vv/vvMainWindow.cxx

   1 /*=========================================================================
   2   Program:   vv                     http://www.creatis.insa-lyon.fr/rio/vv
   3
   4   Authors belong to:
   5   - University of LYON              http://www.universite-lyon.fr/
   6   - Léon Bérard cancer center       http://www.centreleonberard.fr
   7   - CREATIS CNRS laboratory         http://www.creatis.insa-lyon.fr
   8
   9   This software is distributed WITHOUT ANY WARRANTY; without even
  10   the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
  11   PURPOSE.  See the copyright notices for more information.
  12
  13   It is distributed under dual licence
  14
  15   - BSD        See included LICENSE.txt file
  16   - CeCILL-B   http://www.cecill.info/licences/Licence_CeCILL-B_V1-en.html
  17 ===========================================================================**/
  18
  19 #include <algorithm>
  20 #include <QMessageBox>
  21 #include <QInputDialog>
  22 #include <QTimer>
  23 #include "QTreePushButton.h"
  24 #include <QUrl>
  25 #include <QSettings>
  26
  27 // VV include
  28 #include "vvMainWindow.h"
  29 #include "vvHelpDialog.h"
  30 #include "vvRegisterForm.h"
  31 #include "vvDocumentation.h"
  32 #include "vvProgressDialog.h"
  33 #include "vvQDicomSeriesSelector.h"
  34 #include "vvSlicerManager.h"
  35 #include "clitkImageCommon.h"
  36 #include "vvSlicer.h"
  37 #include "vvInteractorStyleNavigator.h"
  38 #include "vvImageWriter.h"
  39 #include "vvSegmentationDialog.h"
  40 #include "vvSurfaceViewerDialog.h"
  41 #include "vvDeformationDialog.h"
  42 #include "vvImageWarp.h"
  43 #include "vvUtils.h"
  44 #include "vvMidPosition.h"
  45 #include "vvMesh.h"
  46 #include "vvStructSelector.h"
  47 #include "vvMeshReader.h"
  48 #include "clitkConfiguration.h"
  49
  50 // ITK include
  51 #include <itkImage.h>
  52 #include <itkImageFileReader.h>
  53 #include <itkByteSwapper.h>
  54 #include <itkCommand.h>
  55 #include <itkNumericSeriesFileNames.h>
  56
  57 // VTK include
  58 #include <vtkImageData.h>
  59 #include <vtkImageActor.h>
  60 #include <vtkCornerAnnotation.h>
  61 #include <vtkRenderWindow.h>
  62 #include <vtkRenderWindowInteractor.h>
  63 #include <vtkRenderer.h>
  64 #include <vtkRendererCollection.h>
  65 #include <vtkWindowToImageFilter.h>
  66 #include <vtkBMPWriter.h>
  67 #include <vtkTIFFWriter.h>
  68 #include <vtkPNMWriter.h>
  69 #include <vtkPNGWriter.h>
  70 #include <vtkJPEGWriter.h>
  71 #include <vtkFFMPEGWriter.h>
  72 #ifdef VTK_USE_MPEG2_ENCODER
  73   #include <vtkMPEG2Writer.h>
  74 #endif
  75 #include <vtkMatrix4x4.h>
  76 #include <vtkTransform.h>
  77
  78 // Standard includes
  79 #include <iostream>
  80 #include <sstream>
  81 #include <iomanip>
  82
  83 #define COLUMN_TREE 0
  84 #define COLUMN_UL_VIEW 1
  85 #define COLUMN_UR_VIEW 2
  86 #define COLUMN_DL_VIEW 3
  87 #define COLUMN_DR_VIEW 4
  88 #define COLUMN_CLOSE_IMAGE 5
  89 #define COLUMN_RELOAD_IMAGE 6
  90 #define COLUMN_IMAGE_NAME 7
  91
  92 #define EXTENSIONS "Images ( *.bmp *.png *.jpeg *.jpg *.tif *.mhd *.mha *.hdr *.vox *.his *.xdr *.SCAN )"
  93
  94 /*Data Tree values
  95   0,Qt::UserRole full filename
  96   1,Qt::CheckStateRole checkbutton UL View
  97   1,Qt::UserRole overlay, fusion or vector
  98   2,Qt::CheckStateRole checkbutton UR View
  99   3,Qt::CheckStateRole checkbutton DL View
 100   4,Qt::CheckStateRole checkbutton DR View
 101   5,0  short filename
 102   5,Qt::UserRole mSlicerManager id*/
 103
 104 //------------------------------------------------------------------------------
 105 vvMainWindow::vvMainWindow():vvMainWindowBase()
 106 {
 107   setupUi(this); // this sets up the GUI
 108
 109   mInputPathName = "";
 110   mMenuTools = menuTools;
