.travis.yml

+sudo: false
+language: c
+os: 
+    - linux
+    - osx
+
+compiler:
+  - gcc
+
+before_install: ./brew/brew_install.sh
+   
+addons:
+  apt:
+    packages:
+      - libnetcdf-dev
+      - libhdf5-serial-dev
+
+script: 
+        - cmake -DCMAKE_BUILD_TYPE:STRING=Release -DLIBMINC_MINC1_SUPPORT:BOOL=OFF -DBUILD_TESTING:BOOL=ON
+        - make
+        - make test
+        - cmake -DCMAKE_BUILD_TYPE:STRING=Release -DLIBMINC_MINC1_SUPPORT:BOOL=ON -DBUILD_TESTING:BOOL=ON
+        - make
+        - make test

CMakeLists.txt

@@ -6,10 +6,10 @@
 PROJECT(LIBMINC)
 
 SET(LIBMINC_PACKAGE_VERSION_MAJOR 2)
-SET(LIBMINC_PACKAGE_VERSION_MINOR 3)
-SET(LIBMINC_PACKAGE_VERSION_PATCH 00)
+SET(LIBMINC_PACKAGE_VERSION_MINOR 4)
+SET(LIBMINC_PACKAGE_VERSION_PATCH 03)
 
-SET(LIBMINC_SOVERSION "4.0.0")
+SET(LIBMINC_SOVERSION "5.2.0")
 
 SET(LIBMINC_PACKAGE "libminc")
 SET(LIBMINC_PACKAGE_BUGREPORT "a.janke@gmail.com")
@@ -22,7 +22,11 @@ INCLUDE(CTest)
 
 ENABLE_TESTING()
 
-CMAKE_MINIMUM_REQUIRED(VERSION 2.6)
+CMAKE_MINIMUM_REQUIRED(VERSION 2.8)
+
+IF( POLICY CMP0063 )
+  CMAKE_POLICY(SET CMP0063 NEW)
+ENDIF()
 
 IF(MINC_TOOLKIT_BUILD)
   SET(LIBMINC_EXTERNALLY_CONFIGURED ON)
@@ -46,6 +50,7 @@ IF(NOT LIBMINC_EXTERNALLY_CONFIGURED)
 
   OPTION(LIBMINC_MINC1_SUPPORT           "Support minc1 file format, requires NETCDF" OFF)
   OPTION(LIBMINC_BUILD_EZMINC_EXAMPLES   "Build EZminc examples" OFF)
+  OPTION(LIBMINC_USE_SYSTEM_NIFTI        "Use system NIfTI-1 library" OFF)
 
   SET (LIBMINC_EXPORTED_TARGETS "LIBMINC-targets")
   SET (LIBMINC_INSTALL_BIN_DIR bin)
@@ -59,12 +64,26 @@ IF(NOT LIBMINC_EXTERNALLY_CONFIGURED)
 
   # external packages
   FIND_PACKAGE(ZLIB REQUIRED)
-  FIND_PACKAGE(HDF5 REQUIRED)
+  SET(HDF5_NO_FIND_PACKAGE_CONFIG_FILE ON)
+  FIND_PACKAGE(HDF5 REQUIRED COMPONENTS C )
+  
+  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)
+  
   SET(HAVE_ZLIB ON)
 ELSE(NOT LIBMINC_EXTERNALLY_CONFIGURED)
   #TODO: set paths for HDF5 etc
 ENDIF(NOT LIBMINC_EXTERNALLY_CONFIGURED)
 
+IF(NOT DEFINED CMAKE_MACOSX_RPATH)
+  set(CMAKE_MACOSX_RPATH ON)
+ENDIF(NOT DEFINED CMAKE_MACOSX_RPATH)
+
 # Configure libminc
 IF(LIBMINC_BUILD_SHARED_LIBS)
   SET(LIBRARY_TYPE SHARED)
@@ -86,6 +105,8 @@ ENDIF(UNIX)
 
 # check for prereqs
 INCLUDE(CheckFunctionExists)
+INCLUDE(CheckSymbolExists)
+INCLUDE(CheckLibraryExists)
 
 CHECK_FUNCTION_EXISTS(mkstemp  HAVE_MKSTEMP)
 CHECK_FUNCTION_EXISTS(tmpnam   HAVE_TMPNAM)
@@ -102,17 +123,32 @@ CHECK_FUNCTION_EXISTS(strerror HAVE_STRERROR)
 CHECK_FUNCTION_EXISTS(sysconf  HAVE_SYSCONF)
 CHECK_FUNCTION_EXISTS(system   HAVE_SYSTEM)
 
+if(NOT MSVC)
+  set(CMAKE_REQUIRED_LIBRARIES m)
+endif()
+
+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)
+unset(CMAKE_REQUIRED_LIBRARIES)
+unset(CMAKE_REQUIRED_DEFINITIONS)
+
+
 CHECK_FUNCTION_EXISTS(srand48   HAVE_SRAND48)
 CHECK_FUNCTION_EXISTS(drand48   HAVE_DRAND48)
 CHECK_FUNCTION_EXISTS(sleep     HAVE_SLEEP)
 
 CHECK_FUNCTION_EXISTS(gettimeofday  HAVE_GETTIMEOFDAY)
 
-INCLUDE(CheckLibraryExists)
-CHECK_LIBRARY_EXISTS(rt clock_gettime "time.h" HAVE_CLOCK_GETTIME)
-IF(HAVE_CLOCK_GETTIME)
+CHECK_LIBRARY_EXISTS(rt clock_gettime "time.h" HAVE_CLOCK_GETTIME_RT)
+IF(HAVE_CLOCK_GETTIME_RT)
   SET(RT_LIBRARY "rt")
-ENDIF(HAVE_CLOCK_GETTIME)
+  SET(HAVE_CLOCK_GETTIME ON)
+ELSE(HAVE_CLOCK_GETTIME_RT)
+  CHECK_SYMBOL_EXISTS(clock_gettime "time.h" HAVE_CLOCK_GETTIME)
+ENDIF(HAVE_CLOCK_GETTIME_RT)
 
