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view_image.cpp
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#include <map>
#include <QTextStream>
#include <QInputDialog>
#include <QFileDialog>
#include "view_image.h"
#include "ui_view_image.h"
#include "prog_interface_static_link.h"
#include <QPlainTextEdit>
#include <QFileInfo>
#include <QMessageBox>
#include <QBuffer>
#include <QImageReader>
#include <filesystem>
std::map<std::string,std::string> dicom_dictionary;
std::vector<view_image*> opened_images;
std::string common_prefix(const std::string& str1,const std::string& str2)
{
std::string result;
for(size_t cur = 0;cur < str1.length() && cur < str2.length();++cur)
{
if(str1[cur] != str2[cur])
break;
result.push_back(str1[cur]);
}
return result;
}
std::string common_prefix(const std::string& str1,const std::string& str2,const std::string& str3)
{
std::string result;
for(size_t cur = 0;cur < str1.length() && cur < str2.length() && cur < str3.length();++cur)
{
if(str1[cur] != str2[cur] || str1[cur] != str3[cur])
break;
result.push_back(str1[cur]);
}
return result;
}
bool match_strings(const std::string& str1,const std::string& str1_match,
const std::string& str2,std::string& str2_match,bool try_reverse = true,bool try_swap = true)
{
// A->A
// B->B
if(str1 == str1_match)
{
str2_match = str2;
return true;
}
// A->B
// A->B
if(str1 == str2)
{
str2_match = str1_match;
return true;
}
// remove common prefix
{
auto cprefix = common_prefix(str1,str1_match,str2);
if(!cprefix.empty())
{
if(!match_strings(str1.substr(cprefix.length()),str1_match.substr(cprefix.length()),
str2.substr(cprefix.length()),str2_match))
return false;
str2_match = cprefix+str2_match;
return true;
}
}
// remove common postfix
{
auto cpostfix = common_prefix(std::string(str1.rbegin(),str1.rend()),
std::string(str1_match.rbegin(),str1_match.rend()),
std::string(str2.rbegin(),str2.rend()));
if(!cpostfix.empty())
{
if(!match_strings(str1.substr(0,str1.length()-cpostfix.length()),
str1_match.substr(0,str1_match.length()-cpostfix.length()),
str2.substr(0,str2.length()-cpostfix.length()),str2_match))
return false;
str2_match += std::string(cpostfix.rbegin(),cpostfix.rend());
return true;
}
}
auto cp1_1 = common_prefix(str1,str1_match);
auto cp1_2 = common_prefix(str1,str2);
// A_B->A_C
// D_B->D_C
if(cp1_1.length() > cp1_2.length())
{
// A->A_C
// D->D_C
if(cp1_1 == str1)
{
str2_match = str2 + str1_match.substr(cp1_1.size());
return true;
}
if(str1.length() == str2.length())
{
if(match_strings(str1.substr(cp1_1.size()),str1_match.substr(cp1_1.size()),
str2.substr(cp1_1.size()),str2_match))
{
str2_match = str2.substr(0,cp1_1.size()) + str2_match;
return true;
}
}
if(match_strings(str1.substr(cp1_1.size()),str1_match.substr(cp1_1.size()),
str2,str2_match))
return true;
}
// try reversed
std::string rev;
if(try_reverse && match_strings(std::string(str1.rbegin(),str1.rend()),
std::string(str1_match.rbegin(),str1_match.rend()),
std::string(str2.rbegin(),str2.rend()),rev,false,try_swap))
{
str2_match = std::string(rev.rbegin(),rev.rend());
return true;
}
// try swap
if(try_swap)
return match_strings(str1,str2,str1_match,str2_match,try_reverse,false);
return false;
}
bool match_files(const std::string& file_path1,const std::string& file_path2,
const std::string& file_path1_others,std::string& file_path2_gen)
{
auto name1 = std::filesystem::path(file_path1).filename().string();
auto name2 = std::filesystem::path(file_path2).filename().string();
auto name1_others = std::filesystem::path(file_path1_others).filename().string();
auto path1 = std::filesystem::path(file_path1).parent_path().string();
auto path2 = std::filesystem::path(file_path2).parent_path().string();
auto path1_others = std::filesystem::path(file_path1_others).parent_path().string();
std::string name2_others,path2_others;
if(!match_strings(name1,name2,name1_others,name2_others) ||
!match_strings(path1,path2,path1_others,path2_others))
return false;
if(!path2_others.empty())
path2_others += "/";
file_path2_gen = path2_others + name2_others;