 111   //  mMenuSegmentation = menuSegmentation;
 112   mContextMenu = &contextMenu;
 113   mMenuExperimentalTools = menuExperimental;
 114   mMainWidget = this;
 115   mCurrentTime = -1;
 116   mCurrentSelectedImageId = "";
 117   mCurrentPickedImageId = "";
 118   mCurrentPickedImageIndex = 0;
 119
 120   //Init the contextMenu
 121   this->setContextMenuPolicy(Qt::CustomContextMenu);
 122   contextActions.resize(0);
 123   QAction* actionOpen_new_image = contextMenu.addAction(QIcon(QString::fromUtf8(":/common/icons/fileopen.png")),
 124                                   tr("O&pen new Image"));
 125   actionOpen_new_image->setShortcut(QKeySequence(tr("Ctrl+O")));
 126   connect(actionOpen_new_image,SIGNAL(triggered()),this,SLOT(OpenImages()));
 127   contextActions.push_back(actionOpen_new_image);
 128   contextMenu.addSeparator();
 129
 130   QAction* actionClose_Image = contextMenu.addAction(QIcon(QString::fromUtf8(":/common/icons/exit.png")),
 131                                tr("Close Current Image"));
 132   connect(actionClose_Image,SIGNAL(triggered()),this,SLOT(CloseImage()));
 133   contextActions.push_back(actionClose_Image);
 134
 135   QAction* actionReload_image = contextMenu.addAction(QIcon(QString::fromUtf8(":/common/icons/rotateright.png")),
 136                                 tr("Reload Current Image"));
 137   connect(actionReload_image,SIGNAL(triggered()),this,SLOT(ReloadImage()));
 138   contextActions.push_back(actionReload_image);
 139
 140   QAction* actionSave_image = contextMenu.addAction(QIcon(QString::fromUtf8(":/common/icons/filesave.png")),
 141                               tr("Save Current Image"));
 142   connect(actionSave_image,SIGNAL(triggered()),this,SLOT(SaveAs()));
 143   contextActions.push_back(actionSave_image);
 144
 145   contextMenu.addSeparator();
 146
 147   contextMenu.addAction(actionAdd_VF_to_current_Image);
 148   contextActions.push_back(actionAdd_VF_to_current_Image);
 149
 150   QAction* actionAdd_Overlay_to_current_Image = menuOverlay->addAction(QIcon(QString::fromUtf8(":/common/icons/GPSup.png")),
 151       tr("Add overlay image to current image"));
 152   contextMenu.addAction(actionAdd_Overlay_to_current_Image);
 153   contextActions.push_back(actionAdd_Overlay_to_current_Image);
 154
 155   connect(actionAdd_Overlay_to_current_Image,SIGNAL(triggered()), this,SLOT(SelectOverlayImage()));
 156
 157   contextMenu.addAction(actionAdd_fusion_image);
 158   connect(actionAdd_fusion_image,SIGNAL(triggered()),this,SLOT(SelectFusionImage()));
 159   contextActions.push_back(actionAdd_fusion_image);
 160
 161   // TRIAL DS
 162   /*
 163   QMenu * m = new QMenu(menubar);
 164   m->setTitle("TOTO");
 165   //  m->setObjectName(QString::fromUtf8("TOTOTO"));
 166   contextMenu.addMenu(m);
 167   QAction * a = m->addAction(QIcon(QString::fromUtf8(":/common/icons/GPSup.png")),
 168                      tr("BIDON"));
 169   QAction * b = m->addAction(QIcon(QString::fromUtf8(":/common/icons/GPSup.png")),
 170                      tr("BIDON2"));
 171   m->addAction(a);
 172   m->addAction(b);
 173   connect(a,SIGNAL(triggered()),this,SLOT(AddFusionImage()));
 174   */
 175
 176   //init the DataTree
 177   mSlicerManagers.resize(0);
 178
 179   QStringList header;
 180   header.append("");
 181   header.append("TL");
 182   header.append("TR");
 183   header.append("BL");
 184   header.append("BR");
 185   header.append("");
 186   header.append("");
 187   header.append("Name");
 188
 189   DataTree->setHeaderLabels(header);
 190   DataTree->resizeColumnToContents(COLUMN_TREE);
 191   DataTree->resizeColumnToContents(COLUMN_UL_VIEW);
 192   DataTree->resizeColumnToContents(COLUMN_UR_VIEW);
 193   DataTree->resizeColumnToContents(COLUMN_DL_VIEW);
 194   DataTree->resizeColumnToContents(COLUMN_DR_VIEW);
