tracking_window::tracking_window(QWidget *parent,ODFModel* new_handle,bool handle_release_) :
QMainWindow(parent),handle(new_handle),handle_release(handle_release_),
ui(new Ui::tracking_window),scene(*this,new_handle),slice(new_handle)
{
ODFModel* odf_model = (ODFModel*)handle;
FibData& fib_data = odf_model->fib_data;
odf_size = fib_data.fib.odf_table.size();
odf_face_size = fib_data.fib.odf_faces.size();
has_odfs = fib_data.fib.has_odfs() ? 1:0;
// check whether first index is "fa0"
is_dti = (fib_data.view_item[0].name[0] == 'f');
ui->setupUi(this);
{
setGeometry(10,10,800,600);
ui->regionDockWidget->setMinimumWidth(0);
ui->dockWidget->setMinimumWidth(0);
ui->dockWidget_3->setMinimumWidth(0);
ui->renderingLayout->addWidget(renderWidget = new RenderingTableWidget(*this,ui->renderingWidgetHolder,has_odfs));
ui->centralLayout->insertWidget(1,glWidget = new GLWidget(renderWidget->getData("anti_aliasing").toInt(),
*this,renderWidget,ui->centralwidget));
ui->verticalLayout_3->addWidget(regionWidget = new RegionTableWidget(*this,ui->regionDockWidget));
ui->tractverticalLayout->addWidget(tractWidget = new TractTableWidget(*this,ui->TractWidgetHolder));
ui->graphicsView->setScene(&scene);
ui->graphicsView->setCursor(Qt::CrossCursor);
scene.statusbar = ui->statusbar;
color_bar.reset(new color_bar_dialog(this));
}
// setup fa threshold
{
for(int index = 0;index < fib_data.fib.index_name.size();++index)
ui->tracking_index->addItem((fib_data.fib.index_name[index]+" threshold").c_str());
ui->tracking_index->setCurrentIndex(0);
ui->step_size->setValue(fib_data.vs[0]/2.0);
}
// setup sliders
{
slice_no_update = true;
ui->SagSlider->setRange(0,slice.geometry[0]-1);
ui->CorSlider->setRange(0,slice.geometry[1]-1);
ui->AxiSlider->setRange(0,slice.geometry[2]-1);
ui->SagSlider->setValue(slice.slice_pos[0]);
ui->CorSlider->setValue(slice.slice_pos[1]);
ui->AxiSlider->setValue(slice.slice_pos[2]);
ui->glSagBox->setRange(0,slice.geometry[0]-1);
ui->glCorBox->setRange(0,slice.geometry[1]-1);
ui->glAxiBox->setRange(0,slice.geometry[2]-1);
ui->glSagBox->setValue(slice.slice_pos[0]);
ui->glCorBox->setValue(slice.slice_pos[1]);
ui->glAxiBox->setValue(slice.slice_pos[2]);
slice_no_update = false;
on_SliceModality_currentIndexChanged(0);
for (unsigned int index = 0;index < fib_data.view_item.size(); ++index)
{
ui->sliceViewBox->addItem(fib_data.view_item[index].name.c_str());
if(fib_data.view_item[index].is_overlay)
ui->overlay->addItem(fib_data.view_item[index].name.c_str());
}
ui->sliceViewBox->setCurrentIndex(0);
ui->overlay->setCurrentIndex(0);
if(ui->overlay->count() == 1)
ui->overlay->hide();
}
is_qsdr = !handle->fib_data.trans_to_mni.empty();
// setup atlas
if(!fa_template_imp.I.empty() && fib_data.vs[0] > 0.5 && !is_qsdr)
{
mi3_arg.scaling[0] = slice.voxel_size[0] / std::fabs(fa_template_imp.tran[0]);
mi3_arg.scaling[1] = slice.voxel_size[1] / std::fabs(fa_template_imp.tran[5]);
mi3_arg.scaling[2] = slice.voxel_size[2] / std::fabs(fa_template_imp.tran[10]);
image::reg::align_center(slice.source_images,fa_template_imp.I,mi3_arg);
mi3.reset(new manual_alignment(this,slice.source_images,fa_template_imp.I,mi3_arg));
is_qsdr = false;
}
else
ui->actionManual_Registration->setEnabled(false);
ui->actionConnectometry->setEnabled(handle->fib_data.fib.has_odfs() && is_qsdr);
for(int index = 0;index < atlas_list.size();++index)
ui->atlasListBox->addItem(atlas_list[index].name.c_str());
{
if(is_dti)
ui->actionQuantitative_anisotropy_QA->setText("Save FA...");