return true;
}
bool resample_mat(gz_mat_read& mat_reader,float resolution);
bool view_image::command(std::string cmd,std::string param1)
{
if(!shape.size())
return true;
error_msg.clear();
bool result = true;
if(mat.size())
{
if(cmd == "regrid")
{
float reso = std::stof(param1);
if(reso <= 0.0f)
return false;
resample_mat(mat,reso);
read_mat();
init_image();
return true;
}
if(cmd == "save")
{
gz_mat_write matfile(file_name.toStdString().c_str());
if(!matfile)
{
QMessageBox::critical(this,"ERROR","Cannot save file");
return false;
}
progress p("saving");
for(unsigned int index = 0;progress::at(index,mat.size());++index)
matfile.write(mat[index]);
QMessageBox::information(this,"DSI Studio","File Save");
return true;
}
}
{
progress prog(cmd.c_str());
if(!param1.empty())
progress::show((std::string("param: ")+param1).c_str());
if(cmd =="change_type")
{
auto new_type = decltype(data_type)(std::stoi(param1));
if(data_type != new_type)
{
std::vector<unsigned char> buf,empty_buf;
size_t pixelbit[4] = {1,2,4,4};
buf.resize(shape.size()*pixelbit[new_type]);
apply([&](auto& I)
{
switch(new_type)
{
case uint8: tipl::copy_mt(I.begin(),I.end(),reinterpret_cast<unsigned char*>(&buf[0]));break;
case uint16: tipl::copy_mt(I.begin(),I.end(),reinterpret_cast<unsigned short*>(&buf[0]));break;
case uint32: tipl::copy_mt(I.begin(),I.end(),reinterpret_cast<unsigned int*>(&buf[0]));break;
case float32: tipl::copy_mt(I.begin(),I.end(),reinterpret_cast<float*>(&buf[0]));break;
}
I.buf().swap(empty_buf);
});
data_type = new_type;
apply([&](auto& I)
{
I.buf().swap(buf);
I.resize(shape);
});
if(!dwi_volume_buf.empty())
dwi_volume_buf = std::move(std::vector<std::vector<unsigned char> >(dwi_volume_buf.size()));
}
}
else
if(cmd == "set_transformation")
{
std::istringstream in(param1);
for(int i = 0;i < 16;++i)
in >> T[i];
}
else
if(cmd == "set_shift")
{
std::istringstream in(param1);
in >> T[3] >> T[7] >> T[11];
}
else
apply([&](auto& I)
{
result = tipl::command<gz_nifti>(I,vs,T,is_mni,cmd,param1,error_msg);
shape = I.shape();
});
show_progress() << "result: " << (result ? "succeeded":"failed") << std::endl;
if(!result)
{
show_progress() << "ERROR:" << error_msg << std::endl;
return false;
}
if(mat.size())
write_mat_image();
}
init_image();
command_list.push_back(cmd);
param_list.push_back(param1);
if(cmd == "save" && !file_names.empty())
{
if(QMessageBox::question(nullptr,"DSI Studio","Applying processing to other images and save them?",
QMessageBox::No | QMessageBox::Yes,QMessageBox::Yes) == QMessageBox::No)
{
file_names.clear();
return true;
}
progress p1("apply to other images");
int file_index = 0;
for(;progress::at(file_index,file_names.size());++file_index)
{
auto file_name2 = file_names[file_index];
progress p2("processing ",file_name2.toStdString().c_str());
std::shared_ptr<view_image> dialog(new view_image(parentWidget()));
dialog->setAttribute(Qt::WA_DeleteOnClose);
if(!dialog->open(QStringList() << file_name2))
{
QMessageBox::critical(this,"ERROR",QString("Cannot open ")+file_name2);
break;
}
for(size_t i = 0;i < param_list.size();++i)
{
std::string param2 = param_list[i];
if(command_list[i] == "save" ||
command_list[i] == "multiply_image" ||
command_list[i] == "add_image" ||
command_list[i] == "minus_image")
{
if(match_files(original_file_name.toStdString(),param_list[i],
file_name2.toStdString(),param2))
{
show_progress() << "matched path: " << std::filesystem::path(param2).parent_path().string() << std::endl;
show_progress() << "matched file name: " << std::filesystem::path(param2).filename().string() << std::endl;
}
}
if(!dialog->command(command_list[i],param2))
{
QMessageBox::critical(this,"ERROR",QString(dialog->error_msg.c_str()) + "\n"
+ command_list[i].c_str() + " at\n"
+ file_name2);
goto end;
}
}
}
end:
if(file_index < file_names.size() && // The processed is aborted, or there is an error happened
file_index && // Some files were processed without a problem. file_index=0 is current image, file_index = 1 is the first to-be processed image.
