int convert_anim(const char *infname)
{
int i, bufsz;
const struct aiScene *aiscn;
struct goat3d *goat;
char *outfname;
bufsz = output_filename(0, 0, infname, "goatanim");
outfname = alloca(bufsz);
output_filename(outfname, bufsz, infname, "goatanim");
printf("converting %s -> %s\n", infname, outfname);
if(!(aiscn = aiImportFile(infname, ANM_PPFLAGS))) {
fprintf(stderr, "failed to import %s\n", infname);
return -1;
}
goat = goat3d_create();
for(i=0; i<(int)aiscn->mRootNode->mNumChildren; i++) {
process_node(goat, 0, aiscn->mRootNode->mChildren[i]);
}
for(i=0; i<aiscn->mNumAnimations; i++) {
if(process_anim(goat, aiscn->mAnimations[i]) == -1) {
return -1;
}
}
goat3d_save_anim(goat, outfname);
goat3d_free(goat);
aiReleaseImport(aiscn);
return 0;
}
void go() override
{
const std::string comp_type = get_arg("type");
std::unique_ptr<Botan::Transform> compress;
#if defined(BOTAN_HAS_COMPRESSION)
compress.reset(Botan::make_compressor(comp_type, get_arg_sz("level")));
#endif
if(!compress)
{
throw CLI_Error_Unsupported("Compression", comp_type);
}
const std::string in_file = get_arg("file");
std::ifstream in(in_file);
if(!in.good())
{
throw CLI_IO_Error("reading", in_file);
}
const std::string out_file = output_filename(in_file, comp_type);
std::ofstream out(out_file);
if(!in.good())
{
throw CLI_IO_Error("writing", out_file);
}
do_compress(*compress, in, out, get_arg_sz("buf-size"));
}
void run_lexer_on_file( const std::string & filename ) {
std::cout << "Parsing file " << filename << "..." << std::endl;
llvm::SmallString<128> output_filename( filename );
llvm::sys::path::replace_extension( output_filename, ".cpp.lex" );
std::ofstream output( output_filename.c_str() );
clang::CompilerInstance ci;
ci.createDiagnostics(0, 0);
clang::TargetOptions * targ_opts = new clang::TargetOptions();
targ_opts->Triple = llvm::sys::getDefaultTargetTriple();
clang::TargetInfo * targ = clang::TargetInfo::CreateTargetInfo( ci.getDiagnostics(),
*targ_opts );
ci.setTarget( targ );
ci.createFileManager();
ci.createSourceManager( ci.getFileManager() );
ci.createPreprocessor();
const clang::FileEntry * file = ci.getFileManager().getFile( filename );
ci.getSourceManager().createMainFileID( file );
ci.getPreprocessor().EnterMainSourceFile();
ci.getDiagnosticClient().BeginSourceFile( ci.getLangOpts(), &ci.getPreprocessor() );
clang::Token tok;
do {
ci.getPreprocessor().Lex( tok );
output << tok.getName() << '\n';
} while( tok.isNot( clang::tok::eof ) );
ci.getDiagnosticClient().EndSourceFile();
}
int convert(const char *infname)
{
int i, bufsz;
const struct aiScene *aiscn;
struct goat3d *goat;
char *outfname;
bufsz = output_filename(0, 0, infname, "goat3d");
outfname = alloca(bufsz);
output_filename(outfname, bufsz, infname, "goat3d");
printf("converting %s -> %s\n", infname, outfname);
if(!(aiscn = aiImportFile(infname, SCE_PPFLAGS))) {
fprintf(stderr, "failed to import %s\n", infname);
return -1;
}
goat = goat3d_create();
for(i=0; i<(int)aiscn->mNumMaterials; i++) {
struct aiMaterial *aimat = aiscn->mMaterials[i];
struct goat3d_material *mat = goat3d_create_mtl();
process_material(mat, aimat);
goat3d_add_mtl(goat, mat);
}
for(i=0; i<(int)aiscn->mNumMeshes; i++) {
struct aiMesh *aimesh = aiscn->mMeshes[i];
struct goat3d_mesh *mesh = goat3d_create_mesh();
process_mesh(goat, mesh, aimesh);
goat3d_add_mesh(goat, mesh);
}
for(i=0; i<(int)aiscn->mRootNode->mNumChildren; i++) {
process_node(goat, 0, aiscn->mRootNode->mChildren[i]);
}
goat3d_save(goat, outfname);
goat3d_free(goat);
aiReleaseImport(aiscn);
return 0;
}
void plot_output(
double *t, ///< time (I)
double *xd, ///< differential states (I)
double *xa, ///< algebraic states (I)
double *u, ///< controls (I)
double *p_free, ///< global model parameters (I)
double *rwh, ///< real work array (I)
long *iwh, ///< integer work array (I)
InfoPtr *info
){
FILE *fp;
stringstream output_filename("");
// Filename
char problemname[50];
get_pname(problemname);
output_filename << "./RES/" << problemname <<".plt";
if (*t == 0)
fp = fopen(output_filename.str().c_str(), "w");
else
fp = fopen(output_filename.str().c_str(), "a");
if (!fp) {
fprintf(stderr, "Error: Could not open file '%s'!\n",
output_filename.str().c_str());
return;
}
if (*t == 0) {
// write header:
/// Get names of model quantities.
