hdf5: dataset: some reorganization + group: add general add/get member functions

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

@@ -22,8 +22,6 @@ namespace CNORXZ
 	Dataset& Dataset::init(const ArrayBase<T>& data)
 	{
 	    const hid_t tid = getTypeId(*data.data());
-	    //VCHECK(tid);
-	    //init(data.range(), tid);
 	    if(data.begin().formatIsTrivial()){
 		init(data.range(), tid, data.data());
 	    }
@@ -41,7 +39,7 @@ namespace CNORXZ
 	template <typename T>
 	MArray<T> SDataset<T>::read() const
 	{
-	    MArray<T> out(mDataRange);
+	    MArray<T> out(mFileRange);
 	    readbase(out.data(), nullptr, nullptr);
 	    return out;
 	}
@@ -50,12 +48,12 @@ namespace CNORXZ
 	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"
+	    CXZ_ASSERT(idx.dim() == mFileRange->dim(), "got index of inconsistent dimension, got"
-		       << idx.dim() << ", expected " << mDataRange->dim());
+		       << idx.dim() << ", expected " << mFileRange->dim());
 	    const RangePtr outrange = idx.range();
-	    CXZ_ASSERT(outrange->size() == mDataRange->size(),
+	    CXZ_ASSERT(outrange->size() == mFileRange->size(),
 		       "got index of range of inconsistent size, expected "
-		       << mDataRange->size() << ", got " << outrange->size());
+		       << mFileRange->size() << ", got " << outrange->size());
 	    MArray<T> out(outrange);
 	    readbase(out.data(), outrange, nullptr);
 	    return out;
@@ -65,8 +63,8 @@ namespace CNORXZ
 	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"
+	    CXZ_ASSERT(beg.dim() == mFileRange->dim(), "got index of inconsistent dimension, got"
-		       << beg.dim() << ", expected " << mDataRange->dim());
+		       << beg.dim() << ", expected " << mFileRange->dim());
 	    const RangePtr outrange = beg.prange(end);
 	    MArray<T> out(outrange);
 	    readbase(out.data(), outrange, toYptr(beg));

src/opt/hdf5/include/h5_dataset.h

@@ -57,6 +57,13 @@ namespace CNORXZ
 	     */
 	    virtual Dataset& init(const RangePtr& dataRange, hid_t type, const void* data);
 
+	    /** Write data into dataset.
+		@param dataRange A potentially multi-dimensional range characterizing the format of the data to be written.
+		@param pos Position on target.
+		@param data Pointer to raw data to be writte.
+	     */
+	    virtual Dataset& writebase(const RangePtr& dataRange, Sptr<YIndex> pos, const void* data);
+	    
 	    /** Read the dataset.
 		@param dest Pointer to destination.
 		@param readrange Range of the destination data.
@@ -78,14 +85,14 @@ namespace CNORXZ
 	protected:
 	    Vector<hsize_t> mkOff(const Sptr<YIndex>& beg) const;
 	    
-	    RangePtr mDataRange; /**< The data range. */
+	    RangePtr mFileRange; /**< The range of the dataset. */
 	    hid_t mType; /**< The data type identifier. */
 	    hid_t mFilespace; /**< The hdf5 file space identifier. */
 	    
 	};
 
 	/** ****
-	    Class to handle hdf5 datasets, the value type is known at compile time.
+	    Class to handle hdf5 datasets, the value type is assumed to be known at compile time.
 	    @tparam T Dataset value type.
 	 */
 	template <typename T>

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

@@ -39,6 +39,13 @@ namespace CNORXZ
 	    return pos - beg;
 	}
 
+	template <class F>
+	decltype(auto) Group::get(const String& name, F&& f)
+	{
+	    auto i = this->getIndexTo(name);
+	    return f(*i);
+	}
+	
 	template <typename... Ts>
 	Sptr<STable<Ts...>> Group::getTable(const String& name, Tuple<Ts...> proto)
 	{
@@ -108,6 +115,17 @@ namespace CNORXZ
 	    return *this;
 	}
 
+	template <class F, typename... Args>
+	Group& Group::add(const String& name, F&& f, const Args&... args)
+	{
+	    CXZ_ASSERT(this->isOpen(), "tried to extend closed group");
+	    Vector<String> nvec({name});
+	    mCont.extend( URangeFactory<String>( nvec ).create() );
+	    auto ii = getIndexTo(name);
+	    *ii = f(args...);
+	    return *this;
+	}
+
 	template <class F>
 	decltype(auto) Group::iter(F&& f) const
 	{

src/opt/hdf5/include/h5_group.h

@@ -96,6 +96,13 @@ namespace CNORXZ
 	     */
 	    const MArray<ContentPtr>& get() const;
 
+	    /** Get object contained by this group.
+		@param name Object name.
+		@param f Function to interpret the object.
+	     */
+	    template <class F>
+	    decltype(auto) get(const String& name, F&& f);
+	    
 	    /** Add a new group to this group.
 		@param name Name of the created group.
 	     */
@@ -119,6 +126,13 @@ namespace CNORXZ
 	    template <typename T>
 	    Group& addDataset(const String& name, const ArrayBase<T>& data);
 
