void main()
{
Super(0);
rlvc_open_system();
rlkb_open_keyboard();
/* rlkb_debug_on(); un-rem this for debuggers! */
rlsc_open_video();
rlsd_open_sound();
rltrk_open_tracker();
init_screen_space();
load_all_files();
test_loop();
rltrk_close_tracker();
rlsd_close_sound();
rlsc_close_video();
rlkb_close_keyboard();
rlvc_close_system();
}
void MainWindow::on_batch_src_clicked()
{
QString dir = QFileDialog::getExistingDirectory(
this,
"Open directory",
ui->workDir->currentText());
if(dir.isEmpty())
return;
add_work_dir(dir);
{
QStringList dir_list;
dir_list << dir;
bool all = false;
bool choice = false;
begin_prog("batch creating src");
for(unsigned int i = 0;check_prog(i,dir_list.size()) && !prog_aborted();++i)
{
QDir cur_dir = dir_list[i];
QStringList new_list = cur_dir.entryList(QStringList(""),QDir::AllDirs|QDir::NoDotAndDotDot);
for(unsigned int index = 0;index < new_list.size();++index)
dir_list << cur_dir.absolutePath() + "/" + new_list[index];
std::vector<std::shared_ptr<DwiHeader> > dwi_files;
if(QFileInfo(dir_list[i] + "/data.nii.gz").exists() &&
QFileInfo(dir_list[i] + "/bvals").exists() &&
QFileInfo(dir_list[i] + "/bvecs").exists() &&
load_4d_nii(QString(dir_list[i] + "/data.nii.gz").toLocal8Bit().begin(),dwi_files))
{
DwiHeader::output_src(QString(dir_list[i] + "/data.src.gz").toLocal8Bit().begin(),dwi_files,0);
continue;
}
QStringList nifti_file_list = cur_dir.entryList(QStringList("*.nii.gz"),QDir::Files|QDir::NoSymLinks);
for (unsigned int index = 0;index < nifti_file_list.size();++index)
{
if(QFileInfo(dir_list[i] + "/" + QFileInfo(nifti_file_list[index]).baseName()+".bval").exists() &&
QFileInfo(dir_list[i] + "/" + QFileInfo(nifti_file_list[index]).baseName()+".bvec").exists() &&
load_4d_nii(QString(dir_list[i] + "/" + nifti_file_list[index]).toLocal8Bit().begin(),dwi_files))
{
DwiHeader::output_src(QString(dir_list[i] + "/" +
QFileInfo(nifti_file_list[index]).baseName() + ".src.gz").toLocal8Bit().begin(),dwi_files,0);
continue;
}
}
QStringList dicom_file_list = cur_dir.entryList(QStringList("*.dcm"),QDir::Files|QDir::NoSymLinks);
if(dicom_file_list.empty())
continue;
for (unsigned int index = 0;index < dicom_file_list.size();++index)
dicom_file_list[index] = dir_list[i] + "/" + dicom_file_list[index];
QString output = dir_list[i] + "/" + QFileInfo(get_src_name(dicom_file_list[0])).baseName()+".src.gz";
if(QFileInfo(output).exists())
{
if(!all)
{
QMessageBox msgBox;
msgBox.setText(QString("Existing SRC file ") + output);
msgBox.setInformativeText("Overwrite?");
msgBox.setStandardButtons(QMessageBox::Yes | QMessageBox::YesToAll | QMessageBox::No | QMessageBox::NoAll);
msgBox.setDefaultButton(QMessageBox::Save);
switch(msgBox.exec())
{
case QMessageBox::YesToAll:
all = true;
case QMessageBox::Yes:
choice = true;
break;
case QMessageBox::NoAll:
all = true;
case QMessageBox::No:
choice = false;
break;
}
}
if(!choice)
continue;
}
if(!load_all_files(dicom_file_list,dwi_files) || prog_aborted())
continue;
if(dwi_files.size() == 1) //MPRAGE or T2W
{
std::sort(dicom_file_list.begin(),dicom_file_list.end(),compare_qstring());
image::io::volume v;
image::io::dicom header;
std::vector<std::string> file_list;
for(unsigned int index = 0;index < dicom_file_list.size();++index)
