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mainwindow.cpp
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#include <QFileDialog>
#include <QDateTime>
#include <QUrl>
#include <QMessageBox>
#include <QProgressDialog>
#include <QDragEnterEvent>
#include <QMimeData>
#include <QAction>
#include <QStyleFactory>
#include <filesystem>
#include "TIPL/tipl.hpp"
#include "mainwindow.h"
#include "ui_mainwindow.h"
#include "regtoolbox.h"
#include "filebrowser.h"
#include "reconstruction/reconstruction_window.h"
#include "prog_interface_static_link.h"
#include "tracking/tracking_window.h"
#include "dicom/dicom_parser.h"
#include "view_image.h"
#include "mapping/atlas.hpp"
#include "libs/gzip_interface.hpp"
#include "libs/tracking/fib_data.hpp"
#include "connectometry/group_connectometry_analysis.h"
#include "connectometry/createdbdialog.h"
#include "connectometry/db_window.h"
#include "connectometry/group_connectometry.hpp"
#include "libs/dsi/image_model.hpp"
#include "manual_alignment.h"
#include "auto_track.h"
#include "xnat_dialog.h"
#include "console.h"
extern std::vector<std::string> fib_template_list;
std::vector<tracking_window*> tracking_windows;
MainWindow::MainWindow(QWidget *parent) :
QMainWindow(parent),
ui(new Ui::MainWindow)
{
setAcceptDrops(true);
ui->setupUi(this);
ui->styles->addItems(QStringList("default") << QStyleFactory::keys());
ui->styles->setCurrentText(settings.value("styles","Fusion").toString());
ui->recentFib->setColumnCount(3);
ui->recentFib->setColumnWidth(0,300);
ui->recentFib->setColumnWidth(1,250);
ui->recentFib->setColumnWidth(2,150);
ui->recentFib->setAlternatingRowColors(true);
ui->recentSrc->setColumnCount(3);
ui->recentSrc->setColumnWidth(0,300);
ui->recentSrc->setColumnWidth(1,250);
ui->recentSrc->setColumnWidth(2,150);
ui->recentSrc->setAlternatingRowColors(true);
QObject::connect(ui->recentFib,SIGNAL(cellDoubleClicked(int,int)),this,SLOT(open_fib_at(int,int)));
QObject::connect(ui->recentSrc,SIGNAL(cellDoubleClicked(int,int)),this,SLOT(open_src_at(int,int)));
updateRecentList();
if (settings.contains("WORK_PATH"))
ui->workDir->addItems(settings.value("WORK_PATH").toStringList());
else
ui->workDir->addItem(QDir::currentPath());
ui->toolBox->setCurrentIndex(0);
for(auto& temp : fib_template_list)
ui->fib_action->addItem(QString("Open ") + QFileInfo(temp.c_str()).baseName() + " template");
}
void MainWindow::openFile(QString file_name)
{
if(QFileInfo(file_name).isDir())
{
QStringList fib_list = QDir(file_name).entryList(QStringList("*fib.gz"),QDir::Files|QDir::NoSymLinks);
QStringList tt_list = QDir(file_name).entryList(
QStringList("*tt.gz") <<
QString("*trk.gz") <<
QString("*trk") <<
QString("*tck"),QDir::Files|QDir::NoSymLinks);
if(!fib_list.empty())
loadFib(file_name + "/" + fib_list[0]);
else
{
loadFib(file_name + "/" + tt_list[0]);
tt_list.removeAt(0);
}
if(!tt_list.empty())
{
for(int i = 0;i < tt_list.size();++i)
tt_list[i] = file_name + "/" + tt_list[i];
tracking_windows.back()->tractWidget->load_tracts(tt_list);
}
return;
}
if(!QFileInfo(file_name).exists())
{
if(file_name[0] == '-') // Mac pass a variable
return;
QMessageBox::critical(this,"ERROR",QString("Cannot find ") +
file_name + " at current dir: " + QDir::current().dirName());
}
else
{
if(QString(file_name).endsWith("tt.gz") ||
QString(file_name).endsWith("trk") ||
QString(file_name).endsWith("trk.gz"))
{
QStringList file_list = QFileInfo(file_name).dir().entryList(QStringList("*fib.gz"),QDir::Files|QDir::NoSymLinks);
if(file_list.size() == 1)
{
loadFib(QFileInfo(file_name).absolutePath() + "/" + file_list[0]);
