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Merge branch 'master' of bitbucket.org:glavaux/cosmotool

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This commit is contained in:
Guilhem Lavaux 2015-04-08 21:02:28 +02:00
commit 5e7437b7d4
4 changed files with 82 additions and 51 deletions
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20
src/CMakeLists.txt
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@ -15,13 +15,15 @@ SET(CosmoTool_SRCS
IF (ENABLE_OPENMP)
ENDIF (ENABLE_OPENMP)
IF(FOUND_NETCDF3)
IF (YORICK_SUPPORT)
IF(FOUND_NETCDF3)
SET(CosmoTool_SRCS ${CosmoTool_SRCS} yorick_nc3.cpp)
ELSE(FOUND_NETCDF3)
IF(FOUND_NETCDF4)
ELSE(FOUND_NETCDF3)
IF(FOUND_NETCDF4)
SET(CosmoTool_SRCS ${CosmoTool_SRCS} yorick_nc4.cpp)
ENDIF(FOUND_NETCDF4)
ENDIF(FOUND_NETCDF3)
ENDIF(FOUND_NETCDF4)
ENDIF(FOUND_NETCDF3)
ENDIF(YORICK_SUPPORT)
if (HDF5_FOUND)
@ -59,9 +61,13 @@ SET(CosmoTool_SRCS ${CosmoTool_SRCS}
growthFactor.hpp
)
include_directories(${GSL_INCLUDE_PATH} ${NETCDF_INCLUDE_PATH} ${NETCDFCPP_INCLUDE_PATH} ${CMAKE_BINARY_DIR}/src)
include_directories(${Boost_INCLUDE_DIRS} ${GSL_INCLUDE_PATH} ${CMAKE_BINARY_DIR}/src)
set(CosmoTool_LIBS ${NETCDFCPP_LIBRARY} ${NETCDF_LIBRARY} ${GSL_LIBRARIES})
set(CosmoTool_LIBS ${GSL_LIBRARIES})
if(YORICK_SUPPORT)
set(CosmoTool_LIBS ${CosmoTool_LIBS} ${NETCDFCPP_LIBRARY} ${NETCDF_LIBRARY} ${GSL_LIBRARIES})
include_directories(${NETCDF_INCLUDE_PATH} ${NETCDFCPP_INCLUDE_PATH})
endif(YORICK_SUPPORT)
if (HDF5_FOUND)
set(CosmoTool_LIBS ${CosmoTool_LIBS} ${HDF5_CXX_LIBRARIES} ${HDF5_LIBRARIES})
include_directories(${HDF5_INCLUDE_DIRS})

51
src/hdf5_array.hpp
View file

@ -90,10 +90,31 @@ namespace CosmoTool {
#undef HDF5_TYPE
// Extent generator
template<std::size_t r>
struct hdf5_extent_gen {
typedef typename boost::detail::multi_array::extent_gen<r> type;
static inline type build(hsize_t *d)
{
return (hdf5_extent_gen<r-1>::build(d))[d[r-1]];
}
};
template<>
struct hdf5_extent_gen<0> {
static inline boost::multi_array_types::extent_gen build(hsize_t *d)
{
return boost::extents;
}
};
//!_______________________________________________________________________________________
//!
//! write_hdf5 multi_array
//!
//! \author Guilhem Lavaux (2014-2015)
//! \author leo Goodstadt (04 March 2013)
//!
//!_______________________________________________________________________________________
@ -216,24 +237,11 @@ namespace CosmoTool {
class InvalidDimensions: virtual std::exception {
};
template<std::size_t r>
struct hdf5_extent_gen {
typedef typename boost::detail::multi_array::extent_gen<r> type;
static inline type build(hsize_t *d)
{
return (hdf5_extent_gen<r-1>::build(d))[d[r-1]];
}
};
template<>
struct hdf5_extent_gen<0> {
static inline boost::multi_array_types::extent_gen build(hsize_t *d)
{
return boost::extents;
}
};
// ----------------------------------------------------------------------
// Conditional resize support
// If the Array type support resize then it is called. Otherwise
// the dimensions are checked and lead to a failure if they are different
template<typename Array> class array_has_resize {
struct Fallback { int resize; };
@ -282,11 +290,13 @@ namespace CosmoTool {
hdf5_resize_array(ArrayType& data, std::vector<hsize_t>& dims) {
hdf5_check_array(data, dims);
}
// ----------------------------------------------------------------------
template<typename ArrayType, typename hdf5_data_type>
void hdf5_read_array_typed(H5::CommonFG& fg, const std::string& data_set_name,
ArrayType& data,
const hdf5_data_type& datatype, bool auto_resize = true)
ArrayType& data,
const hdf5_data_type& datatype, bool auto_resize = true)
{
H5::DataSet dataset = fg.openDataSet(data_set_name);
H5::DataSpace dataspace = dataset.getSpace();
@ -311,8 +321,7 @@ namespace CosmoTool {
{
typedef typename ArrayType::element T;
get_hdf5_data_type<T> hdf_data_type;
hdf5_read_array_typed(fg, data_set_name, data, hdf_data_type.type(), auto_resize);
hdf5_read_array_typed(fg, data_set_name, data, get_hdf5_data_type<T>::type(), auto_resize);
}