 INCLUDE(CheckIncludeFiles)
 CHECK_INCLUDE_FILES(float.h     HAVE_FLOAT_H)
@@ -122,6 +158,7 @@ CHECK_INCLUDE_FILES(sys/stat.h  HAVE_SYS_STAT_H)
 CHECK_INCLUDE_FILES(sys/types.h HAVE_SYS_TYPES_H)
 CHECK_INCLUDE_FILES(sys/wait.h  HAVE_SYS_WAIT_H)
 CHECK_INCLUDE_FILES(sys/time.h  HAVE_SYS_TIME_H)
+CHECK_INCLUDE_FILES(time.h      HAVE_TIME_H)
 CHECK_INCLUDE_FILES(values.h    HAVE_VALUES_H)
 CHECK_INCLUDE_FILES(unistd.h    HAVE_UNISTD_H)
 CHECK_INCLUDE_FILES(dirent.h    HAVE_DIRENT_H)
@@ -134,10 +171,14 @@ CHECK_INCLUDE_FILES(inttypes.h  HAVE_INTTYPES_H)
 CHECK_INCLUDE_FILES(string.h    HAVE_STRING_H)
 CHECK_INCLUDE_FILES(strings.h   HAVE_STRINGS_H)
 CHECK_INCLUDE_FILES(pwd.h       HAVE_PWD_H)
+CHECK_INCLUDE_FILES(sys/select.h    HAVE_SYS_SELECT_H)
+
 
 ADD_DEFINITIONS(-DHAVE_CONFIG_H)
 ADD_DEFINITIONS(-DMINC2=1)
-
+IF(NOT APPLE)
+ADD_DEFINITIONS(-D_XOPEN_SOURCE=500)
+ENDIF(NOT APPLE)
 # aliases
 SET(VERSION "${LIBMINC_EXTERNAL_LIB_PREFIX}${LIBMINC_PACKAGE_VERSION}")
 SET(HAVE_MINC1 ${LIBMINC_MINC1_SUPPORT})
@@ -157,6 +198,15 @@ IF(LIBMINC_BUILD_EZMINC)
    )
 ENDIF(LIBMINC_BUILD_EZMINC)
 
+IF(NIFTI_FOUND)
+    SET(LIBMINC_NIFTI_SUPPORT ON)
+    SET(LIBMINC_NIFTI_SOURCES
+      volume_io/Volumes/input_nifti.c
+      volume_io/Volumes/input_mgh.c
+      volume_io/Volumes/input_nrrd.c
+    )
+ENDIF(NIFTI_FOUND)
+
 # config files for build
 CONFIGURE_FILE(${CMAKE_CURRENT_SOURCE_DIR}/config.h.cmake ${CMAKE_CURRENT_BINARY_DIR}/config.h @ONLY)
 
@@ -167,38 +217,46 @@ CONFIGURE_FILE(${CMAKE_CURRENT_SOURCE_DIR}/config.h.cmake ${CMAKE_CURRENT_BINARY
 INCLUDE_DIRECTORIES(
    ${CMAKE_CURRENT_SOURCE_DIR}
    ${CMAKE_CURRENT_BINARY_DIR}
+   ${CMAKE_CURRENT_SOURCE_DIR}/libcommon
    ${CMAKE_CURRENT_SOURCE_DIR}/libsrc2
    ${CMAKE_CURRENT_SOURCE_DIR}/libsrc
    ${CMAKE_CURRENT_SOURCE_DIR}/volume_io/Include
    ${CMAKE_CURRENT_SOURCE_DIR}/ezminc
-   ${CMAKE_CURRENT_SOURCE_DIR}/nifti
-   ${HDF5_INCLUDE_DIR}
+   ${HDF5_INCLUDE_DIRS}
    )
 
+IF(LIBMINC_NIFTI_SUPPORT)
+    INCLUDE_DIRECTORIES(
+        ${NIFTI_INCLUDE_DIR}
+    )
+ENDIF(LIBMINC_NIFTI_SUPPORT)
+
 SET(minc_common_SRCS
-   libsrc/time_stamp.c
-   libsrc/read_file_names.c
-   libsrc/ParseArgv.c
-   libsrc/restructure.c
+  libcommon/minc2_error.c
+  libcommon/minc_config.c
+  libcommon/minc_error.c
+  libcommon/ParseArgv.c
+  libcommon/read_file_names.c
+  libcommon/restructure.c
+  libcommon/time_stamp.c
 )
 
 SET(minc_common_HEADERS
-  libsrc/time_stamp.h
-  libsrc/ParseArgv.h 
-  libsrc/read_file_names.h
-  libsrc/restructure.h
-  volume_io/Include/volume_io.h
-  nifti/nifti1.h
-  nifti/nifti1_io.h
-  nifti/znzlib.h
+  libcommon/minc2_error.h
+  libcommon/minc_config.h
+  libcommon/minc_error.h
+  libcommon/ParseArgv.h
+  libcommon/read_file_names.h
+  libcommon/restructure.h
+  libcommon/time_stamp.h
+  libcommon/minc_common_defs.h
+  volume_io/Include/volume_io.h # VF: WTF?
 )
 
-# some variables
 SET(minc1_LIB_SRCS
    libsrc/dim_conversion.c
    libsrc/image_conversion.c
    libsrc/minc_convenience.c
-   libsrc/minc_error.c
    libsrc/nd_loop.c
    libsrc/netcdf_convenience.c
    libsrc/value_conversion.c
@@ -232,7 +290,6 @@ SET(minc2_LIB_SRCS
    libsrc2/valid.c
    libsrc2/volprops.c
    libsrc2/volume.c
-   libsrc2/minc2_error.c
    )
 
 SET(minc2_HEADERS
@@ -240,7 +297,6 @@ SET(minc2_HEADERS
   libsrc2/minc2_defs.h 
   libsrc2/minc2_structs.h 
   libsrc2/minc2_api.h 
-  libsrc2/minc2_error.h
 )
 
 # volume_io2
@@ -281,12 +337,16 @@ SET(volume_io_LIB_SRCS
    volume_io/Volumes/volumes.c
    volume_io/Volumes/input_mnc2.c
    volume_io/Volumes/output_mnc2.c
-   volume_io/Volumes/input_mgh.c
-   volume_io/Volumes/input_nifti.c
-   nifti/nifti1_io.c
-   nifti/znzlib.c
 )
 
+IF(LIBMINC_NIFTI_SUPPORT)
+    SET(volume_io_LIB_SRCS 
+        ${volume_io_LIB_SRCS}
+        ${LIBMINC_NIFTI_SOURCES}
+    )
+ENDIF(LIBMINC_NIFTI_SUPPORT)
+
+
 SET(volume_io_HEADERS
     volume_io/Include/volume_io/alloc.h
     volume_io/Include/volume_io/arrays.h 
@@ -314,12 +374,21 @@ ELSE(LIBMINC_BUILD_SHARED_LIBS)
   SET(LIBMINC_LIBRARY_STATIC ${LIBMINC_LIBRARY})
 ENDIF(LIBMINC_BUILD_SHARED_LIBS)
 