 195   DataTree->resizeColumnToContents(COLUMN_CLOSE_IMAGE);
 196   DataTree->resizeColumnToContents(COLUMN_RELOAD_IMAGE);
 197   DataTree->resizeColumnToContents(COLUMN_IMAGE_NAME);
 198
 199   viewMode = 1;
 200   documentation = new vvDocumentation();
 201   help_dialog = new vvHelpDialog();
 202   dicomSeriesSelector = new vvDicomSeriesSelector();
 203
 204   inverseButton->setEnabled(0);
 205   actionAdd_Overlay_to_current_Image->setEnabled(0);
 206   actionSave_As->setEnabled(0);
 207   actionAdd_VF_to_current_Image->setEnabled(0);
 208   actionAdd_fusion_image->setEnabled(0);
 209
 210   //init the sliders
 211   verticalSliders.push_back(NOVerticalSlider);
 212   verticalSliders.push_back(NEVerticalSlider);
 213   verticalSliders.push_back(SOVerticalSlider);
 214   verticalSliders.push_back(SEVerticalSlider);
 215
 216   for (int i =0; i < 4; i++)
 217     verticalSliders[i]->hide();
 218
 219   horizontalSliders.push_back(NOHorizontalSlider);
 220   horizontalSliders.push_back(NEHorizontalSlider);
 221   horizontalSliders.push_back(SOHorizontalSlider);
 222   horizontalSliders.push_back(SEHorizontalSlider);
 223
 224   for (int i =0; i < 4; i++)
 225     horizontalSliders[i]->hide();
 226
 227
 228   connect(NOVerticalSlider,SIGNAL(valueChanged(int)),this,SLOT(NOVerticalSliderChanged()));
 229   connect(NEVerticalSlider,SIGNAL(valueChanged(int)),this,SLOT(NEVerticalSliderChanged()));
 230   connect(SOVerticalSlider,SIGNAL(valueChanged(int)),this,SLOT(SOVerticalSliderChanged()));
 231   connect(SEVerticalSlider,SIGNAL(valueChanged(int)),this,SLOT(SEVerticalSliderChanged()));
 232
 233   connect(NOHorizontalSlider,SIGNAL(valueChanged(int)),this,SLOT(NOHorizontalSliderMoved()));
 234   connect(NEHorizontalSlider,SIGNAL(valueChanged(int)),this,SLOT(NEHorizontalSliderMoved()));
 235   connect(SOHorizontalSlider,SIGNAL(valueChanged(int)),this,SLOT(SOHorizontalSliderMoved()));
 236   connect(SEHorizontalSlider,SIGNAL(valueChanged(int)),this,SLOT(SEHorizontalSliderMoved()));
 237
 238   //connect everything
 239   connect(actionCompute_mid_position_image,SIGNAL(triggered()),this,SLOT(ComputeMidPosition()));
 240   connect(actionDeformable_Registration,SIGNAL(triggered()),this,SLOT(ComputeDeformableRegistration()));
 241   connect(actionWarp_image_with_vector_field,SIGNAL(triggered()),this,SLOT(WarpImage()));
 242   connect(actionLoad_images,SIGNAL(triggered()),this,SLOT(OpenImages()));
 243   connect(actionOpen_Dicom,SIGNAL(triggered()),this,SLOT(OpenDicom()));
 244   connect(actionOpen_Dicom_Struct,SIGNAL(triggered()),this,SLOT(OpenDCStructContour()));
 245   connect(actionOpen_VTK_contour,SIGNAL(triggered()),this,SLOT(OpenVTKContour()));
 246   connect(actionOpen_Multiple_Images_As_One,SIGNAL(triggered()),this,SLOT(MergeImages()));
 247   connect(actionSlice_Image_As_Multiple_Images,SIGNAL(triggered()),this,SLOT(SliceImages()));
 248   connect(actionOpen_Image_With_Time,SIGNAL(triggered()),this,SLOT(OpenImageWithTime()));
 249   connect(actionMerge_images_as_n_dim_t, SIGNAL(triggered()), this, SLOT(MergeImagesWithTime()));
 250   connect(actionSave_As,SIGNAL(triggered()),this,SLOT(SaveAs()));
 251   connect(actionExit,SIGNAL(triggered()),this,SLOT(close()));
 252   connect(actionAdd_VF_to_current_Image,SIGNAL(triggered()),this,SLOT(OpenField()));
 253   connect(actionNavigation_Help,SIGNAL(triggered()),this,SLOT(ShowHelpDialog()));
 254   connect(actionDocumentation,SIGNAL(triggered()),this,SLOT(ShowDocumentation()));
 255   connect(actionRegister_vv,SIGNAL(triggered()),this,SLOT(PopupRegisterForm()));
 256
 257   ///////////////////////////////////////////////
 258   connect(actionSegmentation,SIGNAL(triggered()),this,SLOT(SegmentationOnCurrentImage()));
 259   connect(actionSurface_Viewer,SIGNAL(triggered()),this,SLOT(SurfaceViewerLaunch()));