tracking_windows.back()->tractWidget->load_tracts(QStringList() << file_name);
}
else
loadFib(file_name);
}
else
if(QString(file_name).endsWith("fib.gz") ||
QString(file_name).endsWith("tck"))
{
loadFib(file_name);
}
else
if(QString(file_name).endsWith("src.gz"))
{
loadSrc(QStringList() << file_name);
}
else
if(QString(file_name).endsWith(".nhdr") ||
QString(file_name).endsWith(".nii") ||
QString(file_name).endsWith(".nii.gz") ||
QString(file_name).endsWith(".dcm"))
{
view_image* dialog = new view_image(this);
dialog->setAttribute(Qt::WA_DeleteOnClose);
if(!dialog->open(QStringList() << file_name))
{
delete dialog;
return;
}
dialog->show();
}
else {
QMessageBox::information(this,"error","Unsupported file extension");
}
}
}
void MainWindow::dragEnterEvent(QDragEnterEvent *event)
{
if(event->mimeData()->hasUrls())
{
event->acceptProposedAction();
}
}
void MainWindow::dropEvent(QDropEvent *event)
{
event->acceptProposedAction();
QList<QUrl> droppedUrls = event->mimeData()->urls();
int droppedUrlCnt = droppedUrls.size();
QStringList files;
for(int i = 0; i < droppedUrlCnt; i++)
files << droppedUrls[i].toLocalFile();
if(files.size() == 1)
openFile(files[0]);
}
void MainWindow::open_fib_at(int row,int)
{
loadFib(ui->recentFib->item(row,1)->text() + "/" +
ui->recentFib->item(row,0)->text());
}
void MainWindow::open_src_at(int row,int)
{
loadSrc(QStringList() << (ui->recentSrc->item(row,1)->text() + "/" +
ui->recentSrc->item(row,0)->text()));
}
void MainWindow::closeEvent(QCloseEvent *event)
{
for(size_t index = 0;index < tracking_windows.size();++index)
if(tracking_windows[index])
{
tracking_windows[index]->closeEvent(event);
if(!event->isAccepted())
return;
delete tracking_windows[index];
}
QMainWindow::closeEvent(event);
}
MainWindow::~MainWindow()
{
console.log_window = nullptr;
QStringList workdir_list;
for (int index = 0;index < 10 && index < ui->workDir->count();++index)
workdir_list << ui->workDir->itemText(index);
std::swap(workdir_list[0],workdir_list[ui->workDir->currentIndex()]);
settings.setValue("WORK_PATH", workdir_list);
delete ui;
}
void MainWindow::updateRecentList(void)
{
{
QStringList file_list = settings.value("recentFibFileList").toStringList();
ui->recentFib->clear();
ui->recentFib->setRowCount(file_list.size());
for (int index = 0;index < file_list.size();++index)
{
ui->recentFib->setRowHeight(index,20);
ui->recentFib->setItem(index, 0, new QTableWidgetItem(QFileInfo(file_list[index]).fileName()));
ui->recentFib->setItem(index, 1, new QTableWidgetItem(QFileInfo(file_list[index]).absolutePath()));
ui->recentFib->setItem(index, 2, new QTableWidgetItem(QFileInfo(file_list[index]).lastModified().toString()));
ui->recentFib->item(index,0)->setFlags(ui->recentFib->item(index,0)->flags() & ~Qt::ItemIsEditable);
ui->recentFib->item(index,1)->setFlags(ui->recentFib->item(index,1)->flags() & ~Qt::ItemIsEditable);
ui->recentFib->item(index,2)->setFlags(ui->recentFib->item(index,2)->flags() & ~Qt::ItemIsEditable);
}
}
{
QStringList file_list = settings.value("recentSrcFileList").toStringList();
ui->recentSrc->clear();
ui->recentSrc->setRowCount(file_list.size());
for (int index = 0;index < file_list.size();++index)
{
ui->recentSrc->setRowHeight(index,20);
ui->recentSrc->setItem(index, 0, new QTableWidgetItem(QFileInfo(file_list[index]).fileName()));
ui->recentSrc->setItem(index, 1, new QTableWidgetItem(QFileInfo(file_list[index]).absolutePath()));
ui->recentSrc->setItem(index, 2, new QTableWidgetItem(QFileInfo(file_list[index]).lastModified().toString()));