original_file_name.toStdString() == param1) // those files were overwritten to original file
{
QMessageBox::critical(this,"ERROR","Some files were processed and overwritten. They will be ignored in the next analyses");
#ifdef QT6_PATCH
file_names.remove(0,file_index);
#else
for(int i = 0;i < file_index;++i)
file_names.removeFirst();
#endif
// remove the last save command
command_list.pop_back();
param_list.pop_back();
return true;
}
command_list.clear();
param_list.clear();
}
return true;
}
void show_view(QGraphicsScene& scene,QImage I);
bool load_image_from_files(QStringList filenames,tipl::image<3>& ref,tipl::vector<3>& vs,tipl::matrix<4,4>& trans)
{
if(filenames.size() == 1 && filenames[0].toLower().contains("nii"))
{
gz_nifti in;
if(!in.load_from_file(filenames[0].toLocal8Bit().begin()) || !in.toLPS(ref))
{
QMessageBox::information(nullptr,"Error","Not a valid nifti file");
return false;
}
in.get_voxel_size(vs);
in.get_image_transformation(trans);
return true;
}
else
if(filenames.size() == 1 && filenames[0].contains("2dseq"))
{
tipl::io::bruker_2dseq seq;
if(!seq.load_from_file(filenames[0].toLocal8Bit().begin()))
{
QMessageBox::information(nullptr,"Error","Not a valid 2dseq file");
return false;
}
seq.get_image().swap(ref);
seq.get_voxel_size(vs);
return true;
}
else
{
tipl::io::dicom_volume v;
std::vector<std::string> file_list;
for(int i = 0;i < filenames.size();++i)
file_list.push_back(filenames[i].toStdString());
v.load_from_files(file_list);
v >> ref;
v.get_voxel_size(vs);
return true;
}
}
TableKeyEventWatcher::TableKeyEventWatcher(QTableWidget* table_):table(table_)
{
table_->installEventFilter(this);
}
bool TableKeyEventWatcher::eventFilter(QObject * receiver, QEvent * event)
{
auto table = qobject_cast<QTableWidget*>(receiver);
if (table && event->type() == QEvent::KeyPress)
{
auto keyEvent = static_cast<QKeyEvent*>(event);
if (keyEvent->key() == Qt::Key_Delete && keyEvent->modifiers() & Qt::ControlModifier)
emit DeleteRowPressed(table->currentRow());
}
return false;
}
void view_image::DeleteRowPressed(int row)
{
if(ui->info->currentRow() == -1)
return;
if(ui->info->currentRow() < mat.size())
{
auto index = ui->mat_images->findText(mat.name(ui->info->currentRow()));
if(index != -1)
ui->mat_images->removeItem(index);
mat.remove(ui->info->currentRow());
}
ui->info->removeRow(ui->info->currentRow());
}
view_image::view_image(QWidget *parent) :
QMainWindow(parent),
ui(new Ui::view_image)
{
ui->setupUi(this);
table_event.reset(new TableKeyEventWatcher(ui->info));
connect(table_event.get(),SIGNAL(DeleteRowPressed(int)),this,SLOT(DeleteRowPressed(int)));
ui->mat_images->hide();
ui->info->setColumnWidth(0,120);
ui->info->setColumnWidth(1,200);
ui->info->setHorizontalHeaderLabels(QStringList() << "Header" << "Value");
ui->view->setScene(&source);
ui->max_color->setColor(0xFFFFFFFF);
ui->min_color->setColor(0XFF000000);
ui->dwi_volume->hide();
ui->dwi_label->hide();
connect(ui->max_color,SIGNAL(clicked()),this,SLOT(change_contrast()));
connect(ui->min_color,SIGNAL(clicked()),this,SLOT(change_contrast()));
connect(ui->orientation,SIGNAL(currentIndexChanged(int)),this,SLOT(change_contrast()));
connect(ui->axis_grid,SIGNAL(currentIndexChanged(int)),this,SLOT(change_contrast()));
connect(ui->menuOverlay, SIGNAL(aboutToShow()),this, SLOT(update_overlay_menu()));
connect(ui->actionMorphology_Smoothing, SIGNAL(triggered()),this, SLOT(run_action()));
connect(ui->actionMorphology_Defragment, SIGNAL(triggered()),this, SLOT(run_action()));
