Store name and domain sizes as attribute. (db7edc37) · Commits · NDIP / Tool Sources / Direct-Geometry Spectroscopy / DCA / DCA Main

include/dca/io/hdf5/hdf5_reader.hpp

+11 −3

Original line number	Diff line number	Diff line
		@@ -256,9 +256,17 @@ bool HDF5Reader::execute(const std::string& name, func::function<Scalartype, dom

		std::cout << "\n\tstart reading function : " << name;

		// Check sizes.
		H5::DataSet dataset = file_->openDataSet(full_name.c_str());

		// Read sizes.
		std::vector<hsize_t> dims;
		execute(name + "/" + "domain-sizes", dims);
		auto domain_attribute = dataset.openAttribute("domain-sizes");
		hsize_t n_dims;
		domain_attribute.getSpace().getSimpleExtentDims(&n_dims);
		dims.resize(n_dims);
		domain_attribute.read(HDF5_TYPE<hsize_t>::get_PredType(), dims.data());

		// Check sizes.
		if (dims.size() != f.signature())
		throw(std::length_error("The number of domains is different"));
		for (int i = 0; i < f.signature(); ++i) {
		@@ -266,7 +274,7 @@ bool HDF5Reader::execute(const std::string& name, func::function<Scalartype, dom
		throw(std::length_error("The size of domain " + std::to_string(i) + " is different"));
		}

		read(full_name + "/data", HDF5_TYPE<Scalartype>::get_PredType(), f.values());
		read(full_name, HDF5_TYPE<Scalartype>::get_PredType(), f.values());

		return true;
		}

include/dca/io/hdf5/hdf5_writer.hpp

+35 −28

Original line number	Diff line number	Diff line
		@@ -146,8 +146,11 @@ private:

		bool exists(const std::string& name) const;

		void write(const std::string& name, const std::vector<hsize_t>& size, H5::DataType type,
		H5::DataSet write(const std::string& name, const std::vector<hsize_t>& size, H5::DataType type,
		const void* data);
		void addAttribute(const H5::DataSet& set, const std::string& name,
		const std::vector<hsize_t>& size, H5::DataType type, const void* data);
		void addAttribute(const H5::DataSet& set, const std::string& name, const std::string& value);

		std::unique_ptr<H5::H5File> file_;

		@@ -298,27 +301,22 @@ void HDF5Writer::execute(const std::string& name, const func::function<Scalar, d
		if (f.size() == 0)
		return;

		open_group(name);

		std::string new_path = get_path();

		execute("name", f.get_name());
		const std::string full_name = get_path() + "/" + name;

		std::vector<hsize_t> dims;

		for (int l = 0; l < f.signature(); ++l)
		dims.push_back(f[l]);

		execute("domain-sizes", dims);

		// be carefull --> HDF5 is by default row-major, while the function-class is column-major !
		std::reverse(dims.begin(), dims.end());

		std::string full_name = new_path + "/data";
		auto dataset = write(full_name, dims, HDF5_TYPE<Scalar>::get_PredType(), f.values());

		write(full_name, dims, HDF5_TYPE<Scalar>::get_PredType(), f.values());
		addAttribute(dataset, "name", f.get_name());

		close_group();
		std::reverse(dims.begin(), dims.end());
		auto type = HDF5_TYPE<hsize_t>::get_PredType();
		addAttribute(dataset, "domain-sizes", std::vector<hsize_t>{dims.size()}, type, dims.data());
		}

		template <typename Scalar, typename domain_type>
		@@ -327,41 +325,46 @@ void HDF5Writer::execute(const std::string& name,
		if (f.size() == 0)
		return;

		open_group(name);

		std::string new_path = get_path();

		execute("name", f.get_name());
		const std::string full_name = get_path() + "/" + name;

		std::vector<hsize_t> dims;

		for (int l = 0; l < f.signature(); ++l)
		dims.push_back(f[l]);

		execute("domain-sizes", dims);

		// be carefull --> HDF5 is by default row-major, while the function-class is column-major !
		std::reverse(dims.begin(), dims.end());