ui->recentSrc->item(index,0)->setFlags(ui->recentSrc->item(index,0)->flags() & ~Qt::ItemIsEditable);
ui->recentSrc->item(index,1)->setFlags(ui->recentSrc->item(index,1)->flags() & ~Qt::ItemIsEditable);
ui->recentSrc->item(index,2)->setFlags(ui->recentSrc->item(index,2)->flags() & ~Qt::ItemIsEditable);
}
}
QStringList header;
header << "File Name" << "Directory" << "Date";
ui->recentFib->setHorizontalHeaderLabels(header);
ui->recentSrc->setHorizontalHeaderLabels(header);
}
void MainWindow::addFib(QString filename)
{
// update recent file list
QStringList files = settings.value("recentFibFileList").toStringList();
files.removeAll(filename);
files.prepend(filename);
while (files.size() > MaxRecentFiles)
files.removeLast();
settings.setValue("recentFibFileList", files);
updateRecentList();
}
void MainWindow::addSrc(QString filename)
{
// update recent file list
QStringList files = settings.value("recentSrcFileList").toStringList();
files.removeAll(filename);
files.prepend(filename);
while (files.size() > MaxRecentFiles)
files.removeLast();
settings.setValue("recentSrcFileList", files);
updateRecentList();
}
void shift_track_for_tck(std::vector<std::vector<float> >& loaded_tract_data,tipl::shape<3>& geo);
void MainWindow::loadFib(QString filename,bool presentation_mode)
{
progress p("[Step T3][Fiber Tracking]");
std::string file_name = filename.toStdString();
std::shared_ptr<fib_data> new_handle(new fib_data);
if (!new_handle->load_from_file(&*file_name.begin()))
{
if(!progress::aborted())
QMessageBox::information(this,"ERROR",new_handle->error_msg.c_str());
return;
}
tracking_windows.push_back(new tracking_window(this,new_handle));
tracking_windows.back()->setAttribute(Qt::WA_DeleteOnClose);
tracking_windows.back()->setWindowTitle(filename);
if(presentation_mode)
{
tracking_windows.back()->command("load_workspace",QFileInfo(filename).absolutePath());
tracking_windows.back()->command("presentation_mode");
}
else
if(ui->fib_action->currentIndex() == 0)
{
addFib(filename);
add_work_dir(QFileInfo(filename).absolutePath());
}
tracking_windows.back()->showNormal();
tracking_windows.back()->resize(1200,700);
if(filename.endsWith("trk.gz") || filename.endsWith("trk") || filename.endsWith("tck") || filename.endsWith("tt.gz"))
{
tracking_windows.back()->tractWidget->load_tracts(QStringList() << filename);
if(filename.endsWith("tck"))
{
tipl::shape<3> geo;
shift_track_for_tck(tracking_windows.back()->tractWidget->tract_models.back()->get_tracts(),geo);
}
}
}
void MainWindow::loadSrc(QStringList filenames)
{
if(filenames.empty())
{
QMessageBox::critical(this,"ERROR","Cannot find SRC.gz files in the directory. Please create SRC files first.");
return;
}
try
{
progress p("[Step T2][Reconstruction]");
reconstruction_window* new_mdi = new reconstruction_window(filenames,this);
new_mdi->setAttribute(Qt::WA_DeleteOnClose);
new_mdi->show();
if(filenames.size() == 1)
{
addSrc(filenames[0]);
add_work_dir(QFileInfo(filenames[0]).absolutePath());
}
}
catch(const std::runtime_error& error)
{
QMessageBox::critical(this,"ERROR",error.what());
}
}
void MainWindow::openRecentFibFile(void)
{
QAction *action = qobject_cast<QAction *>(sender());
loadFib(action->data().toString());
}
void MainWindow::openRecentSrcFile(void)
{
QAction *action = qobject_cast<QAction *>(sender());
loadSrc(QStringList() << action->data().toString());
}
void MainWindow::on_OpenDICOM_clicked()
{
QStringList filenames = QFileDialog::getOpenFileNames(
this,
"Open Images files",
ui->workDir->currentText(),
"Image files (*.dcm *.hdr *.nii *nii.gz *.fdf *.nhdr 2dseq subject);;All files (*)" );