char **xd_name[1]; /* differential state names (O) */
char **xa_name[1]; /* algebraic state names (O) */
char **u_name[1]; /* control names (O) */
char **h_name[1]; /* model stage duration names (O) */
char **p_name[1]; /* global model parameter names (O) */
char *of_name[1]; /* objective name (O) */
get_names(xd_name, xa_name, u_name, h_name, p_name, of_name);
fprintf(fp, "//time\t");
for (int i = 0; i<NY; i++){
fprintf(fp, "%s\t",xd_name[0][i]);
}
for (int i = 0; i<NU; i++){
fprintf(fp, "%s\t",u_name[0][i]);
}
fprintf(fp, "\n");
}
fprintf(fp, "%e\t", *t);
for (int i = 0; i<NY; i++){
fprintf(fp, "%e\t",xd[i]);
}
for (int i = 0; i<NU; i++){
fprintf(fp, "%e\t",u[i]);
}
fprintf(fp, "\n");
// Close file
fclose(fp);
}
void go() override
{
const std::string comp_type = get_arg("type");
const size_t buf_size = get_arg_sz("buf-size");
const size_t comp_level = get_arg_sz("level");
std::unique_ptr<Botan::Compression_Algorithm> compress;
compress.reset(Botan::make_compressor(comp_type));
if(!compress)
{
throw CLI_Error_Unsupported("Compression", comp_type);
}
const std::string in_file = get_arg("file");
std::ifstream in(in_file, std::ios::binary);
if(!in.good())
{
throw CLI_IO_Error("reading", in_file);
}
const std::string out_file = output_filename(in_file, comp_type);
std::ofstream out(out_file, std::ios::binary);
if(!in.good())
{
throw CLI_IO_Error("writing", out_file);
}
Botan::secure_vector<uint8_t> buf;
compress->start(comp_level);
while(in.good())
{
buf.resize(buf_size);
in.read(reinterpret_cast<char*>(&buf[0]), buf.size());
buf.resize(in.gcount());
compress->update(buf);
out.write(reinterpret_cast<const char*>(&buf[0]), buf.size());
}
buf.clear();
compress->finish(buf);
out.write(reinterpret_cast<const char*>(&buf[0]), buf.size());
out.close();
}
void getSokolovOfChainsBulk(string path, string input_name) {
string input_filename(path);
input_filename.append(input_name);
std::ifstream input_file;
input_file.open(input_filename);
string line;
getline (input_file, line);
istringstream linestream(line);
int L, l, m;
long double eps;
string output_name;
linestream >> L >> l >> m >> eps >> output_name;
string output_filename(path);
output_filename.append(output_name);
std::ofstream output_file;
output_file.open(output_filename);
output_file.close();
int max_probs_count = 20;
vector<long double> probs;
probs.reserve(max_probs_count);
int probs_count = 0;
do {
getline (input_file, line);
if (!line.empty()) {
vector<int> errors(readChainErrors(line));
long double prob = GetSokolovBound(L, l, m, eps, errors);
probs.push_back(prob);
++probs_count;
}
if ((probs_count == max_probs_count) or (input_file.eof())) {
output_file.open(output_filename, std::ios::app);
copy(probs.begin(), probs.end(), std::ostream_iterator<long double>(output_file, "\n"));
output_file.close();
probs.clear();
probs.reserve(max_probs_count);
probs_count = 0;
}
std::cout << probs.size() << "\n";
}
while (!input_file.eof());
input_file.close();
}
void
Transcoder::run()
{
position_ = eta_ = audio_b_ = video_b_ = -1;
stopping_ = false;
pass_ = extra_args_.contains("--two-pass") ? 0 : -1;
proc_.start(ffmpeg2theora(), QStringList() << "--frontend"
<< extra_args_
<< "--output" << output_filename()
<< input_filename());
if (proc_.waitForStarted())
exec();
else
emit statusUpdate("Encoding failed to start");
}
static void write_log(gpr_timer_log *log) {
size_t i;
if (output_file == NULL) {
output_file = fopen(output_filename(), "w");
}
for (i = 0; i < log->num_entries; i++) {
gpr_timer_entry *entry = &(log->log[i]);
if (gpr_time_cmp(entry->tm, gpr_time_0(entry->tm.clock_type)) < 0) {
entry->tm = gpr_time_0(entry->tm.clock_type);
}
fprintf(output_file,
"{\"t\": %" PRId64
".%09d, \"thd\": \"%d\", \"type\": \"%c\", \"tag\": "
"\"%s\", \"file\": \"%s\", \"line\": %d, \"imp\": %d}\n",
entry->tm.tv_sec, entry->tm.tv_nsec, entry->thd, entry->type,
entry->tagstr, entry->file, entry->line, entry->important);
}
}
int main(int argc, char **argv)
{
try
{
TCLAP::CmdLine cmd("Centers a mesh", ' ', "1.0");
TCLAP::ValueArg<std::string> log_filename("l","logfile", "Log file name (default is convert.log)", false, "convert.log", "string");
cmd.add( log_filename );
TCLAP::UnlabeledValueArg<std::string> input_filename( "input-filename", "Input file name", true, "", "InputFile" );
cmd.add( input_filename );
TCLAP::UnlabeledValueArg<std::string> output_filename( "output-filename", "Output file name", true, "", "OutputFile" );
cmd.add( output_filename );
cmd.parse( argc, argv );
if ( !log_filename.getValue().empty() )
viennamesh_log_add_logging_file(log_filename.getValue().c_str(), NULL);
viennamesh::context_handle context;
viennamesh::algorithm_handle mesh_reader = context.make_algorithm("mesh_reader");
mesh_reader.set_input( "filename", input_filename.getValue() );
mesh_reader.run();
viennamesh::algorithm_handle center_mesh = context.make_algorithm("center_mesh");
center_mesh.set_default_source(mesh_reader);
center_mesh.run();
viennamesh::algorithm_handle mesh_writer = context.make_algorithm("mesh_writer");
mesh_writer.set_default_source(center_mesh);
mesh_writer.set_input( "filename", output_filename.getValue() );
mesh_writer.run();
}
catch (TCLAP::ArgException &e) // catch any exceptions
{
std::cerr << "error: " << e.error() << " for arg " << e.argId() << std::endl;
}
return 0;
}
int main(int argc, char* argv[]) {
if (argc != 2) {
std::cerr << "Usage: " << argv[0] << " INFILE\n";
exit(1);
}
std::string output_format("SQLite");
std::string input_filename(argv[1]);
std::string output_filename("multipolygon.db");
OGRDataSource* data_source = initialize_database(output_format, output_filename);
osmium::area::ProblemReporterOGR problem_reporter(data_source);
osmium::area::Assembler::config_type assembler_config(&problem_reporter);
assembler_config.enable_debug_output();
osmium::area::MultipolygonCollector<osmium::area::Assembler> collector(assembler_config);
std::cerr << "Pass 1...\n";
osmium::io::Reader reader1(input_filename);
collector.read_relations(reader1);
reader1.close();
std::cerr << "Pass 1 done\n";
index_type index_pos;
index_type index_neg;
location_handler_type location_handler(index_pos, index_neg);
location_handler.ignore_errors();
TestHandler test_handler(data_source);
std::cerr << "Pass 2...\n";
osmium::io::Reader reader2(input_filename);
osmium::apply(reader2, location_handler, test_handler, collector.handler([&test_handler](const osmium::memory::Buffer& area_buffer) {
osmium::apply(area_buffer, test_handler);
}));
reader2.close();
std::cerr << "Pass 2 done\n";
OGRDataSource::DestroyDataSource(data_source);
OGRCleanupAll();
}
int main(int argc, char* argv[]) {
if (argc != 2) {
std::cerr << "Usage: " << argv[0] << " INFILE\n";
exit(1);
}
