hdf5: dataset

src/opt/hdf5/include/cnorxz_hdf5.cc.h

@@ -3,3 +3,4 @@
 #include "h5_type_id.cc.h"
 #include "h5_group.cc.h"
 #include "h5_table.cc.h"
+#include "h5_dataset.cc.h"

src/opt/hdf5/include/cnorxz_hdf5.h

@@ -3,6 +3,7 @@
 #include "h5_file.h"
 #include "h5_group.h"
 #include "h5_table.h"
+#include "h5_dataset.h"
 #include "h5_type_id.h"
 
 #include "cnorxz_hdf5.cc.h"

src/opt/hdf5/include/h5_dataset.cc.h

@@ -2,6 +2,8 @@
 #ifndef __cxz_h5_dataset_cc_h__
 #define __cxz_h5_dataset_cc_h__
 
+#include "h5_dataset.h"
+
 namespace CNORXZ
 {
     namespace hdf5
@@ -9,7 +11,89 @@ namespace CNORXZ
 	template <typename T>
 	Dataset& Dataset::init(const ArrayBase<T>& data)
 	{
-	    // !!!!
+	    const hid_t tid = getTypeId(*data.data());
+	    init(data.range(), tid);
+	    if(data.begin().formatIsTrivial()){
+		Vector<hsize_t> dims(mDataRange->dim());
+		for(SizeT i = 0; i != dims.size(); ++i){
+		    dims[i] = mDataRange->sub(i)->size();
+		}
+		const hid_t memspace = H5Screate_simple(dims.size(), dims.data(), NULL);
+		H5Dwrite(mId, mType, memspace, mFilespace, H5P_DEFAULT, data.data());
+		H5Sclose(memspace);
+	    }
+	    else {
+		CXZ_ERROR("IMPLEMENT!!!");
+	    }
+	    return *this;
+	}
+
+	template <typename T>
+	SDataset<T>::SDataset(const String& name, const ContentBase* _parent) :
+	    Dataset(name, _parent)
+	{}
+
+	template <typename T>
+	MArray<T> SDataset<T>::read() const
+	{
+	    Vector<hsize_t> dims(mDataRange->dim());
+	    for(SizeT i = 0; i != dims.size(); ++i){
+		dims[i] = mDataRange->sub(i)->size();
+	    }
+	    const hid_t mem_space_id = H5Screate_simple(static_cast<hsize_t>(dims.size()),
+							dims.data(), nullptr);
+	    const hid_t xfer_plist_id = H5Pcreate(H5P_DATASET_XFER);
+	    MArray<T> out(mDataRange);
+	    const herr_t err = H5Dread(mId, mType, mem_space_id, mFilespace, xfer_plist_id, out.data());
+	    CXZ_ASSERT(err >= 0, "error while reading dataset '" << mName
+		       << "', errorcode :" << err);
+	    H5Pclose(xfer_plist_id);
+	    H5Sclose(mem_space_id);
+	    return out;
+	}
+
+	template <typename T>
+	template <class I, typename M>
+	MArray<T> SDataset<T>::read(const IndexInterface<I,M>& beg, const IndexInterface<I,M>& end) const
+	{
+	    CXZ_ASSERT(beg.dim() == mDataRange->dim(), "got index of inconsistent dimension, got"
+		       << beg.dim() << ", expected " << mDataRange->dim());
+	    const RangePtr outrange = beg.prange(end);
+	    Vector<hsize_t> dims(outrange->dim());
+	    for(SizeT i = 0; i != dims.size(); ++i){
+		dims[i] = outrange->sub(i)->size();
+	    }
+	    const Vector<hsize_t> fpos = mkFPos(beg);
+	    H5Sselect_hyperslab(mFilespace, H5S_SELECT_SET, fpos.data(), NULL, dims.data(), NULL);
+	    const hid_t mem_space_id = H5Screate_simple(static_cast<hsize_t>(dims.size()),
+							dims.data(), nullptr);
+	    const hid_t xfer_plist_id = H5Pcreate(H5P_DATASET_XFER);
+	    MArray<T> out(outrange);
+	    const herr_t err = H5Dread(mId, mType, mem_space_id, mFilespace, xfer_plist_id, out.data());
+	    CXZ_ASSERT(err >= 0, "error while reading dataset '" << mName
+		       << "', errorcode :" << err);
+	    H5Pclose(xfer_plist_id);
+	    H5Sclose(mem_space_id);
+	    return out;
+	}
+
+	template <typename T>
+	template <class I, typename M>
+	Vector<hsize_t> SDataset<T>::mkFPos(const IndexInterface<I,M>& beg) const
+	{
+	    Vector<hsize_t> fpos(beg.dim());
+	    if constexpr(has_static_sub<I>::value){
+		iter<0,index_dim<I>::value> ( [&](auto i) { fpos[i] = beg.pack().get(i).lex(); }, NoF{} );
+	    }
+	    else if constexpr(has_sub<I>::value){
+		for(SizeT i = 0; i != beg.dim(); ++i){
+		    fpos[i] = beg.pack().get(i).lex();
+		}
+	    }
+	    else {
+		fpos[0] = beg.lex();
+	    }
+	    return fpos;
 	}
 