for (int index = fib_data.other_mapping_index; index < fib_data.view_item.size(); ++index)
{
std::string& name = fib_data.view_item[index].name;
QAction* Item = new QAction(this);
Item->setText(QString("Save %1...").arg(name.c_str()));
Item->setData(QString(name.c_str()));
Item->setVisible(true);
connect(Item, SIGNAL(triggered()),tractWidget, SLOT(save_tracts_data_as()));
ui->menuSave->addAction(Item);
}
}
// opengl
{
connect(renderWidget->treemodel,SIGNAL(dataChanged(QModelIndex,QModelIndex)),
glWidget,SLOT(updateGL()));
connect(ui->tbDefaultParam,SIGNAL(clicked()),renderWidget,SLOT(setDefault()));
connect(ui->tbDefaultParam,SIGNAL(clicked()),glWidget,SLOT(updateGL()));
connect(ui->glSagSlider,SIGNAL(valueChanged(int)),this,SLOT(glSliderValueChanged()));
connect(ui->glCorSlider,SIGNAL(valueChanged(int)),this,SLOT(glSliderValueChanged()));
connect(ui->glAxiSlider,SIGNAL(valueChanged(int)),this,SLOT(glSliderValueChanged()));
connect(ui->glSagCheck,SIGNAL(stateChanged(int)),glWidget,SLOT(updateGL()));
connect(ui->glCorCheck,SIGNAL(stateChanged(int)),glWidget,SLOT(updateGL()));
connect(ui->glAxiCheck,SIGNAL(stateChanged(int)),glWidget,SLOT(updateGL()));
connect(ui->glSagView,SIGNAL(clicked()),this,SLOT(on_SagView_clicked()));
connect(ui->glCorView,SIGNAL(clicked()),this,SLOT(on_CorView_clicked()));
connect(ui->glAxiView,SIGNAL(clicked()),this,SLOT(on_AxiView_clicked()));
connect(ui->addSlices,SIGNAL(clicked()),this,SLOT(on_actionInsert_T1_T2_triggered()));
connect(ui->actionAdd_surface,SIGNAL(triggered()),glWidget,SLOT(addSurface()));
connect(ui->SliceModality,SIGNAL(currentIndexChanged(int)),glWidget,SLOT(updateGL()));
connect(ui->actionSave_Screen,SIGNAL(triggered()),glWidget,SLOT(catchScreen()));
connect(ui->actionSave_3D_screen_in_high_resolution,SIGNAL(triggered()),glWidget,SLOT(catchScreen2()));
connect(ui->actionLoad_Camera,SIGNAL(triggered()),glWidget,SLOT(loadCamera()));
connect(ui->actionSave_Camera,SIGNAL(triggered()),glWidget,SLOT(saveCamera()));
connect(ui->actionLoad_mapping,SIGNAL(triggered()),glWidget,SLOT(loadMapping()));
connect(ui->actionSave_mapping,SIGNAL(triggered()),glWidget,SLOT(saveMapping()));
connect(ui->actionSave_Rotation_Images,SIGNAL(triggered()),glWidget,SLOT(saveRotationSeries()));
connect(ui->actionSave_Left_Right_3D_Image,SIGNAL(triggered()),glWidget,SLOT(saveLeftRight3DImage()));
}
// scene view
{
connect(ui->SagSlider,SIGNAL(valueChanged(int)),this,SLOT(SliderValueChanged()));
connect(ui->CorSlider,SIGNAL(valueChanged(int)),this,SLOT(SliderValueChanged()));
connect(ui->AxiSlider,SIGNAL(valueChanged(int)),this,SLOT(SliderValueChanged()));
connect(&scene,SIGNAL(need_update()),&scene,SLOT(show_slice()));
connect(&scene,SIGNAL(need_update()),glWidget,SLOT(updateGL()));
connect(ui->fa_threshold,SIGNAL(valueChanged(double)),&scene,SLOT(show_slice()));
connect(ui->contrast,SIGNAL(valueChanged(int)),&scene,SLOT(show_slice()));
connect(ui->offset,SIGNAL(valueChanged(int)),&scene,SLOT(show_slice()));
connect(ui->show_fiber,SIGNAL(clicked()),&scene,SLOT(show_slice()));
connect(ui->show_pos,SIGNAL(clicked()),&scene,SLOT(show_slice()));
connect(ui->show_lr,SIGNAL(clicked()),&scene,SLOT(show_slice()));
connect(ui->zoom,SIGNAL(valueChanged(double)),&scene,SLOT(show_slice()));
connect(ui->zoom,SIGNAL(valueChanged(double)),&scene,SLOT(center()));
connect(ui->actionAxial_View,SIGNAL(triggered()),this,SLOT(on_AxiView_clicked()));
connect(ui->actionCoronal_View,SIGNAL(triggered()),this,SLOT(on_CorView_clicked()));
connect(ui->actionSagittal_view,SIGNAL(triggered()),this,SLOT(on_SagView_clicked()));