+	    /** Add new object to this group.
+		@param name Object name.
+		@param f Function used to create the object.
+	     */
+	    template <class F, typename... Args>
+	    Group& add(const String& name, F&& f, const Args&... args);
+
 	    /** Iterate over all group elements (const).
 		@param f function object to be executed on each group element.
 	     */

src/opt/hdf5/lib/h5_dataset.cc

@@ -53,7 +53,7 @@ namespace CNORXZ
 		for(SizeT i = 0; i != ndims; ++i){
 		    rs[i] = CRangeFactory(dims[i]).create();
 		}
-		mDataRange = yrange(rs);
+		mFileRange = yrange(rs);
 	    }
 	    return *this;
 	}
@@ -84,18 +84,18 @@ namespace CNORXZ
 	    return H5Lexists(mParent->id(), mName.c_str(), H5P_DEFAULT) > 0;
 	}
 
-	Dataset& Dataset::init(const RangePtr& dataRange, hid_t type)
+	Dataset& Dataset::init(const RangePtr& fileRange, hid_t type)
 	{
 	    CXZ_ASSERT(not isOpen(), "tried to initialize dataset that is already extisting");
-	    mDataRange = dataRange;
+	    mFileRange = fileRange;
 	    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);
 	    // TODO: all sub-ranges explicity!!!:
-	    const SizeT ndim = dataRange->dim();
+	    const SizeT ndim = mFileRange->dim();
 	    Vector<hsize_t> exts(ndim);
 	    for(SizeT i = 0; i != ndim; ++i){
-		exts[i] = static_cast<hsize_t>( dataRange->sub(i)->size() );
+		exts[i] = static_cast<hsize_t>( mFileRange->sub(i)->size() );
 	    }
 	    mFilespace = H5Screate_simple(ndim, exts.data(), NULL);
 	    mType = type;
@@ -105,37 +105,64 @@ namespace CNORXZ
 	    return *this;
 	}
 
-	Dataset& Dataset::init(const RangePtr& dataRange, hid_t type, const void* data)
+	Dataset& Dataset::init(const RangePtr& writeRange, hid_t type, const void* data)
 	{
-	    init(dataRange, type);
+	    init(writeRange, type);
-	    Vector<hsize_t> dims(mDataRange->dim());
+	    writebase(writeRange, std::make_shared<YIndex>(mFileRange), 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);
-	    H5Sclose(memspace);
 	    return *this;
 	}
 
-	void Dataset::readbase(void* dest, RangePtr readrange, Sptr<YIndex> beg) const
+	Dataset& Dataset::writebase(const RangePtr& writeRange, Sptr<YIndex> pos, const void* data)
 	{
-	    // TODO: Check if readrange is compatible with mDataRange!!!
+	    //CXZ_ERROR("TODO!!!");
-	    if(not readrange){
+	    CXZ_ASSERT(writeRange->dim() == mFileRange->dim(), "dimension of data range ("
-		readrange = mDataRange;
+		       << writeRange->dim() << ") different from dimension of file range ("
-	    }
+		       << mFileRange->dim() << ")");
-	    Vector<hsize_t> dims(readrange->dim());
+	    Vector<hsize_t> dims(writeRange->dim());
 	    for(SizeT i = 0; i != dims.size(); ++i){
-		dims[i] = readrange->sub(i)->size();
+		dims[i] = writeRange->sub(i)->size();
+	    }
+	    if(pos){
+		CXZ_ASSERT(pos->range()->dim() == mFileRange->dim(), "dimension of position index ("
+			   << pos->range()->dim() << ") different from dimension of file range ("
+			   << mFileRange->dim() << ")");
+		const Vector<hsize_t> fpos = mkOff(pos);
+		H5Sselect_hyperslab(mFilespace, H5S_SELECT_SET, fpos.data(), NULL, dims.data(), NULL);
+	    }
+	    const hid_t memspace = H5Screate_simple(dims.size(), dims.data(), NULL);
+	    const hid_t xfer_plist_id = H5Pcreate(H5P_DATASET_XFER);
+	    H5Dwrite(mId, mType, memspace, mFilespace, xfer_plist_id, data);
+	    H5Pclose(xfer_plist_id);
+	    H5Sclose(memspace);
+	    return *this;
+	}
+	
+	void Dataset::readbase(void* dest, RangePtr readRange, Sptr<YIndex> beg) const
+	{
+	    // TODO: Check if readRange is compatible with mFileRange!!!
+	    if(not readRange){
+		readRange = mFileRange;
+	    }
+	    else {
+		CXZ_ASSERT(readRange->dim() == mFileRange->dim(), "dimension of data range ("
+			   << readRange->dim() << ") different from dimension of file range ("
+			   << mFileRange->dim() << ")");
+	    }
+	    Vector<hsize_t> dims(readRange->dim());
+	    for(SizeT i = 0; i != dims.size(); ++i){
+		dims[i] = readRange->sub(i)->size();
 	    }
 	    if(beg){
+		CXZ_ASSERT(beg->range()->dim() == mFileRange->dim(), "dimension of position index ("
+			   << beg->range()->dim() << ") different from dimension of file range ("
+			   << mFileRange->dim() << ")");
 		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);
+	    //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);
@@ -145,7 +172,7 @@ namespace CNORXZ
 
 	const RangePtr& Dataset::dataRange() const
 	{
-	    return mDataRange;
+	    return mFileRange;
 	}
 	
         Vector<hsize_t> Dataset::mkOff(const Sptr<YIndex>& beg) const