file_list.push_back(dicom_file_list[index].toLocal8Bit().begin());
if(!v.load_from_files(file_list,file_list.size()) ||
!header.load_from_file(dicom_file_list[0].toLocal8Bit().begin()))
continue;
image::basic_image<float,3> I;
image::vector<3> vs;
v >> I;
v.get_voxel_size(vs.begin());
gz_nifti nii_out;
image::flip_xy(I);
nii_out << I;
nii_out.set_voxel_size(vs);
std::string manu,make,seq,report;
header.get_text(0x0008,0x0070,manu);//Manufacturer
header.get_text(0x0008,0x1090,make);
header.get_text(0x0018,0x1030,seq);
std::replace(manu.begin(),manu.end(),' ',(char)0);
make.erase(std::remove(make.begin(),make.end(),' '),make.end());
std::ostringstream out;
out << manu.c_str() << " " << make.c_str() << " " << seq
<< ".TE=" << header.get_float(0x0018,0x0081) << ".TR=" << header.get_float(0x0018,0x0080) << ".";
report = out.str();
std::copy(report.begin(),report.begin() + std::min<int>(80,report.length()+1),nii_out.nif_header.descrip);
QString output_name = QFileInfo(get_src_name(dicom_file_list[0])).absolutePath() + "/" +
QFileInfo(get_src_name(dicom_file_list[0])).baseName()+ "."+seq.c_str() + ".nii.gz";
nii_out.save_to_file(output_name.toLocal8Bit().begin());
}
else
{
for(unsigned int index = 0;index < dwi_files.size();++index)
if(dwi_files[index]->get_bvalue() < 100)
{
dwi_files[index]->set_bvalue(0);
dwi_files[index]->set_bvec(0,0,0);
}
DwiHeader::output_src(output.toLocal8Bit().begin(),dwi_files,0);
}
}
int src(int ac, char *av[])
{
po::options_description rec_desc("dicom parsing options");
rec_desc.add_options()
("help", "help message")
("action", po::value<std::string>(), "src:dicom parsing")
("source", po::value<std::string>(), "assign the directory for the dicom files")
("recursive", po::value<std::string>(), "search subdirectories")
("b_table", po::value<std::string>(), "assign the b-table")
("bval", po::value<std::string>(), "assign the b value")
("bvec", po::value<std::string>(), "assign the b vector")
("output", po::value<std::string>(), "assign the output filename")
;
if(!ac)
{
std::cout << rec_desc << std::endl;
return 1;
}
po::variables_map vm;
po::store(po::command_line_parser(ac, av).options(rec_desc).run(), vm);
po::notify(vm);
std::string source = vm["source"].as<std::string>();
std::string ext;
if(source.size() > 4)
ext = std::string(source.end()-4,source.end());
boost::ptr_vector<DwiHeader> dwi_files;
QStringList file_list;
if(ext ==".nii" || ext == ".dcm" || ext == "dseq" || ext == "i.gz")
{
std::cout << "image=" << source.c_str() << std::endl;
file_list << source.c_str();
}
else
{
std::cout << "load files in directory " << source.c_str() << std::endl;
QDir directory = QString(source.c_str());
if(vm.count("recursive"))
{
std::cout << "search recursively in the subdir" << std::endl;
file_list = search_files(source.c_str(),"*.dcm");
}
else
{
file_list = directory.entryList(QStringList("*.dcm"),QDir::Files|QDir::NoSymLinks);
if(file_list.empty())
file_list = directory.entryList(QStringList("*.nii.gz"),QDir::Files|QDir::NoSymLinks);
for (unsigned int index = 0;index < file_list.size();++index)
file_list[index] = QString(source.c_str()) + "/" + file_list[index];
}
std::cout << "A total of " << file_list.size() <<" files found in the directory" << std::endl;
