/usr/include/fast5/hdf5_tools.hpp is in libfast5-dev 0~20150918-1.
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#define __HDF5_TOOLS_HPP
#include <cassert>
#include <exception>
#include <functional>
#include <iostream>
#include <sstream>
#include <string>
#include <tuple>
#include <vector>
namespace hdf5
{
#include <hdf5.h>
}
namespace hdf5_tools
{
using namespace hdf5;
/// Exception class thrown by failed hdf5 operations.
class Exception
: public std::exception
{
public:
Exception(const std::string& msg) : _msg(msg) {}
const char* what() const noexcept { return _msg.c_str(); }
private:
std::string _msg;
}; // class Exception
// Forward declaration
class Compound_Map;
namespace detail
{
/// TempMetaFunc: Given destination type, deduce memory type to be used in hdf5 read operation.
/// Only useful for numeric types.
/// HDF5 idiosyncracy:
/// Types such as H5T_NATIVE_INT are not constants(!?), so id() is not a constexpr.
template < typename T > struct get_mem_type { static hid_t id() { return -1; } };
// signed integral:
template <> struct get_mem_type< char > { static hid_t id() { return H5T_NATIVE_CHAR; } };
template <> struct get_mem_type< short > { static hid_t id() { return H5T_NATIVE_SHORT; } };
template <> struct get_mem_type< int > { static hid_t id() { return H5T_NATIVE_INT; } };
template <> struct get_mem_type< long > { static hid_t id() { return H5T_NATIVE_LONG; } };
template <> struct get_mem_type< long long > { static hid_t id() { return H5T_NATIVE_LLONG; } };
// unsigned integral:
template <> struct get_mem_type< unsigned char > { static hid_t id() { return H5T_NATIVE_UCHAR; } };
template <> struct get_mem_type< unsigned short > { static hid_t id() { return H5T_NATIVE_USHORT; } };
template <> struct get_mem_type< unsigned > { static hid_t id() { return H5T_NATIVE_UINT; } };
template <> struct get_mem_type< unsigned long > { static hid_t id() { return H5T_NATIVE_ULONG; } };
template <> struct get_mem_type< unsigned long long > { static hid_t id() { return H5T_NATIVE_ULLONG; } };
// float:
template <> struct get_mem_type< float > { static hid_t id() { return H5T_NATIVE_FLOAT; } };
template <> struct get_mem_type< double > { static hid_t id() { return H5T_NATIVE_DOUBLE; } };
template <> struct get_mem_type< long double > { static hid_t id() { return H5T_NATIVE_LDOUBLE; } };
/// TempMetaFunc: Given destination type, can we read it
template < typename Out_Data_Type >
struct can_read
{
static const bool value =
std::is_integral< Out_Data_Type >::value
or std::is_floating_point< Out_Data_Type >::value
or std::is_same< typename std::remove_extent< Out_Data_Type >::type, char >::value
or std::is_same< Out_Data_Type, std::string >::value
or std::is_class< Out_Data_Type >:: value;
};
/// TempMetaFunc: Given a destination type, does it need a compound map
template < typename Out_Data_Type >
struct read_as_atomic
{
static const bool value =
std::is_integral< Out_Data_Type >::value
or std::is_floating_point< Out_Data_Type >::value
or std::is_same< typename std::remove_extent< Out_Data_Type >::type, char >::value
or std::is_same< Out_Data_Type, std::string >::value;
};
/// Compute offset of a struct member from a member pointer (runtime version).
template < typename T, typename U >
std::size_t offset_of(U T::* mem_ptr)
{
return reinterpret_cast< std::size_t >(&(((T*)0)->*mem_ptr));
}
/// Description of a member inside a compound
/// Only works with numeric, string, and struct types.
