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b2637802be
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e3ad04e56c
6 changed files with 144 additions and 30 deletions
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@ -22,26 +22,25 @@ namespace CNORXZ
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Table(name, _parent)
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{
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constexpr SizeT N = sizeof...(Ts);
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if(mFields == nullptr){
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if(mFields != nullptr){
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CXZ_ASSERT(mFields->size() == N, "expected tuple of size = " << mFields->size()
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<< ", got: " << N);
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Tuple<Ts...> x;
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iter<0,N>( [&](auto i) { CXZ_ASSERT
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( getTupleOffset(x, i) == mOffsets.data()[i],
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"wrong offset for field " << i << ": " << getTupleOffset(x, i)
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<< " vs " << mOffsets.data()[i] ); }, NoF{} );
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iter<0,N>( [&](auto i) { CXZ_ASSERT
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( sizeof(std::get<i>(x)) == mSizes.data()[i],
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"wrong size for field " << i << ": " << sizeof(std::get<i>(x))
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( sizeof(tget<i>(x)) == mSizes.data()[i],
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"wrong size for field " << i << ": " << sizeof(tget<i>(x))
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<< " vs " << mSizes.data()[i] ); }, NoF{} );
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iter<0,N>( [&](auto i) { CXZ_ASSERT
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( getTypeId(std::get<i>(x)) == mTypes.data()[i],
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"wrong type for field " << i << ": " << getTypeId(std::get<i>(x))
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( H5Tget_class(getTypeId(tget<i>(x))) == mTypes.data()[i],
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"wrong type for field " << i
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<< ": " << H5Tget_class(getTypeId(tget<i>(x)))
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<< " vs " << mTypes.data()[i] ); }, NoF{} );
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}
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else {
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CXZ_ASSERT(mFields->size() == N, "expected tuple of size = " << mFields->size()
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<< ", got: " << N);
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}
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}
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template <typename... Ts>
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@ -73,11 +72,11 @@ namespace CNORXZ
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[](const auto&... e) { return Vector<SizeT>({e...}); }) );
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mSizes = MArray<SizeT>
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( mFields, iter<0,N>
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( [&](auto i) { return sizeof(std::get<i>(x)); },
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( [&](auto i) { return sizeof(tget<i>(x)); },
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[](const auto&... e) { return Vector<SizeT>({e...}); }) );
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mTypes = MArray<hid_t>
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( mFields, iter<0,N>
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( [&](auto i) { return getTypeId(std::get<i>(x)); },
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( [&](auto i) { return getTypeId(tget<i>(x)); },
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[](const auto&... e) { return Vector<hid_t>({e...}); }) );
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return *this;
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}
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@ -96,10 +95,12 @@ namespace CNORXZ
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}
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template <typename... Ts>
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MArray<Tuple<Ts...>> STable<Ts...>::read()
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MArray<Tuple<Ts...>> STable<Ts...>::read() const
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{
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CXZ_ASSERT(isOpen(), "attempt to read table that has not been opened");
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MArray<Tuple<Ts...>> out(mRecords);
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//...!!!
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H5TBread_table(mParent->id(), mName.c_str(), mTypesize, mOffsets.data(),
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mSizes.data(), out.data());
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return out;
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}
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}
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@ -29,6 +29,8 @@ namespace CNORXZ
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Table& initTable(SizeT n, const void* data, SizeT dsize, SizeT chunk_size);
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Table& appendRecord(SizeT n, const void* data, SizeT dsize);
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Table& readRecord(SizeT pos, SizeT n, char* data);
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MArray<DType> read() const;
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const RangePtr& fields() const;
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const RangePtr& records() const;
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@ -39,8 +41,11 @@ namespace CNORXZ
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MArray<SizeT> mOffsets;
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MArray<hid_t> mTypes;
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hid_t mType = 0;
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SizeT mTypesize = 0;
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};
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// caution: the memory ordering is the only thing that counts;
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// std::tuple has REVERSE ordering!