-SET(LIBMINC_LIBRARIES ${LIBMINC_LIBRARY} ${HDF5_LIBRARY} ${ZLIB_LIBRARY} ${RT_LIBRARY})
-SET(LIBMINC_STATIC_LIBRARIES ${LIBMINC_LIBRARY_STATIC} ${HDF5_LIBRARY} ${ZLIB_LIBRARY} ${RT_LIBRARY})
+IF(LIBMINC_NIFTI_SUPPORT)
+    SET(NIFTI_LIBRARIES 
+        ${NIFTI_LIBRARY} ${ZNZ_LIBRARY}
+    )
+ELSE(LIBMINC_NIFTI_SUPPORT)
+    SET(NIFTI_LIBRARIES )
+ENDIF(LIBMINC_NIFTI_SUPPORT)
+
+
+SET(LIBMINC_LIBRARIES ${LIBMINC_LIBRARY} ${HDF5_LIBRARIES} ${NIFTI_LIBRARIES} ${ZLIB_LIBRARY})
+SET(LIBMINC_STATIC_LIBRARIES ${LIBMINC_LIBRARY_STATIC} ${HDF5_LIBRARIES} ${NIFTI_LIBRARIES} ${ZLIB_LIBRARY})
 
 IF(UNIX)
-  SET(LIBMINC_LIBRARIES ${LIBMINC_LIBRARIES} m dl)
-  SET(LIBMINC_STATIC_LIBRARIES ${LIBMINC_STATIC_LIBRARIES} m dl)
+  SET(LIBMINC_LIBRARIES ${LIBMINC_LIBRARIES} m dl ${RT_LIBRARY})
+  SET(LIBMINC_STATIC_LIBRARIES ${LIBMINC_STATIC_LIBRARIES} m dl  ${RT_LIBRARY})
 ENDIF(UNIX)
 
 SET(minc_LIB_SRCS ${minc2_LIB_SRCS} ${minc_common_SRCS})
@@ -333,14 +402,26 @@ ENDIF(LIBMINC_MINC1_SUPPORT)
 
 # Keep this variable for compatibility
 SET(VOLUME_IO_LIBRARY  ${LIBMINC_EXTERNAL_LIB_PREFIX}minc2)
+SET(CMAKE_INSTALL_RPATH ${CMAKE_INSTALL_PREFIX}/lib${LIB_SUFFIX})
 
 ADD_LIBRARY(${LIBMINC_LIBRARY} ${LIBRARY_TYPE} ${minc_LIB_SRCS} ${minc_HEADERS} ${volume_io_LIB_SRCS} ${volume_io_HEADERS} )
-TARGET_LINK_LIBRARIES(${LIBMINC_LIBRARY} ${HDF5_LIBRARY} ${ZLIB_LIBRARY} ${RT_LIBRARY}) # 
+
+IF(NIFTI_FOUND AND NOT LIBMINC_USE_SYSTEM_NIFTI)
+    ADD_DEPENDENCIES(${LIBMINC_LIBRARY} NIFTI)
+ENDIF()
+
+
+TARGET_LINK_LIBRARIES(${LIBMINC_LIBRARY} ${HDF5_LIBRARIES} ${NIFTI_LIBRARIES} ${ZLIB_LIBRARY} ${RT_LIBRARY}) #
+
 IF(LIBMINC_MINC1_SUPPORT)
   INCLUDE_DIRECTORIES(${NETCDF_INCLUDE_DIR})
   TARGET_LINK_LIBRARIES(${LIBMINC_LIBRARY} ${NETCDF_LIBRARY})
 ENDIF(LIBMINC_MINC1_SUPPORT)
 
+IF(NOT LIBMINC_USE_SYSTEM_NIFTI AND NOT LIBMINC_EXTERNALLY_CONFIGURED)
+  ADD_DEPENDENCIES(minc2 NIFTI)
+ENDIF(NOT LIBMINC_USE_SYSTEM_NIFTI  AND NOT LIBMINC_EXTERNALLY_CONFIGURED)
+
 EXPORT(TARGETS ${LIBMINC_LIBRARY} FILE "${LIBMINC_EXPORTED_TARGETS}.cmake")
 
 IF(UNIX)
@@ -348,7 +429,7 @@ IF(UNIX)
 
   IF(LIBMINC_BUILD_SHARED_LIBS)
     ADD_LIBRARY(${LIBMINC_LIBRARY_STATIC} STATIC ${minc_LIB_SRCS} ${minc_HEADERS} ${volume_io_LIB_SRCS} ${volume_io_HEADERS} )
-    TARGET_LINK_LIBRARIES(${LIBMINC_LIBRARY_STATIC} ${HDF5_LIBRARY} ${ZLIB_LIBRARY} ${RT_LIBRARY} m dl )
+    TARGET_LINK_LIBRARIES(${LIBMINC_LIBRARY_STATIC} ${HDF5_LIBRARY} ${NIFTI_LIBRARIES} ${ZLIB_LIBRARY} ${RT_LIBRARY} m dl )
     IF(LIBMINC_MINC1_SUPPORT)
       TARGET_LINK_LIBRARIES(${LIBMINC_LIBRARY} ${NETCDF_LIBRARY})
     ENDIF(LIBMINC_MINC1_SUPPORT)
@@ -390,9 +471,9 @@ SET(LIBMINC_USE_FILE_CONFIG  ${CMAKE_CURRENT_BINARY_DIR}/UseLIBMINC.cmake)
 
 SET(LIBMINC_INCLUDE_DIRS_CONFIG
   ${CMAKE_CURRENT_SOURCE_DIR}
+  ${CMAKE_CURRENT_SOURCE_DIR}/libcommon
   ${CMAKE_CURRENT_SOURCE_DIR}/libsrc2
   ${CMAKE_CURRENT_SOURCE_DIR}/volume_io/Include
-  ${CMAKE_CURRENT_SOURCE_DIR}/nifti
 )
 
