CRef<CSeq_id> CSeqIdGenerator::GenerateID(const string& defline, const bool advance)
{
CRef<CSeq_id> seq_id(new CSeq_id);
int n = advance ? m_Counter.Add(1) - 1 : m_Counter.Get();
if (m_Prefix.empty() && m_Suffix.empty()) {
seq_id->SetLocal().SetId(n);
} else {
string& id = seq_id->SetLocal().SetStr();
id.reserve(128);
id += m_Prefix;
id += NStr::IntToString(n);
id += m_Suffix;
}
return seq_id;
}
void
FE_Utils::create_uses_multiple_stuff (AST_Component *c,
AST_Uses *u,
const char *prefix)
{
ACE_CString struct_name (prefix);
if (!struct_name.empty ())
{
struct_name += '_';
}
struct_name += u->local_name ()->get_string ();
struct_name += "Connection";
Identifier struct_id (struct_name.c_str ());
UTL_ScopedName sn (&struct_id, 0);
// In case this call comes from the backend. We
// will pop the scope before returning.
idl_global->scopes ().push (c);
AST_Structure *connection =
idl_global->gen ()->create_structure (&sn, 0, 0);
struct_id.destroy ();
/// If the field type is a param holder, we want
/// to use the lookup to create a fresh one,
/// since the field will own it and destroy it.
UTL_ScopedName *fn = u->uses_type ()->name ();
AST_Decl *d =
idl_global->root ()->lookup_by_name (fn, true, false);
AST_Type *ft = AST_Type::narrow_from_decl (d);
Identifier object_id ("objref");
UTL_ScopedName object_name (&object_id,
0);
AST_Field *object_field =
idl_global->gen ()->create_field (ft,
&object_name,
AST_Field::vis_NA);
(void) DeclAsScope (connection)->fe_add_field (object_field);
object_id.destroy ();
Identifier local_id ("Cookie");
UTL_ScopedName local_name (&local_id,
0);
Identifier module_id ("Components");
UTL_ScopedName scoped_name (&module_id,
&local_name);
d = c->lookup_by_name (&scoped_name, true);
local_id.destroy ();
module_id.destroy ();
if (d == 0)
{
// This would happen if we haven't included Components.idl.
idl_global->err ()->lookup_error (&scoped_name);
return;
}
AST_ValueType *cookie = AST_ValueType::narrow_from_decl (d);
Identifier cookie_id ("ck");
UTL_ScopedName cookie_name (&cookie_id,
0);
AST_Field *cookie_field =
idl_global->gen ()->create_field (cookie,
&cookie_name,
AST_Field::vis_NA);
(void) DeclAsScope (connection)->fe_add_field (cookie_field);
cookie_id.destroy ();
(void) c->fe_add_structure (connection);
ACE_CDR::ULong bound = 0;
AST_Expression *bound_expr =
idl_global->gen ()->create_expr (bound,
AST_Expression::EV_ulong);
AST_Sequence *sequence =
idl_global->gen ()->create_sequence (bound_expr,
connection,
0,
0,
0);
ACE_CString seq_string (struct_name);
seq_string += 's';
Identifier seq_id (seq_string.c_str ());
UTL_ScopedName seq_name (&seq_id,
0);
AST_Typedef *connections =
idl_global->gen ()->create_typedef (sequence,
&seq_name,
0,
0);
seq_id.destroy ();
(void) c->fe_add_typedef (connections);
// In case this call comes from the backend.