connect(ui->actionSave_ROI_Screen,SIGNAL(triggered()),&scene,SLOT(catch_screen()));
connect(ui->actionSave_Anisotrpy_Map_as,SIGNAL(triggered()),&scene,SLOT(save_slice_as()));
connect(ui->overlay,SIGNAL(currentIndexChanged(int)),this,SLOT(on_sliceViewBox_currentIndexChanged(int)));
}
// regions
{
connect(regionWidget,SIGNAL(need_update()),&scene,SLOT(show_slice()));
connect(regionWidget,SIGNAL(need_update()),glWidget,SLOT(updateGL()));
connect(ui->whole_brain,SIGNAL(clicked()),regionWidget,SLOT(whole_brain()));
connect(ui->view_style,SIGNAL(currentIndexChanged(int)),&scene,SLOT(show_slice()));
//atlas
connect(ui->addRegionFromAtlas,SIGNAL(clicked()),regionWidget,SLOT(add_atlas()));
connect(ui->actionNewRegion,SIGNAL(triggered()),regionWidget,SLOT(new_region()));
connect(ui->actionOpenRegion,SIGNAL(triggered()),regionWidget,SLOT(load_region()));
connect(ui->actionSaveRegionAs,SIGNAL(triggered()),regionWidget,SLOT(save_region()));
connect(ui->actionSave_Voxel_Data_As,SIGNAL(triggered()),regionWidget,SLOT(save_region_info()));
connect(ui->actionDeleteRegion,SIGNAL(triggered()),regionWidget,SLOT(delete_region()));
connect(ui->actionDeleteRegionAll,SIGNAL(triggered()),regionWidget,SLOT(delete_all_region()));
// actions
connect(ui->actionShift_X,SIGNAL(triggered()),regionWidget,SLOT(action_shiftx()));
connect(ui->actionShift_X_2,SIGNAL(triggered()),regionWidget,SLOT(action_shiftnx()));
connect(ui->actionShift_Y,SIGNAL(triggered()),regionWidget,SLOT(action_shifty()));
connect(ui->actionShift_Y_2,SIGNAL(triggered()),regionWidget,SLOT(action_shiftny()));
connect(ui->actionShift_Z,SIGNAL(triggered()),regionWidget,SLOT(action_shiftz()));
connect(ui->actionShift_Z_2,SIGNAL(triggered()),regionWidget,SLOT(action_shiftnz()));
connect(ui->actionFlip_X,SIGNAL(triggered()),regionWidget,SLOT(action_flipx()));
connect(ui->actionFlip_Y,SIGNAL(triggered()),regionWidget,SLOT(action_flipy()));
connect(ui->actionFlip_Z,SIGNAL(triggered()),regionWidget,SLOT(action_flipz()));
connect(ui->actionThreshold,SIGNAL(triggered()),regionWidget,SLOT(action_threshold()));
connect(ui->actionSmoothing,SIGNAL(triggered()),regionWidget,SLOT(action_smoothing()));
connect(ui->actionErosion,SIGNAL(triggered()),regionWidget,SLOT(action_erosion()));
connect(ui->actionDilation,SIGNAL(triggered()),regionWidget,SLOT(action_dilation()));
connect(ui->actionNegate,SIGNAL(triggered()),regionWidget,SLOT(action_negate()));
connect(ui->actionDefragment,SIGNAL(triggered()),regionWidget,SLOT(action_defragment()));
connect(ui->actionCheck_all_regions,SIGNAL(triggered()),regionWidget,SLOT(check_all()));
connect(ui->actionUnckech_all_regions,SIGNAL(triggered()),regionWidget,SLOT(uncheck_all()));
connect(ui->actionWhole_brain_seeding,SIGNAL(triggered()),regionWidget,SLOT(whole_brain()));
connect(ui->actionRegion_statistics,SIGNAL(triggered()),regionWidget,SLOT(show_statistics()));
}
// tracts
{
connect(ui->perform_tracking,SIGNAL(clicked()),tractWidget,SLOT(start_tracking()));
connect(ui->stopTracking,SIGNAL(clicked()),tractWidget,SLOT(stop_tracking()));
connect(tractWidget,SIGNAL(need_update()),glWidget,SLOT(makeTracts()));
connect(tractWidget,SIGNAL(need_update()),glWidget,SLOT(updateGL()));
connect(glWidget,SIGNAL(edited()),tractWidget,SLOT(edit_tracts()));
connect(glWidget,SIGNAL(region_edited()),glWidget,SLOT(updateGL()));
connect(glWidget,SIGNAL(region_edited()),&scene,SLOT(show_slice()));
connect(ui->actionOpenTract,SIGNAL(triggered()),tractWidget,SLOT(load_tracts()));
connect(ui->actionMerge_All,SIGNAL(triggered()),tractWidget,SLOT(merge_all()));