 IF(LIBMINC_MINC1_SUPPORT)
@@ -433,8 +514,13 @@ IF(SUPERBUILD_STAGING_PREFIX)
   STRING(REPLACE "${SUPERBUILD_STAGING_PREFIX}/" "" EZMINC_LIBRARIES            "${EZMINC_LIBRARIES}")
   STRING(REPLACE "${SUPERBUILD_STAGING_PREFIX}/" "" NETCDF_INCLUDE_DIR          "${NETCDF_INCLUDE_DIR}")
   STRING(REPLACE "${SUPERBUILD_STAGING_PREFIX}/" "" HDF5_INCLUDE_DIR            "${HDF5_INCLUDE_DIR}")
+  STRING(REPLACE "${SUPERBUILD_STAGING_PREFIX}/" "" HDF5_INCLUDE_DIRS           "${HDF5_INCLUDE_DIRS}")
+  STRING(REPLACE "${SUPERBUILD_STAGING_PREFIX}/" "" NIFTI_INCLUDE_DIR           "${NIFTI_INCLUDE_DIR}")
   STRING(REPLACE "${SUPERBUILD_STAGING_PREFIX}/" "" NETCDF_LIBRARY              "${NETCDF_LIBRARY}")
   STRING(REPLACE "${SUPERBUILD_STAGING_PREFIX}/" "" HDF5_LIBRARY                "${HDF5_LIBRARY}")
+  STRING(REPLACE "${SUPERBUILD_STAGING_PREFIX}/" "" HDF5_LIBRARIES              "${HDF5_LIBRARIES}")
+  STRING(REPLACE "${SUPERBUILD_STAGING_PREFIX}/" "" NIFTI_LIBRARY               "${NIFTI_LIBRARY}")
+  STRING(REPLACE "${SUPERBUILD_STAGING_PREFIX}/" "" ZNZ_LIBRARY                 "${ZNZ_LIBRARY}")
   STRING(REPLACE "${SUPERBUILD_STAGING_PREFIX}/" "" ZLIB_LIBRARY                "${ZLIB_LIBRARY}")
   STRING(REPLACE "${SUPERBUILD_STAGING_PREFIX}/" "" ZLIB_LIBRARIES              "${ZLIB_LIBRARIES}")
 ENDIF(SUPERBUILD_STAGING_PREFIX)

ChangeLog

+2016-05-05  Robert D. Vincent <robert.d.vincent@mcgill.ca>
+   * libsrc/minc_simple.c, libsrc/minc_simple.h: Improved the usefulness
+	of minc_get_world_transform() and added minc_transform_to_world().
+
+2016-02-09  Robert D. Vincent <robert.d.vincent@mcgill.ca>
+   * libsrc2/dimension.c, libsrc2/volume.c, testdir/minc2-dimension-test.c:
+	Existing code did not properly implement miset_dimension_widths()
+	and miget_dimension_widths().
+
+2015-11-16  Robert D. Vincent <robert.d.vincent@mcgill.ca>
+   * volume_io/Volumes/volumes.c,
+     volume_io/Include/volume_io/vol_io_protoypes.h: Added
+	copy_volume_new_type() and declared that
+	get_volume_total_n_voxels() returns size_t.
+   * testdir/volume_test.c: Created a simple test for volume functions.
+   * CMakeLists.txt: Updated LIBMINC_SOVERSION
+
+2015-10-14  Robert D. Vincent <robert.d.vincent@mcgill.ca>
+   * volume_io/Volumes/input_mgh.c: Fix loading of time-varying MGZ files.
+
+2015-10-07  Robert D. Vincent <robert.d.vincent@mcgill.ca>
+   * libsrc2/m2util.c, libsrc2/volume.c: Fix improper handling of
+	label volumes on big-endian architectures.
+
 -- Release of minc 2.3.00 --
+2015-10-01  Vladimir S. FONOV <vladimir.fonov@gmail.com>
+   * Added new configuration environment variable MINC_FILE_CACHE_MB, 
+  it specifies (in megabytes) maximum per file cache for reading MINC2 files
+  default value is 100 Mb. **WARNING** specifying value of 0 will 
+  significantly degrade performance on compressed minc2 files.
+  
+   * Added new configuration environment variable MINC_CHECKSUM, when 
+   set to 1 will enable FLETCHER32 checksum in new MINC2 files, but only when 
+   chunking is enabled
    
 2015-09-11  Robert D. Vincent <robert.d.vincent@mcgill.ca>
    * Remove autoconf/automake support.

LIBMINCConfig.cmake.in

@@ -7,12 +7,17 @@ set(HAVE_MINC2    1)
 set(HAVE_EZMINC   @LIBMINC_MINC1_SUPPORT@)
 set(HAVE_MINC1    @LIBMINC_MINC1_SUPPORT@)
 
+set(LIBMINC_NIFTI_SUPPORT @LIBMINC_NIFTI_SUPPORT@)
+
 set(NETCDF_INCLUDE_DIR "@NETCDF_INCLUDE_DIR@")
 set(HDF5_INCLUDE_DIR   "@HDF5_INCLUDE_DIR@")
+set(NIFTI_INCLUDE_DIR  "@NIFTI_INCLUDE_DIR@")
+
 set(NETCDF_LIBRARY     "@NETCDF_LIBRARY@")
 set(HDF5_LIBRARY       "@HDF5_LIBRARY@")
 set(ZLIB_LIBRARY       "@ZLIB_LIBRARY@")
 set(ZLIB_LIBRARIES     "@ZLIB_LIBRARY@")
+set(NIFTI_LIBRARIES    "@NIFTI_LIBRARIES@")
 
 set(LIBMINC_INCLUDE_DIRS "@LIBMINC_INCLUDE_DIRS_CONFIG@")
 set(LIBMINC_LIBRARY_DIRS "@LIBMINC_LIBRARY_DIRS_CONFIG@")

README

@@ -78,8 +78,32 @@ MINC_LOGFILE = [+]<pathname>|stdout|-
 MINC_LOGLEVEL = 0-4
 
 
+# Maximum memory buffer, used in some minc programs
+#
+MINC_MAX_FILE_BUFFER_KB = <N>
+
+# Maximum allocated memory, used in some minc programs
+#
+MINC_MAX_MEMORY_KB = <N>
+
+# Memory cache for MINC2 files, per open file
+#
+MINC_FILE_CACHE_MB = <N>
+
+# Creation of HDF5 checksums for the volume, only works for MINC2 
+# file format 
+# default 0
+#
+MINC_CHECKSUM = {1,0}
+
+# Prefer using MINC2 API inside Volume IO
+# default 0
+#
+MINC_PREFER_V2_API = {1,0}
+
+
+
 DOCUMENTATION
 -------------
 
 http://en.wikibooks.org/wiki/MINC
-

brew/brew_install.sh

+#!/bin/bash
+if [ "${TRAVIS_OS_NAME}" = "osx" ]; then
+    brew install ./brew/netcdf.rb
+    brew install ./brew/hdf5.rb
+fi
+

brew/hdf5.rb

+class Hdf5 < Formula
+  homepage "https://www.hdfgroup.org/HDF5/"
+  url "https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-1.8/hdf5-1.8.19/src/hdf5-1.8.19.tar.bz2"
+  sha256 "59c03816105d57990329537ad1049ba22c2b8afe1890085f0c022b75f1727238"
+  def install
+    system "./configure", "--prefix=#{prefix}"
+    system "make", "install"
+  end
+end

brew/netcdf.rb

+class Netcdf < Formula
+  homepage "http://www.unidata.ucar.edu/software/netcdf/"
+  url "ftp://ftp.unidata.ucar.edu/pub/netcdf/netcdf-4.3.3.1.tar.gz"
+  sha256 "bdde3d8b0e48eed2948ead65f82c5cfb7590313bc32c4cf6c6546e4cea47ba19"
+  def install
+    system "./configure", "--prefix=#{prefix}", "--disable-netcdf-4"
+    system "make", "install"
+  end
+end

