[ismrmrd] 113/177: merge from development

[Ghislain Vaillant]

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ghisvail-guest pushed a commit to annotated tag v1.1.0.beta.1
in repository ismrmrd.

commit 44cd3323b22110f43f65fe03be8a09092a7bc99d
Merge: 8c4590b 141ea78
Author: Hui Xue <hui.xue at nih.gov>
Date:   Mon Sep 29 13:17:50 2014 -0400

    merge from development

 CMakeLists.txt                               |  35 +-
 bindings/CMakeLists.txt                      |   7 -
 bindings/java/CMakeLists.txt                 |  46 --
 bindings/java/JNILibLoader.java              |  34 --
 bindings/java/XMLString.java                 |  42 --
 bindings/java/cfg.jxb                        |  10 -
 bindings/java/ismrmrd_java.i                 | 780 ---------------------------
 bindings/java/make_jar.sh.in                 |  10 -
 cmake/FindPugiXML.cmake                      |  27 +
 examples/java/ismrmrd_test.java              |  55 --
 include/ismrmrd/dataset.h                    |   2 +-
 include/ismrmrd/ismrmrd.h                    |  18 +-
 libsrc/dataset.c                             | 152 ++----
 libsrc/ismrmrd.c                             | 266 +++++----
 utilities/CMakeLists.txt                     |  16 +
 utilities/generate_cartesian_shepp_logan.cpp |  18 +-
 utilities/recon_cartesian_2d.cpp             | 150 ++++++
 utilities/test_recon_dataset.cpp             | 159 ------
 18 files changed, 451 insertions(+), 1376 deletions(-)

diff --cc CMakeLists.txt
index 8874909,2461dc8..0f19d7e
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@@ -1,17 -1,11 +1,20 @@@
  cmake_minimum_required(VERSION 2.8)
  project(ISMRMRD)
  
 +# set project specific cmake module path
 +set (ISMRMRD_CMAKE_DIR ${PROJECT_SOURCE_DIR}/cmake CACHE PATH
 +  "Location of CMake scripts")
 +
+ # command line options
+ option(USE_SYSTEM_PUGIXML "Use pugixml installed on the system" OFF)
+ 
 -# add project specific cmake find modules
 -list(APPEND CMAKE_MODULE_PATH ${CMAKE_SOURCE_DIR}/cmake)
 +# and include it to the search list
 +list(APPEND CMAKE_MODULE_PATH ${ISMRMRD_CMAKE_DIR})
 +
 +# whether to install dependencies
 +if (WIN32)
 +    OPTION(ISMRMRD_INSTALL_DEPENDENCIES "Install ismrmrd dependencies in windows" Off)
 +endif (WIN32)
  
  # set the build type to Release if not specified
  IF(NOT CMAKE_BUILD_TYPE)
@@@ -93,23 -87,8 +96,23 @@@ set(ISMRMRD_SOVERSION ${ISMRMRD_VERSION
  # required packages for main library
  find_package(HDF5 1.8 COMPONENTS C REQUIRED)
  
 +# in windows, install the HDF5 dependencies
 +if (WIN32)
 +    if (ISMRMRD_INSTALL_DEPENDENCIES)
 +        if ( HDF5_FOUND )
 +            if(DEFINED ENV{HDF5_ROOT})
 +                set(HDF5_BIN_DIR $ENV{HDF5_ROOT}/bin)
 +            else (DEFINED ENV{HDF5_ROOT})
 +                set(HDF5_BIN_DIR ${HDF5_C_INCLUDE_DIR}/../bin)
 +            endif (DEFINED ENV{HDF5_ROOT})
 +            message("Install hdf5 libraries from ${HDF5_BIN_DIR} ")
 +            install( DIRECTORY ${HDF5_BIN_DIR} DESTINATION bin/.. FILES_MATCHING PATTERN "*.dll" )
 +        endif (HDF5_FOUND)
 +    endif (ISMRMRD_INSTALL_DEPENDENCIES)
 +endif (WIN32)
 +
  # include directories for main library
- include_directories(
+ set(ISMRMRD_TARGET_INCLUDE_DIRS
    include
    ${HDF5_C_INCLUDE_DIR}
  )

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