idl_global->scopes ().pop ();
}
int CSampleLds2Application::Run(void)
{
// Process command line args
const CArgs& args = GetArgs();
const string& db_path = args["db"].AsString();
//
// Initialize the local data storage
//
if ( args["data_dir"] ) {
try {
CRef<CLDS2_Manager> mgr(new CLDS2_Manager(db_path));
// Allow to split GB release bioseq-sets
mgr->SetGBReleaseMode(CLDS2_Manager::eGB_Guess);
if ( args["group_aligns"] ) {
mgr->SetSeqAlignGroupSize(args["group_aligns"].AsInteger());
}
mgr->AddDataDir(args["data_dir"].AsString());
mgr->UpdateData();
}
catch(CException& e) {
ERR_POST("Error initializing local data storage: " << e.what());
return 1;
}
}
// Create OM and LDS2 data loader
CRef<CObjectManager> object_manager = CObjectManager::GetInstance();
try {
CLDS2_DataLoader::RegisterInObjectManager(*object_manager,
db_path, -1, CObjectManager::eDefault);
}
catch (CException& e) {
ERR_POST("Error registering LDS2 data loader: " << e.what());
return 2;
}
// Check if an id was requested, try to fetch some data
if ( args["id"] ) {
string id = args["id"].AsString();
// Create Seq-id, set it to the GI specified on the command line
CSeq_id seq_id(id);
// Create a new scope ("attached" to our OM).
CScope scope(*object_manager);
// Add default loaders (GB loader in this demo) to the scope.
scope.AddDefaults();
// Get synonyms
CBioseq_Handle::TId bh_ids = scope.GetIds(seq_id);
NcbiCout << "Synonyms for " << id << ": ";
string sep = "";
ITERATE (CBioseq_Handle::TId, id_it, bh_ids) {
cout << sep << id_it->AsString();
sep = ", ";
}
cout << endl;
// Get Bioseq handle for the Seq-id.
CBioseq_Handle bioseq_handle = scope.GetBioseqHandle(seq_id);
if ( !bioseq_handle ) {
ERR_POST("Bioseq not found, with id=" << id);
}
else {
// Dump the seq-entry.
if ( args["print_entry"] ) {
cout << MSerial_AsnText <<
*bioseq_handle.GetTopLevelEntry().GetCompleteSeq_entry();
}
}
// Test features
SAnnotSelector sel;
sel.SetSearchUnresolved()
.SetResolveAll();
CSeq_loc loc;
loc.SetWhole().Assign(seq_id);
cout << "Features by location:" << endl;
CFeat_CI fit(scope, loc, sel);
int fcount = 0;
for (; fit; ++fit) {
if ( args["print_feats"] ) {
cout << MSerial_AsnText << fit->GetOriginalFeature();
}
fcount++;
}
cout << fcount << " features found" << endl;
cout << "Features by product:" << endl;
sel.SetByProduct(true);
CFeat_CI fitp(scope, loc, sel);
fcount = 0;
for (; fitp; ++fitp) {
if ( args["print_feats"] ) {
cout << MSerial_AsnText << fitp->GetOriginalFeature();
}
fcount++;
}
cout << fcount << " features found" << endl;
// Test alignments
cout << "Alignments:" << endl;
sel.SetByProduct(false);
CAlign_CI ait(scope, loc, sel);
int acount = 0;
for (; ait; ++ait) {
if ( args["print_aligns"] ) {
cout << MSerial_AsnText << ait.GetOriginalSeq_align();
}
acount++;
}
cout << acount << " alignments found" << endl;
}
CRef<CBioseq> MakeMaskingBioseq(const CSeq_id& new_id,
TSeqPos seq_length,
const CSeq_id& original_id,
const vector<CRange<TSeqPos> >& mask_ranges)
{