std::string output_format("SQLite");
std::string input_filename(argv[1]);
std::string output_filename("testdata-overview.db");
::unlink(output_filename.c_str());
osmium::io::Reader reader(input_filename);
index_type index;
location_handler_type location_handler(index);
location_handler.ignore_errors();
TestOverviewHandler handler(output_format, output_filename);
osmium::apply(reader, location_handler, handler);
reader.close();
}
int main(int argc, char** argv)
{
if (argc != 3) {
std::cerr << "Usage: urdf_to_collada input.urdf output.dae" << std::endl;
return -1;
}
ros::init(argc, argv, "urdf_to_collada");
std::string input_filename(argv[1]);
std::string output_filename(argv[2]);
urdf::Model robot_model;
if( !robot_model.initFile(input_filename) ) {
ROS_ERROR("failed to open urdf file %s",input_filename.c_str());
}
collada_urdf::WriteUrdfModelToColladaFile(robot_model, output_filename);
std::cout << std::endl << "Document successfully written to " << output_filename << std::endl;
return 0;
}
void dot_graph(const binspector_analyzer_t::structure_map_t& struct_map,
const std::string& starting_struct,
const boost::filesystem::path& output_root)
{
boost::filesystem::path output_filename(output_root / "graph.gv");
boost::filesystem::ofstream output(output_filename);
dot_graph_t graph;
assert (output);
graph.name_m = "G";
graph.type_m = "digraph";
//graph.setting_vector_m.push_back("node [shape=box]");
//graph.setting_vector_m.push_back("rankdir=TB");
//graph.setting_vector_m.push_back("packMode=clust");
graph.setting_vector_m.push_back("outputMode=nodesfirst");
adobe::name_t starting_name(starting_struct.c_str());
std::string starting_id(name_map(starting_name));
dot_node_t node;
node.attribute_map_m["label"] = starting_name.c_str();
node.id_m = starting_id;
graph.node_vector_m.push_back(node);
graph_struct(struct_map,
starting_name,
starting_id,
binspector_analyzer_t::typedef_map_t(),
0,
graph);
format_graph(graph, output);
std::cerr << "File written to " << output_filename.string() << '\n';
}
int main(int argc, char* argv[]) {
static struct option long_options[] = {
{"help", no_argument, 0, 'h'},
{"format", required_argument, 0, 'f'},
{0, 0, 0, 0}
};
std::string output_format("SQLite");
while (true) {
int c = getopt_long(argc, argv, "hf:", long_options, 0);
if (c == -1) {
break;
}
switch (c) {
case 'h':
print_help();
exit(0);
case 'f':
output_format = optarg;
break;
default:
exit(1);
}
}
std::string input_filename;
std::string output_filename("ogr_out");
int remaining_args = argc - optind;
if (remaining_args > 2) {
std::cerr << "Usage: " << argv[0] << " [OPTIONS] [INFILE [OUTFILE]]" << std::endl;
exit(1);
} else if (remaining_args == 2) {
input_filename = argv[optind];
output_filename = argv[optind+1];
} else if (remaining_args == 1) {
input_filename = argv[optind];
} else {
input_filename = "-";
}
index_type index_pos;
location_handler_type location_handler(index_pos);
osmium::experimental::FlexReader<location_handler_type> exr(input_filename, location_handler, osmium::osm_entity_bits::object);
MyOGRHandler ogr_handler(output_format, output_filename);
while (auto buffer = exr.read()) {
osmium::apply(buffer, ogr_handler);
}
exr.close();
std::vector<const osmium::Relation*> incomplete_relations = exr.collector().get_incomplete_relations();
if (!incomplete_relations.empty()) {
std::cerr << "Warning! Some member ways missing for these multipolygon relations:";
for (const auto* relation : incomplete_relations) {
std::cerr << " " << relation->id();
}
std::cerr << "\n";
}
google::protobuf::ShutdownProtobufLibrary();
}
po::variables_map ParseCommandLineOptions(int argc, char* argv[])
{/*{{{*/
////////////////////////////////////////////////////////////////////////////////
//{{{ record command line options
string output_filename("EnsNVeBath");
string command_opt("");
for(int i=1; i<argc; ++i)
command_opt += argv[i];
cout << "Command line options recieved: " << command_opt << endl;
output_filename += command_opt;
//}}}
////////////////////////////////////////////////////////////////////////////////
////////////////////////////////////////////////////////////////////////////////
//{{{ Set path
char *env_path = std::getenv("CCE_PROJ_PATH");
if(env_path!=NULL)
{
PROJECT_PATH = env_path;
cout << "PROJECT_PATH got from environment varialbe: ";
}
else
{
char pwd[500];
getcwd(pwd, sizeof(pwd));
PROJECT_PATH = pwd;
cout << "PROJECT_PATH set as present working directory (pwd): ";
}
cout << PROJECT_PATH << endl;
LOG_PATH = PROJECT_PATH + "/dat/log/";
INPUT_PATH = PROJECT_PATH + "/dat/input/";
OUTPUT_PATH = PROJECT_PATH + "/dat/output/";
CONFIG_PATH = PROJECT_PATH + "/dat/config/";
DEBUG_PATH = PROJECT_PATH + "/dat/debug/";
//}}}
////////////////////////////////////////////////////////////////////////////////
////////////////////////////////////////////////////////////////////////////////
//{{{ Parse command line options
po::variables_map para;
po::options_description desc("Allowed options");
desc.add_options()
("help,h", "Print help message")
("input,i", po::value<string>()->default_value("None"), "Input file name (not used)")
("output,o", po::value<string>()->default_value(output_filename), "Output .mat file of results")
("logfile,l", po::value<string>()->default_value("EnsembleCCE.conf"), "Config. file of logging")
("position,P", po::value<string>()->default_value("0.0 0.0 0.0"), "Central spin position")
("state0,a", po::value<int>()->default_value(0), "Central spin state index - a")
("state1,b", po::value<int>()->default_value(1), "Central spin state index - b")
("cce,c", po::value<int>()->default_value(3), "CCE order")
("cutoff,d", po::value<double>()->default_value(300.0), "Cut-off distance of bath spins")
("polarization,z", po::value<string>()->default_value("0.0 0.0 0.0"), "bath spin polarization")
("dephasing_rate,r", po::value<double>()->default_value(10000.0), "dephasing rate of bath spins")
("dephasing_axis,x", po::value<string>()->default_value("1.0 1.0 1.0"), "dephasing axis of bath spins")
("length,L", po::value<double>()->default_value(3.57), "size of unit cell in angstrom (default diamond)")
("num_cell,u", po::value<int>()->default_value(8), "atom num in unit cell (default diamond)")
("concentration,C", po::value<double>()->default_value(1.0), "bath concentration in ppm")
("max_number,M", po::value<int>()->default_value(2000), "Max bath spin number")
("number,N", po::value<int>()->default_value(100), "bath spin number")
("seed,D", po::value<int>()->default_value(1), "bath seed")
("isotope", po::value<string>()->default_value("E"), "bath spin isotope")
("nTime,n", po::value<int>()->default_value(101), "Number of time points")
("start,s", po::value<double>()->default_value(0.0), "Start time (in unit of sec.)")
