C++ h5::DataSpace类代码示例

void Bundle2::storeParameters(H5::H5File& file) const {
	H5::Group root = file.openGroup("/");

	H5::DataSpace scalar;

	H5::Attribute attr = root.createAttribute("version", H5::PredType::STD_U32LE, scalar);
	attr.write(H5::PredType::NATIVE_UINT, &version_);
	attr.close();

	unsigned char r2 = parameters_.reduce2?1:0;
	attr = root.createAttribute("reduce2", H5::PredType::STD_U8LE, scalar);
	attr.write(H5::PredType::NATIVE_UCHAR, &r2);
	attr.close();

	attr = root.createAttribute("xROI", H5::PredType::STD_U32LE, scalar);
	attr.write(H5::PredType::NATIVE_UINT, &parameters_.xROI);
	attr.close();

	attr = root.createAttribute("yROI", H5::PredType::STD_U32LE, scalar);
	attr.write(H5::PredType::NATIVE_UINT, &parameters_.yROI);
	attr.close();

	scalar.close();
	root.close();
}

void HDFAtom<std::vector<std::string> >::Read(std::vector<std::string> &values) {
	std::string value;
	/*
	 * This attribute is an array of std::strings. They are read in by
	 * storing pointers to std::strings in memory controlled by HDF.  To read
	 * the std::strings, read the pointers into a temporary array, then copy
	 * those std::strings to the values array. This way when the values array
	 * is destroyed, it will not try and get rid of space that is under
	 * HDF control.
	 */
    H5::DataSpace attributeSpace = attribute.getSpace();
	hsize_t nPoints;
	nPoints = attributeSpace.getSelectNpoints();
	H5::DataType attrType = attribute.getDataType(); // necessary for attr.read()

	// Declare and initialize std::vector of pointers to std::string attribute list.
	std::vector<char*> ptrsToHDFControlledMemory;
	ptrsToHDFControlledMemory.resize(nPoints);
	// Copy the pointers.
	attribute.read(attrType, &ptrsToHDFControlledMemory[0]);
	// Copy the std::strings into memory the main program has control over.
	unsigned int i;
	for (i = 0; i < ptrsToHDFControlledMemory.size(); i++ ){
		values.push_back(ptrsToHDFControlledMemory[i]);
		free(ptrsToHDFControlledMemory[i]);
	}
}

void addrow( H5::DataSet& ds, const std::vector<double>& rowtowrite )
{
  //Get the space (since it may have grown in length since last time of course )
  H5::DataSpace origspace = ds.getSpace();

  //get the rank, even though I know it is 2
  int rank = origspace.getSimpleExtentNdims();

  //Get the actual dimensions of the ranks.
  hsize_t dims[rank];
  int ndims = origspace.getSimpleExtentDims( dims, NULL);

  //Want to ADD a row, so need to offset at row = nrows, and col = 0;
  hsize_t offset[rank] = { dims[0], 0 }; 
  hsize_t dims_toadd[rank] = { 1, rowtowrite.size() }; //will write 1 row, ncols columns.

  //Compute "new" size (extended by 1 row).
  hsize_t size[rank] = { dims[0]+dims_toadd[0], rowtowrite.size() };

  //Do the extension.
  ds.extend( size );

  //Get the new (extended) space, and select the hyperslab to write the row to.
  origspace = ds.getSpace();
  origspace.selectHyperslab( H5S_SELECT_SET, dims_toadd, offset );

  //Make the "memory" data space?
  H5::DataSpace toaddspace(rank, dims_toadd);

  ds.write(  rowtowrite.data(), H5::PredType::NATIVE_DOUBLE, toaddspace, origspace );

  //Can close toaddspace/origspace with no effect.
  //Can also close/open data set at the beginning of each time with no effect.
}

void ossim_hdf5::getExtents( const H5::DataSet* dataset,
                             std::vector<ossim_uint32>& extents )
{
   extents.clear();
   
   if ( dataset )
   {
      // Get dataspace of the dataset.
      H5::DataSpace dataspace = dataset->getSpace();
      
      // Number of dimensions:
      int ndims = dataspace.getSimpleExtentNdims();
      if ( ndims )
      {
         //hsize_t dims_out[ndims];
         std::vector<hsize_t> dims_out(ndims);
         dataspace.getSimpleExtentDims( &dims_out.front(), 0 );
         for ( ossim_int32 i = 0; i < ndims; ++i )
         {
            extents.push_back(static_cast<ossim_uint32>(dims_out[i]));
         }
      }

      dataspace.close();
   }
}

void Hdf5Handler::getColumnEntries(
        void* data,
        const std::string& dataSetName,
        const hsize_t numEntries,
        const hsize_t offset) const
{
    try
    {
        const ColumnData& columnData(getColumnData(dataSetName));

        columnData.dataSpace.selectHyperslab(
                H5S_SELECT_SET,
                &numEntries,
                &offset);

        const hsize_t outOffset = 0;
        const H5::DataSpace outSpace(1, &numEntries);
        outSpace.selectHyperslab(H5S_SELECT_SET, &numEntries, &outOffset);

        columnData.dataSet.read(
                data,
                columnData.predType,
                outSpace, 
                columnData.dataSpace);
    }
    catch (const H5::Exception&)
    {
        throw hdf5_error("Could not read from dataset");
    }
}

