dicom_parser::dicom_parser(QStringList file_list,QWidget *parent) :
QDialog(parent),
ui(new Ui::dicom_parser)
{
ui->setupUi(this);
cur_path = QFileInfo(file_list[0]).absolutePath();
std::sort(file_list.begin(),file_list.end(),compare_qstring());
load_files(file_list);
if (!dwi_files.empty())
{
ui->SrcName->setText(get_src_name(file_list[0]));
image::io::dicom header;
if (header.load_from_file(file_list[0].toLocal8Bit().begin()))
{
slice_orientation.resize(9);
header.get_image_orientation(slice_orientation.begin());
}
}
}
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);
}
}