connect(ui->actionCopyTrack,SIGNAL(triggered()),tractWidget,SLOT(copy_track()));
connect(ui->actionDeleteTract,SIGNAL(triggered()),tractWidget,SLOT(delete_tract()));
connect(ui->actionDeleteTractAll,SIGNAL(triggered()),tractWidget,SLOT(delete_all_tract()));
connect(ui->actionOpen_Colors,SIGNAL(triggered()),tractWidget,SLOT(load_tracts_color()));
connect(ui->actionSave_Tracts_Colors_As,SIGNAL(triggered()),tractWidget,SLOT(save_tracts_color_as()));
connect(ui->actionUndo,SIGNAL(triggered()),tractWidget,SLOT(undo_tracts()));
connect(ui->actionRedo,SIGNAL(triggered()),tractWidget,SLOT(redo_tracts()));
connect(ui->actionTrim,SIGNAL(triggered()),tractWidget,SLOT(trim_tracts()));
connect(ui->actionSet_Color,SIGNAL(triggered()),tractWidget,SLOT(set_color()));
connect(ui->actionK_means,SIGNAL(triggered()),tractWidget,SLOT(clustering_kmeans()));
connect(ui->actionEM,SIGNAL(triggered()),tractWidget,SLOT(clustering_EM()));
connect(ui->actionHierarchical,SIGNAL(triggered()),tractWidget,SLOT(clustering_hie()));
connect(ui->actionOpen_Cluster_Labels,SIGNAL(triggered()),tractWidget,SLOT(open_cluster_label()));
//setup menu
connect(ui->actionSaveTractAs,SIGNAL(triggered()),tractWidget,SLOT(save_tracts_as()));
connect(ui->actionSave_All_Tracts_As,SIGNAL(triggered()),tractWidget,SLOT(save_all_tracts_as()));
connect(ui->actionQuantitative_anisotropy_QA,SIGNAL(triggered()),tractWidget,SLOT(save_fa_as()));
connect(ui->actionSave_End_Points_As,SIGNAL(triggered()),tractWidget,SLOT(save_end_point_as()));
connect(ui->actionStatistics,SIGNAL(triggered()),tractWidget,SLOT(show_tracts_statistics()));
connect(ui->track_up,SIGNAL(clicked()),tractWidget,SLOT(move_up()));
connect(ui->track_down,SIGNAL(clicked()),tractWidget,SLOT(move_down()));
}
// recall the setting
{
QSettings settings;
if(!default_geo.size())
default_geo = saveGeometry();
if(!default_state.size())
default_state = saveState();
restoreGeometry(settings.value("geometry").toByteArray());
restoreState(settings.value("state").toByteArray());
ui->turning_angle->setValue(settings.value("turning_angle",60).toDouble());
ui->smoothing->setValue(settings.value("smoothing",0.0).toDouble());
ui->min_length->setValue(settings.value("min_length",0.0).toDouble());
ui->max_length->setValue(settings.value("max_length",500).toDouble());
ui->tracking_method->setCurrentIndex(settings.value("tracking_method",0).toInt());
ui->seed_plan->setCurrentIndex(settings.value("seed_plan",0).toInt());
ui->initial_direction->setCurrentIndex(settings.value("initial_direction",0).toInt());
ui->interpolation->setCurrentIndex(settings.value("interpolation",0).toInt());
ui->tracking_plan->setCurrentIndex(settings.value("tracking_plan",0).toInt());
ui->track_count->setValue(settings.value("track_count",2000).toInt());
ui->thread_count->setCurrentIndex(settings.value("thread_count",0).toInt());
ui->glSagCheck->setChecked(settings.value("SagSlice",1).toBool());
ui->glCorCheck->setChecked(settings.value("CorSlice",1).toBool());
ui->glAxiCheck->setChecked(settings.value("AxiSlice",1).toBool());
ui->RenderingQualityBox->setCurrentIndex(settings.value("RenderingQuality",1).toInt());
ui->view_style->setCurrentIndex((settings.value("view_style",0).toInt()));
ui->RAS->setChecked(settings.value("RAS",0).toBool());
}
{
scene.center();
slice_no_update = false;
copy_target = 0;
}
on_glAxiView_clicked();
if(scene.neurology_convention)
on_glAxiView_clicked();
qApp->installEventFilter(this);
}
void SlaveMapper::createMapping(int processID, int numberOfProcesses)
{