struct Compound_Member_Description
{
public:
Compound_Member_Description(const std::string& _name, size_t _offset, hid_t _numeric_type_id)
: name(_name), offset(_offset), numeric_type_id(_numeric_type_id)
{
type = numeric;
}
Compound_Member_Description(const std::string& _name, size_t _offset, size_t _char_array_size)
: name(_name), offset(_offset), char_array_size(_char_array_size)
{
type = char_array;
}
Compound_Member_Description(const std::string& _name, size_t _offset)
: name(_name), offset(_offset)
{
type = string;
}
Compound_Member_Description(const std::string& _name, size_t _offset, const Compound_Map* _compound_map_ptr)
: name(_name), offset(_offset), compound_map_ptr(_compound_map_ptr)
{
type = compound;
}
bool is_numeric() const { return type == numeric; }
bool is_char_array() const { return type == char_array; }
bool is_string() const { return type == string; }
bool is_compound() const { return type == compound; }
std::string name;
size_t offset;
union
{
hid_t numeric_type_id;
size_t char_array_size;
const Compound_Map* compound_map_ptr;
};
private:
enum member_type
{
numeric,
char_array,
string,
compound
};
member_type type;
}; // Compound_Member_Description
} // namespace detail
/// A map of struct fields to tags that is used to read compound datatypes
class Compound_Map
{
public:
Compound_Map() = default;
Compound_Map(const Compound_Map&) = delete;
Compound_Map(Compound_Map&&) = default;
Compound_Map& operator = (const Compound_Map&) = delete;
Compound_Map& operator = (Compound_Map&&) = default;
~Compound_Map() = default;
template < typename T, typename U >
void add_member(const std::string& name, U T::* mem_ptr)
{
static_assert(std::is_integral< U >::value
or std::is_floating_point< U >::value
or std::is_same< typename std::remove_extent< U >::type, char >::value
or std::is_same< U, std::string >::value,
"add_member(name, mem_ptr) overload expects numerical or string types only ");
if (std::is_integral< U >::value or std::is_floating_point< U >::value)
{
_members.emplace_back(name, detail::offset_of(mem_ptr), detail::get_mem_type< U >::id());
}
else if (std::is_same< typename std::remove_extent< U >::type, char >::value)
{
_members.emplace_back(name, detail::offset_of(mem_ptr), sizeof(U));
}
else if (std::is_same< U, std::string >::value)
{
_members.emplace_back(name, detail::offset_of(mem_ptr));
}
}
template < typename T, typename U >
void add_member(const std::string& name, U T::* mem_ptr, const Compound_Map* compound_map_ptr)
{
assert(false); // not currently implemented
static_assert(std::is_class< U >::value,
"add_member(name, mem_ptr, compound_map_ptr) overload expects class types only ");
_members.emplace_back(name, detail::offset_of(mem_ptr), compound_map_ptr);
}
const std::vector< detail::Compound_Member_Description >& members() const { return _members; }
private:
std::vector< detail::Compound_Member_Description > _members;
}; // Compound_Map
namespace detail
{
// TempSpec: reading numerics
template < typename Out_Data_Type, typename Out_Data_Storage >
struct Extent_Atomic_Reader
{
void operator () (const std::string& loc_full_name, Out_Data_Storage& dest,
const Compound_Map*, hid_t obj_id, hid_t,
const std::string&, std::function< hid_t(hid_t) >,
const std::string& read_fcn_name, std::function< herr_t(hid_t, hid_t, void*) > read_fcn)
{
hid_t mem_type_id = get_mem_type< Out_Data_Type >::id();
assert(mem_type_id != -1);
int status = read_fcn(obj_id, mem_type_id, static_cast< void* >(dest.data()));
if (status < 0) throw Exception(loc_full_name + ": error in " + read_fcn_name);
}