if ( !s_is_sorted(mask_ranges.begin(), mask_ranges.end(), ByFrom()) ) {
vector<CRange<TSeqPos> > ranges(mask_ranges);
sort(ranges.begin(), ranges.end(), ByFrom());
return MakeMaskingBioseq(new_id, seq_length, original_id, ranges);
}
_ASSERT(s_is_sorted(mask_ranges.begin(), mask_ranges.end(), ByFrom()));
CRef<CBioseq> seq(new CBioseq);
CRef<CSeq_id> seq_id(new CSeq_id);
seq->SetId().push_back(seq_id);
seq_id->Assign(new_id);
CSeq_inst& inst = seq->SetInst();
inst.SetRepr(inst.eRepr_delta);
inst.SetMol(inst.eMol_not_set);
inst.SetLength(seq_length);
CDelta_ext& delta = inst.SetExt().SetDelta();
TSeqPos cur_pos = 0, last_pos = 0;
vector<CRange<TSeqPos> >::const_iterator mask_it = mask_ranges.begin();
while ( cur_pos < seq_length && mask_it != mask_ranges.end() ) {
if ( !mask_it->Empty() ) {
TSeqPos mask_start = mask_it->GetFrom();
if ( mask_start <= cur_pos ) {
TSeqPos mask_end = mask_it->GetToOpen();
if ( mask_end > cur_pos ) {
cur_pos = mask_it->GetToOpen();
}
}
else {
if ( last_pos < cur_pos ) {
// add gap
CRef<CDelta_seq> seg(new CDelta_seq);
delta.Set().push_back(seg);
seg->SetLiteral().SetLength(cur_pos-last_pos);
}
CRef<CDelta_seq> seg(new CDelta_seq);
delta.Set().push_back(seg);
CSeq_interval& ref_int = seg->SetLoc().SetInt();
ref_int.SetId().Assign(original_id);
ref_int.SetFrom(cur_pos);
if ( mask_start >= seq_length ) {
ref_int.SetTo(seq_length-1);
last_pos = cur_pos = seq_length;
break;
}
ref_int.SetTo(mask_start-1);
last_pos = cur_pos = mask_start;
}
}
++mask_it;
}
if ( last_pos < cur_pos ) {
// trailing gap
CRef<CDelta_seq> seg(new CDelta_seq);
delta.Set().push_back(seg);
seg->SetLiteral().SetLength(cur_pos-last_pos);
}
return seq;
}
int main(int argc, char** argv)
{
std::string path("/home/chi/arco/test/build/temp/");
std::string filename("temp_0_0");
pcl::console::parse_argument(argc, argv, "--f", filename);
pcl::PointCloud<PointT>::Ptr cloud(new pcl::PointCloud<PointT>());
pcl::io::loadPCDFile(path+filename+".pcd", *cloud);
int w = cloud->width;
int h = cloud->height;
cv::Mat img = cv::Mat::zeros(h, w, CV_8UC3);
for( size_t i = 0 ; i < cloud->size() ; i++ )
{
int r = i / w;
int c = i % w;
uint32_t rgb_tmp = cloud->at(i).rgba;
img.at<uchar>(r, c*3+2) = (rgb_tmp >> 16) & 0x0000ff;
img.at<uchar>(r, c*3+1) = (rgb_tmp >> 8) & 0x0000ff;
img.at<uchar>(r, c*3+0) = (rgb_tmp) & 0x0000ff;
}
cv::imwrite(filename+".png", img);
return 0;
std::string in_path("/home/chi/JHUIT/raw/");
std::string out_path("img_tmp/");
std::string inst_name("driller_kel_0");
std::string seq_id("1");;
float elev = ELEV;
int max_frames = 200;
pcl::console::parse_argument(argc, argv, "--p", in_path);
pcl::console::parse_argument(argc, argv, "--s", seq_id);
pcl::console::parse_argument(argc, argv, "--i", inst_name);
pcl::console::parse_argument(argc, argv, "--elev", elev);
pcl::console::parse_argument(argc, argv, "--max", max_frames);
std::cerr << "Loading-"<< inst_name << std::endl;
if( exists_dir(out_path) == false )
boost::filesystem::create_directories(out_path);