if ( filenames.isEmpty() )
return;
progress p("[Step T1][Open Source Images]");
add_work_dir(QFileInfo(filenames[0]).absolutePath());
if(QFileInfo(filenames[0]).completeBaseName() == "subject")
{
tipl::io::bruker_info subject_file;
if(!subject_file.load_from_file(filenames[0].toLocal8Bit().begin()))
return;
QString dir = QFileInfo(filenames[0]).absolutePath();
filenames.clear();
for(unsigned int i = 1;i < 100;++i)
if(QDir(dir + "/" +QString::number(i)).exists())
{
bool is_dwi =false;
// has dif info in the method file
{
tipl::io::bruker_info method_file;
QString method_name = dir + "/" +QString::number(i)+"/method";
if(method_file.load_from_file(method_name.toLocal8Bit().begin()) &&
method_file["PVM_DwEffBval"].length())
is_dwi = true;
}
// has dif info in the imnd file
{
tipl::io::bruker_info imnd_file;
QString imnd_name = dir + "/" +QString::number(i)+"/imnd";
if(imnd_file.load_from_file(imnd_name.toLocal8Bit().begin()) &&
imnd_file["IMND_diff_b_value"].length())
is_dwi = true;
}
if(is_dwi)
filenames.push_back(dir + "/" +QString::number(i)+"/pdata/1/2dseq");
}
if(filenames.size() == 0)
{
QMessageBox::critical(this,"ERROR","No diffusion data in this subject");
return;
}
std::string file_name(subject_file["SUBJECT_study_name"]);
file_name.erase(std::remove(file_name.begin(),file_name.end(),' '),file_name.end());
dicom_parser* dp = new dicom_parser(filenames,this);
dp->set_name(dir + "/" + file_name.c_str() + ".src.gz");
dp->setAttribute(Qt::WA_DeleteOnClose);
dp->showNormal();
return;
}
if(QFileInfo(filenames[0]).completeSuffix() == "dcm")
{
QString sel = QString("*.")+QFileInfo(filenames[0]).suffix();
QDir directory = QFileInfo(filenames[0]).absoluteDir();
QStringList file_list = directory.entryList(QStringList(sel),QDir::Files|QDir::NoSymLinks);
if(file_list.size() > filenames.size())
{
QString msg =
QString("There are %1 %2 files in the directory. Select all?").arg(file_list.size()).arg(QFileInfo(filenames[0]).suffix());
int result = QMessageBox::information(this,"Input images",msg,
QMessageBox::Yes|QMessageBox::No|QMessageBox::Cancel);
if(result == QMessageBox::Cancel)
return;
if(result == QMessageBox::Yes)
{
filenames = file_list;
for(int index = 0;index < filenames.size();++index)
filenames[index] = directory.absolutePath() + "/" + filenames[index];
}
}
}
dicom_parser* dp = new dicom_parser(filenames,this);
dp->setAttribute(Qt::WA_DeleteOnClose);
dp->showNormal();
if(dp->dwi_files.empty())
dp->close();
}
void MainWindow::on_Reconstruction_clicked()
{
QStringList filenames = QFileDialog::getOpenFileNames(
this,
"Open Src files",
ui->workDir->currentText(),
"Src files (*src.gz *.src);;Histology images (*.jpg *.tif);;All files (*)" );
if (filenames.isEmpty())
return;
add_work_dir(QFileInfo(filenames[0]).absolutePath());
loadSrc(filenames);
}
void MainWindow::on_FiberTracking_clicked()
{
if(ui->fib_action->currentIndex() > 0)
{
loadFib(fib_template_list[ui->fib_action->currentIndex()-1].c_str());
tracking_windows.back()->work_path = ui->workDir->currentText() + "/";
return;
}
QString filename = QFileDialog::getOpenFileName(
this,
"Open Fib files",
ui->workDir->currentText(),
"Fib files (*fib.gz *.fib);;Image files (*nii.gz *.nii 2dseq);;All files (*)");
if (filename.isEmpty())
return;
add_work_dir(QFileInfo(filename).absolutePath());
loadFib(filename);
}
void check_name(std::string& name)
{
for(unsigned int index = 0;index < name.size();++index)
if((name[index] < '0' || name[index] > '9') &&
(name[index] < 'a' || name[index] > 'z') &&
(name[index] < 'A' || name[index] > 'Z') &&
name[index] != '.')
