Compartment_Report_Binary_File_Reader::Compartment_Report_Binary_File_Reader
(const Report_Specification & specs)
: _sequence_start_frame(0),
_frame_counter(0),
_frame_skip(1.0f),
_current_frame(UNDEFINED_FRAME_NUMBER)
{
static Report_Specialization_Register<
Compartment_Report_Binary_File_Reader,
float
> register_float_buffer;
namespace fs = boost::filesystem;
Filepath path = uri_to_filename(specs.data_source());
Filepath filename;
enum Binary_Type
{
Multi_Split,
Unknown
};
Binary_Type binary_type = Unknown;
// Checking which type of file
if (fs::is_directory(path))
{
if (fs::exists((filename = path / (specs.label() + ".rep"))))
{
binary_type = Multi_Split;
}
else if (fs::exists((filename = path / (specs.label() + ".bbp"))))
{
binary_type = Multi_Split;
}
}
else if (fs::exists(path))
{
filename = path;
if (fs::extension(path) == ".rep")
{
binary_type = Multi_Split;
}
else if (fs::extension(path) == ".bbp")
{
binary_type = Multi_Split;
}
}
if (binary_type == Multi_Split)
{
_parser.open(filename.string());
}
else
{
throw_exception(Bad_Data("Compartment_Binary_File_Report_Reader: "
"no proper binary file for " +
specs.data_source() + " found"),
FATAL_LEVEL, __FILE__, __LINE__);
}
}
//-----------------------------------------------------------------------------
void Mesh_Binary_File_Parser::read_mesh(
const Filepath & file,
bool vertex_flag,
bool triangle_flag,
bool triangle_strip_flag,
bool mapping_flag,
Vertex_Index & vertex_count,
Triangle_Index & triangle_count,
Triangle_Index & triangle_strip_length,
Vector_3D_Micron_Array & vertices,
Section_ID_Array & vertex_sections,
Float_Array & vertex_relative_distances,
Vertex_Index_Array & triangles,
Vertex_Index_Array & triangle_strips
)
throw (IO_Error)
{
vertex_count = 0;
triangle_count = 0;
// local variable to store the element count
Vertex_Index vertex_count_tmp = 0 ;
Triangle_Index triangle_count_tmp = 0 ;
Triangle_Index triangle_strip_length_tmp = 0 ;
std::ifstream dataStream((char*)file.string().c_str(), std::ios::binary);
if (!dataStream)
{
throw_exception(
File_Access_Error("Mesh_Binary_File_Parser: cannot "
"open binary file: " + file.string()),
FATAL_LEVEL, __FILE__, __LINE__);
}
dataStream.read((char*)&vertex_count_tmp, sizeof(Vertex_Index));
dataStream.read((char*)&triangle_count_tmp, sizeof(Triangle_Index));
dataStream.read((char*)&triangle_strip_length_tmp, sizeof(Triangle_Index));
// set the seeks
unsigned long vertexseek =
sizeof(Vertex_Index) + sizeof(Triangle_Index) * 2;
unsigned long mappingseek = vertexseek +
vertex_count_tmp * 3 * sizeof(Micron);
unsigned long triangleseek = mappingseek +
vertex_count_tmp * (sizeof(Section_ID) + sizeof(float));
unsigned long trianglestripseek = triangleseek +
triangle_count_tmp * 3 * sizeof(Vertex_Index);
//----------------------------------
// load the vertex data
//----------------------------------
if (vertex_flag) {
// allocating memory
Vector_3D_Micron_Array vertices_tmp(new Vector_3D<Micron>[vertex_count_tmp]) ;
// store the data
dataStream.seekg(vertexseek) ;
for ( Vertex_Index i = 0 ; i < vertex_count_tmp ; ++i )
{
Micron position[3] ;
dataStream.read((char*) &position, 3 * sizeof(Micron));
vertices_tmp[i].x() = position[0];
vertices_tmp[i].y() = position[1];
vertices_tmp[i].z() = position[2];
}
// copying local variables to final result
vertex_count = vertex_count_tmp;
vertices = vertices_tmp ;
}
//----------------------------------
// load the triangle data
//----------------------------------
if (triangle_flag) {
// allocating memory
Vertex_Index_Array triangles_tmp(new Vertex_Index[triangle_count_tmp * 3]) ;
// store the data
dataStream.seekg(triangleseek) ;
dataStream.read((char*)triangles_tmp.get(),
triangle_count_tmp * 3 * sizeof(Vertex_Index));
// copying local variables to final result
triangle_count = triangle_count_tmp;
triangles = triangles_tmp ;
}
if (triangle_strip_flag) {
// allocating memory
Vertex_Index_Array triangles_tmp
(new Vertex_Index[triangle_strip_length_tmp]) ;
// store the data
dataStream.seekg(trianglestripseek) ;
dataStream.read((char*)triangles_tmp.get(),
triangle_strip_length_tmp * sizeof(Vertex_Index));
// copying local variables to final result
triangle_strip_length = triangle_strip_length_tmp;
triangle_strips = triangles_tmp ;
}
//----------------------------------
// load the mapping data
//----------------------------------
if (mapping_flag) {
// allocating memory
Section_ID_Array vertex_sections_tmp(new Section_ID[vertex_count]) ;
Float_Array vertex_relative_distances_tmp(new float[vertex_count]) ;
// store the data
dataStream.seekg(mappingseek) ;
dataStream.read((char*)vertex_sections_tmp.get(),
vertex_count_tmp * sizeof(Section_ID)) ;
dataStream.read((char*)vertex_relative_distances_tmp.get(),
vertex_count_tmp * sizeof(float)) ;
// copying local variables to final result
vertex_sections = vertex_sections_tmp;
vertex_relative_distances = vertex_relative_distances_tmp;
}
if (dataStream.fail())
{
throw_exception(
File_Parse_Error("Mesh_Binary_File_Parser: parse error in file :"
+ file.string()),
FATAL_LEVEL, __FILE__, __LINE__);
}
dataStream.close() ;
}