std::ifstream fp;
fp.open((in_path+"/PlaneCoef_"+ seq_id + ".txt").c_str(), std::ios::in);
if( fp.is_open() == false )
{
std::cerr << "Failed to open: " << in_path+"/PlaneCoef_"+ seq_id + ".txt" << std::endl;
exit(0);
}
pcl::ModelCoefficients::Ptr planeCoef(new pcl::ModelCoefficients());
planeCoef->values.resize(4);
fp >> planeCoef->values[0] >> planeCoef->values[1] >> planeCoef->values[2] >> planeCoef->values[3];
fp.close();
std::vector< pcl::PointCloud<PointT>::Ptr > cloud_set;
std::vector< KEYSET > keypt_set;
std::vector< cv::Mat > keydescr_set;
for( size_t j = 0 ; j < max_frames ; j++ )
{
std::stringstream ss;
ss << j;
if( j % 3 != 0 )
continue;
std::string filename(in_path + inst_name + "/" + inst_name + "_" + seq_id + "_" + ss.str() + ".pcd");
if( exists_test(filename) == false )
continue;
pcl::PointCloud<PointT>::Ptr cloud(new pcl::PointCloud<PointT>());
pcl::io::loadPCDFile(filename, *cloud);
int w = cloud->width;
int h = cloud->height;
//std::cerr << w << " " << h << " " << cloud->size() << std::endl;
cv::Mat rgb = cv::Mat::zeros(h, w, CV_8UC3);
cv::Mat gray = cv::Mat::zeros(h, w, CV_8UC1);
for(size_t i = 0 ; i < cloud->size() ; i++ )
{
int r_idx = i / w;
int c_idx = i % w;
uint32_t rgb_tmp = cloud->at(i).rgba;
rgb.at<uchar>(r_idx, c_idx*3+2) = (rgb_tmp >> 16) & 0x0000ff;
rgb.at<uchar>(r_idx, c_idx*3+1) = (rgb_tmp >> 8) & 0x0000ff;
rgb.at<uchar>(r_idx, c_idx*3+0) = (rgb_tmp) & 0x0000ff;
}
cv::cvtColor(rgb,gray,CV_BGR2GRAY);
//cv::imshow("GRAY", rgb);
//cv::waitKey();
cv::SiftFeatureDetector *sift_det = new cv::SiftFeatureDetector(
0, // nFeatures
4, // nOctaveLayers
0.04, // contrastThreshold
10, //edgeThreshold
1.6 //sigma
);
cv::SiftDescriptorExtractor * sift_ext = new cv::SiftDescriptorExtractor();
KEYSET keypoints;
cv::Mat descriptors;
sift_det->detect(gray, keypoints);
sift_ext->compute(gray, keypoints, descriptors);
printf("%d sift keypoints are found.\n", (int)keypoints.size());
keypt_set.push_back(keypoints);
keydescr_set.push_back(descriptors);
cloud = cropCloud(cloud, planeCoef, 0.114);
cloud_set.push_back(cloud);
//cv::imshow("GRAY", in_rgb);
//cv::waitKey();
//cv::imwrite(out_path + ss.str() + ".jpg", in_rgb);
//viewer->addPointCloud(cloud, "cloud");
//viewer->spin();
//if( show_keys )
/*
{
cv::Mat out_image;
cv::drawKeypoints(gray, keypoints, out_image);
cv::imshow("keypoints", out_image);
cv::waitKey();
}
//*/
}
int total = cloud_set.size();
/*
std::vector< pcl::PointCloud<PointT>::Ptr > first_half, second_half;
std::vector< KEYSET > first_keypt, second_keypt;
std::vector< cv::Mat > first_keydescr, second_keydescr;
first_half.insert(first_half.end(), cloud_set.begin(), cloud_set.begin()+total/2);
first_keypt.insert(first_keypt.end(), keypt_set.begin(), keypt_set.begin()+total/2);
first_keydescr.insert(first_keydescr.end(), keydescr_set.begin(), keydescr_set.begin()+total/2);
second_half.push_back(cloud_set[0]);
second_keypt.push_back(keypt_set[0]);
second_keydescr.push_back(keydescr_set[0]);
