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e2e233b931
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6f3601daa4
9 changed files with 155 additions and 25 deletions
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@ -3,3 +3,4 @@
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#include "h5_type_id.cc.h"
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#include "h5_group.cc.h"
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#include "h5_table.cc.h"
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#include "h5_dataset.cc.h"
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@ -3,6 +3,7 @@
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#include "h5_file.h"
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#include "h5_group.h"
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#include "h5_table.h"
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#include "h5_dataset.h"
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#include "h5_type_id.h"
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#include "cnorxz_hdf5.cc.h"
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@ -2,6 +2,8 @@
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#ifndef __cxz_h5_dataset_cc_h__
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#define __cxz_h5_dataset_cc_h__
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#include "h5_dataset.h"
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namespace CNORXZ
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{
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namespace hdf5
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@ -9,9 +11,91 @@ namespace CNORXZ
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template <typename T>
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Dataset& Dataset::init(const ArrayBase<T>& data)
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{
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// !!!!
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const hid_t tid = getTypeId(*data.data());
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init(data.range(), tid);
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if(data.begin().formatIsTrivial()){
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Vector<hsize_t> dims(mDataRange->dim());
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for(SizeT i = 0; i != dims.size(); ++i){
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dims[i] = mDataRange->sub(i)->size();
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}
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const hid_t memspace = H5Screate_simple(dims.size(), dims.data(), NULL);
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H5Dwrite(mId, mType, memspace, mFilespace, H5P_DEFAULT, data.data());
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H5Sclose(memspace);
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}
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else {
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CXZ_ERROR("IMPLEMENT!!!");
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}
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return *this;
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}
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template <typename T>
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SDataset<T>::SDataset(const String& name, const ContentBase* _parent) :
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Dataset(name, _parent)
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{}
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template <typename T>
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MArray<T> SDataset<T>::read() const
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{
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Vector<hsize_t> dims(mDataRange->dim());
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for(SizeT i = 0; i != dims.size(); ++i){
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dims[i] = mDataRange->sub(i)->size();
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}
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const hid_t mem_space_id = H5Screate_simple(static_cast<hsize_t>(dims.size()),
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dims.data(), nullptr);
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const hid_t xfer_plist_id = H5Pcreate(H5P_DATASET_XFER);
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MArray<T> out(mDataRange);
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const herr_t err = H5Dread(mId, mType, mem_space_id, mFilespace, xfer_plist_id, out.data());
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CXZ_ASSERT(err >= 0, "error while reading dataset '" << mName
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<< "', errorcode :" << err);
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H5Pclose(xfer_plist_id);
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H5Sclose(mem_space_id);
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return out;
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}
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template <typename T>
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template <class I, typename M>
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MArray<T> SDataset<T>::read(const IndexInterface<I,M>& beg, const IndexInterface<I,M>& end) const
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{
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CXZ_ASSERT(beg.dim() == mDataRange->dim(), "got index of inconsistent dimension, got"
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<< beg.dim() << ", expected " << mDataRange->dim());
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const RangePtr outrange = beg.prange(end);
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Vector<hsize_t> dims(outrange->dim());
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for(SizeT i = 0; i != dims.size(); ++i){
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dims[i] = outrange->sub(i)->size();
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}
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const Vector<hsize_t> fpos = mkFPos(beg);
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H5Sselect_hyperslab(mFilespace, H5S_SELECT_SET, fpos.data(), NULL, dims.data(), NULL);
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const hid_t mem_space_id = H5Screate_simple(static_cast<hsize_t>(dims.size()),
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dims.data(), nullptr);
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const hid_t xfer_plist_id = H5Pcreate(H5P_DATASET_XFER);
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MArray<T> out(outrange);
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const herr_t err = H5Dread(mId, mType, mem_space_id, mFilespace, xfer_plist_id, out.data());
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CXZ_ASSERT(err >= 0, "error while reading dataset '" << mName
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<< "', errorcode :" << err);
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H5Pclose(xfer_plist_id);
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H5Sclose(mem_space_id);
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return out;
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}
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template <typename T>
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template <class I, typename M>
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Vector<hsize_t> SDataset<T>::mkFPos(const IndexInterface<I,M>& beg) const
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{
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Vector<hsize_t> fpos(beg.dim());
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if constexpr(has_static_sub<I>::value){
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iter<0,index_dim<I>::value> ( [&](auto i) { fpos[i] = beg.pack().get(i).lex(); }, NoF{} );
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}
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else if constexpr(has_sub<I>::value){
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for(SizeT i = 0; i != beg.dim(); ++i){
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fpos[i] = beg.pack().get(i).lex();
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}
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}
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else {
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fpos[0] = beg.lex();
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}
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return fpos;
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}
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}
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}
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@ -47,6 +47,14 @@ namespace CNORXZ
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SDataset(const String& name, const ContentBase* _parent);
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MArray<T> read() const;
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template <class I, typename M>
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MArray<T> read(const IndexInterface<I,M>& beg, const IndexInterface<I,M>& end) const;
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private:
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template <class I, typename M>
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Vector<hsize_t> mkFPos(const IndexInterface<I,M>& beg) const;
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};
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}
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}
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@ -13,9 +13,9 @@ namespace CNORXZ
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Sptr<STable<Ts...>> Group::getTable(const String& name, Tuple<Ts...> proto)
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{
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auto i = this->getIndexTo(name);
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auto tab = std::dynamic_pointer_cast<Table>( *i );
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CXZ_ASSERT(tab->type() == ContentType::TABLE,
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CXZ_ASSERT((*i)->type() == ContentType::TABLE,
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"element '" << name << "' is not of type TABLE");
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auto tab = std::dynamic_pointer_cast<Table>( *i );
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if(tab == nullptr){
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auto stab = std::dynamic_pointer_cast<STable<Ts...>>(*i);
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CXZ_ASSERT(stab != nullptr, "wrong format for table '" << name << "'");
