cmode & MI2_CREATE_V1) != 0) {
-        fd = nccreate(path, cmode);
+        fd = nccreate(path, cmode & 0xffff);
     }
     else if (miget_cfg_bool(MICFG_FORCE_V2) || (cmode & MI2_CREATE_V2) != 0) {
 	fd = hdf_create(path, cmode, opts_ptr);
@@ -612,7 +612,7 @@ MNCAPI int micreatex(const char *path, int cmode, struct mi2opts *opts_ptr)
         }
         else {
             /* Create a NetCDF file. */
-            fd = nccreate(path, cmode);
+            fd = nccreate(path, cmode & 0xffff);
         }
     }
     if (fd < 0) {
@@ -644,7 +644,7 @@ MNCAPI int micreate(char *path, int cmode)
     MI_SAVE_ROUTINE_NAME("micreate");
 
     /* Create a NetCDF file. */
-    fd = nccreate(path, cmode);
+    fd = nccreate(path, cmode & 0xffff);
     if (fd < 0) {
 	MI_LOG_ERROR(MI_MSG_CREATEFILE, path);
     }

libsrc2/minc2_private.h

@@ -210,9 +210,12 @@ void miinit_default_range(mitype_t mitype, double *valid_max, double *valid_min)
 double rint(double v);
 #endif
 
-#ifdef _MSC_VER
+#if  defined(_MSC_VER) && _MSC_VER < 1900
 #define snprintf _snprintf 
 #define vsnprintf _vsnprintf 
+#endif
+
+#ifdef _MSC_VER
 #define strcasecmp _stricmp 
 #define strncasecmp _strnicmp 
 #endif