for( int i = 1 ; i < total/2 ; i++ )
{
second_half.push_back(cloud_set[total-i]);
second_keypt.push_back(keypt_set[total-i]);
second_keydescr.push_back(keydescr_set[total-i]);
}
pcl::PointCloud<PointT>::Ptr first_model = Meshing(first_half, first_keypt, first_keydescr);
pcl::PointCloud<PointT>::Ptr second_model = Meshing(second_half, second_keypt, second_keydescr);
pcl::PointCloud<PointT>::Ptr full_model (new pcl::PointCloud<PointT>());
full_model->insert(full_model->end(), first_model->begin(), first_model->end());
full_model->insert(full_model->end(), second_model->begin(), second_model->end());
*/
pcl::PointCloud<PointT>::Ptr full_model = Meshing(cloud_set, keypt_set, keydescr_set);
full_model = cropCloud(full_model, planeCoef, elev);
pcl::io::savePCDFile("temp_full.pcd", *full_model);
pcl::PLYWriter ply_writer;
ply_writer.write("temp_full.ply", *full_model, true);
/*
pcl::PointCloud<PointT>::Ptr full_model(new pcl::PointCloud<PointT>());
pcl::io::loadPCDFile("temp_full.pcd", *full_model);
std::vector<int> idx_ff;
pcl::removeNaNFromPointCloud(*full_model, *full_model, idx_ff);
pcl::PointCloud<NormalT>::Ptr full_model_normals (new pcl::PointCloud<NormalT>());
computeNormals(full_model, full_model_normals, 0.02);
AdjustCloudNormal(full_model, full_model_normals);
pcl::visualization::PCLVisualizer::Ptr viewer(new pcl::visualization::PCLVisualizer());
viewer->initCameraParameters();
viewer->addCoordinateSystem(0.1);
viewer->setCameraPosition(0, 0, 0.1, 0, 0, 1, 0, -1, 0);
//viewer->addPointCloud(full_model, "full_model");
//viewer->setPointCloudRenderingProperties(pcl::visualization::PCL_VISUALIZER_COLOR, 1.0, 1.0, 1.0, "full_model");
//viewer->addPointCloudNormals<PointT, NormalT> (full_model, full_model_normals, 5, 0.01, "normals");
//viewer->spin();
pcl::PointCloud<pcl::PointNormal>::Ptr joint_model (new pcl::PointCloud<pcl::PointNormal>());
pcl::copyPointCloud(*full_model, *joint_model);
pcl::copyPointCloud(*full_model_normals, *joint_model);
//std::cerr << full_model->size() << " " << full_model_normals->size() << " " << joint_model->size() << std::endl;
//pcl::concatenateFields (*full_model, *full_model_normals, *joint_model);
pcl::search::KdTree<pcl::PointNormal>::Ptr tree2(new pcl::search::KdTree<pcl::PointNormal>);
tree2->setInputCloud (joint_model);
pcl::GreedyProjectionTriangulation<pcl::PointNormal> gp3;
pcl::PolygonMesh model_mesh;
gp3.setMu(2.5);
gp3.setMaximumNearestNeighbors(100);
gp3.setSearchRadius(0.03);
gp3.setMaximumSurfaceAngle(M_PI/4); // 45 degrees
gp3.setMinimumAngle(M_PI/18); // 10 degrees
gp3.setMaximumAngle(2*M_PI/3); // 120 degrees
gp3.setNormalConsistency(false);
// Get result
gp3.setInputCloud (joint_model);
gp3.setSearchMethod (tree2);
gp3.reconstruct (model_mesh);
//viewer->addPointCloud(full_model, "model");
viewer->addPolygonMesh(model_mesh, "full_model_mesh");
viewer->setPointCloudRenderingProperties(pcl::visualization::PCL_VISUALIZER_COLOR, 1.0, 0.55, 0.05, "full_model_mesh");
viewer->spin();
*/
return 0;
}