cmake-modules/BuildNIFTI.cmake

+macro(build_nifti install_prefix staging_prefix)
+
+  if(CMAKE_EXTRA_GENERATOR)
+    set(CMAKE_GEN "${CMAKE_EXTRA_GENERATOR} - ${CMAKE_GENERATOR}")
+  else()
+    set(CMAKE_GEN "${CMAKE_GENERATOR}")
+  endif()
+
+  SET(NIFTI_CMAKE_CXX_FLAGS_RELEASE ${CMAKE_CXX_FLAGS_RELEASE})
+  SET(NIFTI_CMAKE_C_FLAGS_RELEASE   ${CMAKE_C_FLAGS_RELEASE})
+  
+  SET(NIFTI_CMAKE_CXX_FLAGS_DEBUG   ${CMAKE_CXX_FLAGS_DEBUG})
+  SET(NIFTI_CMAKE_C_FLAGS_DEBUG     ${CMAKE_C_FLAGS_DEBUG})
+  
+  SET(NIFTI_CMAKE_CXX_FLAGS "-fPIC ${CMAKE_CXX_FLAGS}")
+  SET(NIFTI_CMAKE_C_FLAGS   "-fPIC ${CMAKE_C_FLAGS}")
+
+ExternalProject_Add(NIFTI
+  SOURCE_DIR NIFTI
+  BINARY_DIR NIFTI-build
+  URL "http://downloads.sourceforge.net/project/niftilib/nifticlib/nifticlib_2_0_0/nifticlib-2.0.0.tar.gz"
+  URL_MD5 "425a711f8f92fb1e1f088cbc55bea53a"
+  CMAKE_GENERATOR ${CMAKE_GEN}
+  CMAKE_ARGS
+        -DCMAKE_BUILD_TYPE:STRING=${CMAKE_BUILD_TYPE}
+        -DBUILD_SHARED_LIBS:BOOL=OFF
+        -DCMAKE_SKIP_RPATH:BOOL=YES
+        -DMACOSX_RPATH:BOOL=ON
+        -DCMAKE_INSTALL_RPATH:PATH=${install_prefix}/lib${LIB_SUFFIX}
+        -DCMAKE_INSTALL_PREFIX:PATH=${install_prefix}
+        "-DCMAKE_CXX_FLAGS_RELEASE:STRING=${NIFTI_CMAKE_CXX_FLAGS_RELEASE}"
+        "-DCMAKE_C_FLAGS_RELEASE:STRING=${NIFTI_CMAKE_C_FLAGS_RELEASE}"
+        "-DCMAKE_CXX_FLAGS_DEBUG:STRING=${NIFTI_CMAKE_CXX_FLAGS_DEBUG}"
+        "-DCMAKE_C_FLAGS_DEBUG:STRING=${NIFTI_CMAKE_C_FLAGS_DEBUG}"
+        "-DCMAKE_CXX_FLAGS:STRING=${NIFTI_CMAKE_CXX_FLAGS}"
+        "-DCMAKE_C_FLAGS:STRING=${NIFTI_CMAKE_C_FLAGS}"
+        -DCMAKE_EXE_LINKER_FLAGS:STRING=${CMAKE_EXE_LINKER_FLAGS}
+        -DCMAKE_MODULE_LINKER_FLAGS:STRING=${CMAKE_MODULE_LINKER_FLAGS}
+        -DCMAKE_SHARED_LINKER_FLAGS:STRING=${CMAKE_SHARED_LINKER_FLAGS}
+        -DCMAKE_C_COMPILER:FILEPATH=${CMAKE_C_COMPILER}
+        -DCMAKE_CXX_COMPILER:FILEPATH=${CMAKE_CXX_COMPILER}
+        -DZLIB_INCLUDE_DIR:PATH=${ZLIB_INCLUDE_DIR}
+        -DZLIB_LIBRARY:FILEPATH=${ZLIB_LIBRARY}
+   
+   INSTALL_COMMAND $(MAKE) install DESTDIR=${staging_prefix}
+   INSTALL_DIR ${staging_prefix}/${install_prefix}
+)
+
+SET(NIFTI_LIBRARY     ${staging_prefix}/${install_prefix}/lib${LIB_SUFFIX}/libniftiio.a )
+SET(NIFTI_INCLUDE_DIR ${staging_prefix}/${install_prefix}/include/nifti )
+SET(ZNZ_LIBRARY       ${staging_prefix}/${install_prefix}/lib${LIB_SUFFIX}/libznz.a )
+SET(ZNZ_INCLUDE_DIR   ${staging_prefix}/${install_prefix}/include/nifti )
+SET(NIFTI_FOUND ON)
+message("NIFTI_INCLUDE_DIR=${NIFTI_INCLUDE_DIR}")
+
+endmacro(build_nifti)
+