name[index] = '_';
}
bool RenameDICOMToDir(QString FileName, QString ToDir)
{
QString NewName;
{
std::string person, sequence, imagename;
{
tipl::io::dicom header;
if (!header.load_from_file(FileName.toLocal8Bit().begin()))
{
show_progress() << "not a DICOM file. Skipping" << std::endl;
return true;
}
header.get_patient(person);
header.get_sequence(sequence);
header.get_image_name(imagename);
}
check_name(person);
check_name(sequence);
check_name(imagename);
QString Person(person.c_str()), Sequence(sequence.c_str()),
ImageName(imagename.c_str());
ToDir += "/";
ToDir += Person;
if (!QDir(ToDir).exists() && !std::filesystem::create_directory(std::filesystem::path(ToDir.toStdString())))
show_progress() << "ERROR: cannot create dir " << ToDir.toStdString() << std::endl;
ToDir += "/";
ToDir += Sequence;
if (!QDir(ToDir).exists() && !std::filesystem::create_directory(std::filesystem::path(ToDir.toStdString())))
show_progress() << "ERROR: cannot create dir " << ToDir.toStdString() << std::endl;
ToDir += "/";
ToDir += ImageName;
NewName = ToDir;
}
if(FileName == NewName)
return true;
show_progress() << FileName.toStdString() << "->" << NewName.toStdString() << std::endl;
return QFile::rename(FileName,NewName);
}
void MainWindow::on_RenameDICOM_clicked()
{
QStringList filenames = QFileDialog::getOpenFileNames(
this,
"Open DICOM files",
ui->workDir->currentText(),
"All files (*)" );
if ( filenames.isEmpty() )
return;
add_work_dir(QFileInfo(filenames[0]).absolutePath());
progress prog_("Rename DICOM Files");
for (unsigned int index = 0;progress::at(index,filenames.size());++index)
if(!RenameDICOMToDir(filenames[index],QFileInfo(filenames[index]).absolutePath()))
show_progress() << "ERROR: cannot rename the file." << std::endl;
}
void MainWindow::add_work_dir(QString dir)
{
if(ui->workDir->findText(dir) != -1)
ui->workDir->removeItem(ui->workDir->findText(dir));
ui->workDir->insertItem(0,dir);
ui->workDir->setCurrentIndex(0);
}
void MainWindow::on_browseDir_clicked()
{
QString filename =
QFileDialog::getExistingDirectory(this,"Browse Directory",
ui->workDir->currentText());
if ( filename.isEmpty() )
return;
add_work_dir(filename);
}
QStringList GetSubDir(QString Dir,bool recursive = true)
{
QStringList sub_dirs;
QStringList dirs = QDir(Dir).entryList(QStringList("*"),
QDir::Dirs | QDir::NoSymLinks | QDir::NoDotAndDotDot);
if(recursive)
sub_dirs << Dir;
for(int index = 0;index < dirs.size();++index)
{
QString new_dir = Dir + "/" + dirs[index];
if(recursive)
sub_dirs << GetSubDir(new_dir,recursive);
else
sub_dirs << new_dir;
}
return sub_dirs;
}
void rename_dicom_at_dir(QString path,QString output)
{
progress prog_("Renaming DICOM");
show_progress() << "current directory is " << std::filesystem::current_path() << std::endl
<< "source directory is " << path.toStdString() << std::endl
<< "output directory is " << output.toStdString() << std::endl;
QStringList dirs = GetSubDir(path);
for(int index = 0;progress::at(index,dirs.size());++index)
{
QStringList files = QDir(dirs[index]).entryList(QStringList("*"),
QDir::Files | QDir::NoSymLinks);
for(int j = 0;j < files.size() && index < dirs.size();++j)
{
progress::show(files[j].toStdString().c_str());
if(!RenameDICOMToDir(dirs[index] + "/" + files[j],output))
show_progress() << "ERROR: cannot rename the file." << std::endl;
}
}
}
void MainWindow::on_RenameDICOMDir_clicked()
{
QString path =
QFileDialog::getExistingDirectory(this,"Browse Directory",
ui->workDir->currentText());
if ( path.isEmpty() )
return;
add_work_dir(path);
rename_dicom_at_dir(path,path);
