Commit 550ab08c authored by gbalduzz's avatar gbalduzz
Browse files

Write strings with the native H5 type readable from hdfview.

parent e4650522

include/dca/io/hdf5/hdf5_writer.hpp

+1 −1
Original line number Diff line number Diff line
@@ -146,7 +146,7 @@ private: 


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



  void write(const std::string& name, const std::vector<hsize_t>& size, H5::PredType type,

  void write(const std::string& name, const std::vector<hsize_t>& size, H5::DataType type,

             const void* data);



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

include/dca/phys/parameters/output_parameters.hpp

+6 −6
Original line number Diff line number Diff line
@@ -194,8 +194,8 @@ void OutputParameters::readWrite(ReaderOrWriter& reader_or_writer) { 
  }

}



}  // params

}  // phys

}  // dca

}  // namespace params

}  // namespace phys

}  // namespace dca



#endif  // DCA_PHYS_PARAMETERS_OUTPUT_PARAMETERS_HPP

src/io/hdf5/hdf5_reader.cpp

+11 −5
Original line number Diff line number Diff line
@@ -59,16 +59,22 @@ std::string HDF5Reader::get_path() { 


bool HDF5Reader::execute(const std::string& name, std::string& value) {

  std::string full_name = get_path() + "/" + name;



  if (!exists(full_name)) {

    return false;

  }



  auto dims = readSize(full_name);

  assert(dims.size() == 1);

  value.resize(dims.at(0));

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

  const auto type = dataset.getDataType();



  const auto size = type.getSize();

  value.resize(size);



  dataset.read(value.data(), type);



  // Null string case.

  if (value == std::string{0})

    value = "";



  read(full_name, HDF5_TYPE<char>::get_PredType(), value.data());

  return true;

}

src/io/hdf5/hdf5_writer.cpp

+9 −2
Original line number Diff line number Diff line
@@ -83,9 +83,16 @@ std::string HDF5Writer::get_path() { 
void HDF5Writer::execute(const std::string& name,

                         const std::string& value)  //, H5File& file, std::string path)

{

  // HDF5 does not allow a datatype of size 0.

  if (value.size() == 0)

    return execute(name, std::string{0});



  std::string full_name = get_path() + '/' + name;



  write(full_name, std::vector<hsize_t>{value.size()}, HDF5_TYPE<char>::get_PredType(), value.data());

  // String type.

  H5::StrType datatype(H5::PredType::C_S1, value.size());



  write(full_name, std::vector<hsize_t>{1}, datatype, value.data());

}



void HDF5Writer::execute(const std::string& name,
@@ -106,7 +113,7 @@ void HDF5Writer::execute(const std::string& name, 
  }

}



void HDF5Writer::write(const std::string& name, const std::vector<hsize_t>& dims, H5::PredType type,

void 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());

test/unit/io/hdf5_reader_writer_test.cpp

+11 −6
Original line number Diff line number Diff line
@@ -143,22 +143,27 @@ TEST(HDF5ReaderWriterTest, VectorOfArraysReadWrite) { 
  reader.close_file();

}



TEST(HDF5ReaderWriterTest, VectorOfStringsReadWrite) {

  std::vector<std::string> s1{"foo", "bar", "baz"};

TEST(HDF5ReaderWriterTest, StringAndVectorOfStringsReadWrite) {

  std::vector<std::string> s_vec1{"foo", "", "baz"};

  std::string s1{"bazinga"};

  const std::string filename = "test_vec_of_strings.hdf5";



  // Create test file.

  dca::io::HDF5Writer writer;

  writer.open_file(filename);

  writer.execute("strings", s1);

  writer.execute("single-string", s1);

  writer.execute("strings", s_vec1);

  writer.close_file();



  // Read test file.

  dca::io::HDF5Reader reader;

  reader.open_file(filename);



  std::vector<std::string> s2;

  EXPECT_TRUE(reader.execute("strings", s2));

  //

  std::vector<std::string> s_vec2;

  std::string s2;

  EXPECT_TRUE(reader.execute("strings", s_vec2));

  EXPECT_TRUE(reader.execute("single-string", s2));

  EXPECT_EQ(s_vec1, s_vec2);

  EXPECT_EQ(s1, s2);

}