("finish,f", po::value<double>()->default_value(0.0002), "Finish time (in unit of sec.)")
("magnetic_field,B", po::value<string>()->default_value("0.1 0.1 0.1"), "magnetic field vector in Tesla")
("pulse,p", po::value<string>()->default_value("CPMG"), "Pulse name")
("pulse_num,m", po::value<int>()->default_value(1), "Pulse number")
;
po::store(parse_command_line(argc, argv, desc), para);
ifstream ifs("config.cfg");
if (ifs!=NULL)
po::store(parse_config_file(ifs,desc),para);
else
cout << "No configure file found." << endl;
po::notify(para);
PrintVariableMap(para);
if (para.count("help")) {
cout << desc;
exit(0);
}
//}}}
////////////////////////////////////////////////////////////////////////////////
return para;
}/*}}}*/
int
export_png_rgb_16(image *i, output *output)
{
const char *fn;
int shouldclose;
png_structp png_ptr;
png_infop info_ptr;
png_uint_32 n, x, y, pi;
pixelref src;
colour rgb;
png_bytep pp;
uint16_t *bp;
FILE *fp;
pixel_converter_fn converter;
converter = convert_pixels(i->format, PF_RGB, 16);
if(!converter)
{
fprintf(stderr, "cannot locate a suitable format converter for RGB-16\n");
return -1;
}
fn = output_filename(output, i, &shouldclose);
fp = fopen(fn, "wb");
if(!fp)
{
return -1;
}
png_ptr = png_create_write_struct(PNG_LIBPNG_VER_STRING, NULL, NULL, NULL);
if(!png_ptr)
{
return -1;
}
info_ptr = png_create_info_struct(png_ptr);
if(!info_ptr)
{
return -1;
}
png_init_io(png_ptr, fp);
png_set_IHDR(png_ptr, info_ptr, i->width, i->height, 16, PNG_COLOR_TYPE_RGB, PNG_INTERLACE_NONE, PNG_COMPRESSION_TYPE_BASE, PNG_FILTER_TYPE_BASE);
png_write_info(png_ptr, info_ptr);
pp = (png_bytep) malloc(i->width * 3 * sizeof(uint16_t));
bp = (uint16_t *) pp;
src.pixel[0] = i->pixels[0];
src.pixel[1] = i->pixels[1];
src.pixel[2] = i->pixels[2];
for(y = 0, pi = 0; y < i->height; y++)
{
for(n = 0, x = 0; x < i->width; x++, pi++)
{
converter(src, &rgb);
src.pixel[0]++;
src.pixel[1]++;
src.pixel[2]++;
bp[n] = htons(rgb.p.rgb.r);
n++;
bp[n] = htons(rgb.p.rgb.g);
n++;
bp[n] = htons(rgb.p.rgb.b);
n++;
}
png_write_row(png_ptr, pp);
}
png_write_end(png_ptr, NULL);
free(pp);
fclose(fp);
png_free_data(png_ptr, info_ptr, PNG_FREE_ALL, -1);
png_destroy_write_struct(&png_ptr, NULL);
return 0;
}
int main(int argc, char **argv)
{
try
{
TCLAP::CmdLine cmd("Clips elements based on a hyperplane", ' ', "1.0");
TCLAP::ValueArg<std::string> log_filename("l","logfile", "Log file name (default is convert.log)", false, "convert.log", "string");
cmd.add( log_filename );
TCLAP::ValueArg<std::string> input_filetype("","inputtype", "Input file type. Can be\nauto - ViennaMesh automatically detects the file format (default)\nvtk - for VTK files\nmesh - for Netgen .mesh files\npoly - for Tetgen .poly files\ndeva - for GTS deva files", false, "auto", "string");
cmd.add( input_filetype );
TCLAP::ValueArg<std::string> output_filetype("","outputtype", "Output file type. Can be\nauto - ViennaMesh automatically detects the file format (default)\nvtk - for VTK files\nvmesh - for Vienna vmesh files", false, "auto", "string");
cmd.add( output_filetype );
TCLAP::ValueArg<std::string> hyperplane_point_string("p","hyperplane_point", "Point of the clip hyperplane", true, "", "string");
cmd.add( hyperplane_point_string );
TCLAP::ValueArg<std::string> hyperplane_normal_string("n","hyperplane_normal", "Normal vector of the clip hyperplane", true, "", "string");
cmd.add( hyperplane_normal_string );
TCLAP::UnlabeledValueArg<std::string> input_filename( "input-filename", "Input file name", true, "", "InputFile" );
cmd.add( input_filename );
TCLAP::UnlabeledValueArg<std::string> output_filename( "output-filename", "Output file name", true, "", "OutputFile" );
cmd.add( output_filename );
cmd.parse( argc, argv );
viennamesh::logger().register_callback( new viennamesh::FileStreamCallback<viennamesh::FileStreamFormater>( log_filename.getValue() ) );
viennamesh::algorithm_handle reader( new viennamesh::io::mesh_reader() );
reader->set_input( "filename", input_filename.getValue() );
if (input_filetype.isSet() && (input_filetype.getValue() != "auto"))
reader->set_input( "file_type", input_filetype.getValue() );
reader->run();
viennamesh::dynamic_point hyperplane_point = viennamesh::dynamic_point_from_string( hyperplane_point_string.getValue() );
viennamesh::dynamic_point hyperplane_normal = viennamesh::dynamic_point_from_string( hyperplane_normal_string.getValue() );
viennamesh::algorithm_handle clip( new viennamesh::hyperplane_clip() );
clip->set_input( "mesh", reader->get_output("mesh") );
clip->set_input( "hyperplane_point", hyperplane_point );
clip->set_input( "hyperplane_normal", hyperplane_normal );