cmake-modules/FindHDF5.cmake

-#
-# this module look for HDF5 (http://hdf.ncsa.uiuc.edu) support
-# it will define the following values
-#
-# HDF5_INCLUDE_DIR  = where hdf5.h can be found
-# HDF5_LIBRARY      = the library to link against (hdf5 etc)
-# HDF5_FOUND        = set to true after finding the library
-#
-
-IF(EXISTS ${PROJECT_CMAKE}/Hdf5Config.cmake)
-  INCLUDE(${PROJECT_CMAKE}/Hdf5Config.cmake)
-ENDIF(EXISTS ${PROJECT_CMAKE}/Hdf5Config.cmake)
-
-IF(Hdf5_INCLUDE_DIRS)
-
-  FIND_PATH(HDF5_INCLUDE_DIR hdf5.h ${Hdf5_INCLUDE_DIRS})
-  FIND_LIBRARY(HDF5_LIBRARY hdf5 ${Hdf5_LIBRARY_DIRS})
-
-ELSE(Hdf5_INCLUDE_DIRS)
-
-  SET(TRIAL_LIBRARY_PATHS
-    $ENV{HDF5_HOME}/lib
-    /usr/apps/lib
-    /usr/lib 
-    /usr/local/lib
-    /opt/lib
-    /sw/lib
-    )
-
-  SET(TRIAL_INCLUDE_PATHS
-    $ENV{HDF5_HOME}/include
-    /usr/apps/include
-    /usr/include
-    /opt/include
-    /usr/local/include
-    /sw/include
-    )
-
-  IF($ENV{HDF5_DIR} MATCHES "hdf")
-    MESSAGE(STATUS "Using environment variable HDF5_DIR.")
-    SET(TRIAL_LIBRARY_PATHS $ENV{HDF5_DIR}/lib ${TRIAL_LIBRARY_PATHS} )
-    SET(TRIAL_INCLUDE_PATHS $ENV{HDF5_DIR}/include ${TRIAL_INCLUDE_PATHS} )
-  ENDIF($ENV{HDF5_DIR} MATCHES "hdf")
-  
-  FIND_LIBRARY(HDF5_LIBRARY hdf5 ${TRIAL_LIBRARY_PATHS})
-  FIND_PATH(HDF5_INCLUDE_DIR hdf5.h ${TRIAL_INCLUDE_PATHS} )
-
-ENDIF(Hdf5_INCLUDE_DIRS)
-
-## -----------------------------------------------------------------------------
-## Assign status of the search
-
-IF(HDF5_INCLUDE_DIR AND HDF5_LIBRARY)
-  SET(HDF5_FOUND 1 CACHE BOOL "Found hdf5 library")
-ELSE(HDF5_INCLUDE_DIR AND HDF5_LIBRARY)
-  SET(HDF5_FOUND 0 CACHE BOOL "Not fount hdf5 library")
-ENDIF(HDF5_INCLUDE_DIR AND HDF5_LIBRARY)
-
-## -----------------------------------------------------------------------------
-## Feedback
-
-IF (HDF5_FOUND)
-  IF (NOT HDF5_FIND_QUIETLY)
-    MESSAGE (STATUS "Found components for HDF5")
-    MESSAGE (STATUS "HDF5 library : ${HDF5_LIBRARY}")
-    MESSAGE (STATUS "HDF5 headers : ${HDF5_INCLUDE_DIR}")
-  ENDIF (NOT HDF5_FIND_QUIETLY)
-ELSE (HDF5_FOUND)
-  IF (HDF5_FIND_REQUIRED)
-    MESSAGE (FATAL_ERROR "Could not find HDF5!")
-  ENDIF (HDF5_FIND_REQUIRED)
-ENDIF (HDF5_FOUND)
-
-## -----------------------------------------------------------------------------
-## Variables marked as advanced
-
-MARK_AS_ADVANCED(
-  HDF5_INCLUDE_DIR 
-  HDF5_LIBRARY 
-  HDF5_FOUND
-)

cmake-modules/FindNIFTI.cmake

+# FindNIFTI.cmake module
+
+
+FIND_PATH(NIFTI_INCLUDE_DIR nifti1_io.h /usr/include /usr/local/include /usr/local/bic/include)
+
+FIND_LIBRARY(NIFTI_LIBRARY NAMES niftiio PATHS /usr/lib /usr/local/lib /usr/local/bic/lib)
+
+FIND_PATH(ZNZ_INCLUDE_DIR znzlib.h /usr/include /usr/local/include /usr/local/bic/include)
+
+FIND_LIBRARY(ZNZ_LIBRARY NAMES znz PATHS /usr/lib /usr/local/lib /usr/local/bic/lib)
+
+
+IF (NIFTI_INCLUDE_DIR AND NIFTI_LIBRARY AND ZNZ_INCLUDE_DIR AND ZNZ_LIBRARY)
+   SET(NIFTI_FOUND TRUE)
+ENDIF (NIFTI_INCLUDE_DIR AND NIFTI_LIBRARY AND ZNZ_INCLUDE_DIR AND ZNZ_LIBRARY)
+
+
+IF (NIFTI_FOUND)
+   IF (NOT NIFTI_FIND_QUIETLY)
+      MESSAGE(STATUS "Found NetCDF headers: ${NIFTI_INCLUDE_DIR}")
+      MESSAGE(STATUS "Found NetCDF library: ${NIFTI_LIBRARY}")
+      MESSAGE(STATUS "Found znzlib headers: ${ZNZ_INCLUDE_DIR}")
+      MESSAGE(STATUS "Found znzlib library: ${ZNZ_LIBRARY}")
+   ENDIF (NOT NIFTI_FIND_QUIETLY)
+ELSE (NIFTI_FOUND)
+   IF (NIFTI_FIND_REQUIRED)
+      MESSAGE(FATAL_ERROR "Cound not find NIfTI-1 I/O library")
+   ENDIF (NIFTI_FIND_REQUIRED)
+ENDIF (NIFTI_FOUND)

config.h.cmake

@@ -14,6 +14,7 @@
 
 #cmakedefine HAVE_MINC1 1 
 #cmakedefine HAVE_MINC2 1
+#cmakedefine LIBMINC_NIFTI_SUPPORT 1
 
 #ifndef H5Acreate_vers
 #define H5Acreate_vers 2
@@ -23,6 +24,9 @@
 #cmakedefine HAVE_STRERROR 1 
 #cmakedefine HAVE_FLOAT_H 1 
 
+#cmakedefine HAVE_COPYSIGN 1 
+#cmakedefine HAVE_ROUND 1 
+
 #cmakedefine HAVE_DIRENT_H 1 
 #cmakedefine HAVE_DLFCN_H 1 
 #cmakedefine HAVE_FCNTL_H 1 
@@ -46,8 +50,10 @@
 #cmakedefine HAVE_SYS_NDIR_H 1 
 #cmakedefine HAVE_SYS_STAT_H 1 
 #cmakedefine HAVE_SYS_TIME_H 1 
+#cmakedefine HAVE_TIME_H 1 
 #cmakedefine HAVE_SYS_TYPES_H 1 
 #cmakedefine HAVE_SYS_WAIT_H 1 
+#cmakedefine HAVE_SYS_SELECT_H 1
 #cmakedefine HAVE_TEMPNAM 1 
 #cmakedefine HAVE_TMPNAM 1 
 #cmakedefine HAVE_UNISTD_H 1 
@@ -64,3 +70,5 @@
 #cmakedefine HAVE_SLEEP 1 
 #cmakedefine HAVE_CLOCK_GETTIME 1
 #cmakedefine HAVE_GETTIMEOFDAY 1
+#cmakedefine HAVE_RINT 1
+

debian/changelog

+libminc (2.4.03-1~exp1) UNRELEASED; urgency=medium
+
+  * Team upload.
+  * New upstream version 2.4.03
+  * d/p: remove patches resolved upstream
+  * d/rules: Enable system nifti from build rules
+  * d/control: cme fix dpkg: Update urls and standard (no changes needed)
+  * d/rules, *.install: Move to use install files
+  * d/p/remove-rpath: Don't set rpath when installing
+  * Correct *.cmake install location
+  * d/rules: add -ffloat-store in i386 build to pass tests
+
+ -- Gert Wollny <gewo@debian.org>  Sat, 19 May 2018 22:12:40 +0200
+
 libminc (2.3.00-5) unstable; urgency=medium
 
