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453 lines (402 loc) · 14 KB
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/* This file is part of PyMesh. Copyright (c) 2015 by Qingnan Zhou */
#include "MshLoader.h"
#include <iostream>
#include <sstream>
#include <vector>
#include <Core/Exception.h>
#include "IOUtils.h"
using namespace PyMesh;
MshLoader::MshLoader(const std::string& filename) {
std::ifstream fin(filename.c_str(), std::ios::in | std::ios::binary);
if (!fin.is_open()) {
std::stringstream err_msg;
err_msg << "failed to open file \"" << filename << "\"";
throw IOError(err_msg.str());
}
// Parse header
std::string buf;
double version;
int type;
fin >> buf;
if (buf != "$MeshFormat") { throw INVALID_FORMAT; }
fin >> version >> type >> m_data_size;
m_binary = (type == 1);
// Some sanity check.
if (m_data_size != 8) {
std::cerr << "Error: data size must be 8 bytes." << std::endl;
throw NOT_IMPLEMENTED;
}
if (sizeof(int) != 4) {
std::cerr << "Error: code must be compiled with int size 4 bytes." << std::endl;
throw NOT_IMPLEMENTED;
}
// Read in extra info from binary header.
if (m_binary) {
int one;
IOUtils::eat_white_space(fin);
fin.read(reinterpret_cast<char*>(&one), sizeof(int));
if (one != 1) {
std::cerr << "Warning: binary msh file " << filename
<< " is saved with different endianness than this machine."
<< std::endl;
throw NOT_IMPLEMENTED;
}
}
fin >> buf;
if (buf != "$EndMeshFormat") { throw NOT_IMPLEMENTED; }
while (!fin.eof()) {
buf.clear();
fin >> buf;
if (buf == "$Nodes") {
parse_nodes(fin);
fin >> buf;
if (buf != "$EndNodes") { throw INVALID_FORMAT; }
} else if (buf == "$Elements") {
parse_elements(fin);
fin >> buf;
if (buf != "$EndElements") { throw INVALID_FORMAT; }
} else if (buf == "$NodeData") {
parse_node_field(fin);
fin >> buf;
if (buf != "$EndNodeData") { throw INVALID_FORMAT; }
} else if (buf == "$ElementData") {
parse_element_field(fin);
fin >> buf;
if (buf != "$EndElementData") { throw INVALID_FORMAT; }
} else if (fin.eof()) {
break;
} else {
parse_unknown_field(fin, buf);
}
}
fin.close();
}
MshLoader::FieldNames MshLoader::get_node_field_names() const {
FieldNames result;
for (FieldMap::const_iterator itr = m_node_fields.begin();
itr != m_node_fields.end(); itr++) {
result.push_back(itr->first);
}
return result;
}
MshLoader::FieldNames MshLoader::get_element_field_names() const {
FieldNames result;
for (FieldMap::const_iterator itr = m_element_fields.begin();
itr != m_element_fields.end(); itr++) {
result.push_back(itr->first);
}
return result;
}
void MshLoader::parse_nodes(std::ifstream& fin) {
size_t num_nodes;
fin >> num_nodes;
m_nodes.resize(num_nodes*3);
if (m_binary) {
size_t num_bytes = (4+3*m_data_size) * num_nodes;
char* data = new char[num_bytes];
IOUtils::eat_white_space(fin);
fin.read(data, num_bytes);
for (size_t i=0; i<num_nodes; i++) {
int node_idx = *reinterpret_cast<int*> (&data[i*(4+3*m_data_size)]) - 1;
m_nodes[node_idx*3] = *reinterpret_cast<Float*>(&data[i*(4+3*m_data_size) + 4]);
m_nodes[node_idx*3+1] = *reinterpret_cast<Float*>(&data[i*(4+3*m_data_size) + 4 + m_data_size]);
m_nodes[node_idx*3+2] = *reinterpret_cast<Float*>(&data[i*(4+3*m_data_size) + 4 + 2*m_data_size]);
}
delete [] data;
} else {
int node_idx;
for (size_t i=0; i<num_nodes; i++) {
fin >> node_idx;
node_idx -= 1;
fin >> m_nodes[node_idx*3]
>> m_nodes[node_idx*3+1]
>> m_nodes[node_idx*3+2];
}
}
if (!m_nodes.allFinite()) {
throw IOError("NaN or Inf detected in input file.");
}
}
void MshLoader::parse_elements(std::ifstream& fin) {
size_t num_elements;
fin >> num_elements;
// Tmp storage of elements;
std::vector<int> triangle_element_idx;
std::vector<int> triangle_elements;
std::vector<int> quad_element_idx;
std::vector<int> quad_elements;
std::vector<int> tet_element_idx;
std::vector<int> tet_elements;
std::vector<int> hex_element_idx;
std::vector<int> hex_elements;
auto get_element_storage = [&](int elem_type) -> std::vector<int>* {
switch (elem_type) {
case 2:
return &triangle_elements;
case 3:
return &quad_elements;
case 4:
return &tet_elements;
case 5:
return &hex_elements;
default:
throw IOError("Unsupported element type encountered");
};
};
auto get_element_idx_storage = [&](int elem_type) -> std::vector<int>* {
switch (elem_type) {
case 2:
return &triangle_element_idx;
case 3:
return &quad_element_idx;
case 4:
return &tet_element_idx;
case 5:
return &hex_element_idx;
default:
throw IOError("Unsupported element type encountered");
};
};
size_t nodes_per_element;
if (m_binary) {
IOUtils::eat_white_space(fin);
int elem_read = 0;
while (elem_read < num_elements) {
// Parse element header.