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template <typename... Ts>
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class STable : public Table
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{
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@ -51,11 +56,11 @@ namespace CNORXZ
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const Arr<String,sizeof...(Ts)>& fnames);
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STable& initFields(const Arr<String,sizeof...(Ts)>& fnames);
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STable& appendRecord(const Tuple<Ts...>& t);
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STable& appendRecord(const MArray<Tuple<Ts...>>& t);
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MArray<Tuple<Ts...>> read();
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MArray<Tuple<Ts...>> read() const;
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template <class F>
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decltype(auto) iterRecords(F&& f) const;
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@ -8,11 +8,31 @@ namespace CNORXZ
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{
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namespace hdf5
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{
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template <typename... Ts>
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decltype(auto) reverseTuple(const Tuple<Ts...>& t)
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{
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return iter<0,sizeof...(Ts)>
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( [&](auto i) { return tget<i>(t); },
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[](const auto&... e) { return std::make_tuple(e...); } );
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}
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template <SizeT I, typename... Ts>
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constexpr const auto& tget(const Tuple<Ts...>& t)
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{
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return std::get<sizeof...(Ts)-I-1>(t);
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}
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template <SizeT I, typename... Ts>
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constexpr auto& tget(Tuple<Ts...>& t)
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{
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return std::get<sizeof...(Ts)-I-1>(t);
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}
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template <SizeT N, typename... Ts>
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SizeT getTupleOffset(const Tuple<Ts...>& t, CSizeT<N> i)
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{
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const PtrId beg = reinterpret_cast<PtrId>(&t);
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const PtrId pos = reinterpret_cast<PtrId>(&std::get<i>(t));
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const PtrId pos = reinterpret_cast<PtrId>(&tget<i>(t));
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return pos - beg;
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}
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@ -2,10 +2,23 @@
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#ifndef __cxz_h5_type_id_h__
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#define __cxz_h5_type_id_h__
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#include "base/types.h"
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namespace CNORXZ
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{
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namespace hdf5
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{
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template <typename... Ts>
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decltype(auto) reverseTuple(const Tuple<Ts...>& t);
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template <typename... Ts>
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using RTuple = typename std::remove_reference<decltype(reverseTuple(Tuple<Ts...>()))>::type;
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template <SizeT I, typename... Ts>
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constexpr const auto& tget(const Tuple<Ts...>& t);
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template <SizeT I, typename... Ts>
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constexpr auto& tget(Tuple<Ts...>& t);
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template <SizeT N, typename... Ts>
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SizeT getTupleOffset(const Tuple<Ts...>& t, CSizeT<N> i);
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@ -21,9 +21,8 @@ namespace CNORXZ
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}
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Vector<SizeT> offsets(nfields);
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Vector<SizeT> sizes(nfields);
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SizeT typesize = 0;
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H5TBget_field_info(mParent->id(), mName.c_str(), fieldsptr.data(), sizes.data(),
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offsets.data(), &typesize);
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offsets.data(), &mTypesize);
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Vector<FieldID> fields(nfields);
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for(SizeT i = 0; i != nfields; ++i){
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fields[i].first = i;
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@ -132,6 +131,59 @@ namespace CNORXZ
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CXZ_ERROR("not implemented!!!");
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return *this;
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}
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MArray<DType> Table::read() const
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{
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Vector<char> buf(mTypesize*mRecords->size());
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H5TBread_table(mParent->id(), mName.c_str(), mTypesize, mOffsets.data(),
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mSizes.data(), buf.data());
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const hid_t dset_id = H5Dopen(mParent->id(), mName.c_str(), H5P_DEFAULT);
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const hid_t type_id = H5Dget_type(dset_id);
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MArray<DType> out(mRecords*mFields);
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CIndex fi(mFields);
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CIndex ri(mRecords);
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const char* b = nullptr;
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for(fi = 0; fi.lex() != mFields->size(); ++fi){
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const SizeT off = mOffsets[fi];
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const hid_t tp = H5Tget_member_type( type_id, fi.lex() );
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const hid_t tc = H5Tget_class(tp);
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const size_t ts = H5Tget_size(tp);
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//const bool sig = H5Tget_sign(tp);
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DType x;
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switch(tc){
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case H5T_INTEGER: {