clip->run();
viennamesh::algorithm_handle writer( new viennamesh::io::mesh_writer() );
writer->set_input( "mesh", clip->get_output("mesh") );
writer->set_input( "filename", output_filename.getValue() );
if (output_filetype.isSet() && (output_filetype.getValue() != "auto"))
writer->set_input( "file_type", output_filetype.getValue() );
writer->run();
}
catch (TCLAP::ArgException &e) // catch any exceptions
{
std::cerr << "error: " << e.error() << " for arg " << e.argId() << std::endl;
}
return 0;
}
int main(int argc, char **argv)
{
try
{
TCLAP::CmdLine cmd("Maps/Renames segments", ' ', "1.0");
TCLAP::ValueArg<std::string> log_filename("l","logfile", "Log file name (default is convert.log)", false, "convert.log", "string");
cmd.add( log_filename );
TCLAP::ValueArg<std::string> input_filetype("","inputtype", "Input file type. Can be\nauto - ViennaMesh automatically detects the file format (default)\nvtk - for VTK files\nmesh - for Netgen .mesh files\npoly - for Tetgen .poly files\ndeva - for GTS deva files", false, "auto", "string");
cmd.add( input_filetype );
TCLAP::ValueArg<std::string> output_filetype("","outputtype", "Output file type. Can be\nauto - ViennaMesh automatically detects the file format (default)\nvtk - for VTK files\nvmesh - for Vienna vmesh files", false, "auto", "string");
cmd.add( output_filetype );
TCLAP::ValueArg<std::string> segment_mapping_string("m","segment-mapping", "Segment mapping. Syntax: \"src_id,dst_id;src_id,dst_id\"", true, "", "string");
cmd.add( segment_mapping_string );
TCLAP::UnlabeledValueArg<std::string> input_filename( "input-filename", "Input file name", true, "", "InputFile" );
cmd.add( input_filename );
TCLAP::UnlabeledValueArg<std::string> output_filename( "output-filename", "Output file name", true, "", "OutputFile" );
cmd.add( output_filename );
cmd.parse( argc, argv );
viennamesh::logger().register_callback( new viennamesh::FileStreamCallback<viennamesh::FileStreamFormater>( log_filename.getValue() ) );
viennamesh::algorithm_handle reader( new viennamesh::io::mesh_reader() );
reader->set_input( "filename", input_filename.getValue() );
if (input_filetype.isSet() && (input_filetype.getValue() != "auto"))
reader->set_input( "file_type", input_filetype.getValue() );
reader->run();
std::map<int, int> segment_mapping;
std::list<std::string> split_mappings = stringtools::split_string( segment_mapping_string.getValue(), ";" );
for (std::list<std::string>::const_iterator mit = split_mappings.begin(); mit != split_mappings.end(); ++mit)
{
std::list<std::string> from_to = stringtools::split_string( *mit, "," );
std::list<std::string>::const_iterator it = from_to.begin();
if (it == from_to.end())
continue;
int src_segment_id = lexical_cast<int>(*it);
++it;
if (it == from_to.end())
continue;
int dst_segment_id = lexical_cast<int>(*it);
segment_mapping[src_segment_id] = dst_segment_id;
}
viennamesh::algorithm_handle map_segments( new viennamesh::map_segments() );
map_segments->set_input( "mesh", reader->get_output("mesh") );
map_segments->set_input( "segment_mapping", segment_mapping );
map_segments->run();
viennamesh::algorithm_handle writer( new viennamesh::io::mesh_writer() );
writer->set_input( "mesh", map_segments->get_output("mesh") );
writer->set_input( "quantities", reader->get_output("quantities") );
writer->set_input( "filename", output_filename.getValue() );
if (output_filetype.isSet() && (output_filetype.getValue() != "auto"))
writer->set_input( "file_type", output_filetype.getValue() );
writer->run();
}
catch (TCLAP::ArgException &e) // catch any exceptions
{
std::cerr << "error: " << e.error() << " for arg " << e.argId() << std::endl;
}
return 0;
}
int main() {
//std::vector<int> items = {1,2,3,4,5,6,7,8,9,10};
std::string filename("sampleEmbedding_200.txt");
//std::string filename("iris.data");
std::vector< std::vector<double> > items = load_data(filename);
// generate similarity matrix
unsigned int size = items.size();
Eigen::MatrixXd m = Eigen::MatrixXd::Zero(size,size);
std::cout << "------------" << std::endl;
for (unsigned int i=0; i < size; i++) {
for (unsigned int j=0; j < size; j++) {
// generate similarity
//int d = items[i] - items[j];
double d = eculidean_distance(items[i], items[j]);
int similarity = exp(-d*d / 1);
m(i,j) = similarity;
m(j,i) = similarity;
}
}
// the number of eigenvectors to consider. This should be near (but greater) than the number of clusters you expect. Fewer dimensions will speed up the clustering
int numDims = size;
// do eigenvalue decomposition
SpectralClustering* c = new SpectralClustering(m, numDims);
