void Compartment_Report_HDF5_File_Reader::open_data_set
(Cell_GID cell_ID, const char * dataset_name, H5ID & file, H5ID & dataset) const
{
// Opening file for current cell
std::string cell_name = "a" + boost::lexical_cast<std::string>(cell_ID);
Filename filename = _path / (cell_name + ".h5");
file.reset(H5Fopen(filename.string().c_str(), H5F_ACC_RDONLY, H5P_DEFAULT),
H5Fclose);
if (!file)
{
throw_exception(
File_Open_Error("Compartment_Report_HDF5_File_Reader: error "
"opening file:" + filename.string()),
FATAL_LEVEL, __FILE__, __LINE__);
}
// Opening the dataset
std::string dataset_full_name =
"/" + cell_name + "/" + (_report_name + "/") + dataset_name;
H5E_BEGIN_TRY
dataset.reset(H5Dopen(file, dataset_full_name.c_str()), H5Dclose);
H5E_END_TRY;
if (!dataset)
{
throw_exception(
File_Parse_Error("Compartment_Report_HDF5_File_Reader: "
"Dataset " + dataset_full_name + " not found "
"in file: " + filename.string()),
FATAL_LEVEL, __FILE__, __LINE__);
}
}
void Mesh_Binary_File_Writer::write_mesh(
const Filename & file,
Mesh & mesh
)
{
std::ofstream datastream((char*)file.string().c_str(), std::ios::binary);
if (!datastream)
{
throw_exception(
IO_Error("Mesh_Binary_File_Writer: cannot create "
"binary file: " + file.string()),
WARNING_LEVEL, __FILE__, __LINE__);
}
// write header infos for the current mesh
Vertex_Index vertex_count = mesh.vertex_count();
Triangle_Index triangle_count = mesh.triangle_count();
Triangle_Index triangle_strip_length = mesh.triangle_strip_length();
datastream.write((char*)&vertex_count, sizeof(Vertex_Index));
datastream.write((char*)&triangle_count, sizeof(Triangle_Index));
datastream.write((char*)&triangle_strip_length, sizeof(Triangle_Index));
// write the vertices data
datastream.write((char*)mesh.vertices().pointer(),
vertex_count * 3 * sizeof(Micron));
datastream.write((char*)mesh.vertex_sections().pointer(),
vertex_count * sizeof(Section_ID));
datastream.write((char*)mesh.vertex_relative_distances().pointer(),
vertex_count * sizeof(float));
// write the triangles data
datastream.write((char*)mesh.triangles().pointer(),
triangle_count * 3 * sizeof(Vertex_Index));
datastream.write((char*)mesh.triangle_strip().pointer(),
triangle_strip_length * sizeof(Vertex_Index));
}
void Compartment_Voltage_Voxel_Average::open(Filename mapping_filename,
bool portable_format)
{
std::ifstream file(mapping_filename.string().c_str());
if (file.is_open() == false)
{
std::cerr << "Volume compartment mapping file could not be opened ("
<< mapping_filename << ")" << std::endl;
throw std::runtime_error( std::string("Volume compartment mapping file"
" could not be opened (")
+ mapping_filename.string() + ")");
}
if (portable_format)
{
boost::archive::text_iarchive ia(file);
std::cout << "Volume Compartment Mapping: reading from portable text"
"file (" << mapping_filename.string() << ")" << std::endl;
ia >> * this;
std::cout << "Volume Compartment Mapping: in memory" << std::endl;
}
else
{