     }

src/opt/hdf5/include/h5_dataset.h

@@ -47,6 +47,14 @@ namespace CNORXZ
 	    SDataset(const String& name, const ContentBase* _parent);
 
 	    MArray<T> read() const;
+
+	    template <class I, typename M>
+	    MArray<T> read(const IndexInterface<I,M>& beg, const IndexInterface<I,M>& end) const;
+
+	private:
+
+	    template <class I, typename M>
+	    Vector<hsize_t> mkFPos(const IndexInterface<I,M>& beg) const;
 	};
     }
 }

src/opt/hdf5/include/h5_group.cc.h

@@ -13,9 +13,9 @@ namespace CNORXZ
 	Sptr<STable<Ts...>> Group::getTable(const String& name, Tuple<Ts...> proto)
 	{
 	    auto i = this->getIndexTo(name);
-	    auto tab = std::dynamic_pointer_cast<Table>( *i );
+	    CXZ_ASSERT((*i)->type() == ContentType::TABLE,
-	    CXZ_ASSERT(tab->type() == ContentType::TABLE,
 		       "element '" << name << "' is not of type TABLE");
+	    auto tab = std::dynamic_pointer_cast<Table>( *i );
 	    if(tab == nullptr){
 		auto stab = std::dynamic_pointer_cast<STable<Ts...>>(*i);
 		CXZ_ASSERT(stab != nullptr, "wrong format for table '" << name << "'");
@@ -30,10 +30,35 @@ namespace CNORXZ
 	}
 
 	template <typename T>
-	Group& Group::addData(const String& name, const ArrayBase<T>& data)
+	Sptr<SDataset<T>> Group::getDataset(const String& name, T proto)
+	{
+	    auto i = this->getIndexTo(name);
+	    CXZ_ASSERT((*i)->type() == ContentType::DSET,
+		       "element '" << name << "' is not of type DSET");
+	    auto dset = std::dynamic_pointer_cast<Dataset>( *i );
+	    if(dset == nullptr){
+		auto sdset = std::dynamic_pointer_cast<SDataset<T>>(*i);
+		CXZ_ASSERT(sdset != nullptr, "wrong format for dataset '" << name << "'");
+		return sdset;
+	    }
+	    else {
+		(*i)->close();
+		auto sdset = std::make_shared<SDataset<T>>(name, this);
+		*i = sdset;
+		return sdset;
+	    }
+	}
+
+	template <typename T>
+	Group& Group::addDataset(const String& name, const ArrayBase<T>& data)
 	{
 	    CXZ_ASSERT(this->isOpen(), "tried to extend closed group");
-	    CXZ_ERROR("not implemented!!!");
+	    Vector<String> nvec({name});
+	    mCont.extend( URangeFactory<String>( nvec ).create() );
+	    auto ii = getIndexTo(name);
+	    auto dset = std::make_shared<SDataset<T>>(name, this);
+	    dset->init(data);
+	    *ii = dset;
 	    return *this;
 	}
 