}
if(file_list.empty())
{
std::cout << "No file found for creating src" << std::endl;
return -1;
}
if(!load_all_files(file_list,dwi_files))
{
std::cout << "Invalid file format" << std::endl;
return -1;
}
if(vm.count("b_table"))
{
std::string table_file_name = vm["b_table"].as<std::string>();
std::ifstream in(table_file_name.c_str());
if(!in)
{
std::cout << "Failed to open b-table" <<std::endl;
return -1;
}
std::string line;
std::vector<double> b_table;
while(std::getline(in,line))
{
std::istringstream read_line(line);
std::copy(std::istream_iterator<double>(read_line),
std::istream_iterator<double>(),
std::back_inserter(b_table));
}
if(b_table.size() != dwi_files.size()*4)
{
std::cout << "Mismatch between b-table and the loaded images" << std::endl;
return -1;
}
for(unsigned int index = 0,b_index = 0;index < dwi_files.size();++index,b_index += 4)
{
dwi_files[index].set_bvalue(b_table[b_index]);
dwi_files[index].set_bvec(b_table[b_index+1],b_table[b_index+2],b_table[b_index+3]);
}
std::cout << "B-table " << table_file_name << " loaded" << std::endl;
}
if(vm.count("bval") && vm.count("bvec"))
{
std::vector<double> bval,bvec;
std::cout << "load bval=" << vm["bval"].as<std::string>() << std::endl;
std::cout << "load bvec=" << vm["bvec"].as<std::string>() << std::endl;
load_bval(vm["bval"].as<std::string>().c_str(),bval);
load_bvec(vm["bvec"].as<std::string>().c_str(),bvec);
if(bval.size() != dwi_files.size())
{
std::cout << "Mismatch between bval file and the loaded images" << std::endl;
return -1;
}
if(bvec.size() != dwi_files.size()*3)
{
std::cout << "Mismatch between bvec file and the loaded images" << std::endl;
return -1;
}
for(unsigned int index = 0;index < dwi_files.size();++index)
{
dwi_files[index].set_bvalue(bval[index]);
dwi_files[index].set_bvec(bvec[index*3],bvec[index*3+1],bvec[index*3+2]);
}
}
if(dwi_files.empty())
{
std::cout << "No file readed. Abort." << std::endl;
return 1;
}
double max_b = 0;
for(unsigned int index = 0;index < dwi_files.size();++index)
{
if(dwi_files[index].get_bvalue() < 100)
dwi_files[index].set_bvalue(0);
max_b = std::max(max_b,(double)dwi_files[index].get_bvalue());
}
if(max_b == 0.0)
{
std::cout << "Cannot find b-table from the header. You may need to load an external b-table using--b_table or --bval and --bvec." << std::endl;
return 1;
}
std::cout << "Output src " << vm["output"].as<std::string>().c_str() << std::endl;
DwiHeader::output_src(vm["output"].as<std::string>().c_str(),dwi_files,0);
return 0;
}
int src(void)
{
std::string source = po.get("source");
std::string ext;
if(source.size() > 4)
ext = std::string(source.end()-4,source.end());
std::string output;
if(po.has("output"))
output = po.get("output");
if(QFileInfo(output.c_str()).exists())
{
std::cout << output << " exists. skipping..." << std::endl;
return 1;
}
std::vector<std::shared_ptr<DwiHeader> > dwi_files;
QStringList file_list;
if(ext ==".nii" || ext == ".dcm" || ext == "dseq" || ext == "i.gz")
{
std::cout << "image=" << source.c_str() << std::endl;
std::istringstream ss(source);
std::string token;
while(std::getline(ss, token, ','))
file_list << source.c_str();
if(!po.has("output"))
output = file_list.front().toStdString() + ".src.gz";
}
else
{