   * Team upload

debian/control

@@ -10,12 +10,12 @@ Build-Depends: debhelper (>= 10),
                libnifti-dev,
                zlib1g-dev,
                libhdf5-dev
-Standards-Version: 4.1.1
-Vcs-Browser: https://anonscm.debian.org/cgit/debian-med/libminc.git
-Vcs-Git: https://anonscm.debian.org/git/debian-med/libminc.git
+Standards-Version: 4.1.4
+Vcs-Browser: https://salsa.debian.org/med-team/libminc
+Vcs-Git: https://salsa.debian.org/med-team/libminc.git
 Homepage: https://github.com/BIC-MNI/libminc
 
-Package: libminc2-4.0.0
+Package: libminc2-5.2.0
 Architecture: any
 Multi-Arch: same
 Section: libs
@@ -41,7 +41,7 @@ Package: libminc-dev
 Architecture: any
 Section: libdevel
 Depends: ${misc:Depends},
-         libminc2-4.0.0 (= ${binary:Version}),
+         libminc2-5.2.0 (= ${binary:Version}),
          libnetcdf-dev,
          libhdf5-dev
 Conflicts: libminc0-dev

debian/libminc-dev.install

+usr/lib/*/lib*.so
+usr/lib/*/cmake/*.cmake
+usr/include/*
+
+

debian/libminc2-5.2.0.install

+usr/lib/*/lib*.so.*

debian/patches/Use-system-FindHDF5-CMake-module.patch

-From: Ghislain Antony Vaillant <ghisvail@gmail.com>
-Date: Thu, 25 Aug 2016 13:20:22 +0100
-Subject: Use system FindHDF5 CMake module.
-
----
- CMakeLists.txt               |  5 +--
- cmake-modules/FindHDF5.cmake | 81 --------------------------------------------
- 2 files changed, 3 insertions(+), 83 deletions(-)
- delete mode 100644 cmake-modules/FindHDF5.cmake
-
-diff --git a/CMakeLists.txt b/CMakeLists.txt
-index df996ed..8eeb50b 100644
---- a/CMakeLists.txt
-+++ b/CMakeLists.txt
-@@ -59,9 +59,10 @@ IF(NOT LIBMINC_EXTERNALLY_CONFIGURED)
- 
-   # external packages
-   FIND_PACKAGE(ZLIB REQUIRED)
--  FIND_PACKAGE(HDF5 REQUIRED)
-+  FIND_PACKAGE(HDF5 COMPONENTS C REQUIRED)
-   SET(HAVE_ZLIB ON)
--  set(HDF5_LIBRARY ${HDF5_C_LIBRARIES})
-+  set(HDF5_LIBRARY ${HDF5_LIBRARIES})
-+  set(HDF5_INCLUDE_DIR ${HDF5_INCLUDE_DIRS})
- ELSE(NOT LIBMINC_EXTERNALLY_CONFIGURED)
-   #TODO: set paths for HDF5 etc
- ENDIF(NOT LIBMINC_EXTERNALLY_CONFIGURED)
-diff --git a/cmake-modules/FindHDF5.cmake b/cmake-modules/FindHDF5.cmake
-deleted file mode 100644
-index 6de68d0..0000000
---- a/cmake-modules/FindHDF5.cmake
-+++ /dev/null
-@@ -1,81 +0,0 @@
--#
--# this module look for HDF5 (http://hdf.ncsa.uiuc.edu) support
--# it will define the following values
--#
--# HDF5_INCLUDE_DIR  = where hdf5.h can be found
--# HDF5_LIBRARY      = the library to link against (hdf5 etc)
--# HDF5_FOUND        = set to true after finding the library
--#
--
--IF(EXISTS ${PROJECT_CMAKE}/Hdf5Config.cmake)
--  INCLUDE(${PROJECT_CMAKE}/Hdf5Config.cmake)
--ENDIF(EXISTS ${PROJECT_CMAKE}/Hdf5Config.cmake)
--
--IF(Hdf5_INCLUDE_DIRS)
--
--  FIND_PATH(HDF5_INCLUDE_DIR hdf5.h ${Hdf5_INCLUDE_DIRS})
--  FIND_LIBRARY(HDF5_LIBRARY hdf5 ${Hdf5_LIBRARY_DIRS})
--
--ELSE(Hdf5_INCLUDE_DIRS)
--
--  SET(TRIAL_LIBRARY_PATHS
--    $ENV{HDF5_HOME}/lib
--    /usr/apps/lib
--    /usr/lib 
--    /usr/local/lib
--    /opt/lib
--    /sw/lib
--    )
--
--  SET(TRIAL_INCLUDE_PATHS
--    $ENV{HDF5_HOME}/include
--    /usr/apps/include
--    /usr/include
--    /opt/include
--    /usr/local/include
--    /sw/include
--    )
--
--  IF($ENV{HDF5_DIR} MATCHES "hdf")
--    MESSAGE(STATUS "Using environment variable HDF5_DIR.")
--    SET(TRIAL_LIBRARY_PATHS $ENV{HDF5_DIR}/lib ${TRIAL_LIBRARY_PATHS} )
--    SET(TRIAL_INCLUDE_PATHS $ENV{HDF5_DIR}/include ${TRIAL_INCLUDE_PATHS} )
--  ENDIF($ENV{HDF5_DIR} MATCHES "hdf")
--  
--  FIND_LIBRARY(HDF5_LIBRARY hdf5 ${TRIAL_LIBRARY_PATHS})
--  FIND_PATH(HDF5_INCLUDE_DIR hdf5.h ${TRIAL_INCLUDE_PATHS} )
--
--ENDIF(Hdf5_INCLUDE_DIRS)
--
--## -----------------------------------------------------------------------------
--## Assign status of the search
--
--IF(HDF5_INCLUDE_DIR AND HDF5_LIBRARY)
--  SET(HDF5_FOUND 1 CACHE BOOL "Found hdf5 library")
--ELSE(HDF5_INCLUDE_DIR AND HDF5_LIBRARY)
--  SET(HDF5_FOUND 0 CACHE BOOL "Not fount hdf5 library")
--ENDIF(HDF5_INCLUDE_DIR AND HDF5_LIBRARY)
--
--## -----------------------------------------------------------------------------
--## Feedback
--
--IF (HDF5_FOUND)
--  IF (NOT HDF5_FIND_QUIETLY)
--    MESSAGE (STATUS "Found components for HDF5")
--    MESSAGE (STATUS "HDF5 library : ${HDF5_LIBRARY}")
--    MESSAGE (STATUS "HDF5 headers : ${HDF5_INCLUDE_DIR}")
--  ENDIF (NOT HDF5_FIND_QUIETLY)
--ELSE (HDF5_FOUND)
--  IF (HDF5_FIND_REQUIRED)
--    MESSAGE (FATAL_ERROR "Could not find HDF5!")
--  ENDIF (HDF5_FIND_REQUIRED)
--ENDIF (HDF5_FOUND)
--
--## -----------------------------------------------------------------------------
--## Variables marked as advanced
--
--MARK_AS_ADVANCED(
--  HDF5_INCLUDE_DIR 
--  HDF5_LIBRARY 
--  HDF5_FOUND
--)

debian/patches/build-using-system-find-dot-cmake

@@ -9,11 +9,11 @@ version, but also require this patch so that the newer
 variable HDF5_C_LIBRARIES is used.
 
