bool output_odfs(const tipl::image<unsigned char,3>& mni_mask,
const char* out_name,
const char* ext,
std::vector<std::vector<float> >& odfs,
const tessellated_icosahedron& ti,
const float* vs,
const float* mni,
const std::string& report,
bool record_odf = true)
{
begin_prog("output");
ImageModel image_model;
if(report.length())
image_model.voxel.report = report.c_str();
image_model.voxel.dim = mni_mask.geometry();
image_model.voxel.ti = ti;
image_model.voxel.max_fiber_number = 5;
image_model.voxel.need_odf = record_odf;
image_model.voxel.template_odfs.swap(odfs);
image_model.file_name = out_name;
image_model.voxel.mask = mni_mask;
std::copy(mni,mni+16,image_model.voxel.trans_to_mni);
std::copy(vs,vs+3,image_model.voxel.vs.begin());
if (prog_aborted() || !image_model.reconstruct<reprocess_odf>())
return false;
image_model.save_fib(ext);
image_model.voxel.template_odfs.swap(odfs);
return true;
}
bool output_odfs(const image::basic_image<unsigned char,3>& mni_mask,
const char* out_name,
const char* ext,
std::vector<std::vector<float> >& odfs,
const tessellated_icosahedron& ti,
const float* vs,
const float* mni,
const std::string& report,
bool record_odf = true)
{
begin_prog("output");
ImageModel image_model;
if(report.length())
image_model.voxel.report = report.c_str();
image_model.voxel.dim = mni_mask.geometry();
image_model.voxel.ti = ti;
image_model.voxel.odf_decomposition = false;
image_model.voxel.odf_deconvolusion = false;
image_model.voxel.half_sphere = false;
image_model.voxel.max_fiber_number = 5;
image_model.voxel.z0 = 0.0;
image_model.voxel.need_odf = record_odf;
image_model.voxel.template_odfs.swap(odfs);
image_model.voxel.param = mni;
image_model.file_name = out_name;
image_model.mask = mni_mask;
std::copy(vs,vs+3,image_model.voxel.vs.begin());
if (prog_aborted() || !image_model.reconstruct<reprocess_odf>(1))
return false;
image_model.save_fib(ext);
image_model.voxel.template_odfs.swap(odfs);
return true;
}
bool reconstruct(unsigned int thread_count)
{
begin_prog("reconstruction");
voxel.image_model = this;
voxel.CreateProcesses<ProcessType>();
voxel.init(thread_count);
boost::thread_group threads;
for (unsigned int index = 1;index < thread_count;++index)
threads.add_thread(new boost::thread(&Voxel::thread_run,&voxel,
index,thread_count,mask));
voxel.thread_run(0,thread_count,mask);
threads.join_all();
return !prog_aborted();
}
void MainWindow::loadFib(QString filename)
{
std::string file_name = filename.toLocal8Bit().begin();
begin_prog("load fib");
std::shared_ptr<fib_data> new_handle(new fib_data);
if (!new_handle->load_from_file(&*file_name.begin()))
{
if(!prog_aborted())
QMessageBox::information(this,"error",new_handle->error_msg.c_str(),0);
return;
}
tracking_window* new_mdi = new tracking_window(this,new_handle);
new_mdi->setAttribute(Qt::WA_DeleteOnClose);
new_mdi->setWindowTitle(filename);
new_mdi->showNormal();
addFib(filename);
add_work_dir(QFileInfo(filename).absolutePath());
QDir::setCurrent(QFileInfo(filename).absolutePath());
}
void thread_run(unsigned char thread_index,unsigned char thread_count,
const std::vector<unsigned char>& mask)
{
unsigned int sum_mask = std::accumulate(mask.begin(),mask.end(),(unsigned int)0)/thread_count;
unsigned int cur = 0;
for(unsigned int voxel_index = thread_index;
voxel_index < dim.size() &&
(thread_index != 0 || check_prog(cur,sum_mask));voxel_index += thread_count)
{
if (!mask[voxel_index])
continue;
cur += mask[voxel_index];
voxel_data[thread_index].init();
voxel_data[thread_index].voxel_index = voxel_index;
for (int index = 0; index < process_list.size(); ++index)
process_list[index].run(*this,voxel_data[thread_index]);
if(prog_aborted())
break;
}
}
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);
}
}