connect(ui->actionMorphology_Dilation, SIGNAL(triggered()),this, SLOT(run_action()));
connect(ui->actionMorphology_Erosion, SIGNAL(triggered()),this, SLOT(run_action()));
connect(ui->actionMorphology_Edge, SIGNAL(triggered()),this, SLOT(run_action()));
connect(ui->actionMorphology_XY, SIGNAL(triggered()),this, SLOT(run_action()));
connect(ui->actionMorphology_XZ, SIGNAL(triggered()),this, SLOT(run_action()));
connect(ui->actionFlip_X, SIGNAL(triggered()),this, SLOT(run_action()));
connect(ui->actionFlip_Y, SIGNAL(triggered()),this, SLOT(run_action()));
connect(ui->actionFlip_Z, SIGNAL(triggered()),this, SLOT(run_action()));
connect(ui->actionSwap_XY, SIGNAL(triggered()),this, SLOT(run_action()));
connect(ui->actionSwap_XZ, SIGNAL(triggered()),this, SLOT(run_action()));
connect(ui->actionSwap_YZ, SIGNAL(triggered()),this, SLOT(run_action()));
connect(ui->actionDownsample_by_2, SIGNAL(triggered()),this, SLOT(run_action()));
connect(ui->actionUpsample_by_2, SIGNAL(triggered()),this, SLOT(run_action()));
connect(ui->actionNormalize_Intensity, SIGNAL(triggered()),this, SLOT(run_action()));
connect(ui->actionMean_Filter, SIGNAL(triggered()),this, SLOT(run_action()));
connect(ui->actionGaussian_Filter, SIGNAL(triggered()),this, SLOT(run_action()));
connect(ui->actionSobel_Filter, SIGNAL(triggered()),this, SLOT(run_action()));
// ask for a value and run action
connect(ui->actionIntensity_shift, SIGNAL(triggered()),this, SLOT(run_action2()));
connect(ui->actionIntensity_scale, SIGNAL(triggered()),this, SLOT(run_action2()));
connect(ui->actionLower_threshold, SIGNAL(triggered()),this, SLOT(run_action2()));
connect(ui->actionUpper_Threshold, SIGNAL(triggered()),this, SLOT(run_action2()));
connect(ui->actionRegrid, SIGNAL(triggered()),this, SLOT(run_action2()));
connect(ui->actionThreshold, SIGNAL(triggered()),this, SLOT(run_action2()));
connect(ui->actionTranslocate, SIGNAL(triggered()),this, SLOT(run_action2()));
connect(ui->actionResize, SIGNAL(triggered()),this, SLOT(run_action2()));
connect(ui->actionMultiplyImage, SIGNAL(triggered()),this, SLOT(run_action2()));
connect(ui->actionAddImage, SIGNAL(triggered()),this, SLOT(run_action2()));
connect(ui->actionMinusImage, SIGNAL(triggered()),this, SLOT(run_action2()));
connect(ui->actionCropToFit, SIGNAL(triggered()),this, SLOT(run_action2()));
ui->tabWidget->setCurrentIndex(0);
qApp->installEventFilter(this);
this_index = opened_images.size();
opened_images.push_back(this);
}
void save_idx(const char* file_name,std::shared_ptr<gz_istream> in);
view_image::~view_image()
{
opened_images[this_index] = nullptr;
update_other_images();
qApp->removeEventFilter(this);
delete ui;
}
bool view_image::eventFilter(QObject *obj, QEvent *event)
{
if (event->type() == QEvent::Wheel && obj->parent() == ui->view)
{
QWheelEvent* we = dynamic_cast<QWheelEvent*>(event);
if(!we)
return false;
if(we->angleDelta().y() < 0)
ui->zoom->setValue(ui->zoom->value()*0.8f);
else
ui->zoom->setValue(ui->zoom->value()*1.2f);
event->accept();
return true;
}
if (event->type() != QEvent::MouseMove || obj->parent() != ui->view)
return false;
QMouseEvent *mouseEvent = static_cast<QMouseEvent*>(event);
QPointF point = ui->view->mapToScene(mouseEvent->pos().x(),mouseEvent->pos().y());
tipl::vector<3,float> pos,mni;
auto x = point.x();
auto y = point.y();
if(has_flip_x())
x = source.width() - x;
if(has_flip_y())
y = source.height() - y;
tipl::slice2space(cur_dim,