 
---- libminc-2.3.00~2015-08-24.orig/CMakeLists.txt
-+++ libminc-2.3.00~2015-08-24/CMakeLists.txt
-@@ -61,6 +61,7 @@
-   FIND_PACKAGE(ZLIB REQUIRED)
-   FIND_PACKAGE(HDF5 REQUIRED)
+--- a/CMakeLists.txt
++++ b/CMakeLists.txt
+@@ -76,6 +76,7 @@
+   ENDIF(LIBMINC_USE_SYSTEM_NIFTI)
+   
    SET(HAVE_ZLIB ON)
 +  set(HDF5_LIBRARY ${HDF5_C_LIBRARIES})
  ELSE(NOT LIBMINC_EXTERNALLY_CONFIGURED)

debian/patches/fix-endian-issues-label-data.patch

-From 166aca9f4c33bc5642047ceafd5c6bae0d888187 Mon Sep 17 00:00:00 2001
-From: "Robert D. Vincent" <robert.d.vincent@mcgill.ca>
-Date: Wed, 7 Oct 2015 22:06:38 +0000
-Subject: [PATCH] Fix endian issues with label data.
-
----
- libsrc2/m2util.c | 83 ++++++++++++++++++++++++++++++++++++++++++++------------
- libsrc2/volume.c |  4 +--
- 2 files changed, 66 insertions(+), 21 deletions(-)
-
---- a/libsrc2/m2util.c
-+++ b/libsrc2/m2util.c
-@@ -1343,33 +1343,80 @@ void miinit ( void )
-                 mi2_dbl_to_int ),"H5Tregister")
- }
- 
--/** HDF5 type conversion function for converting an arbitrary integer type to
--* an arbitrary enumerated type.  The beauty part of this is that it is
--* not necessary to actually perform any real conversion!
--*/
--static herr_t mi2_null_conv ( hid_t src_id,
--                              hid_t dst_id,
--                              H5T_cdata_t *cdata,
--                              size_t nelements,
--                              size_t buf_stride,
--                              size_t bkg_stride,
--                              void *buf_ptr,
--                              void *bkg_ptr,
--                              hid_t dset_xfer_plist )
-+/** HDF5 type conversion function for converting among integer types.
-+ * This handles byte-swapping for enumerated types where needed.
-+ */
-+static herr_t mi2_int_to_int ( hid_t src_id,
-+			       hid_t dst_id,
-+			       H5T_cdata_t *cdata,
-+			       size_t nelements,
-+			       size_t buf_stride,
-+			       size_t bkg_stride,
-+			       void *buf_ptr,
-+			       void *bkg_ptr,
-+			       hid_t dset_xfer_plist )
- {
-+  unsigned char *dst_ptr;
-+  size_t dst_cnt;
-+  size_t dst_sz;
-+
-   switch ( cdata->command ) {
-   case H5T_CONV_INIT:
-     break;
-   case H5T_CONV_CONV:
-+    dst_ptr = ( unsigned char * ) buf_ptr;
-+    dst_sz = H5Tget_size( dst_id );
-+
-+    if (dst_sz != H5Tget_size( src_id )) {
-+      return -1;		/* Can't change size for now. */
-+    }
-+    if ( H5Tget_order ( dst_id ) == H5Tget_order ( src_id ) ) {
-+      return 0;			/* Nothing to do. */
-+    }
-+
-+    /* The logic of HDF5 seems to be that if a stride is specified,
-+    * both the source and destination pointers should advance by that
-+    * amount.  This seems wrong to me, but I've examined the HDF5 sources
-+    * and that's what their own type converters do.
-+    */
-+    if ( buf_stride == 0 ) {
-+      dst_cnt = dst_sz;
-+    } else {
-+      dst_cnt = buf_stride;
-+    }
-+
-+    switch ( dst_sz ) {
-+    case 8:
-+      while ( nelements-- > 0 ) {
-+	miswap8 ( dst_ptr );
-+	dst_ptr += dst_cnt;
-+      }
-+      break;
-+    case 4:
-+      while ( nelements-- > 0 ) {
-+	miswap4 ( dst_ptr );
-+	dst_ptr += dst_cnt;
-+      }
-+      break;
-+    case 2:
-+      while ( nelements-- > 0 ) {
-+	miswap2 ( dst_ptr );
-+	dst_ptr += dst_cnt;
-+      }
-+      break;
-+    case 1:
-+      break;
-+    default:
-+      return (-1);
-+    }
-     break;
-+
-   case H5T_CONV_FREE:
-     break;
- 
-   default:
--    /* Unknown command */
--    return ( -1 );
-+    return (-1);                /* Unknown command. */
-   }
--
-   return ( 0 );
- }
- 
-@@ -1380,9 +1427,9 @@ in order to facilitate conversions from
- void miinit_enum ( hid_t type_id )
- {
-   H5Tregister ( H5T_PERS_SOFT, "i2e", H5T_NATIVE_INT, type_id,
--                mi2_null_conv );
-+                mi2_int_to_int );
-   H5Tregister ( H5T_PERS_SOFT, "e2i", type_id, H5T_NATIVE_INT,
--                mi2_null_conv );
-+                mi2_int_to_int );
-   H5Tregister ( H5T_PERS_SOFT, "d2e", H5T_NATIVE_DOUBLE, type_id,
-                 mi2_dbl_to_int );
-   H5Tregister ( H5T_PERS_SOFT, "e2d", type_id, H5T_NATIVE_DOUBLE,
---- a/libsrc2/volume.c
-+++ b/libsrc2/volume.c
-@@ -1409,11 +1409,9 @@ int miopen_volume(const char *filename,
-     break;
- 
-   case H5T_ENUM:
--    handle->mtype_id = H5Tcopy(handle->ftype_id);
-+    handle->mtype_id = H5Tget_native_type(handle->ftype_id, H5T_DIR_ASCEND);
-     miinit_enum(handle->ftype_id);
-     miinit_enum(handle->mtype_id);
--    /* Set native order ---> is not allowed after order is set */
--    //H5Tset_order(handle->mtype_id, H5Tget_order(H5T_NATIVE_INT));
-     break;
- 
-   default: