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e3ad04e56c
commit
f7c00eab8c
3 changed files with 97 additions and 53 deletions
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@ -89,7 +89,7 @@ namespace CNORXZ
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initTable(1, &t, sizeof(t), sizeof(t));
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initTable(1, &t, sizeof(t), sizeof(t));
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}
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}
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else {
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else {
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Table::appendRecord(1, &t, sizeof(t));
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Table::appendRecords(1, &t);
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}
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}
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return *this;
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return *this;
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}
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}
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@ -27,8 +27,9 @@ namespace CNORXZ
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Table& initFieldNames(const Vector<String>& fnames);
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Table& initFieldNames(const Vector<String>& fnames);
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Table& initTable(SizeT n, const void* data, SizeT dsize, SizeT chunk_size);
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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& appendRecords(SizeT n, const void* data);
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Table& readRecord(SizeT pos, SizeT n, char* data);
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Table& readRecords(SizeT pos, SizeT n, char* data);
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MArray<DType> readRecord(SizeT pos) const;
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MArray<DType> read() const;
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MArray<DType> read() const;
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const RangePtr& fields() const;
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const RangePtr& fields() const;
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@ -42,6 +43,9 @@ namespace CNORXZ
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MArray<hid_t> mTypes;
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MArray<hid_t> mTypes;
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hid_t mType = 0;
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hid_t mType = 0;
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SizeT mTypesize = 0;
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SizeT mTypesize = 0;
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MArray<std::function<DType(const char*)>> mInterpret;
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void mkTypes();
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};
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};
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// caution: the memory ordering is the only thing that counts;
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// caution: the memory ordering is the only thing that counts;
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@ -65,6 +65,7 @@ namespace CNORXZ
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if(mId == 0){
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if(mId == 0){
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mId = H5Dopen(mParent->id(), mName.c_str(), H5P_DEFAULT);
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mId = H5Dopen(mParent->id(), mName.c_str(), H5P_DEFAULT);
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mType = H5Dget_type(mId);
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mType = H5Dget_type(mId);
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mkTypes();
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}
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}
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return *this;
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return *this;
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}
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}
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@ -110,78 +111,58 @@ namespace CNORXZ
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for(auto fi = fr->begin(); fi != fr->end(); ++fi){
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for(auto fi = fr->begin(); fi != fr->end(); ++fi){
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fields[fi.lex()] = (*fi).second.c_str();
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fields[fi.lex()] = (*fi).second.c_str();
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}
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}
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mTypesize = dsize;
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const herr_t err = H5TBmake_table
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const herr_t err = H5TBmake_table
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(mName.c_str(), mParent->id(), mName.c_str(), mFields->size(), mRecords->size(), dsize,
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(mName.c_str(), mParent->id(), mName.c_str(), mFields->size(), mRecords->size(), mTypesize,
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fields.data(), mOffsets.data(), mTypes.data(), chunk_size, NULL, compress, data);
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fields.data(), mOffsets.data(), mTypes.data(), chunk_size, NULL, compress, data);
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CXZ_ASSERT(err >= 0, "error while initialzing table: error code = " << err);
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CXZ_ASSERT(err >= 0, "error while initialzing table: error code = " << err);
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return *this;
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return *this;
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}
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}
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Table& Table::appendRecord(SizeT n, const void* data, SizeT dsize)
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Table& Table::appendRecords(SizeT n, const void* data)
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{
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{
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mRecords = mRecords->extend( CRangeFactory(1).create() );
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mRecords = mRecords->extend( CRangeFactory(n).create() );
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const herr_t err = H5TBappend_records(mParent->id(), mName.c_str(), n, dsize,
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const herr_t err = H5TBappend_records(mParent->id(), mName.c_str(), n, mTypesize,
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mOffsets.data(), mSizes.data(), data);
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mOffsets.data(), mSizes.data(), data);
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CXZ_ASSERT(err >= 0, "error while appending record to table: error code = " << err);
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CXZ_ASSERT(err >= 0, "error while appending record to table: error code = " << err);
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return *this;
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return *this;
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}
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}
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Table& Table::readRecord(SizeT pos, SizeT n, char* data)
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Table& Table::readRecords(SizeT pos, SizeT n, char* data)
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{
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{
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CXZ_ERROR("not implemented!!!");
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H5TBread_records(mParent->id(), mName.c_str(), pos, n, mTypesize, mOffsets.data(),
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mSizes.data(), data);
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return *this;
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return *this;
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}
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}
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MArray<DType> Table::readRecord(SizeT pos) const
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{
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Vector<char> buf(mTypesize);
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H5TBread_records(mParent->id(), mName.c_str(), pos, 1, mTypesize, mOffsets.data(),
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mSizes.data(), buf.data());
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MArray<DType> out(mFields);
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auto fi = std::make_shared<CIndex>(mFields);
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out(fi) = operation( [&](const SizeT& off, const std::function<DType(const char*)>& f){
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return f( buf.data() + off );
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}, mOffsets(fi), mInterpret(fi) );
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return out;
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}
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MArray<DType> Table::read() const
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MArray<DType> Table::read() const
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{
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{
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Vector<char> buf(mTypesize*mRecords->size());
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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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H5TBread_table(mParent->id(), mName.c_str(), mTypesize, mOffsets.data(),
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mSizes.data(), buf.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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MArray<DType> out(mRecords*mFields);
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CIndex fi(mFields);
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auto fi = std::make_shared<CIndex>(mFields);
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CIndex ri(mRecords);
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auto ri = std::make_shared<CIndex>(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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out(ri*fi) = operation( [&](const SizeT& off, const std::function<DType(const char*)>& f, const SizeT r){
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const SizeT off = mOffsets[fi];
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return f( buf.data() + r*mTypesize + off );
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const hid_t tp = H5Tget_member_type( type_id, fi.lex() );
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}, mOffsets(fi), mInterpret(fi), xpr(ri) );
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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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return out;
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}
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}
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@ -195,5 +176,64 @@ namespace CNORXZ
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return mRecords;
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return mRecords;
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}
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}
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void Table::mkTypes()
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{
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mTypes = MArray<hid_t>(mFields);
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auto i = std::make_shared<CIndex>(mFields);
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mTypes(i) = operation( [&](const SizeT n){ return H5Tget_member_type( mType, n ); } , xpr(i) );
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mInterpret = MArray<std::function<DType(const char*)>>(mFields);
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mInterpret(i) = operation( [](const hid_t tid){
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const hid_t tc = H5Tget_class(tid);
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const size_t ts = H5Tget_size(tid);
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const bool sig = H5Tget_sign(tid);
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std::function<DType(const char*)> of;
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switch(tc){
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case H5T_INTEGER:{
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switch(ts){
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case 1:{ // 8-bit
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of = sig ?
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[](const char* d){ const int8_t x = *reinterpret_cast<const int8_t*>(d); return DType(static_cast<Int>(x)); } :
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[](const char* d){ const uint8_t x = *reinterpret_cast<const uint8_t*>(d); return DType(static_cast<SizeT>(x)); };
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break;
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}
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case 2:{ // 16-bit
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of = sig ?
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[](const char* d){ const int16_t x = *reinterpret_cast<const int16_t*>(d); return DType(static_cast<Int>(x)); } :
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[](const char* d){ const uint16_t x = *reinterpret_cast<const uint16_t*>(d); return DType(static_cast<SizeT>(x)); };
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break;
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}
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case 4:{ // 32-bit
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of = sig ?
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[](const char* d){ const int32_t x = *reinterpret_cast<const int32_t*>(d); return DType(static_cast<Int>(x)); } :
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[](const char* d){ const uint32_t x = *reinterpret_cast<const uint32_t*>(d); return DType(static_cast<SizeT>(x)); };
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break;
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}
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case 8:{ // 64-bit
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of = sig ?
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[](const char* d){ const int64_t x = *reinterpret_cast<const int64_t*>(d); return DType(static_cast<LInt>(x)); } :
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[](const char* d){ const uint64_t x = *reinterpret_cast<const uint64_t*>(d); return DType(static_cast<SizeT>(x)); };
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break;
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}
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default:
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CXZ_ERROR("got integer of weird size: " << ts);
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}
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break;
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}
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case H5T_FLOAT:{
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if(ts == 4) {
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of = [](const char* d){ const float x = *reinterpret_cast<const float*>(d); return DType(static_cast<Double>(x)); };
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}
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else {
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CXZ_ASSERT(ts == 8, "got float of weird size: " << ts);
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of = [](const char* d){ const double x = *reinterpret_cast<const double*>(d); return DType(static_cast<Double>(x)); };
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}
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break;
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}
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default:
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CXZ_ERROR("got unsupported type");
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};
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return of;
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}, mTypes(i) );
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}
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}
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}
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}
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}
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