void NEURONSEGlugin::domenu(const QString &menu_name, V3DPluginCallback &callback, QWidget *parent)
{
if (menu_name == tr("Swc segment"))
{
swc_to_segments(callback, parent,1);
}
else if (menu_name == tr("Help"))
{
v3d_msg("(version 0.11)Neuronseg Plugin 1.0 developed by Jinzhu Yang. (Peng Lab, Janelia Research Farm Campus, HHMI), save swc files according to different segments of swc file");
return;
}
}
//ConsensusBuilder::ConsensusBuilder(DIR *directory){
ConsensusBuilder::ConsensusBuilder(string &directory){
ready_to_run = false;
logger->set_write_level(true);
Composite::set_logger(logger);
struct dirent *ep;
logger->debug("opening directory");
DIR * dir = opendir(directory.c_str());
if (dir){
logger->debug("directory exists, going through");
unsigned char isFile =0x8;
while ((ep = readdir(dir)) != NULL){
logger->debug("File char 0 %c",ep->d_name[0]);
if (ep->d_type == DT_REG && ep->d_name[0] != '.'){
logger->debug("Processing file");
string filename = string(ep->d_name);
// Check file extension
pair<string,string> name_ext = split_final(filename);
string name = name_ext.first, extension = name_ext.second;
if (name.length() > 0 && (extension.compare("swc") == 0 || extension.compare("SWC") == 0)){
printf("%s\n",ep->d_name);
logger->debug2("extension %s",extension.c_str());
string filepath = directory;
// filepath.append("/");
filepath.append(filename);
//logger->debug2("Adding reconstruction from file %s to list", filepath.c_str());
// Read neuron points
vector<MyMarker *> neuronPts = readSWC_file(directory+string("/")+filename);
if (neuronPts.size() > 0){
logger->debug2("%d neuron points",neuronPts.size());
NeuronSegment * neuron;
vector<NeuronSegment*> segments;
// Convert points into segments
swc_to_segments(neuronPts, segments);
neuron = segments[segments.size()-1]; // #CHECK: Get root, which should be last segments
// Create reconstruction
Reconstruction * reconstruction = new Reconstruction(name, neuron);
cb_reconstructions.insert(std::pair<string, Reconstruction *>(name, reconstruction));
}
}
}
logger->debug("End of loop");
}
logger->debug("Done loop");
(void) closedir (dir);
}else{
logger->error("Null directory provided");
}
if (cb_reconstructions.size() > 1){
ready_to_run = true;
}else{
logger->error("Not enough reconstructions");
// #TODO: warning message saying that there are only n swc files in the directory, not enough to run the ConsensusBuilder
}
};