int numberOfReceivedTriples = 0;
std::set<int> visitedTriples;
std::tr1::hash<std::string> hashFunction;
char *message1Master2Slaves = (char*)malloc(GlobalConstants::MAX_CHARS_PER_LINE * sizeof(char));
int message2All2Slave[4], message2AllToSlaveResult[4];
std::string separationSymbol = MappingConfigurationFileManager::getInstance()->getSeparationSymbol();
std::string subject, predicate, object, line, triple, tripleReverse;
int designedProcess, hashSubj, hashPred, hashObj, hashTriple, hashTripleReverse;
while (true)
{
MPI_Bcast(message1Master2Slaves, GlobalConstants::MAX_CHARS_PER_LINE, MPI_CHAR, GlobalConstants::MASTER, MPI_COMM_WORLD);
line.assign(message1Master2Slaves);
if (line.find(INPUT_FILE_OVER) != line.npos)
{
break;
}
subject = line.substr(0, line.find(separationSymbol));
line = line.erase(0, subject.length() + separationSymbol.length());
predicate = line.substr(0, line.find(separationSymbol));
line = line.erase(0, predicate.length() + separationSymbol.length());
object = line.substr(0, line.find(separationSymbol));
triple = subject + separationSymbol + predicate + separationSymbol + object;
tripleReverse = object + separationSymbol + predicate + separationSymbol + subject;
hashSubj = hashFunction(subject);
hashPred = hashFunction(predicate);
hashObj = hashFunction(object);
hashTriple = hashFunction(triple);
hashTripleReverse = hashFunction(tripleReverse);
designedProcess = ((numberOfReceivedTriples % (numberOfProcesses - 1)) + 1);
message2All2Slave[0] = (visitedTriples.find(hashTriple) != visitedTriples.end() || visitedTriples.find(hashTripleReverse) != visitedTriples.end()) ? 1 : 0;
message2All2Slave[1] = (mappingId2Node->find(hashSubj) != mappingId2Node->end()) ? 1 : 0;
message2All2Slave[2] = (mappingId2Predicate->find(hashPred) != mappingId2Predicate->end()) ? 1 : 0;
message2All2Slave[3] = (mappingId2Node->find(hashObj) != mappingId2Node->end()) ? 1 : 0;
MPI_Reduce(message2All2Slave, message2AllToSlaveResult, 4, MPI_INT, MPI_MAX, designedProcess, MPI_COMM_WORLD);
if (processID == designedProcess && message2AllToSlaveResult[0] == 0)
{
if (message2AllToSlaveResult[1] == 0)
{
mappingId2Node->operator [](hashSubj) = subject;
}
if (message2AllToSlaveResult[2] == 0)
{
mappingId2Predicate->operator [](hashPred) = predicate;
}
if (message2AllToSlaveResult[3] == 0)
{
mappingId2Node->operator [](hashObj) = object;
}
predicates->push_back(hashPred);
objects->push_back(hashObj);
if (mappingNode2Positions->find(hashSubj) == mappingNode2Positions->end())
{
mappingNode2Positions->operator [](hashSubj) = *(new std::vector<int>);
}
mappingNode2Positions->operator [](hashSubj).push_back(predicates->size() - 1);
predicates->push_back(hashPred);
objects->push_back(hashSubj);
if (mappingNode2Positions->find(hashObj) == mappingNode2Positions->end())
{
mappingNode2Positions->operator [](hashObj) = *(new std::vector<int>);
}
mappingNode2Positions->operator [](hashObj).push_back(predicates->size() - 1);
visitedTriples.insert(hashTriple);
}
numberOfReceivedTriples++;
}
visitedTriples.clear();
free(message1Master2Slaves);
int numberOfNodes = mappingId2Node->size(), numberOfPredicates = mappingId2Predicate->size(), numberOfCorrectTriples = objects->size() / 2;
MPI_Reduce(&numberOfNodes, NULL, 1, MPI_INT, MPI_SUM, GlobalConstants::MASTER, MPI_COMM_WORLD);
MPI_Reduce(&numberOfPredicates, NULL, 1, MPI_INT, MPI_SUM, GlobalConstants::MASTER, MPI_COMM_WORLD);
MPI_Reduce(&numberOfCorrectTriples, NULL, 1, MPI_INT, MPI_SUM, GlobalConstants::MASTER, MPI_COMM_WORLD);
saveMapping(processID);
}