}; // struct Extent_Atomic_Reader
// TempSpec: for reading strings
template < typename Out_Data_Storage >
struct Extent_Atomic_Reader< std::string, Out_Data_Storage >
{
void operator () (const std::string& loc_full_name, Out_Data_Storage& dest,
const Compound_Map*, hid_t obj_id, hid_t obj_space_id,
const std::string& get_type_fcn_name, std::function< hid_t(hid_t) > get_type_fcn,
const std::string& read_fcn_name, std::function< herr_t(hid_t, hid_t, void*) > read_fcn)
{
int status;
int file_type_id = get_type_fcn(obj_id);
if (file_type_id < 0) throw Exception(loc_full_name + ": error in " + get_type_fcn_name);
int is_vlen_str = H5Tis_variable_str(file_type_id);
if (is_vlen_str < 0) throw Exception(loc_full_name + ": error in H5Tis_variable_str");
hid_t mem_type_id = H5Tcopy(H5T_C_S1);
if (mem_type_id < 0) throw Exception(loc_full_name + ": error in H5Tcopy");
if (is_vlen_str) // stored as variable-length string
{
// compute mem_type
status = H5Tset_size(mem_type_id, H5T_VARIABLE);
if (status < 0) throw Exception(loc_full_name + ": error in H5Tset_size(variable)");
// prepare buffer to receive data
std::vector< char* > char_p_buff(dest.size(), nullptr);
// perform the read
status = read_fcn(obj_id, mem_type_id, static_cast< void* >(char_p_buff.data()));
if (status < 0) throw Exception(loc_full_name + ": error in " + read_fcn_name);
// transfer strings to destination
for (size_t i = 0; i < dest.size(); ++i)
{
if (not char_p_buff[i]) throw Exception(loc_full_name + ": " + read_fcn_name + " did not fill buffer");
dest[i] = char_p_buff[i];
}
// reclaim memory allocated by libhdf5
status = H5Dvlen_reclaim(mem_type_id, obj_space_id, H5P_DEFAULT, char_p_buff.data());
if (status < 0) throw Exception(loc_full_name + ": error in H5Dvlen_reclaim");
}
else // stored as fixed-length string
{
// compute mem_type
size_t sz = H5Tget_size(file_type_id);
if (sz == 0) throw Exception(loc_full_name + ": H5Tget_size returned 0; is this an error?!");
status = H5Tset_size(mem_type_id, sz + 1);
if (status < 0) throw Exception(loc_full_name + ": error in H5Tset_size(fixed)");
// prepare buffer to receieve data
std::vector< char > char_buff(dest.size() * (sz + 1));
// perform the read
status = read_fcn(obj_id, mem_type_id, static_cast< void* >(char_buff.data()));
if (status < 0) throw Exception(loc_full_name + ": error in " + read_fcn_name);
// transfer strings to destination
for (size_t i = 0; i < dest.size(); ++i)
{
dest[i] = std::string(&char_buff[i * (sz + 1)], sz);
}
}
status = H5Tclose(mem_type_id);
if (status < 0) throw Exception(loc_full_name + ": error in H5Tclose(mem_type_id)");
status = H5Tclose(file_type_id);
if (status < 0) throw Exception(loc_full_name + ": error in H5Tclose(file_type_id)");
}
}; // struct Extent_Atomic_Reader< std::string >
template < typename Out_Data_Type, typename Out_Data_Storage >
struct Extent_Compound_Reader
{
void operator () (const std::string& loc_full_name, Out_Data_Storage& dest,
const Compound_Map* compound_map_ptr, hid_t obj_id, hid_t,
const std::string& get_type_fcn_name, std::function< hid_t(hid_t) > get_type_fcn,
const std::string& read_fcn_name, std::function< herr_t(hid_t, hid_t, void*) > read_fcn)
{
int status;
assert(compound_map_ptr);
hid_t file_type_id = get_type_fcn(obj_id);
if (file_type_id < 0) throw Exception(loc_full_name + ": error in " + get_type_fcn_name);
H5T_class_t file_type_class = H5Tget_class(file_type_id);
if (file_type_class == H5T_NO_CLASS) throw Exception(loc_full_name + ": error in H5Tget_class(file_type)");
if (file_type_class != H5T_COMPOUND) throw Exception(loc_full_name + ": expected H5T_COMPOUND datatype");