std::round(float(x) / ui->zoom->value()),
std::round(float(y) / ui->zoom->value()),ui->slice_pos->value(),pos[0],pos[1],pos[2]);
if(!shape.is_valid(pos))
return true;
mni = pos;
mni.to(T);
apply([&](auto& data)
{
ui->info_label->setText(QString("(i,j,k)=(%1,%2,%3) (x,y,z)=(%4,%5,%6) value=%7").arg(pos[0]).arg(pos[1]).arg(pos[2])
.arg(mni[0]).arg(mni[1]).arg(mni[2])
.arg(data.at(pos)));
});
return true;
}
bool get_compressed_image(tipl::io::dicom& dicom,tipl::image<2,short>& I)
{
QByteArray array((char*)&*dicom.compressed_buf.begin(),dicom.buf_size);
QBuffer qbuff(&array);
QImageReader qimg;
qimg.setDecideFormatFromContent(true);
qimg.setDevice(&qbuff);
QImage img;
if(!qimg.read(&img))
{
std::cout << "Unsupported transfer syntax:" << dicom.encoding;
return false;
}
QImage buf = img.convertToFormat(QImage::Format_RGB32);
I.resize(tipl::shape<2>(buf.width(),buf.height()));
const uchar* ptr = buf.bits();
for(int j = 0;j < I.size();++j,ptr += 4)
I[j] = *ptr;
return true;
}
void view_image::read_mat_info(void)
{
QString info;
for(unsigned int index = 0;index < mat.size();++index)
{
std::string data;
mat[index].get_info(data);
info += data.c_str();
info += "\n";
}
show_info(info);
}
bool view_image::read_mat_image(void)
{
auto cur_metric = ui->mat_images->currentText().toStdString();
unsigned int row(0), col(0);
if(!mat.get_col_row(cur_metric.c_str(),row,col) || row*col != shape.size())
return false;
if(mat.type_compatible<float>(cur_metric.c_str()))
{
I_float32.resize(shape);
mat.read(cur_metric.c_str(),I_float32.begin(),I_float32.end());
data_type = float32;
ui->type->setCurrentIndex(data_type);
return true;
}
if(mat.type_compatible<unsigned int>(cur_metric.c_str()))
{
I_uint32.resize(shape);
mat.read(cur_metric.c_str(),I_uint32.begin(),I_uint32.end());
data_type = uint32;
ui->type->setCurrentIndex(data_type);
return true;
}
if(mat.type_compatible<unsigned short>(cur_metric.c_str()))
{
I_uint16.resize(shape);
mat.read(cur_metric.c_str(),I_uint16.begin(),I_uint16.end());
data_type = uint16;
ui->type->setCurrentIndex(data_type);
return true;
}
if(mat.type_compatible<unsigned char>(cur_metric.c_str()))
{
I_uint8.resize(shape);
mat.read(cur_metric.c_str(),I_uint8.begin(),I_uint8.end());
data_type = uint8;
ui->type->setCurrentIndex(data_type);
return true;
}
if(mat.type_compatible<double>(cur_metric.c_str()))
{
I_float32.resize(shape);
mat.read(cur_metric.c_str(),I_float32.begin(),I_float32.end());
data_type = float32;
ui->type->setCurrentIndex(data_type);
return true;
}
return false;
}
void view_image::write_mat_image(void)
{
auto cur_metric = ui->mat_images->currentText().toStdString();
unsigned int row(0), col(0);
if(!mat.get_col_row(cur_metric.c_str(),row,col) || row*col != shape.size())
return;
switch(data_type)
{
case float32:
std::copy(I_float32.begin(),I_float32.end(),const_cast<float*>(mat.read_as_type<float>(cur_metric.c_str(),row,col)));
break;
case uint32:
std::copy(I_uint32.begin(),I_uint32.end(),const_cast<unsigned int*>(mat.read_as_type<unsigned int>(cur_metric.c_str(),row,col)));
break;
case uint16:
std::copy(I_uint16.begin(),I_uint16.end(),const_cast<unsigned short*>(mat.read_as_type<unsigned short>(cur_metric.c_str(),row,col)));
break;
case uint8:
std::copy(I_uint8.begin(),I_uint8.end(),const_cast<unsigned char*>(mat.read_as_type<unsigned char>(cur_metric.c_str(),row,col)));
break;
}
}
void initial_LPS_nifti_srow(tipl::matrix<4,4>& T,const tipl::shape<3>& geo,const tipl::vector<3>& vs);
bool view_image::read_mat(void)