std::cout << "load files in directory " << source.c_str() << std::endl;
QDir directory = QString(source.c_str());
if(po.has("recursive"))
{
std::cout << "search recursively in the subdir" << std::endl;
file_list = search_files(source.c_str(),"*.dcm");
}
else
{
file_list = directory.entryList(QStringList("*.dcm"),QDir::Files|QDir::NoSymLinks);
if(file_list.empty())
file_list = directory.entryList(QStringList("*.nii.gz"),QDir::Files|QDir::NoSymLinks);
if(file_list.empty())
file_list = directory.entryList(QStringList("*.fdf"),QDir::Files|QDir::NoSymLinks);
for (unsigned int index = 0;index < file_list.size();++index)
file_list[index] = QString(source.c_str()) + "/" + file_list[index];
}
std::cout << "A total of " << file_list.size() <<" files found in the directory" << std::endl;
if(!po.has("output"))
output = source + ".src.gz";
}
if(file_list.empty())
{
std::cout << "No file found for creating src" << std::endl;
return 1;
}
if(!load_all_files(file_list,dwi_files))
{
std::cout << "Invalid file format" << std::endl;
return 1;
}
if(po.has("b_table"))
{
std::string table_file_name = po.get("b_table");
std::ifstream in(table_file_name.c_str());
if(!in)
{
std::cout << "Failed to open b-table" <<std::endl;
return 1;
}
std::string line;
std::vector<double> b_table;
while(std::getline(in,line))
{
std::istringstream read_line(line);
std::copy(std::istream_iterator<double>(read_line),
std::istream_iterator<double>(),
std::back_inserter(b_table));
}
if(b_table.size() != dwi_files.size()*4)
{
std::cout << "Mismatch between b-table and the loaded images" << std::endl;
return 1;
}
for(unsigned int index = 0,b_index = 0;index < dwi_files.size();++index,b_index += 4)
{
dwi_files[index]->set_bvalue(b_table[b_index]);
dwi_files[index]->set_bvec(b_table[b_index+1],b_table[b_index+2],b_table[b_index+3]);
}
std::cout << "B-table " << table_file_name << " loaded" << std::endl;
}
if(po.has("bval") && po.has("bvec"))
{
std::vector<double> bval,bvec;
std::cout << "load bval=" << po.get("bval") << std::endl;
std::cout << "load bvec=" << po.get("bvec") << std::endl;
load_bval(po.get("bval").c_str(),bval);
load_bvec(po.get("bvec").c_str(),bvec);
if(bval.size() != dwi_files.size())
{
std::cout << "Mismatch between bval file and the loaded images" << std::endl;
return 1;
}
if(bvec.size() != dwi_files.size()*3)
{
std::cout << "Mismatch between bvec file and the loaded images" << std::endl;
return 1;
}
for(unsigned int index = 0;index < dwi_files.size();++index)
{
dwi_files[index]->set_bvalue(bval[index]);
dwi_files[index]->set_bvec(bvec[index*3],bvec[index*3+1],bvec[index*3+2]);
}
}
if(dwi_files.empty())
{
std::cout << "No file readed. Abort." << std::endl;
return 1;
}
double max_b = 0;
for(unsigned int index = 0;index < dwi_files.size();++index)
{
if(dwi_files[index]->get_bvalue() < 100)
dwi_files[index]->set_bvalue(0);
max_b = std::max(max_b,(double)dwi_files[index]->get_bvalue());
}
if(max_b == 0.0)
{
std::cout << "Cannot find b-table from the header. You may need to load an external b-table using--b_table or --bval and --bvec." << std::endl;
return 1;
}
std::cout << "Output src to " << output << std::endl;
DwiHeader::output_src(output.c_str(),dwi_files,
po.get<int>("up_sampling",0),
po.get<int>("sort_b_table",0));
return 0;
}