// pass 1
// read numeric and char_array members only
hid_t mem_type_id = H5Tcreate(H5T_COMPOUND, sizeof(Out_Data_Type));
std::vector< hid_t > mem_stype_id_v;
for (const auto& e : compound_map_ptr->members())
{
assert(not e.is_compound()); // not implemented yet
if (e.is_string()) continue;
int file_stype_idx = H5Tget_member_index(file_type_id, e.name.c_str());
if (file_stype_idx < 0) throw Exception(loc_full_name + ": missing member \"" + e.name + "\"");
hid_t file_stype_id = H5Tget_member_type(file_type_id, file_stype_idx);
if (file_stype_id < 0) throw Exception(loc_full_name + ": error in H5Tget_member_type");
H5T_class_t file_stype_class = H5Tget_class(file_stype_id);
if (file_stype_class == H5T_NO_CLASS) throw Exception(loc_full_name + ": error in H5Tget_class(file_stype)");
if (e.is_numeric())
{
if (file_stype_class != H5T_INTEGER and file_stype_class != H5T_FLOAT)
throw Exception(loc_full_name + ": member \"" + e.name + "\" is numeric, but file_stype is not numeric");
status = H5Tinsert(mem_type_id, e.name.c_str(), e.offset, e.numeric_type_id);
if (status < 0) throw Exception(loc_full_name + ": error in H5Tinsert(\"" + e.name + "\")");
}
if (e.is_char_array())
{
if (file_stype_class != H5T_STRING)
throw Exception(loc_full_name + ": member \"" + e.name + "\" is char_array, but file_stype is not H5T_STRING");
status = H5Tis_variable_str(file_stype_id);
if (status < 0) throw Exception(loc_full_name + ": error in H5Tis_variable_str(\"" + e.name + "\")");
if (status) throw Exception(loc_full_name + ": member \"" + e.name + "\" is a char_array, but file_stype is a variable len string");
//size_t file_stype_size = H5Tget_size(file_stype_id);
//if (file_stype_size == 0) throw Exception(loc_full_name + ": H5Tget_size(\"" + e.name + "\") returned 0");
hid_t mem_stype_id = H5Tcopy(H5T_C_S1);
if (mem_stype_id < 0) throw Exception(loc_full_name + ": member \"" + e.name + "\": error in H5Tcopy");
status = H5Tset_size(mem_stype_id, e.char_array_size);
if (status < 0) throw Exception(loc_full_name + ": error in H5Tset_size(\"" + e.name + "\")");
status = H5Tinsert(mem_type_id, e.name.c_str(), e.offset, mem_stype_id);
if (status < 0) throw Exception(loc_full_name + ": error in H5Tinsert(\"" + e.name + "\")");
mem_stype_id_v.push_back(mem_stype_id);
}
status = H5Tclose(file_stype_id);
if (status < 0) throw Exception(loc_full_name + ": member \"" + e.name + "\": error in H5Tclose(file_stype)");
}
// perform the actual read
status = read_fcn(obj_id, mem_type_id, static_cast< void* >(dest.data()));
if (status < 0) throw Exception(loc_full_name + ": pass 1: error in " + read_fcn_name);
// release the memory types
for (const auto& mem_stype_id : mem_stype_id_v)
{
status = H5Tclose(mem_stype_id);
if (status < 0) throw Exception(loc_full_name + ": error in H5Tclose(mem_stype)");
}
mem_stype_id_v.clear();
status = H5Tclose(mem_type_id);
if (status < 0) throw Exception(loc_full_name + ": error in H5Tclose(mem_type)");
// pass 2
// read strings
for (const auto& e : compound_map_ptr->members())
{
assert(not e.is_compound()); // not implemented yet
if (e.is_numeric() or e.is_char_array()) continue;
//TODO
assert(false);
}
status = H5Tclose(file_type_id);
if (status < 0) throw Exception(loc_full_name + ": error in H5Tclose(file_type_id)");
}
}; //struct Extent_Compound_Reader
// TempSpec: read extent of atomic types
template < typename Out_Data_Type, typename Out_Data_Storage, bool = true >
struct Extent_Reader_as_atomic
: Extent_Atomic_Reader< Out_Data_Type, Out_Data_Storage >
{};