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if(ts == 4){
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for(ri = 0, b = buf.data(); ri.lex() != mRecords->size(); ++ri, b += mTypesize){
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const Int xi = *reinterpret_cast<const Int*>(b+off);
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out[ri*fi] = DType(xi);
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}
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break;
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}
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else if(ts == 8){
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for(ri = 0, b = buf.data(); ri.lex() != mRecords->size(); ++ri, b += mTypesize){
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const LInt xi = *reinterpret_cast<const LInt*>(b+off);
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out[ri*fi] = DType(xi);
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}
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break;
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}
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}
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case H5T_FLOAT: {
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if(ts == 8){
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for(ri = 0, b = buf.data(); ri.lex() != mRecords->size(); ++ri, b += mTypesize){
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const Double xi = *reinterpret_cast<const Double*>(b+off);
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out[ri*fi] = DType(xi);
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}
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break;
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}
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}
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default:
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CXZ_ERROR("type " << tp << " not supported");
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}
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}
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H5Tclose(type_id);
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H5Dclose(dset_id);
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return out;
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}
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const RangePtr& Table::fields() const
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{
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@ -39,24 +39,32 @@ namespace
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Group_Test()
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{
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mFileName = testh5file;
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//mGrps = { "gr1", "gr2", "foo", "bar", "moregroups" };
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mFs = {"field1","second","real"};
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Vector<Tuple<SizeT,Int,Double>> v
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( { {0, -6, 3.141},
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{3, -8, 0.789},
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{34, 4, 10.009},
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{2, -777, -9.77},
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{321, 0, -0.003}
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// Tuple has reverse (!) memory ordering:
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Vector<Tuple<Double,Int,SizeT>> v
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( { { 3.141, -6, 0 },
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{ 0.789, -8, 3 },
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{ 10.009, 4, 34 },
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{ -9.77, -777, 2 },
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{ -0.003, 0, 321 }
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} );
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RangePtr rs = CRangeFactory(v.size()).create();
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mTabA = MArray<Tuple<SizeT,Int,Double>>(rs, std::move(v));
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RangePtr fs = CRangeFactory(mFs.size()).create();
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mTabA = MArray<Tuple<Double,Int,SizeT>>(rs, std::move(v));
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mTabD = MArray<DType>(rs*fs);
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CIndex i(rs);
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CIndex j(fs);
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for(i = 0; i.lex() != rs->size(); ++i){
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iter<0,3>( [&](auto jj)
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{ j = jj; mTabD[i*j] = DType(tget<jj>(v[i.lex()])); }, NoF{} );
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}
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}
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String mFileName;
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//Vector<String> mGrps;
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Arr<String,3> mFs;
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MArray<Tuple<SizeT,Int,Double>> mTabA;
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MArray<Tuple<Double,Int,SizeT>> mTabA;
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MArray<DType> mTabD;
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};
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TEST_F(Group_Test, ReadTable)
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{
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typedef Tuple<SizeT,Int,Double> RecType;
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typedef Tuple<Double,Int,SizeT> RecType;
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File h5f(mFileName, true);
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h5f.open();
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auto tab = h5f.getGroup("gr1")->open().getTable("tab1", RecType());
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EXPECT_EQ(tab->fields()->size(), 3u);
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EXPECT_EQ(tab->records()->size(), 5u);
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tab->open();
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auto cont = tab->read();
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EXPECT_EQ(cont.size(), mTabA.size());
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CIndex i(mTabA.range());
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for(; i.lex() != i.lmax().val(); ++i){
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EXPECT_EQ( cont[i], mTabA[i] );
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}
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auto dtab = h5f.getGroup("gr1")->open().getTable("tab1");
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auto dcont = dtab->read();
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EXPECT_EQ(dcont.range()->dim(), 2u);
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EXPECT_EQ(dcont.range()->sub(0)->size(), 5u);
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EXPECT_EQ(dcont.range()->sub(1)->size(), 3u);
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for(auto ai = dcont.begin(); ai != dcont.end(); ++ai){
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EXPECT_EQ(dcont[ai].str(), mTabD[ai].str());
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}
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h5f.close();
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}
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}
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