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Allow for weak HDF5 array reading

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This commit is contained in:
Guilhem Lavaux 2016-02-23 17:34:53 +01:00
parent 0174cdc8d6
commit 43d77feafe
2 changed files with 52 additions and 7 deletions
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39
src/hdf5_array.hpp
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@ -283,6 +283,20 @@ namespace CosmoTool {
}
}
template<typename ArrayType>
void hdf5_weak_check_array(ArrayType& data, std::vector<hsize_t>& dims) {
for (long i = 0; i < data.num_dimensions(); i++) {
if (data.index_bases()[i] < 0) {
// Negative indexes are not supported right now.
throw InvalidDimensions();
}
if (data.index_bases()[i]+data.shape()[i] > dims[i]) {
throw InvalidDimensions();
}
}
}
template<typename ArrayType>
typename boost::disable_if<
array_has_resize<ArrayType>
@ -296,7 +310,7 @@ namespace CosmoTool {
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)
const hdf5_data_type& datatype, bool auto_resize = true, bool useBases = false)
{
H5::DataSet dataset = fg.openDataSet(data_set_name);
H5::DataSpace dataspace = dataset.getSpace();
@ -310,18 +324,31 @@ namespace CosmoTool {
dataspace.getSimpleExtentDims(dimensions.data());
if (auto_resize)
hdf5_resize_array(data, dimensions);
else
hdf5_check_array(data, dimensions);
else {
if (useBases) {
hdf5_weak_check_array(data, dimensions);
std::vector<hsize_t> memdims(data.shape(), data.shape() + data.num_dimensions());
H5::DataSpace memspace(memdims.size(), memdims.data());
std::vector<hsize_t> offsets(data.index_bases(), data.index_bases() + data.num_dimensions());
dataspace.selectHyperslab(H5S_SELECT_SET, memdims.data(), offsets.data());
dataset.read(data.data(), datatype, memspace, dataspace);
} else {
hdf5_check_array(data, dimensions);
}
}
dataset.read(data.data(), datatype);
}
template<typename ArrayType>
void hdf5_read_array(H5::CommonFG& fg, const std::string& data_set_name, ArrayType& data, bool auto_resize = true )
void hdf5_read_array(H5::CommonFG& fg, const std::string& data_set_name, ArrayType& data, bool auto_resize = true,
bool useBases = false )
{
typedef typename ArrayType::element T;
hdf5_read_array_typed(fg, data_set_name, data, get_hdf5_data_type<T>::type(), auto_resize);
hdf5_read_array_typed(fg, data_set_name, data, get_hdf5_data_type<T>::type(), auto_resize, useBases);
}