// TempSpec: read extent of compound types
template < typename Out_Data_Type, typename Out_Data_Storage >
struct Extent_Reader_as_atomic< Out_Data_Type, Out_Data_Storage, false >
: Extent_Compound_Reader< Out_Data_Type, Out_Data_Storage >
{};
// branch on atomic/compound destination
template < typename Out_Data_Type, typename Out_Data_Storage >
struct Extent_Reader
: public Extent_Reader_as_atomic< Out_Data_Type, Out_Data_Storage, read_as_atomic< Out_Data_Type >::value >
{};
template < typename, typename, bool >
struct Object_Reader_impl;
// TempSpec: reading scalars
template < typename Out_Data_Type >
struct Object_Reader_impl< Out_Data_Type, Out_Data_Type, true >
{
void operator () (const std::string& loc_full_name, Out_Data_Type& dest,
const Compound_Map* compound_map_ptr, hid_t obj_id, hid_t obj_space_id,
const std::string& get_type_fcn_name, std::function< hid_t(hid_t) > get_type_fcn,
const std::string& read_fcn_name, std::function< herr_t(hid_t, hid_t, void*) > read_fcn)
{
H5S_class_t obj_class_t = H5Sget_simple_extent_type(obj_space_id);
if (obj_class_t == H5S_NO_CLASS) throw Exception(loc_full_name + ": error in H5Sget_simple_extent_type");
if (obj_class_t != H5S_SCALAR)
throw Exception(loc_full_name + ": reading as scalar, but dataspace not H5S_SCALAR");
std::vector< Out_Data_Type > tmp(1);
Extent_Reader< Out_Data_Type, std::vector< Out_Data_Type > >()(
loc_full_name, tmp, compound_map_ptr, obj_id, obj_space_id,
get_type_fcn_name, get_type_fcn,
read_fcn_name, read_fcn);
dest = std::move(tmp[0]);
}
};
// TempSpec: reading vectors
template < typename Out_Data_Type, typename Out_Data_Storage >
struct Object_Reader_impl< Out_Data_Type, Out_Data_Storage, false >
{
void operator () (const std::string& loc_full_name, Out_Data_Storage& dest,
const Compound_Map* compound_map_ptr, hid_t obj_id, hid_t obj_space_id,
const std::string& get_type_fcn_name, std::function< hid_t(hid_t) > get_type_fcn,
const std::string& read_fcn_name, std::function< herr_t(hid_t, hid_t, void*) > read_fcn)
{
H5S_class_t obj_class_t = H5Sget_simple_extent_type(obj_space_id);
if (obj_class_t == H5S_NO_CLASS) throw Exception(loc_full_name + ": error in H5Sget_simple_extent_type");
if (obj_class_t != H5S_SIMPLE)
throw Exception(loc_full_name + ": reading as vector, but dataspace not H5S_SIMPLE");
int status = H5Sget_simple_extent_dims(obj_space_id, nullptr, nullptr);
if (status < 0) throw Exception(loc_full_name + ": error in H5Sget_simple_extent_dims");
if (status != 1) throw Exception(loc_full_name + ": expected extent of dimension 1");
hsize_t sz;
H5Sget_simple_extent_dims(obj_space_id, &sz, nullptr);
dest.clear();
dest.resize(sz);
Extent_Reader< Out_Data_Type, Out_Data_Storage >()(
loc_full_name, dest, compound_map_ptr, obj_id, obj_space_id,
get_type_fcn_name, get_type_fcn,
read_fcn_name, read_fcn);
}
};
// TempMetaFunc: split scalar & vector reading branches
template < typename Out_Data_Type, typename Out_Data_Storage >
struct Object_Reader
: public Object_Reader_impl< Out_Data_Type, Out_Data_Storage, std::is_same< Out_Data_Type, Out_Data_Storage >::value > {};
// open object and object space, then delegate
template < typename Out_Data_Type, typename Out_Data_Storage >
void read_obj_helper(const std::string& loc_full_name, Out_Data_Storage& dest, const Compound_Map* compound_map_ptr,
const std::string& open_fcn_name, std::function< hid_t(void) > open_fcn,
const std::string& close_fcn_name, std::function< herr_t(hid_t) > close_fcn,
const std::string& get_space_fcn_name, std::function< hid_t(hid_t) > get_space_fcn,
