Compartment_Report_HDF5_File_Reader::Compartment_Report_HDF5_File_Reader
(const Report_Specification & specs) :
_path(uri_to_filename(specs.data_source())),
_report_name(specs.label()),
_sequence_start_frame(0),
_frame_counter(0),
_frame_skip(1.0),
_current_framestamp(UNDEFINED_FRAME_NUMBER)
{
namespace fs = boost::filesystem;
static Report_Specialization_Register<
Compartment_Report_HDF5_File_Reader,
float
> register_float_buffer;
// Finding a suitable cell name from which has a h5 inside the search path.
bool h5_file_found = false;
if (!fs::is_directory(_path))
{
throw_exception(
IO_Error("Compartment_Report_HDF5_File_Reader: data source "
"is not a directory: " + specs.data_source()),
FATAL_LEVEL, __FILE__, __LINE__);
}
fs::directory_iterator entry(_path), end_entry;
Cell_GID cell_GID = UNDEFINED_CELL_GID;
while (cell_GID == UNDEFINED_CELL_GID && entry != end_entry)
{
fs::path filename = entry->path();
std::string cell_name = fs::basename(filename);
char * endptr;
if (fs::is_regular(entry->status()) &&
fs::extension(filename) == ".h5" &&
// Checking if name matches a[0-9]+ pattern and storing the GID
cell_name.size() > 1 && cell_name[0] == 'a' &&
(cell_GID = strtol(&cell_name[1], &endptr, 10)) > 0 &&
*endptr == '\0')
h5_file_found = true;
++entry;
}
if (cell_GID == UNDEFINED_CELL_GID)
{
throw_exception(
Bad_Data("Compartment_Report_HDF5_File_Reader: source path "
"doesn't contain any valid .h5 file" +
specs.data_source()), FATAL_LEVEL, __FILE__, __LINE__);
}
// Not catching any exception here
H5ID file, dataset;
open_data_set(cell_GID, "data", file, dataset);
float start_time, end_time, delta_time;
if (// Trying to read attributes
!read_attribute("tstart", dataset, start_time) ||
!read_attribute("tstop", dataset, end_time) ||
!read_attribute("Dt", dataset, delta_time) ||
// And checking them
start_time != specs.start_time() ||
end_time != specs.end_time() ||
delta_time != specs.timestep())
{
/*!
\todo Exception commented because the forward_skip is not taken into
account in the HDF5. SL - 24.07.08
throw_exception(
Bad_Data("Compartment_Report_HDF5_File_Reader: inconsistent"
" report metadata found for '" + specs.label() +
"' in path " + specs.data_source()),
FATAL_LEVEL, __FILE__, __LINE__);
*/
}
}