		// Add real-imaginary dimension
		dims.push_back(2);
		std::string full_name = get_path() + "/data";
		write(full_name, dims, HDF5_TYPE<Scalar>::get_PredType(), f.values());

		close_group();
		auto dataset = write(full_name, dims, HDF5_TYPE<Scalar>::get_PredType(), f.values());

		addAttribute(dataset, "name", f.get_name());

		dims.pop_back();
		std::reverse(dims.begin(), dims.end());
		auto type = HDF5_TYPE<hsize_t>::get_PredType();
		addAttribute(dataset, "domain-sizes", std::vector<hsize_t>{dims.size()}, type, dims.data());
		}

		template <typename Scalar>
		void HDF5Writer::execute(const std::string& name,
		const dca::linalg::Vector<Scalar, dca::linalg::CPU>& V) {
		std::string full_name = get_path() + "/" + name;
		auto dataset =
		write(full_name, std::vector<hsize_t>{V.size()}, HDF5_TYPE<Scalar>::get_PredType(), V.ptr());

		addAttribute(dataset, "name", V.get_name());
		}

		template <typename Scalar>
		void HDF5Writer::execute(const std::string& name,
		const dca::linalg::Vector<std::complex<Scalar>, dca::linalg::CPU>& V) {
		std::string full_name = get_path() + "/" + name;
		write(full_name, std::vector<hsize_t>{V.size(), 2}, HDF5_TYPE<Scalar>::get_PredType(), V.ptr());
		auto dataset = write(full_name, std::vector<hsize_t>{V.size(), 2},
		HDF5_TYPE<Scalar>::get_PredType(), V.ptr());

		addAttribute(dataset, "name", V.get_name());
		}

		template <typename Scalar>
		@@ -377,7 +380,9 @@ void HDF5Writer::execute(const std::string& name,
		linearized[linindex++] = A(i, j);

		std::string full_name = get_path() + "/" + name;
		write(full_name, dims, HDF5_TYPE<Scalar>::get_PredType(), linearized.data());
		auto dataset = write(full_name, dims, HDF5_TYPE<Scalar>::get_PredType(), linearized.data());

		addAttribute(dataset, "name", A.get_name());
		}

		template <typename Scalar>
		@@ -393,7 +398,9 @@ void HDF5Writer::execute(const std::string& name,
		linearized[linindex++] = A(i, j);

		std::string full_name = get_path() + "/" + name;
		write(full_name, dims, HDF5_TYPE<Scalar>::get_PredType(), linearized.data());
		auto dataset = write(full_name, dims, HDF5_TYPE<Scalar>::get_PredType(), linearized.data());

		addAttribute(dataset, "name", A.get_name());
		}

		template <class T>

src/io/hdf5/hdf5_writer.cpp

+21 −2

Original line number	Diff line number	Diff line
		@@ -113,8 +113,8 @@ void HDF5Writer::execute(const std::string& name,
		}
		}

		void HDF5Writer::write(const std::string& name, const std::vector<hsize_t>& dims, H5::DataType type,
		const void* data) {
		H5::DataSet HDF5Writer::write(const std::string& name, const std::vector<hsize_t>& dims,
		H5::DataType type, const void* data) {
		if (exists(name)) {
		H5::DataSet dataset = file_->openDataSet(name.c_str());
		H5::DataSpace dataspace = dataset.getSpace();
		@@ -127,15 +127,34 @@ void HDF5Writer::write(const std::string& name, const std::vector<hsize_t>& dims
		}

		dataset.write(data, type, dataspace, H5P_DEFAULT);
		return dataset;
		}
		else {
		H5::DataSpace dataspace(dims.size(), dims.data());
		H5::DataSet dataset(file_->createDataSet(name.c_str(), type, dataspace));

		dataset.write(data, type, dataspace, H5P_DEFAULT);
		return dataset;
		}
		}

		void HDF5Writer::addAttribute(const H5::DataSet& set, const std::string& name,
		const std::vector<hsize_t>& size, H5::DataType type, const void* data) {
		if (set.attrExists(name)) {
		return;
		}

		H5::DataSpace space(size.size(), size.data());
		auto attribute = set.createAttribute(name, type, space);
		attribute.write(type, data);
		}

		void HDF5Writer::addAttribute(const H5::DataSet& set, const std::string& name,
		const std::string& value) {
		H5::StrType str_type(H5::PredType::C_S1, value.size());
		addAttribute(set, name, std::vector<hsize_t>{1}, str_type, value.c_str());
		}

		bool HDF5Writer::exists(const std::string& name) const {
		auto code = H5Gget_objinfo(file_id_, name.c_str(), 0, NULL);
		return code == 0;