@@ -43,11 +68,8 @@ namespace CNORXZ
 	{
 	    CXZ_ASSERT(this->isOpen(), "tried to extend closed group");
 	    Vector<String> nvec({name});
-	    Vector<DType> dvec({DType(name)});
+	    mCont.extend( URangeFactory<String>( nvec ).create() );
-	    auto extr = URangeFactory<String>( nvec ).create();
+	    auto ii = getIndexTo(name);
-	    mCont.extend(extr);
-	    auto ii = mCont.begin();
-	    ii.at(dvec); // 'at' returns YIndex&, so cannot use it inline...
 	    auto tab = std::make_shared<STable<Ts...>>(name, this, fnames);
 	    for(auto& d: data){
 		tab->appendRecord(d);

src/opt/hdf5/include/h5_group.h

@@ -28,20 +28,24 @@ namespace CNORXZ
 	    const ContentPtr& get(const String& name) const;
 	    Sptr<Group> getGroup(const String& name) const;
 	    Sptr<Table> getTable(const String& name) const;
+	    Sptr<Dataset> getDataset(const String& name) const;
 
 	    template <typename... Ts>
 	    Sptr<STable<Ts...>> getTable(const String& name, Tuple<Ts...> proto);
 
+	    template <typename T>
+	    Sptr<SDataset<T>> getDataset(const String& name, T proto);
+
 	    const MArray<ContentPtr>& get() const;
 	    Group& addGroup(const String& name);
 
-	    template <typename T>
-	    Group& addData(const String& name, const ArrayBase<T>& data);
-
 	    template <typename... Ts>
 	    Group& addTable(const String& name, const ArrayBase<Tuple<Ts...>>& data,
 			    const Arr<String,sizeof...(Ts)>& fnames);
 
+	    template <typename T>
+	    Group& addDataset(const String& name, const ArrayBase<T>& data);
+
 	    template <class F>
 	    decltype(auto) iter(F&& f) const;
 

src/opt/hdf5/include/h5_types.h

@@ -22,6 +22,13 @@ namespace CNORXZ
 	template <typename... Ts>
 	class STable;
 
+	// definition -> h5_dataset.h
+	class Dataset;
+
+	// definition -> h5_dataset.h
+	template <typename T>
+	class SDataset;
+
     }
 }
 

src/opt/hdf5/lib/h5_dataset.cc

@@ -44,10 +44,6 @@ namespace CNORXZ
 		    rs[i] = CRangeFactory(dims[i]).create();
 		}
 		mDataRange = yrange(rs);
-
-		// use when reading!!!:
-		//hid_t mem_space_id = H5Screate_simple(static_cast<hsize_t>(ndims), dims.data(), nullptr);
-		//hid_t xfer_plist_id = H5Pcreate(H5P_DATASET_XFER);
 	    }
 	    return *this;
 	}
@@ -55,7 +51,6 @@ namespace CNORXZ
 	Dataset& Dataset::close()
 	{
 	    if(mId != 0){
-		//!!!
 		H5Sclose(mFilespace);
 		H5Tclose(mType);
 		H5Dclose(mId);
@@ -81,7 +76,7 @@ namespace CNORXZ
 
 	Dataset& Dataset::init(const RangePtr& dataRange, hid_t type)
 	{
-	    CXZ_ASSERT(not open(), "tried to initialize dataset that is already extisting");
+	    CXZ_ASSERT(not isOpen(), "tried to initialize dataset that is already extisting");
 	    const H5T_class_t tc = H5Tget_class(type);
 	    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)...
 	    const hid_t dcpl_id = H5Pcreate(H5P_DATASET_CREATE);

src/opt/hdf5/lib/h5_group.cc

@@ -1,6 +1,7 @@
 
 #include "h5_group.h"
 #include "h5_table.h"
+#include "h5_dataset.h"
 
 namespace CNORXZ
 {
@@ -104,6 +105,14 @@ namespace CNORXZ
 	    return std::dynamic_pointer_cast<Table>( table );
 	}
 
+	Sptr<Dataset> Group::getDataset(const String& name) const
+	{
+	    auto dset = this->get(name);
+	    CXZ_ASSERT(dset->type() == ContentType::DSET,
+		       "element '" << name << "' is not of type DSET");
+	    return std::dynamic_pointer_cast<Dataset>( dset );
+	}
+
 	const MArray<ContentPtr>& Group::get() const
 	{
 	    CXZ_ASSERT(this->isOpen(), "tried to get content of closed group");
@@ -186,8 +195,7 @@ namespace CNORXZ
 		    *index = std::make_shared<Table>(sname, icd->parent);
 		}
 		else {
-		    CXZ_ERROR("IMPLEMENT!!!");
+		    *index = std::make_shared<Dataset>(sname, icd->parent);
-		    //*index = std::make_shared<DSet>(sname, icd->parent);
 		}
 		break;
 	    }