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return stab;
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}
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}
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template <typename T>
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Group& Group::addData(const String& name, const ArrayBase<T>& data)
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Sptr<SDataset<T>> Group::getDataset(const String& name, T proto)
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{
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auto i = this->getIndexTo(name);
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CXZ_ASSERT((*i)->type() == ContentType::DSET,
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"element '" << name << "' is not of type DSET");
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auto dset = std::dynamic_pointer_cast<Dataset>( *i );
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if(dset == nullptr){
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auto sdset = std::dynamic_pointer_cast<SDataset<T>>(*i);
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CXZ_ASSERT(sdset != nullptr, "wrong format for dataset '" << name << "'");
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return sdset;
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}
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else {
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(*i)->close();
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auto sdset = std::make_shared<SDataset<T>>(name, this);
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*i = sdset;
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return sdset;
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}
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}
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template <typename T>
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Group& Group::addDataset(const String& name, const ArrayBase<T>& data)
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{
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CXZ_ASSERT(this->isOpen(), "tried to extend closed group");
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CXZ_ERROR("not implemented!!!");
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Vector<String> nvec({name});
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mCont.extend( URangeFactory<String>( nvec ).create() );
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auto ii = getIndexTo(name);
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auto dset = std::make_shared<SDataset<T>>(name, this);
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dset->init(data);
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*ii = dset;
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return *this;
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}
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{
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CXZ_ASSERT(this->isOpen(), "tried to extend closed group");
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Vector<String> nvec({name});
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Vector<DType> dvec({DType(name)});
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auto extr = URangeFactory<String>( nvec ).create();
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mCont.extend(extr);
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auto ii = mCont.begin();
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ii.at(dvec); // 'at' returns YIndex&, so cannot use it inline...
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mCont.extend( URangeFactory<String>( nvec ).create() );
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auto ii = getIndexTo(name);
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auto tab = std::make_shared<STable<Ts...>>(name, this, fnames);
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for(auto& d: data){
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tab->appendRecord(d);
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@ -28,20 +28,24 @@ namespace CNORXZ
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const ContentPtr& get(const String& name) const;
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Sptr<Group> getGroup(const String& name) const;
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Sptr<Table> getTable(const String& name) const;
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Sptr<Dataset> getDataset(const String& name) const;
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template <typename... Ts>
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Sptr<STable<Ts...>> getTable(const String& name, Tuple<Ts...> proto);
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const MArray<ContentPtr>& get() const;
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Group& addGroup(const String& name);
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template <typename T>
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Group& addData(const String& name, const ArrayBase<T>& data);
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Sptr<SDataset<T>> getDataset(const String& name, T proto);
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const MArray<ContentPtr>& get() const;
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Group& addGroup(const String& name);
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template <typename... Ts>
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Group& addTable(const String& name, const ArrayBase<Tuple<Ts...>>& data,
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const Arr<String,sizeof...(Ts)>& fnames);
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template <typename T>
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Group& addDataset(const String& name, const ArrayBase<T>& data);
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template <class F>
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decltype(auto) iter(F&& f) const;
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// definition -> h5_table.h
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template <typename... Ts>
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class STable;
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// definition -> h5_dataset.h
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class Dataset;
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// definition -> h5_dataset.h
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template <typename T>
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class SDataset;
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}
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}
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rs[i] = CRangeFactory(dims[i]).create();
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}
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mDataRange = yrange(rs);
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// use when reading!!!:
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//hid_t mem_space_id = H5Screate_simple(static_cast<hsize_t>(ndims), dims.data(), nullptr);
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//hid_t xfer_plist_id = H5Pcreate(H5P_DATASET_XFER);
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}
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return *this;
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}
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Dataset& Dataset::close()
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{
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if(mId != 0){
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//!!!
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H5Sclose(mFilespace);
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H5Tclose(mType);
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H5Dclose(mId);
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Dataset& Dataset::init(const RangePtr& dataRange, hid_t type)
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{
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CXZ_ASSERT(not open(), "tried to initialize dataset that is already extisting");
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CXZ_ASSERT(not isOpen(), "tried to initialize dataset that is already extisting");
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const H5T_class_t tc = H5Tget_class(type);
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CXZ_ASSERT(tc != H5T_NO_CLASS, "id does not correspond to a data type"); // (did not found anythng better to check if type id is valid)...
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const hid_t dcpl_id = H5Pcreate(H5P_DATASET_CREATE);
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#include "h5_group.h"
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#include "h5_table.h"
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#include "h5_dataset.h"
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namespace CNORXZ
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{
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return std::dynamic_pointer_cast<Table>( table );
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}
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Sptr<Dataset> Group::getDataset(const String& name) const
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{
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auto dset = this->get(name);
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CXZ_ASSERT(dset->type() == ContentType::DSET,
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"element '" << name << "' is not of type DSET");
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return std::dynamic_pointer_cast<Dataset>( dset );
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}
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const MArray<ContentPtr>& Group::get() const
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{
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CXZ_ASSERT(this->isOpen(), "tried to get content of closed group");
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@ -186,8 +195,7 @@ namespace CNORXZ
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*index = std::make_shared<Table>(sname, icd->parent);
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}
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else {
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CXZ_ERROR("IMPLEMENT!!!");
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//*index = std::make_shared<DSet>(sname, icd->parent);
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*index = std::make_shared<Dataset>(sname, icd->parent);
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}
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break;
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}
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