// whether to use auto-tuning spectral clustering or kmeans spectral clustering
bool autotune = false;
std::vector<std::vector<int> > clusters;
if (autotune) {
// auto-tuning clustering
clusters = c->clusterRotate();
} else {
// how many clusters you want
int numClusters = 10;
clusters = c->clusterKmeans(numClusters);
}
// output clustered items
// items are ordered according to distance from cluster centre
for (unsigned int i=0; i < clusters.size(); i++) {
std::cout << "Cluster " << i << ": " << "Item ";
std::copy(clusters[i].begin(), clusters[i].end(), std::ostream_iterator<int>(std::cout, ", "));
std::cout << std::endl;
}
std::map<int, int> sampleid_to_clusterid;
for (unsigned int i = 0; i < clusters.size(); i++) {
for (unsigned int j = 0; j < clusters[i].size(); j++){
sampleid_to_clusterid.insert(std::make_pair(clusters[i][j], i));
}
}
std::string output_filename("sample_assignment.txt");
std::ofstream out(output_filename.c_str(), std::ios::out);
if(!out) {
std::cerr << "Can't open output file " << output_filename << std::endl;
return 0;
}
std::map<int, int>::iterator it;
for(it = sampleid_to_clusterid.begin(); it != sampleid_to_clusterid.end(); it++) {
out << it->second << std::endl;
}
out.close();
}
void motion_output(long *imos, ///< index of model stage (I)
long *imsn, ///< index of m.s. node on current model stage (I)
double *ts, ///< time at m.s. node (I)
double *te, ///< time at end of m.s. interval (I)
double *sd, ///< differential states at m.s. node (I)
double *sa, ///< algebraic states at m.s. node (I)
double *u, ///< controls at m.s. node (I)
double *udot, ///< control slopes at m.s. node (I)
double *ue, ///< controls at end of m.s. interval (I)
double *uedot, ///< control slopes at end of m.s. interval (I)
double *p_free, ///< global model parameters (I)
double *pr, ///< local i.p.c. parameters (I)
double *ccxd, double *mul_ccxd, ///< multipliers of continuity conditions (I)
#if defined(PRSQP) || defined(EXTPRSQP)
double *ares, double *mul_ares,
#endif
double *rd, double *mul_rd, ///< multipliers of decoupled i.p.c. (I)
double *rc, double *mul_rc, ///< multipliers of coupled i.p.c. (I)
double *obj, double *rwh, ///< real work array (I)
long *iwh ///< integer work array (I)
) {
FILE *fp;
stringstream output_filename("");
// Filename
char problemname[50];
get_pname(problemname);
output_filename << "./RES/" << problemname <<".mot";
if ((*imsn == 0) && (*imos == 0))
fp = fopen(output_filename.str().c_str(), "w");
else
fp = fopen(output_filename.str().c_str(), "a");
if (!fp) {
fprintf(stderr, "Error: Could not open file '%s'!\n",
output_filename.str().c_str());
return;
}
/* Create and reset file when we're in the first MS-knot.
* otherwise just append data
*/
if ((*imsn == 0) && (*imos == 0)) {
// write header:
/// Get names of model quantities.
char **xd_name[1]; /* differential state names (O) */
char **xa_name[1]; /* algebraic state names (O) */
char **u_name[1]; /* control names (O) */
char **h_name[1]; /* model stage duration names (O) */
char **p_name[1]; /* global model parameter names (O) */
char *of_name[1]; /* objective name (O) */
get_names(xd_name, xa_name, u_name, h_name, p_name, of_name);
// Objective:
fprintf(fp, "COT: %e\n", *obj);
// Print parameters first:
fprintf(fp, "//");
for (int i = 0; i<NPFree; i++){
fprintf(fp, "%s\t",p_name[0][i]);
}
fprintf(fp, "\n");
for (int i = 0; i<NPFree; i++){
fprintf(fp, "%e\t",p_free[i]);
}
fprintf(fp, "\n");
// States and timing:
fprintf(fp, "//imos\t");
fprintf(fp, "imsn\t");
fprintf(fp, "time\t");
for (int i = 0; i<NY; i++){
fprintf(fp, "%s\t",xd_name[0][i]);
}
for (int i = 0; i<NU; i++){
fprintf(fp, "%s\t",u_name[0][i]);
}
fprintf(fp, "\n");
}
fprintf(fp, "%li\t", *imos);
fprintf(fp, "%li\t", *imsn);
fprintf(fp, "%e\t", *ts);
for (int i = 0; i<NY; i++){
fprintf(fp, "%e\t",sd[i]);
}
for (int i = 0; i<NU; i++){
fprintf(fp, "%e\t",u[i]);
}
fprintf(fp, "\n");
// Close file
fclose(fp);
}
int main(int argc, char** argv)
{
// abort if the user didn't pass the correct number of command line args
if (argc != 4)
{
fprintf
(
stderr,
"Error! Invalid command line arguments.\n"
"Usage: %s [initial_grid.png] [output_pattern] [iterations]\n",
argv[0]
);
return -1;
} else if (argc > 4) {
fprintf
(
stderr,
"Warning! Ignoring all but the first 3 command line arguments\n"
"Usage: %s [initial_grid.png] [output_pattern] [iterations]\n",
argv[0]
);
}
// detect the number of iterations
unsigned iterations = atoi(argv[3]);
if (iterations < 1)
{
fprintf(stderr, "Error! Iteration count must be at least 1\n");
return -1;
}
unsigned width;
unsigned height;
// double buffered cell memory.