}
void MainWindow::on_vbc_clicked()
{
CreateDBDialog* new_mdi = new CreateDBDialog(this,true);
new_mdi->setAttribute(Qt::WA_DeleteOnClose);
new_mdi->show();
}
void MainWindow::on_averagefib_clicked()
{
CreateDBDialog* new_mdi = new CreateDBDialog(this,false);
new_mdi->setAttribute(Qt::WA_DeleteOnClose);
new_mdi->show();
}
bool parse_dwi(QStringList file_list,std::vector<std::shared_ptr<DwiHeader> >& dwi_files);
bool load_4d_nii(const char* file_name,std::vector<std::shared_ptr<DwiHeader> >& dwi_files,bool need_bvalbvec);
QString get_dicom_output_name(QString file_name,QString file_extension,bool add_path);
QStringList search_files(QString dir,QString filter);
void MainWindow::on_batch_reconstruction_clicked()
{
QString dir = QFileDialog::getExistingDirectory(
this,
"Open directory",
ui->workDir->currentText());
if(dir.isEmpty())
return;
add_work_dir(dir);
loadSrc(search_files(dir,"*src.gz"));
}
void MainWindow::on_view_image_clicked()
{
QStringList filename = QFileDialog::getOpenFileNames(
this,
"Open Image",
ui->workDir->currentText(),
"image files (*.nii *nii.gz *.dcm *.nhdr 2dseq *fib.gz *src.gz)" );
if(filename.isEmpty())
return;
add_work_dir(QFileInfo(filename[0]).absolutePath());
view_image* dialog = new view_image(this);
dialog->setAttribute(Qt::WA_DeleteOnClose);
if(!dialog->open(filename))
{
delete dialog;
return;
}
dialog->show();
}
void MainWindow::on_workDir_currentTextChanged(const QString &arg1)
{
QDir::setCurrent(arg1);
}
bool MainWindow::load_db(std::shared_ptr<group_connectometry_analysis>& database,QString& filename)
{
filename = QFileDialog::getOpenFileName(
this,
"Open Database files",
ui->workDir->currentText(),
"Database files (*db?fib.gz);;All files (*)");
if (filename.isEmpty())
return false;
add_work_dir(QFileInfo(filename).absolutePath());
database = std::make_shared<group_connectometry_analysis>();
progress prog_("reading connectometry db");
if(!database->load_database(filename.toLocal8Bit().begin()))
{
QMessageBox::critical(this,"ERROR",database->error_msg.c_str());
return false;
}
return true;
}
void MainWindow::on_open_db_clicked()
{
QString filename;
std::shared_ptr<group_connectometry_analysis> database;
if(!load_db(database,filename))
return;
db_window* db = new db_window(this,database);
db->setWindowTitle(filename);
db->setAttribute(Qt::WA_DeleteOnClose);
db->show();
}
void MainWindow::on_group_connectometry_clicked()
{
QString filename;
std::shared_ptr<group_connectometry_analysis> database;
if(!load_db(database,filename))
return;
group_connectometry* group_cnt = new group_connectometry(this,database,filename);
group_cnt->setAttribute(Qt::WA_DeleteOnClose);
group_cnt->show();
}
bool load_image_from_files(QStringList filenames,tipl::image<3>& ref,tipl::vector<3>& vs,tipl::matrix<4,4>& trans);
void MainWindow::on_linear_reg_clicked()
{
QStringList filename1 = QFileDialog::getOpenFileNames(
this,"Open Subject Image",ui->workDir->currentText(),
"Images (*.nii *nii.gz *.dcm);;All files (*)" );
if(filename1.isEmpty())
return;
QStringList filename2 = QFileDialog::getOpenFileNames(
this,"Open Template Image",QFileInfo(filename1[0]).absolutePath(),
"Images (*.nii *nii.gz *.dcm);;All files (*)" );
if(filename2.isEmpty())
return;
tipl::image<3> ref1,ref2;
tipl::vector<3> vs1,vs2;
tipl::matrix<4,4> t1,t2;
if(!load_image_from_files(filename1,ref1,vs1,t1) ||
!load_image_from_files(filename2,ref2,vs2,t2))
return;
std::shared_ptr<manual_alignment> manual(new manual_alignment(this,ref1,vs1,ref2,vs2,tipl::reg::affine,tipl::reg::mutual_info));
manual->nifti_srow = t2;