{
if(!mat.read("dimension",shape))
{
error_msg = "cannot find dimension matrix";
return false;
}
bool has_data = true;
ui->mat_images->clear();
for(size_t i = 0;i < mat.size();++i)
if(mat[i].get_cols()*mat[i].get_rows() == shape.size())
ui->mat_images->addItem(mat[i].get_name().c_str());
if(!ui->mat_images->count())
{
error_msg = "cannot find images";
return false;
}
ui->mat_images->setCurrentIndex(0);
mat.get_voxel_size(vs);
if(mat.has("trans"))
mat.read("trans",T);
else
initial_LPS_nifti_srow(T,shape,vs);
read_mat_info();
ui->mat_images->show();
return true;
}
void prepare_idx(const char* file_name,std::shared_ptr<gz_istream> in);
bool view_image::open(QStringList file_names_)
{
if(file_names_.empty())
return false;
file_names = file_names_;
original_file_name = file_name = file_names[0];
file_names.removeFirst();
tipl::io::dicom dicom;
is_mni = false;
T.identity();
QString info;
setWindowTitle(QFileInfo(file_name).fileName());
progress prog("open image file ",std::filesystem::path(file_name.toStdString()).filename().string().c_str());
if(file_names_.size() > 1 && QString(file_name).endsWith(".bmp"))
{
for(unsigned int i = 0;progress::at(i,file_names_.size());++i)
{
tipl::color_image I;
tipl::io::bitmap bmp;
if(!bmp.load_from_file(file_names_[i].toStdString().c_str()))
return false;
bmp >> I;
data_type = uint8;
if(i == 0)
{
shape = tipl::shape<3>(I.width(),I.height(),file_names_.size());
I_uint8.resize(shape);
}
unsigned int pos = i*I.size();
for(unsigned int j = 0;j < I.size();++j)
I_uint8[pos+j] = ((float)I[j].r+(float)I[j].r+(float)I[j].r)/3.0;
}
file_names.clear();
}
if(QString(file_name).endsWith(".nhdr"))
{
tipl::io::nrrd<progress> nrrd;
if(!nrrd.load_from_file(file_name.toStdString().c_str()))
{
QMessageBox::critical(this,"ERROR",nrrd.error_msg.c_str());
return false;
}
shape = nrrd.size;
data_type = float32;
if(nrrd.values["type"] == "int" || nrrd.values["type"] == "unsigned int")
data_type = uint32;
if(nrrd.values["type"] == "short" || nrrd.values["type"] == "unsigned short")
data_type = uint16;
if(nrrd.values["type"] == "uchar")
data_type = uint8;
apply([&](auto& data)
{
nrrd >> data;
});
if(progress::aborted())
return false;
if(!nrrd.error_msg.empty())
{
QMessageBox::critical(this,"ERROR",nrrd.error_msg.c_str());
return false;
}
nrrd.get_voxel_size(vs);
nrrd.get_image_transformation(T);
info.clear();
for(const auto& iter : nrrd.values)
info += QString("%1=%2\n").arg(iter.first.c_str()).arg(iter.second.c_str());
}
else
if(QString(file_name).endsWith(".nii.gz") || QString(file_name).endsWith(".nii"))
{
prepare_idx(file_name.toStdString().c_str(),nifti.input_stream);
if(!nifti.load_from_file(file_name.toStdString().c_str()))
{
QMessageBox::critical(this,"ERROR",nifti.error_msg.c_str());
return false;
}
if(nifti.dim(4) > 1)
{
ui->dwi_volume->setMaximum(nifti.dim(4)-1);
dwi_volume_buf.resize(nifti.dim(4));
nifti.input_stream->sample_access_point = true;
ui->dwi_volume->show();
ui->dwi_label->show();
}
nifti.get_image_dimension(shape);
switch (nifti.nif_header.datatype)
{
case 2://DT_UNSIGNED_CHAR 2
case 256: // DT_INT8
data_type = uint8;
break;
case 4://DT_SIGNED_SHORT 4
case 512: // DT_UINT16
data_type = uint16;
break;
case 8://DT_SIGNED_INT 8
case 768: // DT_UINT32
case 1024: // DT_INT64
case 1280: // DT_UINT64
data_type = uint32;
break;
case 16://DT_FLOAT 16
case 64://DT_DOUBLE 64
data_type = float32;
break;
default:
QMessageBox::critical(this,"ERROR","Unsupported pixel format");