// cell_grid_read is NULL to tell pngrw_read_file() to allocate new memory for us
unsigned char* cell_grid_read = NULL;
unsigned char* cell_grid_write;
// attempt to load the inital cell grid. cell_grid_read will be allocated
unsigned bytes = pngrw_read_file(&cell_grid_read, &width, &height, argv[1]);
if (bytes == 0)
// error messages printed from inside pngrw_read_file()
return -1;
if (width < 1)
{
fprintf(stderr, "Error! %s must have a width >= 1\n", argv[1]);
delete[] cell_grid_read;
return -1;
}
if (height < 1)
{
fprintf(stderr, "Error! %s must have a height >= 1\n", argv[1]);
delete[] cell_grid_read;
return -1;
}
// we're double buffering, pngrw_read_file only allocated the input buffer
cell_grid_write = new unsigned char[bytes];
// need to init to 0 so valgrind won't complain (it can't track single-bit initializations)
memset(cell_grid_write, 0, bytes);
// simulate the cell grid for 'iterations' steps
output_filename_t output_filename(argv[2], iterations);
double start = get_timestamp();
for (unsigned ix = 0; ix < iterations; ix++)
{
// simulate one time step (generation)
recalculate_grid_cpu(cell_grid_write, cell_grid_read, width, height);
// write the new cell grid to a png file
pngrw_write_file
(
output_filename.str,
cell_grid_write,
width,
height
);
output_filename.next_filename();
// swap buffers
unsigned char* swap = cell_grid_read;
cell_grid_read = cell_grid_write;
cell_grid_write = swap;
}
double elapsed_sec = get_timestamp() - start;
// cleanup
delete[] cell_grid_read;
delete[] cell_grid_write;
printf
(
"Success! Finished %s ~ %u iterations in %lf seconds ~ %lf cells/sec\n",
argv[1],
iterations,
elapsed_sec,
((double)width * (double)height * (double)iterations) / elapsed_sec
);
return 0;
}
int main(int argc, char *argv[])
{
int iOS = 0;
char *pInputFile = NULL;
char *pOutputFile = NULL;
/* Figure out arguments.
* [REQUIRED] First argument is input file.
* [OPTIONAL] Second argument is output file.
*/
if(argc > 1) {
FILE *pInputStream = NULL;
FILE *pOutputStream = NULL;
/* Form respective filenames.
*/
pInputFile = input_filename(argv[1]);
pOutputFile = output_filename(pInputFile, argc > 2 ? argv[2] : NULL);
if(pInputFile == NULL) {
fprintf(stderr, "MANTOMAK: Unable to form input filename\n");
iOS = 1;
}
else {
pInputStream = fopen(pInputFile, "rb");
if(pInputStream == NULL) {
fprintf(stderr, "MANTOMAK: Unable to open input file %s\n", pInputFile);
iOS = 1;
}
}
if(pOutputFile == NULL) {
fprintf(stderr, "MANTOMAK: Unable to form output filename\n");
iOS = 1;
}
else if(pInputStream != NULL) {
pOutputStream = fopen(pOutputFile, "wt");
if(pOutputStream == NULL) {
fprintf(stderr, "MANTOMAK: Unable to open output file %s\n", pOutputFile);
iOS = 1;
}
}
/* Only do the real processing if our error code is not
* already set.
*/
if(iOS == 0) {
iOS = input_to_output(pInputStream, pOutputStream);
}
if(pInputStream != NULL) {
fclose(pInputStream);
pInputStream = NULL;
}
if(pOutputStream != NULL) {
fclose(pOutputStream);
pOutputStream = NULL;
}
}
else {
help();
iOS = 1;
}
if(pInputFile) {
free(pInputFile);
pInputFile = NULL;
}
if(pOutputFile) {
free(pOutputFile);
pOutputFile = NULL;
}
return(iOS);
}
int main(int argc, char* argv[]) {
const auto& map_factory = osmium::index::MapFactory<osmium::unsigned_object_id_type, osmium::Location>::instance();
static struct option long_options[] = {
{"help", no_argument, 0, 'h'},
{"format", required_argument, 0, 'f'},
{"location_store", required_argument, 0, 'l'},
{"list_location_stores", no_argument, 0, 'L'},
{0, 0, 0, 0}
};
std::string output_format { "SQLite" };
std::string location_store { "sparse_mem_array" };
while (true) {
int c = getopt_long(argc, argv, "hf:l:L", long_options, 0);
if (c == -1) {
break;
}
switch (c) {
case 'h':
print_help();
exit(0);
case 'f':
output_format = optarg;
break;
case 'l':
location_store = optarg;
break;
case 'L':
std::cout << "Available map types:\n";
for (const auto& map_type : map_factory.map_types()) {
std::cout << " " << map_type << "\n";
}
exit(0);
default:
exit(1);
}
}
std::string input_filename;
std::string output_filename("ogr_out");
int remaining_args = argc - optind;
if (remaining_args > 2) {
std::cerr << "Usage: " << argv[0] << " [OPTIONS] [INFILE [OUTFILE]]" << std::endl;
exit(1);
} else if (remaining_args == 2) {
input_filename = argv[optind];
output_filename = argv[optind+1];
} else if (remaining_args == 1) {
input_filename = argv[optind];
} else {
input_filename = "-";
}
osmium::io::Reader reader(input_filename);
std::unique_ptr<index_pos_type> index_pos = map_factory.create_map(location_store);
index_neg_type index_neg;
location_handler_type location_handler(*index_pos, index_neg);
location_handler.ignore_errors();
MyOGRHandler ogr_handler(output_format, output_filename);
osmium::apply(reader, location_handler, ogr_handler);
reader.close();
int locations_fd = open("locations.dump", O_WRONLY | O_CREAT, 0644);
if (locations_fd < 0) {
throw std::system_error(errno, std::system_category(), "Open failed");
}
index_pos->dump_as_list(locations_fd);
close(locations_fd);
}
int main(int argc, char **argv)
{
try
{
TCLAP::CmdLine cmd("Geometrically transforms a mesh", ' ', "1.0");
TCLAP::ValueArg<std::string> log_filename("l","logfile", "Log file name (default is convert.log)", false, "convert.log", "string");
cmd.add( log_filename );
TCLAP::ValueArg<std::string> input_filetype("","inputtype", "Input file type. Can be\nauto - ViennaMesh automatically detects the file format (default)\nvtk - for VTK files\nmesh - for Netgen .mesh files\npoly - for Tetgen .poly files\ndeva - for GTS deva files", false, "auto", "string");
cmd.add( input_filetype );