if(manual->exec() != QDialog::Accepted)
return;
}
void MainWindow::on_nonlinear_reg_clicked()
{
RegToolBox* rt = new RegToolBox(this);
rt->setAttribute(Qt::WA_DeleteOnClose);
rt->showNormal();
}
std::string quality_check_src_files(QString dir);
void show_info_dialog(const std::string& title,const std::string& result);
void MainWindow::on_SRC_qc_clicked()
{
QString dir = QFileDialog::getExistingDirectory(
this,
"Open directory",
ui->workDir->currentText());
if(dir.isEmpty())
return;
progress prog_("checking SRC files");
show_info_dialog("SRC report",quality_check_src_files(dir));
}
void MainWindow::on_parse_network_measures_clicked()
{
QStringList filename = QFileDialog::getOpenFileNames(
this,"Open Network Measures",ui->workDir->currentText(),
"Text files (*.txt);;All files (*)" );
if(filename.isEmpty())
return;
std::ofstream out((filename[0]+".collected.txt").toStdString().c_str());
out << "Field\t";
for(int i = 0;i < filename.size();++i)
out << QFileInfo(filename[i]).baseName().toStdString() << "\t";
out << std::endl;
std::vector<std::string> line_output;
for(int i = 0;i < filename.size();++i)
{
std::ifstream in(filename[i].toStdString().c_str());
std::vector<std::string> node_list;
// global measures
size_t line_index = 0;
while(in)
{
std::string t1,t2;
in >> t1;
if(t1 == "network_measures")
{
std::string nodes;
std::getline(in,nodes);
std::istringstream nodestream(nodes);
std::copy(std::istream_iterator<std::string>(nodestream),
std::istream_iterator<std::string>(),std::back_inserter(node_list));
break;
}
in >> t2;
if(i == 0)
{
line_output.push_back(t1);
line_output.back() += "\t";
}
line_output[line_index] += t2;
line_output[line_index] += "\t";
++line_index;
}
// nodal measures
std::string line;
while(std::getline(in,line))
{
std::istringstream in2(line);
std::string t1;
in2 >> t1;
if(t1[0] == '#' || t1[0] == ' ')
continue;
for(size_t k = 0;k < node_list.size();++k,++line_index)
{
std::string t2;
in2 >> t2;
if(i==0)
{
line_output.push_back(t1);
line_output.back() += "_";
line_output.back() += node_list[k];
line_output.back() += "\t";
}
line_output[line_index] += t2;
line_output[line_index] += "\t";
}
}
}
for(size_t i = 0;i < line_output.size();++i)
out << line_output[i] << std::endl;
QMessageBox::information(this,"DSI Studio",QString("File saved to")+filename[0]+".collected.txt");
}
void MainWindow::on_auto_track_clicked()
{
auto_track* at = new auto_track(this);
at->setAttribute(Qt::WA_DeleteOnClose);
at->showNormal();
}
extern std::string src_error_msg;
void nii2src(const std::vector<std::string>& nii_names,std::string src_name,std::ostream& out)
{
std::vector<std::shared_ptr<DwiHeader> > dwi_files;
for(auto& nii_name : nii_names)
{
if(!load_4d_nii(nii_name.c_str(),dwi_files,true))
{
out << "ERROR: " << src_error_msg << std::endl;
return;
}
}
out << std::filesystem::path(src_name).filename().string() << std::endl;
if(!DwiHeader::output_src(src_name.c_str(),dwi_files,0,false))
out << "ERROR: " << src_error_msg << std::endl;
}
void nii2src(std::string nii_name,std::string src_name,std::ostream& out)
{
std::vector<std::string> nii_names;
nii_names.push_back(nii_name);
nii2src(nii_names,src_name,out);
}
void nii2src(const std::vector<std::string>& nii1,
const std::vector<std::string>& nii2,
std::string src_name,
std::ostream& out)
{
std::vector<std::shared_ptr<DwiHeader> > dwi_files1,dwi_files2;
for(auto& nii_name : nii1)
{
if(!load_4d_nii(nii_name.c_str(),dwi_files1,true))
{
out << "ERROR: " << src_error_msg << std::endl;
return;
}
}
for(auto& nii_name : nii2)
{