UInt GetDatasetNDim(H5::CommonFG &parentGroup, std::string datasetName) {
    HDFData tmpDataset;
    tmpDataset.InitializeDataset(parentGroup, datasetName);
    H5::DataSpace dataspace = tmpDataset.dataset.getSpace();
    UInt nDims = dataspace.getSimpleExtentNdims();
    dataspace.close();
    tmpDataset.dataset.close();
    return nDims;
}

int H5Signal::signal_count(void)
/*----------------------------*/
{
  H5::DataSpace uspace = dataset.openAttribute("uri").getSpace() ;
  int udims = uspace.getSimpleExtentNdims() ;
  if (udims == 0) return 1 ;  // SCALAR
  else {
    if (udims != 1) throw H5Exception("Dataset's 'uri' attribute has wrong shape: " + uri) ;
    return uspace.getSimpleExtentNpoints() ;
    }
  }

	/**
	 * @brief Returns a pointer to a std::vector<float> containing the values of the selected variable
	 *
	 * This allocates a new std::vector<float> pointer.  Make sure you
	 * delete the contents when you done using it, or you will have a memory leak.
	 *
	 * @param variable
	 * @return std::vector<float> containing the values of the selected variable.
	 */
	std::vector<float>* HDF5FileReader::getVariable(const std::string& variable)
	{
		std::vector<float>* variableData = new std::vector<float>();

		if (this->doesVariableExist(variable))
		{
			//std::cout << "reading " << variable << std::endl;
			//get variable number
//			long variableNum = this->getVariableID(variable);

			//std::cout << "variableNum for " << variable << ": " << variableNum << std::endl;
			//get dim sizes

			H5::Group group = this->current_file->openGroup("Variables");
			//cout << "variable: " << variable << ": " << counts[0] << endl;
			H5::DataSet * dataset = new H5::DataSet(group.openDataSet(variable));
			H5::DataSpace dataspace = dataset->getSpace();
			int rank = dataspace.getSimpleExtentNdims(); //should be 1
			hsize_t count[1];
			hsize_t offset[1] = {0};
//			int ndims = dataspace.getSimpleExtentDims(count, NULL);

			//std::cout << "count[0]: " << count[0] << std::endl;
			float * buffer = new float[count[0]];



			dataspace.selectHyperslab(H5S_SELECT_SET, count, offset);

			H5::DataSpace memspace( rank, count);
			memspace.selectHyperslab(H5S_SELECT_SET, count, offset);

			dataset->read(buffer, H5::PredType::NATIVE_FLOAT, memspace, dataspace);
			//std::cout << "after read" << std::endl;

			//add data to vector type, and delete original array
			variableData->reserve(count[0]);
			for (int i = 0; i < count[0]; i++)
			{
				variableData->push_back(buffer[i]);
			}
			//std::cout << "after adding to variableData vector" << std::endl;

			delete[] buffer;
			delete dataset;
			//std::cout << "finished reading " << variable << std::endl;
			//std::cout << "size of variable: " << variableData.size() << std::endl;
			//std::cout << "dimSizes[0]: " << dimSizes[0] << std::endl;

		}

		return variableData;
	}

   const std::vector<hsize_t> TableDims(){

      if(flags_ != hdf5::READ) 
         throw std::runtime_error("TableDims() is only valid in READ mode");

      H5::DataSet dSet = file_->openDataSet("T00000000");
      H5::DataSpace dSpace = dSet.getSpace();

      std::vector<hsize_t> dims(dSpace.getSimpleExtentNdims());
      dSpace.getSimpleExtentDims(&dims[0]);

      return dims;
   }

 H5::DataSpace dataspace_from_LS (  
   mini_vector<hsize_t, R> const & Ltot, 
   mini_vector<hsize_t, R> const & L, 
   mini_vector<hsize_t, R> const & S, 
   mini_vector<hsize_t, R> const & offset = mini_vector<hsize_t,R>() ) 
 { 
  static const unsigned int rank = R + (IsComplex ? 1 : 0);
  hsize_t totdimsf[rank], dimsf [rank], stridesf[rank], offsetf[rank];  // dataset dimensions
  for (size_t u=0; u<R ; ++u) { offsetf[u] = offset[u]; dimsf[u] = L[u]; totdimsf[u] = Ltot[u]; stridesf[u] = S[u]; }
  if (IsComplex) { offsetf[rank-1]=0; dimsf[rank-1]=2; totdimsf[rank-1] = 2; stridesf[rank-1]=1; }
  H5::DataSpace ds ( rank, totdimsf );
  ds.selectHyperslab (H5S_SELECT_SET , dimsf, offsetf, stridesf);
  return ds;
 }