int elem_type, num_elems, num_tags;
fin.read((char*)&elem_type, sizeof(int));
fin.read((char*)&num_elems, sizeof(int));
fin.read((char*)&num_tags, sizeof(int));
nodes_per_element = num_nodes_per_elem_type(elem_type);
std::vector<int>& elements = *get_element_storage(elem_type);
std::vector<int>& element_idx = *get_element_idx_storage(elem_type);
for (size_t i=0; i<num_elems; i++) {
int elem_idx;
fin.read((char*)&elem_idx, sizeof(int));
elem_idx -= 1;
element_idx.push_back(elem_idx);
// Eat up tags.
for (size_t j=0; j<num_tags; j++) {
int tag;
fin.read((char*)&tag, sizeof(int));
}
// Element values.
for (size_t j=0; j<nodes_per_element; j++) {
int idx;
fin.read((char*)&idx, sizeof(int));
elements.push_back(idx-1);
}
}
elem_read += num_elems;
}
} else {
for (size_t i=0; i<num_elements; i++) {
// Parse per element header
int elem_num, elem_type, num_tags;
fin >> elem_num >> elem_type >> num_tags;
for (size_t j=0; j<num_tags; j++) {
int tag;
fin >> tag;
}
nodes_per_element = num_nodes_per_elem_type(elem_type);
std::vector<int>& elements = *get_element_storage(elem_type);
std::vector<int>& element_idx = *get_element_idx_storage(elem_type);
elem_num -= 1;
element_idx.push_back(elem_num);
// Parse node idx.
for (size_t j=0; j<nodes_per_element; j++) {
int idx;
fin >> idx;
elements.push_back(idx-1); // msh index starts from 1.
}
}
}
auto copy_to_array = [&](
const std::vector<int>& elements,
const int nodes_per_element) {
if (elements.size() % nodes_per_element != 0) {
throw IOError("Parsing elements failed!");
}
m_elements.resize(elements.size());
std::copy(elements.begin(), elements.end(), m_elements.data());
m_nodes_per_element = nodes_per_element;
};
if (!tet_elements.empty()) {
copy_to_array(tet_elements, 4);
m_element_type = 4;
} else if (!hex_elements.empty()) {
copy_to_array(hex_elements, 8);
m_element_type = 5;
} else if (!triangle_elements.empty()) {
copy_to_array(triangle_elements, 3);
m_element_type = 2;
} else if (!quad_elements.empty()) {
copy_to_array(quad_elements, 4);
m_element_type = 3;
} else {
// 0 elements, use triangle by default.
m_element_type = 2;
}
}
void MshLoader::parse_node_field(std::ifstream& fin) {
size_t num_string_tags;
size_t num_real_tags;
size_t num_int_tags;
fin >> num_string_tags;
std::string* str_tags = new std::string[num_string_tags];
for (size_t i=0; i<num_string_tags; i++) {
IOUtils::eat_white_space(fin);
if (fin.peek() == '\"') {
// Handle field name between quoates.
char buf[128];
fin.get(); // remove the quote at the beginning.