const std::string& get_type_fcn_name, std::function< hid_t(hid_t) > get_type_fcn,
const std::string& read_fcn_name, std::function< herr_t(hid_t, hid_t, void*) > read_fcn)
{
int status;
// open object
hid_t obj_id = open_fcn();
if (obj_id < 0) throw Exception(loc_full_name + ": error in " + open_fcn_name);
// open object space, check reading ode matches storage mode (scalar/vector)
hid_t obj_space_id = get_space_fcn(obj_id);
if (obj_space_id < 0) throw Exception(loc_full_name + ": error in " + get_space_fcn_name);
// read object
Object_Reader< Out_Data_Type, Out_Data_Storage >()(
loc_full_name, dest, compound_map_ptr, obj_id, obj_space_id,
get_type_fcn_name, get_type_fcn,
read_fcn_name, read_fcn);
// close object space & object
status = H5Sclose(obj_space_id);
if (status < 0) throw Exception(loc_full_name + ": error in H5Sclose");
status = close_fcn(obj_id);
if (status < 0) throw Exception(loc_full_name + ": error in " + close_fcn_name);
}
// determine if address is attribute or dataset, then delegate
template < typename Out_Data_Type, typename Out_Data_Storage >
void read_addr(hid_t root_id, const std::string& loc_path, const std::string& loc_name,
Out_Data_Storage& dest, const Compound_Map* compound_map_ptr)
{
assert(root_id > 0);
std::string loc_full_name = loc_path + loc_name;
// determine if object is an attribute; otherwise, assume it's a dataset
int status;
status = H5Aexists_by_name(root_id, loc_path.c_str(), loc_name.c_str(), H5P_DEFAULT);
if (status < 0) throw Exception(loc_full_name + ": error in H5Aexists_by_name");
bool is_attr = status > 0;
if (is_attr)
{
read_obj_helper< Out_Data_Type, Out_Data_Storage >(
loc_full_name, dest, compound_map_ptr,
"H5Aopen_by_name",
[&root_id, &loc_path, &loc_name] ()
{
return H5Aopen_by_name(root_id, loc_path.c_str(), loc_name.c_str(), H5P_DEFAULT, H5P_DEFAULT);
},
"H5Aclose", &H5Aclose,
"H5Aget_space", &H5Aget_space,
"H5Aget_type", &H5Aget_type,
"H5Aread",
[] (hid_t id, hid_t mem_type_id, void* dest_p)
{
return H5Aread(id, mem_type_id, dest_p);
});
}
else
{
read_obj_helper< Out_Data_Type, Out_Data_Storage >(
loc_full_name, dest, compound_map_ptr,
"H5Dopen",
[&root_id, &loc_full_name] ()
{
return H5Dopen(root_id, loc_full_name.c_str(), H5P_DEFAULT);
},
"H5Dclose", &H5Dclose,
"H5Dget_space", &H5Dget_space,
"H5Dget_type", &H5Dget_type,
"H5Dread",
[] (hid_t id, hid_t mem_type_id, void* dest_p)
{
return H5Dread(id, mem_type_id, H5S_ALL, H5S_ALL, H5P_DEFAULT, dest_p);
});
}
} // read_addr
// TempSpec: for atomic types
template < typename Out_Data_Type, bool = true >
struct Reader_as_atomic
{
template < typename Out_Data_Storage >
void operator () (hid_t root_id, const std::string& loc_path, const std::string& loc_name,
Out_Data_Storage& dest)
{
static_assert(can_read< Out_Data_Type >::value,
"Reader_impl<Out_Data_Type,true>: expected a readable destination");
static_assert(read_as_atomic< Out_Data_Type >::value,
"Reader_impl<Out_Data_Type,true>: expected a type readable as atomic");
read_addr< Out_Data_Type, Out_Data_Storage >(root_id, loc_path, loc_name, dest, nullptr);
}
};
// TempSpec: for compound types
template < typename Out_Data_Type >
struct Reader_as_atomic< Out_Data_Type, false >
{
template < typename Out_Data_Storage >
void operator () (hid_t root_id, const std::string& loc_path, const std::string& loc_name,
Out_Data_Storage& dest, const Compound_Map* compound_map_ptr)
{
static_assert(can_read< Out_Data_Type >::value,
"Reader_impl<Out_Data_Type,false>: expected a readable destination");
static_assert(not read_as_atomic< Out_Data_Type >::value,
"Reader_impl<Out_Data_Type,false>: expected a type readable as compound");