NDArray<T, Nd> NDArray<T,Nd>::ReadFromH5(const H5::DataSet& h5Dset) {
  H5::DataSpace dspace = h5Dset.getSpace(); 
  int ndim = dspace.getSimpleExtentNdims(); 
  if (ndim>Nd) 
      throw std::range_error("Too many dimensions in H5 dataset for NDArray");
  hsize_t dimSize[ndim];
  dspace.getSimpleExtentDims(dimSize); 
  std::array<std::size_t, Nd> dimSizeArr;
  for (int i=0; i<Nd; ++i) dimSizeArr[i] = dimSize[i];
  NDArray<T, Nd> arr(dimSizeArr);
  // Read in data here
  H5::DataType h5DType = GetH5DataType<T>();
  h5Dset.read(arr.mData, h5DType);
  return arr;
}

void HDF5IO::loadStdVector(const std::string& GroupName, const std::string& Name,
    std::vector<RealType>& V)
{
  try{
    H5::Group FG = getGroup( GroupName );
    H5::DataSet DataSet = FG.openDataSet(Name.c_str());
    H5::DataSpace DataSpace = DataSet.getSpace();
    if(DataSpace.getSimpleExtentNdims() != 1)
      throw(H5::DataSpaceIException("HDF5IO::loadRealVector()","Unexpected multidimentional dataspace."));
    V.resize(DataSpace.getSimpleExtentNpoints());
    DataSet.read(V.data(),H5::PredType::NATIVE_DOUBLE);
    FG.close();
  } catch( const H5::Exception err ){
    RUNTIME_ERROR("HDF5IO::loadRealStdVector");
  }
}

    inline void
    read_values(H5::DataSet& dataset, H5::DataSpace& data_space,
        dimension const& dimx, dimension const& dimy, dimension const& dimz,
        double* values)
    {
        using namespace H5;

        // Define the hyperslab for file based data.
        hsize_t data_offset[dimension::dim] = {
            dimx.offset_, dimy.offset_, dimz.offset_
        };
        hsize_t data_count[dimension::dim] = {
            dimx.count_, dimy.count_, dimz.count_
        };
        data_space.selectHyperslab(H5S_SELECT_SET, data_count, data_offset);

        // Memory dataspace.
        DataSpace mem_space (dimension::dim, data_count);

        // Define the hyperslab for data in memory.
        hsize_t mem_offset[dimension::dim] = { 0, 0, 0 };
        mem_space.selectHyperslab(H5S_SELECT_SET, data_count, mem_offset);

        // Read data to memory.
        dataset.read(values, PredType::NATIVE_DOUBLE, mem_space, data_space);
    }

size_t H5Signal::clock_size(void)
/*-----------------------------*/
{
  try {
    H5::Attribute attr = dataset.openAttribute("clock") ;
    hobj_ref_t ref ;
    attr.read(H5::PredType::STD_REF_OBJ, &ref) ;
    attr.close() ;
    H5::DataSet clk(H5Rdereference(H5Iget_file_id(dataset.getId()), H5R_OBJECT, &ref)) ;
    H5::DataSpace cspace = clk.getSpace() ;
    int cdims = cspace.getSimpleExtentNdims() ;
    hsize_t cshape[cdims] ;
    cspace.getSimpleExtentDims(cshape) ;
    return cshape[0] ;
    }
  catch (H5::AttributeIException e) { }
  return -1 ;
  }

/** Retrieves the dimensions of the dataset */
int hdfutil::GetDsDims (const H5::DataSet & dataset, int dims[3]) {
	H5::DataSpace dataspace = dataset.getSpace();
    bool simple = dataspace.isSimple();
    if (!simple)
        throw std::runtime_error("complex HDF5 dataspace");
	int rank = (int)dataspace.getSimpleExtentNdims();
	if (rank > 3)
        throw std::runtime_error("unsupported dimensionality");

    hsize_t h5_dims[3];
	dataspace.getSimpleExtentDims(h5_dims, NULL);
    for (int i = 0; i < rank; i++)
        dims[i] = (int)h5_dims[i];
    for (int i = rank; i < 3; i++)
        dims[i] =      -1;

    return rank;
}