hdf5: some reorganization of the code + new member functions

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

@@ -23,15 +23,9 @@ namespace CNORXZ
 	{
 	    const hid_t tid = getTypeId(*data.data());
 	    //VCHECK(tid);
-	    init(data.range(), tid);
+	    //init(data.range(), tid);
 	    if(data.begin().formatIsTrivial()){
-		Vector<hsize_t> dims(mDataRange->dim());
+		init(data.range(), tid, data.data());
-		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("Got array type with non-trivial format; non-contiguous data formats are not supported yet!");
@@ -47,19 +41,23 @@ namespace CNORXZ
 	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());
+	    readbase(out.data(), nullptr, nullptr);
-	    CXZ_ASSERT(err >= 0, "error while reading dataset '" << mName
+	    return out;
-		       << "', errorcode :" << err);
+	}
-	    H5Pclose(xfer_plist_id);
+
-	    H5Sclose(mem_space_id);
+	template <typename T>
+	template <class I, typename M>
+	MArray<T> SDataset<T>::read(const IndexInterface<I,M>& idx) const
+	{
+	    CXZ_ASSERT(idx.dim() == mDataRange->dim(), "got index of inconsistent dimension, got"
+		       << idx.dim() << ", expected " << mDataRange->dim());
+	    const RangePtr outrange = idx.range();
+	    CXZ_ASSERT(outrange->size() == mDataRange->size(),
+		       "got index of range of inconsistent size, expected "
+		       << mDataRange->size() << ", got " << outrange->size());
+	    MArray<T> out(outrange);
+	    readbase(out.data(), outrange, nullptr);
 	    return out;
 	}
 
@@ -70,43 +68,25 @@ namespace CNORXZ
 	    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());
+	    readbase(out.data(), outrange, toYptr(beg));
-	    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
+	Sptr<YIndex> SDataset<T>::toYptr(const IndexInterface<I,M>& beg) const
 	{
-	    Vector<hsize_t> fpos(beg.dim());
+	    if constexpr(std::is_same<YIndex,I>::value){
-	    if constexpr(has_static_sub<I>::value){
+		return std::make_shared<YIndex>(beg.THIS());
-		iter<0,index_dim<I>::value> ( [&](auto i) { fpos[i] = beg.THIS().pack().get(i)->lex(); }, NoF{} );
 	    }
-	    else if constexpr(has_sub<I>::value){
+	    else if constexpr(has_sub<I>::value) {
-		for(SizeT i = 0; i != beg.dim(); ++i){
+		return yindexPtr(beg.pack());
-		    fpos[i] = beg.THIS().pack().get(i)->lex();
-		}
 	    }
 	    else {
-		fpos[0] = beg.lex();
+		return yindexPtr(DPack(std::make_shared<I>(beg)));
 	    }
-	    return fpos;
 	}
-
     }
 }
 

src/opt/hdf5/include/h5_dataset.h

@@ -48,8 +48,22 @@ namespace CNORXZ
 		@param dataRange A potentially multi-dimensional range characterizing the dataset.
 		@param type Data type id.
 	     */
-	    Dataset& init(const RangePtr& dataRange, hid_t type);
+	    virtual Dataset& init(const RangePtr& dataRange, hid_t type);
 
+	    /** Initalize the dataset.
+		@param dataRange A potentially multi-dimensional range characterizing the dataset.
+		@param type Data type id.
+		@param data Pointer to raw data.
+	     */
+	    virtual Dataset& init(const RangePtr& dataRange, hid_t type, const void* data);
+
+	    /** Read the dataset.
+		@param dest Pointer to destination.
+		@param readrange Range of the destination data.
+		@param beg Position within the file space.
+	     */
+	    virtual void readbase(void* dest, RangePtr readrange, Sptr<YIndex> beg) const;
+	    
 	    /** Initalize the dataset.
 		@param data Array containing the dataset.
 	    */
@@ -62,6 +76,8 @@ namespace CNORXZ
 	    const RangePtr& dataRange() const;
 	    
 	protected:
+	    Vector<hsize_t> mkOff(const Sptr<YIndex>& beg) const;
+	    
 	    RangePtr mDataRange; /**< The data range. */
 	    hid_t mType; /**< The data type identifier. */
 	    hid_t mFilespace; /**< The hdf5 file space identifier. */
@@ -89,6 +105,14 @@ namespace CNORXZ
 	     */
 	    MArray<T> read() const;
 
+	    /** Read the dataset using range of given index.
+		The index position is ignored.
+		@param idx Index specifying the range type.
+		@return Array containing the dataset values.
+	     */
+	    template <class I, typename M>
+	    MArray<T> read(const IndexInterface<I,M>& idx) const;
+
 	    /** Read a given subset of the dataset.
 		The subset needs to be hypercubic.
 		@param beg Index indicating the begin edge of the hypercube.
@@ -100,8 +124,10 @@ namespace CNORXZ
 
 	private:
 
+	    //template <class I, typename M>
+	    //Vector<hsize_t> mkFPos(const IndexInterface<I,M>& beg) const;
 	    template <class I, typename M>
-	    Vector<hsize_t> mkFPos(const IndexInterface<I,M>& beg) const;
+	    Sptr<YIndex> toYptr(const IndexInterface<I,M>& beg) const;
 	};
     }
 }

src/opt/hdf5/lib/h5_dataset.cc

@@ -105,10 +105,57 @@ namespace CNORXZ
 	    return *this;
 	}
 
+	Dataset& Dataset::init(const RangePtr& dataRange, hid_t type, const void* data)
+	{
+	    init(dataRange, type);
+	    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);
+	    H5Sclose(memspace);
+	    return *this;
+	}
+
+	void Dataset::readbase(void* dest, RangePtr readrange, Sptr<YIndex> beg) const
+	{
+	    // TODO: Check if readrange is compatible with mDataRange!!!
+	    if(not readrange){
+		readrange = mDataRange;
+	    }
+	    Vector<hsize_t> dims(readrange->dim());
+	    for(SizeT i = 0; i != dims.size(); ++i){
+		dims[i] = readrange->sub(i)->size();
+	    }
+	    if(beg){
+		const Vector<hsize_t> fpos = mkOff(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(readrange);
+	    const herr_t err = H5Dread(mId, mType, mem_space_id, mFilespace, xfer_plist_id, dest);
+	    CXZ_ASSERT(err >= 0, "error while reading dataset '" << mName
+		       << "', errorcode :" << err);
+	    H5Pclose(xfer_plist_id);
+	    H5Sclose(mem_space_id);
+	}
+
 	const RangePtr& Dataset::dataRange() const
 	{
 	    return mDataRange;
 	}
 	
+        Vector<hsize_t> Dataset::mkOff(const Sptr<YIndex>& beg) const
+	{
+	    Vector<hsize_t> off(beg->dim());
+	    for(SizeT i = 0; i != beg->dim(); ++i){
+		off[i] = beg->pack().get(i)->lex();
+	    }
+	    return off;
+	}
+	
     }
 }