return false;
}
if(std::floor(nifti.nif_header.scl_inter) != nifti.nif_header.scl_inter ||
std::floor(nifti.nif_header.scl_slope) != nifti.nif_header.scl_slope)
data_type = float32;
bool succeed = true;
apply([&](auto& data)
{
succeed = nifti.get_untouched_image(data);
});
if(!succeed)
{
QMessageBox::critical(this,"ERROR",nifti.error_msg.c_str());
return false;
}
if(nifti.dim(4) == 1)
save_idx(file_name.toStdString().c_str(),nifti.input_stream);
nifti.get_voxel_size(vs);
nifti.get_image_transformation(T);
is_mni = nifti.is_mni();
std::ostringstream out;
out << nifti;
info = out.str().c_str();
}
else
if(dicom.load_from_file(file_name.toStdString()))
{
data_type = uint16;
dicom.get_image_dimension(shape);
apply([&](auto& data){dicom >> data;});
if(dicom.is_compressed)
{
tipl::image<2,short> I;
if(!get_compressed_image(dicom,I))
{
QMessageBox::critical(this,"ERROR",QString("Unsupported transfer syntax:") + QString(dicom.encoding.c_str()));
return false;
}
if(I.size() == shape.size())
std::copy(I.begin(),I.end(),I_uint16.begin());
}
dicom.get_voxel_size(vs);
std::string info_;
dicom >> info_;
if(dicom_dictionary.empty())
{
QFile data(":/data/dicom_tag.txt");
if (data.open(QIODevice::ReadOnly | QIODevice::Text))
{
QTextStream in(&data);
while (!in.atEnd())
{
QStringList list = in.readLine().split('\t');
if(list.size() < 3)
continue;
std::string value = list[2].toStdString();
std::replace(value.begin(),value.end(),' ','_');
dicom_dictionary[list[0].toStdString()] = value;
}
}
}
std::ostringstream out;
std::istringstream in(info_);
std::string line;
while(std::getline(in,line))
{
for(size_t pos = 0;(pos = line.find('(',pos)) != std::string::npos;++pos)
{
std::string tag = line.substr(pos,11);
if(tag.length() != 11)
continue;
std::string tag2 = tag;
tag2[3] = 'x';
tag2[4] = 'x';
auto iter = dicom_dictionary.find(tag);
if(iter == dicom_dictionary.end())
iter = dicom_dictionary.find(tag2);
if(iter != dicom_dictionary.end())
line.replace(pos,11,tag+iter->second);
}
out << line << std::endl;
}
info_ = out.str();
info = info_.c_str();
}
else
if(QString(file_name).endsWith(".mat") || QString(file_name).endsWith("fib.gz") || QString(file_name).endsWith("src.gz"))
{
if(!mat.load_from_file(file_name.toStdString().c_str()))
{
error_msg = "invalid format";
return false;
}
data_type = float32;
if(!read_mat())
return false;
}
else
if(QString(file_name).endsWith("2dseq"))
{
tipl::io::bruker_2dseq seq;
if(seq.load_from_file(file_name.toLocal8Bit().begin()))
{
error_msg = "cannot parse file";
return false;
}
data_type = float32;
shape = seq.get_image().shape();
I_float32 = seq.get_image();
seq.get_voxel_size(vs);
}
else
{
error_msg = "unsupported file format";
return false;
}
if(!info.isEmpty())
show_info(info);
no_update = true;
ui->type->setCurrentIndex(data_type);
ui->zoom->setValue(0.9f*width()/shape.width());
if(shape.size())
init_image();
return shape.size() || !info.isEmpty();
}
void view_image::init_image(void)
{
no_update = true;
float min_value = 0.0f;
float max_value = 0.0f;
apply([&](auto& data)
{
auto minmax = tipl::minmax_value_mt(data);
min_value = minmax.first;
max_value = minmax.second;
});
float range = max_value-min_value;
QString dim_text = QString("%1,%2,%3").arg(shape.width()).arg(shape.height()).arg(shape.depth());
if(!dwi_volume_buf.empty())
dim_text += QString(",%1").arg(dwi_volume_buf.size());
ui->image_info->setText(QString("dim=(%1) vs=(%4,%5,%6) srow=[%7 %8 %9 %10][%11 %12 %13 %14][%15 %16 %17 %18]").