if(!load_4d_nii(nii_name.c_str(),dwi_files2,true))
{
out << "ERROR: " << src_error_msg << std::endl;
return;
}
}
if(dwi_files2.size() > dwi_files1.size())
dwi_files1.swap(dwi_files2);
{
out << std::filesystem::path(src_name).filename().string() << ".src.gz" << std::endl;
if(!DwiHeader::output_src((src_name+".src.gz").c_str(),dwi_files1,0,false))
out << "ERROR: " << src_error_msg << std::endl;
}
{
out << "\t" << std::filesystem::path(src_name).filename().string() << ".rsrc.gz" << std::endl;
if(!DwiHeader::output_src((src_name+".rsrc.gz").c_str(),dwi_files2,0,false))
out << "ERROR: " << src_error_msg << std::endl;
}
}
bool get_pe_dir(const std::string& nii_name,size_t& pe_dir,bool& is_neg)
{
const char pe_coding[3][2][5] = { { "\"i\"","\"i-\"" },
{ "\"j\"","\"j-\"" },
{ "\"k\"","\"k-\"" }};
std::string jason_name = nii_name.substr(0,nii_name.find_last_of(".nii")-4) + ".json";
if(!std::filesystem::exists(jason_name))
return false;
std::stringstream buffer;
buffer << std::ifstream(jason_name).rdbuf();
std::string jason_content(buffer.str());
for(pe_dir = 0;pe_dir < 3;++pe_dir)
{
if(jason_content.find(pe_coding[pe_dir][0]) != std::string::npos)
{
is_neg = false;
return true;
}
if(jason_content.find(pe_coding[pe_dir][1]) != std::string::npos)
{
is_neg = true;
return true;
}
}
return false;
}
void nii2src(QStringList nifti_file_list,QString output_dir,std::ofstream& out)
{
std::string output_file_base_name = output_dir.toStdString() + "/" + QFileInfo(nifti_file_list[0]).baseName().toStdString();
if(nifti_file_list.size() == 1)
{
out << "\t" << nifti_file_list[0].toStdString() << " -> " << output_file_base_name + ".src.gz" << std::endl;
nii2src(nifti_file_list[0].toStdString(),output_file_base_name + ".src.gz",out);
return;
}
std::vector<std::string> nii1,nii2;
size_t pe_dir = 4;
out << "\tParsing phase encoding directions" << std::endl;
for (QString nii_file_name : nifti_file_list)
{
std::string nii_name = nii_file_name.toStdString();
size_t cur_pe_dir;
bool is_neg;
if(!get_pe_dir(nii_name,cur_pe_dir,is_neg))
{
out << "\tCannot parse phase encoding direction for " << nii_file_name.toStdString() << std::endl;
nii1.clear();
break;
}
if(pe_dir == 4)
pe_dir = cur_pe_dir;
else
{
if(pe_dir != cur_pe_dir)
{
out << "\t[WARNING] Inconsistent phase encoding directions found at " << nii_file_name.toStdString() << std::endl;
nii1.clear();
break;
}
}
out << "\t" << nii_file_name.toStdString() << " pe dir=" << cur_pe_dir << " neg=" << (is_neg ? "true":"false") << std::endl;
if(is_neg)
nii1.push_back(nii_name);
else
nii2.push_back(nii_name);
}
if(nii1.empty() || nii2.empty())
{
nii1.clear();
for(auto& file : nifti_file_list)
{
nii1.push_back(file.toStdString());
out << "\t" << nii1.back() << std::endl;
}
out << "\tNo reversed phase encoding direction dataset found. Create one SRC file -> ";
nii2src(nii1,output_file_base_name + ".src.gz",out);
}
else
{
out << "\tReversed phase encoding direction data found. Create SRC and RSRC files -> ";
nii2src(nii1,nii2,output_file_base_name,out);
}
}
bool nii2src_bids(QString dir,QString output_dir,std::string& error_msg)
{
QStringList sub_dir = QDir(dir).entryList(QStringList("sub-*"),
QDir::Dirs | QDir::NoSymLinks | QDir::NoDotAndDotDot);
if(sub_dir.isEmpty())
{
error_msg = "No subject folder (sub-*) found.";
return false;
}
if(!QDir(output_dir).exists() && !std::filesystem::create_directory(std::filesystem::path(output_dir.toStdString())))
{
error_msg = "Cannot create the output folder. Please check write privileges";
return false;
}
auto get_nifti_dim = [&](QString file_name)