fin.getline(buf, 128, '\"');
str_tags[i] = std::string(buf);
} else {
fin >> str_tags[i];
}
}
fin >> num_real_tags;
Float* real_tags = new Float[num_real_tags];
for (size_t i=0; i<num_real_tags; i++)
fin >> real_tags[i];
fin >> num_int_tags;
int* int_tags = new int[num_int_tags];
for (size_t i=0; i<num_int_tags; i++)
fin >> int_tags[i];
if (num_string_tags <= 0 || num_int_tags <= 2) {
delete [] str_tags;
delete [] real_tags;
delete [] int_tags;
throw INVALID_FORMAT;
}
std::string fieldname = str_tags[0];
int num_components = int_tags[1];
int num_entries = int_tags[2];
VectorF field(num_entries * num_components);
delete [] str_tags;
delete [] real_tags;
delete [] int_tags;
if (m_binary) {
size_t num_bytes = (num_components * m_data_size + 4) * num_entries;
char* data = new char[num_bytes];
IOUtils::eat_white_space(fin);
fin.read(data, num_bytes);
for (size_t i=0; i<num_entries; i++) {
int node_idx = *reinterpret_cast<int*>(&data[i*(4+num_components*m_data_size)]);
node_idx -= 1;
size_t base_idx = i*(4+num_components*m_data_size) + 4;
for (size_t j=0; j<num_components; j++) {
field[node_idx * num_components + j] = *reinterpret_cast<Float*>(&data[base_idx+j*m_data_size]);
}
}
delete [] data;
} else {
int node_idx;
for (size_t i=0; i<num_entries; i++) {
fin >> node_idx;
node_idx -= 1;
for (size_t j=0; j<num_components; j++) {
fin >> field[node_idx * num_components + j];
}
}
}
m_node_fields[fieldname] = field;
}
void MshLoader::parse_element_field(std::ifstream& fin) {
size_t num_string_tags;
size_t num_real_tags;
size_t num_int_tags;
fin >> num_string_tags;
std::string* str_tags = new std::string[num_string_tags];
for (size_t i=0; i<num_string_tags; i++) {
IOUtils::eat_white_space(fin);
if (fin.peek() == '\"') {
// Handle field name between quoates.
char buf[128];
fin.get(); // remove the quote at the beginning.
fin.getline(buf, 128, '\"');
str_tags[i] = std::string(buf);
} else {
fin >> str_tags[i];
}
}
fin >> num_real_tags;
Float* real_tags = new Float[num_real_tags];
for (size_t i=0; i<num_real_tags; i++)
fin >> real_tags[i];
fin >> num_int_tags;
int* int_tags = new int[num_int_tags];
for (size_t i=0; i<num_int_tags; i++)
fin >> int_tags[i];
if (num_string_tags <= 0 || num_int_tags <= 2) {
delete [] str_tags;
delete [] real_tags;
delete [] int_tags;
throw INVALID_FORMAT;
}
std::string fieldname = str_tags[0];
int num_components = int_tags[1];
int num_entries = int_tags[2];
VectorF field(num_entries * num_components);
delete [] str_tags;
delete [] real_tags;
delete [] int_tags;
if (m_binary) {
size_t num_bytes = (num_components * m_data_size + 4) * num_entries;
char* data = new char[num_bytes];
IOUtils::eat_white_space(fin);
fin.read(data, num_bytes);
for (size_t i=0; i<num_entries; i++) {
int elem_idx = *reinterpret_cast<int*>(&data[i*(4+num_components*m_data_size)]);
elem_idx -= 1;
size_t base_idx = i*(4+num_components*m_data_size) + 4;
for (size_t j=0; j<num_components; j++) {
field[elem_idx * num_components + j] = *reinterpret_cast<Float*>(&data[base_idx+j*m_data_size]);
}
}
delete [] data;
} else {
int elem_idx;
for (size_t i=0; i<num_entries; i++) {
fin >> elem_idx;
elem_idx -= 1;
for (size_t j=0; j<num_components; j++) {
fin >> field[elem_idx * num_components + j];
}
}
}
m_element_fields[fieldname] = field;
}
void MshLoader::parse_unknown_field(std::ifstream& fin,
const std::string& fieldname) {
std::cerr << "Warning: \"" << fieldname << "\" not supported yet. Ignored." << std::endl;
std::string endmark = fieldname.substr(0,1) + "End"
+ fieldname.substr(1,fieldname.size()-1);
std::string buf("");
while (buf != endmark && !fin.eof()) {
fin >> buf;
}
}
int MshLoader::num_nodes_per_elem_type(int elem_type) {
size_t nodes_per_element = 0;
switch (elem_type) {
case 2:
nodes_per_element = 3; // Triangle
break;
case 3:
nodes_per_element = 4; // Quad
break;
case 4:
nodes_per_element = 4; // Tet
break;
case 5:
nodes_per_element = 8; // hexahedron
break;
default:
std::cerr << "Warning: Element type (" << elem_type << ") is not supported yet."
<< std::endl;
throw NOT_IMPLEMENTED;
}
return nodes_per_element;
}