TCLAP::ValueArg<std::string> output_filetype("","outputtype", "Output file type. Can be\nauto - ViennaMesh automatically detects the file format (default)\nvtk - for VTK files\nvmesh - for Vienna vmesh files", false, "auto", "string");
cmd.add( output_filetype );
TCLAP::ValueArg<std::string> matrix_string("m","matrix", "Translate matrix", false, "", "string");
cmd.add( matrix_string );
TCLAP::ValueArg<double> scale("s","scale", "Scale the mesh", false, 0.0, "double");
cmd.add( scale );
TCLAP::ValueArg<std::string> translate_string("t","translate", "Translate the mesh", false, "", "string");
cmd.add( translate_string );
TCLAP::UnlabeledValueArg<std::string> input_filename( "input-filename", "Input file name", true, "", "InputFile" );
cmd.add( input_filename );
TCLAP::UnlabeledValueArg<std::string> output_filename( "output-filename", "Output file name", true, "", "OutputFile" );
cmd.add( output_filename );
cmd.parse( argc, argv );
viennamesh::logger().register_callback( new viennamesh::FileStreamCallback<viennamesh::FileStreamFormater>( log_filename.getValue() ) );
viennamesh::algorithm_handle reader( new viennamesh::io::mesh_reader() );
reader->set_input( "filename", input_filename.getValue() );
if (input_filetype.isSet() && (input_filetype.getValue() != "auto"))
reader->set_input( "file_type", input_filetype.getValue() );
reader->run();
int dimension = lexical_cast<int>(reader->get_output("mesh")->get_property("geometric_dimension").first);
viennamesh::algorithm_handle transform( new viennamesh::affine_transform() );
viennamesh::dynamic_point matrix(dimension*dimension, 0.0);
for (int i = 0; i < dimension; ++i)
matrix[dimension*i+i] = 1.0;
if ( matrix_string.isSet() )
{
matrix = stringtools::vector_from_string<double>( matrix_string.getValue() );
}
else if (scale.isSet())
{
for (int i = 0; i < dimension*dimension; ++i)
matrix[i] *= scale.getValue();
}
viennamesh::dynamic_point translate( dimension, 0.0 );
if ( translate_string.isSet() )
{
translate = stringtools::vector_from_string<double>( translate_string.getValue() );
}
transform->set_input( "mesh", reader->get_output("mesh") );
transform->set_output( "mesh", reader->get_output("mesh") );
transform->set_input( "matrix", matrix );
transform->set_input( "translate", translate );
transform->run();
viennamesh::algorithm_handle writer( new viennamesh::io::mesh_writer() );
writer->set_input( "mesh", transform->get_output("mesh") );
writer->set_input( "quantities", reader->get_output("quantities") );
writer->set_input( "filename", output_filename.getValue() );
if (output_filetype.isSet() && (output_filetype.getValue() != "auto"))
writer->set_input( "file_type", output_filetype.getValue() );
writer->run();
}
catch (TCLAP::ArgException &e) // catch any exceptions
{
std::cerr << "error: " << e.error() << " for arg " << e.argId() << std::endl;
}
return 0;
}
/*********************************
* Output Functions
*********************************/
void figureview_output(long *imos, ///< index of model stage (I)
long *imsn, ///< index of m.s. node on current model stage (I)
double *ts, ///< time at m.s. node (I)
double *te, ///< time at end of m.s. interval (I)
double *sd, ///< differential states at m.s. node (I)
double *sa, ///< algebraic states at m.s. node (I)
double *u, ///< controls at m.s. node (I)
double *udot, ///< control slopes at m.s. node (I)
double *ue, ///< controls at end of m.s. interval (I)
double *uedot, ///< control slopes at end of m.s. interval (I)
double *p_free, ///< global model parameters (I)
double *pr, ///< local i.p.c. parameters (I)
double *ccxd, double *mul_ccxd, ///< multipliers of continuity conditions (I)
#if defined(PRSQP) || defined(EXTPRSQP)
double *ares, double *mul_ares,
#endif
double *rd, double *mul_rd, ///< multipliers of decoupled i.p.c. (I)
double *rc, double *mul_rc, ///< multipliers of coupled i.p.c. (I)
double *obj, double *rwh, ///< real work array (I)
long *iwh ///< integer work array (I)
) {
FILE *fp;
stringstream output_filename("");
const char* fv_header_state_names = "# Time\n"
"# LowerTrunk_TX\n"
"# LowerTrunk_TY\n"
"# LowerTrunk_RZ\n"
"# UpperLeg_R_RZ\n"
"# UpperLeg_R_TY\n"
"# UpperLeg_L_RZ\n"
"# UpperLeg_L_TY\n"
"# LowerLeg_R_RZ\n"
"# LowerLeg_R_TY\n"
"# LowerLeg_L_RZ\n"
"# LowerLeg_L_TY\n";
// Filename
output_filename << "./RES/" << figureview_file_name;
/* Create and reset file when we're in the first MS-knot.
* otherwise just append data
*/
if ((*imsn == 0) && (*imos == 0)) {
fp = fopen(output_filename.str().c_str(), "w");
if (!fp) {
fprintf(stderr, "Error: Could not open file '%s'!\n",
output_filename.str().c_str());
return;
}
// Write the header of the figureview file
fprintf(
fp,
"# JAFV Format: DOF_0 DOF_1 ... DOF_N TAG0_x TAG0_y ... TAGN_z\n");
fprintf(fp, "# Format for cal3dview:\n");
fprintf(fp, "# MODEL hopper\n");
fprintf(fp, "# SYMMETRIC_DATA\n");
fprintf(fp, "# BEGIN_FORMAT\n");
// the degrees of freedom
fprintf(fp, "%s", fv_header_state_names);
fprintf(fp, "# END_FORMAT\n");
// More header information
fprintf(
fp,
"#\n#\n# Articulating biped hopper\n#\n# Variables per frame: \n#\n# %d\n#\n",
1 + NQ + 2);
} else {
fp = fopen(output_filename.str().c_str(), "a");
if (!fp) {
fprintf(stderr, "Error: Could not open file '%s'!\n",
output_filename.str().c_str());
return;
}
}
// Write a line of data:
fprintf(fp, "%e\t", *ts);
fprintf(fp, "%e\t", sd[x]);
fprintf(fp, "%e\t", sd[y]);
fprintf(fp, "%e\t", sd[phi]);
fprintf(fp, "%e\t", sd[alphaR]);
fprintf(fp, "0\t");
fprintf(fp, "%e\t", sd[alphaL]);
fprintf(fp, "0\t");
fprintf(fp, "0\t");
fprintf(fp, "%e\t", 1 - sd[betaR]);
fprintf(fp, "0\t");
fprintf(fp, "%e\t", 1 - sd[betaL]);
fprintf(fp, "\n");
// Close file
fclose(fp);
}
