void Mesh_File_Reader::load(
Meshes & final_meshes,
const Cell_Target & cells,
const URI & circuit_source,
bool load_vertices,
bool load_triangles,
bool load_mapping,
bool load_triangle_strips)
{
Meshes meshes;
boost::filesystem::path mvd_file = uri_to_filename(circuit_source);
if (mvd_file == "" || boost::filesystem::extension(mvd_file) != ".mvd2")
{
throw_exception(Bad_Data_Source("Loading meshes: circuit_source '" +
circuit_source + "' "),
FATAL_LEVEL, __FILE__, __LINE__);
}
MVD_File_Parser mvd_parser(mvd_file);
mvd_parser.parse_file(cells);
for (Cell_Target::iterator cell_gid = cells.begin();
cell_gid != cells.end();
++cell_gid)
{
MVD_Cell_Index index = mvd_parser.cell_index(*cell_gid);
if (index == UNDEFINED_MVD_CELL_INDEX)
{
std::stringstream msg;
msg << "Loading meshes: bad cell target, neuron gid "
<< *cell_gid << " not in mvd file '" << mvd_file << "'";
throw_exception(Bad_Data(msg.str()),
FATAL_LEVEL, __FILE__, __LINE__);
}
const Label & label = mvd_parser.morphology_names()[index];
if (meshes.find(label) == meshes.end())
{
insert_new_or_updated(label, final_meshes, meshes,
load_vertices, load_triangles,
load_triangle_strips, load_mapping);
}
}
// Final insertion from local container to result
for (Meshes::iterator i = meshes.begin();
i != meshes.end();
++i)
{
// This insertion replaces old existing meshes with its updated
// version also
final_meshes.insert(i.label(), i.ptr());
}
}
void Neurons::load_from_cell_target_and_microcircuit(const Cell_Target & cell_target, Microcircuit & microcircuit)
{
_label =cell_target.label();
Neurons & neurons = microcircuit.neurons();
_microcircuit = neurons._microcircuit;
for (Cell_Target::const_iterator i = cell_target.begin();
i != cell_target.end();
++i)
{
Neurons::iterator neuron = neurons.find(*i);
/** \bug This situation may happen in user code quite easily,
how do we deal with it? */
bbp_assert(neuron != neurons.end());
insert(neuron);
}
}
void test_reader(const char * file_path)
{
Neurons neurons;
Structure_Dataset_Ptr structure = Structure_Dataset_Ptr (new Structure_Dataset());
Microcircuit_Composition_Reader_Ptr reader = Microcircuit_Composition_Reader::create_reader(file_path);
bbp_assert(reader.get());
reader->open();
Cell_Target target;
target.insert(1);
target.insert(3);
reader->load(neurons, target, structure);
// for (Neurons::const_iterator neuron = neurons.begin();
// neuron != neurons.end();
// ++neuron)
// {
// std::cout << *neuron << std::endl;
// }
}
void Compartment_Report_HDF5_File_Reader::update_mapping_and_framesize
(const Cell_Target & target)
{
Cell_Index cell_index = 0;
Report_Frame_Index next_compartment_index = 0;
Compartment_Report_Mapping_Ptr mapping(new Compartment_Report_Mapping);
std::vector<std::vector<Report_Frame_Index> > offset_mapping;
offset_mapping.resize(target.size());
for (Cell_Target::iterator cell_ID = target.begin();
cell_ID != target.end();
++cell_ID, ++cell_index)
{
H5ID file, dataset;
try
{
open_data_set(*cell_ID, "mapping", file, dataset);
}
catch (File_Open_Error)
{
continue;
}
// Opening the dataspace
H5ID space(H5Dget_space(dataset), H5Sclose);
int rank = H5Sget_simple_extent_ndims(space);
if (rank != 2)
{
std::string cell_name =
"a" + boost::lexical_cast<std::string>(*cell_ID);
std::string dataset_name =
"/" + cell_name + "/" + (_report_name + "/") + "mapping";
throw_exception(
File_Parse_Error("Compartment_Report_HDF5_File_Reader: "
"Error, not 2 dimensional array on " +
dataset_name),
FATAL_LEVEL, __FILE__, __LINE__);
}
hsize_t dims[2];
H5Sget_simple_extent_dims(space, dims, NULL);
boost::shared_array<float> data(new float[dims[1]]);
H5Dread(dataset, H5T_NATIVE_FLOAT, H5S_ALL, H5S_ALL, H5P_DEFAULT,
data.get());
// Getting the last section id;
size_t largest_section_id = 0;
for(size_t i = 0; i < dims[1]; ++i)
{
if (data[i] > largest_section_id)
largest_section_id = (size_t) data[i];
}
std::vector<Report_Frame_Index> & offsets = offset_mapping[cell_index];
offsets.resize(largest_section_id + 1, UNDEFINED_REPORT_FRAME_INDEX);
size_t last_section = UNDEFINED_SECTION_ID;
for(size_t i = 0; i < dims[1]; ++i, ++next_compartment_index)
{
size_t section = (size_t) data[i];
if (last_section != section)
{
last_section = section;
// Storing the start index of a new section with at
// least 1 compartment
offsets[section] = next_compartment_index;
}
}
}
// next_compartment_index contains the total number of compartments
_frame_size = next_compartment_index;
// Updating internal mapping pointer.
mapping->swap_mapping(offset_mapping, next_compartment_index);
_mapping = mapping;
_current_cell_target = target;
}