read_addr< Out_Data_Type, Out_Data_Storage >(root_id, loc_path, loc_name, dest, compound_map_ptr);
}
};
template < typename Out_Data_Type >
struct Reader : public Reader_as_atomic< Out_Data_Type, read_as_atomic< Out_Data_Type >::value >
{};
} // namespace detail
/// An HDF5 file reader
class File_Reader
{
public:
File_Reader() : _file_id(0) {}
File_Reader(const std::string& file_name) : _file_id(0) { open(file_name); }
File_Reader(const File_Reader&) = delete;
File_Reader& operator = (const File_Reader&) = delete;
~File_Reader() { if (is_open()) close(); }
bool is_open() const { return _file_id > 0; }
const std::string& file_name() const { return _file_name; }
void open(const std::string& file_name)
{
assert(not is_open());
_file_name = file_name;
_file_id = H5Fopen(file_name.c_str(), H5F_ACC_RDONLY, H5P_DEFAULT);
if (not is_open()) throw Exception(_file_name + ": error in H5Fopen");
}
void close()
{
assert(is_open());
assert(H5Fget_obj_count(_file_id, H5F_OBJ_ALL | H5F_OBJ_LOCAL) == 1);
int status = H5Fclose(_file_id);
if (status < 0) throw Exception(_file_name + ": error in H5Fclose");
_file_id = 0;
_file_name.clear();
}
/// Determine if address is an attribute or dataset
bool exists(const std::string& loc_full_name) const
{
assert(is_open());
assert(not loc_full_name.empty() and loc_full_name[0] == '/');
std::string loc_path;
std::string loc_name;
std::tie(loc_path, loc_name) = split_full_name(loc_full_name);
int status;
// check all path elements exist, except for what is to the right of the last '/'
size_t pos = 0;
while (true)
{
++pos;
pos = loc_full_name.find('/', pos);
if (pos == std::string::npos) break;
std::string tmp = loc_full_name.substr(0, pos);
status = H5Lexists(_file_id, tmp.c_str(), H5P_DEFAULT);
if (status < 0) throw Exception(loc_full_name + ": error in H5Lexists");
if (not status) return false;
status = H5Oexists_by_name(_file_id, tmp.c_str(), H5P_DEFAULT);
if (status < 0) throw Exception(loc_full_name + ": error in H5Oexists_by_name");
if (not status) return false;
}
status = H5Aexists_by_name(_file_id, loc_path.c_str(), loc_name.c_str(), H5P_DEFAULT);
if (status < 0) throw Exception(loc_full_name + ": error in H5Aexists_by_name");
if (status) return true;
// not an attribute: try to open as a dataset
hid_t ds_id = H5Dopen(_file_id, loc_full_name.c_str(), H5P_DEFAULT);
if (ds_id < 0) return false;
status = H5Dclose(ds_id);
if (status < 0) throw Exception(loc_full_name + ": error in H5Dclose");
return true;
}
/// Read attribute or dataset at address
template < typename Out_Data_Type, typename ...Args >
void read(const std::string& loc_full_name, Args&& ...args) const
{
assert(is_open());
assert(not loc_full_name.empty() and loc_full_name[0] == '/');
std::string loc_path;
std::string loc_name;
std::tie(loc_path, loc_name) = split_full_name(loc_full_name);
detail::Reader< Out_Data_Type >()(_file_id, loc_path, loc_name, std::forward< Args >(args)...);
}
private:
std::string _file_name;
hid_t _file_id;
/// Split a full name into path and name
static std::pair< std::string, std::string > split_full_name(const std::string& full_name)
{
auto last_slash_pos = full_name.find_last_of('/');
std::string path = last_slash_pos != std::string::npos? full_name.substr(0, last_slash_pos + 1) : std::string();
std::string name = last_slash_pos != std::string::npos? full_name.substr(last_slash_pos + 1) : full_name;
return std::make_pair(path, name);
} // split_full_name
}; // class File_Reader
} // namespace hdf5_tools
#endif
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