arg(dim_text).
arg(double(vs[0])).arg(double(vs[1])).arg(double(vs[2])).
arg(double(T[0])).arg(double(T[1])).arg(double(T[2])).arg(double(T[3])).
arg(double(T[4])).arg(double(T[5])).arg(double(T[6])).arg(double(T[7])).
arg(double(T[8])).arg(double(T[9])).arg(double(T[10])).arg(double(T[11])));
if(ui->min->maximum() != double(max_value) ||
ui->max->minimum() != double(min_value))
{
ui->min->setRange(double(min_value),double(max_value));
ui->max->setRange(double(min_value),double(max_value));
ui->min->setSingleStep(double(range/20));
ui->max->setSingleStep(double(range/20));
ui->min->setValue(double(min_value));
ui->max->setValue(double(max_value));
}
if(ui->slice_pos->maximum() != int(shape[cur_dim]-1))
{
ui->slice_pos->setRange(0,shape[cur_dim]-1);
slice_pos[0] = shape.width()/2;
slice_pos[1] = shape.height()/2;
slice_pos[2] = shape.depth()/2;
ui->slice_pos->setValue(slice_pos[cur_dim]);
ui->actionResize->setStatusTip(QString("%1 %2 %3").arg(shape.width()).arg(shape.height()).arg(shape.depth()));
}
no_update = false;
show_image(true);
}
void view_image::set_overlay(void)
{
QAction *action = qobject_cast<QAction *>(sender());
overlay_images_visible[action->data().toInt()] = action->isChecked();
show_image(false);
}
void view_image::update_overlay_menu(void)
{
{
std::vector<size_t> new_overlay_images;
std::vector<bool> new_overlay_images_visible;
for(size_t i = 0;i < opened_images.size();++i)
if(opened_images[i] && this_index != i &&
opened_images[i]->shape == shape)
{
new_overlay_images.push_back(i);
auto pos = std::find(overlay_images.begin(),overlay_images.end(),i);
new_overlay_images_visible.push_back(pos != overlay_images.end() && overlay_images_visible[pos-overlay_images.begin()]);
}
overlay_images.swap(new_overlay_images);
overlay_images_visible.swap(new_overlay_images_visible);
}
while(ui->menuOverlay->actions().size() > int(overlay_images.size()))
ui->menuOverlay->removeAction(ui->menuOverlay->actions()[ui->menuOverlay->actions().size()-1]);
for (size_t index = 0; index < overlay_images.size(); ++index)
{
if(index >= size_t(ui->menuOverlay->actions().size()))
{
QAction* Item = new QAction(this);
Item->setVisible(true);
Item->setData(int(index));
Item->setCheckable(true);
connect(Item, SIGNAL(triggered()),this, SLOT(set_overlay()));
ui->menuOverlay->addAction(Item);
}
auto action = ui->menuOverlay->actions()[index];
action->setText(opened_images[overlay_images[index]]->windowTitle());
action->setChecked(overlay_images_visible[index]);
}
}
bool view_image::has_flip_x(void)
{
bool flip_x = false;