 260   ///////////////////////////////////////////////
 261
 262   actionNorth_East_Window->setEnabled(0);
 263   actionNorth_West_Window->setEnabled(0);
 264   actionSouth_East_Window->setEnabled(0);
 265   actionSouth_West_Window->setEnabled(0);
 266
 267   connect(actionNorth_East_Window,SIGNAL(triggered()),this,SLOT(SaveNEScreenshot()));
 268   connect(actionNorth_West_Window,SIGNAL(triggered()),this,SLOT(SaveNOScreenshot()));
 269   connect(actionSouth_East_Window,SIGNAL(triggered()),this,SLOT(SaveSEScreenshot()));
 270   connect(actionSouth_West_Window,SIGNAL(triggered()),this,SLOT(SaveSOScreenshot()));
 271
 272   connect(DataTree,SIGNAL(itemSelectionChanged()),this,SLOT(ImageInfoChanged()));
 273   connect(DataTree,SIGNAL(itemClicked(QTreeWidgetItem*, int)),this,
 274           SLOT(DisplayChanged(QTreeWidgetItem*, int)));
 275
 276   connect(viewButton,SIGNAL(clicked()),this, SLOT(ChangeViewMode()) );
 277   connect(windowSpinBox,SIGNAL(editingFinished()),this,SLOT(WindowLevelEdited()));
 278   connect(levelSpinBox,SIGNAL(editingFinished()),this,SLOT(WindowLevelEdited()));
 279   connect(colorMapComboBox,SIGNAL(currentIndexChanged(int)),this,SLOT(UpdateColorMap()));
 280   connect(presetComboBox,SIGNAL(currentIndexChanged(int)),this,SLOT(UpdateWindowLevel()));
 281   connect(inverseButton,SIGNAL(clicked()),this,SLOT(SwitchWindowLevel()));
 282   connect(applyWindowLevelToAllButton,SIGNAL(clicked()),this,SLOT(ApplyWindowLevelToAllImages()));
 283
 284
 285   connect(this,SIGNAL(customContextMenuRequested(QPoint)),this,SLOT(ShowContextMenu(QPoint)));
 286
 287   connect(linkPanel,SIGNAL(addLink(QString,QString)),this,SLOT(AddLink(QString,QString)));
 288   connect(linkPanel,SIGNAL(removeLink(QString,QString)),this,SLOT(RemoveLink(QString,QString)));
 289   connect(overlayPanel,SIGNAL(VFPropertyUpdated(int,int,int,int,double,double,double)),this,SLOT(SetVFProperty(int,int,int,int,double,double,double)));
 290   connect(overlayPanel,SIGNAL(OverlayPropertyUpdated(int)),this,SLOT(SetOverlayProperty(int)));
 291   connect(overlayPanel,SIGNAL(FusionPropertyUpdated(int,int,double,double)),
 292           this,SLOT(SetFusionProperty(int,int,double,double)));
 293   connect(landmarksPanel,SIGNAL(UpdateRenderWindows()),this,SLOT(UpdateRenderWindows()));
 294
 295   playMode = 0;//pause
 296   mFrameRate = 10;
 297   playButton->setEnabled(0);
 298   frameRateLabel->setEnabled(0);
 299   frameRateSpinBox->setEnabled(0);
 300   connect(playButton, SIGNAL(clicked()),this,SLOT(PlayPause()));
 301   connect(frameRateSpinBox, SIGNAL(valueChanged(int)),this,SLOT(ChangeFrameRate(int)));
 302
 303   goToCursorPushButton->setEnabled(0);
 304   connect(goToCursorPushButton, SIGNAL(clicked()),this,SLOT(GoToCursor()));
 305
 306   NOViewWidget->hide();
 307   NEViewWidget->hide();
 308   SOViewWidget->hide();
 309   SEViewWidget->hide();
 310
 311   //Recently opened files
 312   std::list<std::string> recent_files = GetRecentlyOpenedImages();
 313   recentlyOpenedFilesMenu=NULL;
 314   if ( !recent_files.empty() ) {
 315     createRecentlyOpenedFilesMenu();
 316     updateRecentlyOpenedFilesMenu(recent_files);
 317   }
 318
 319   // Adding all new tools (insertion in the menu)
 320   vvToolManager::GetInstance()->InsertToolsInMenu(this);
 321   vvToolManager::GetInstance()->EnableToolsInMenu(this, false);
 322
 323   if (!CLITK_EXPERIMENTAL)
 324     menuExperimental->menuAction()->setVisible(false);
 325
 326
 327   QTimer * timerMemory = new QTimer(this);
 328   //timerMemory->setInterval(5);
 329   connect(timerMemory, SIGNAL(timeout()), this, SLOT(UpdateMemoryUsage()));
 330   timerMemory->start(2000);
 331 }
 332 //------------------------------------------------------------------------------
 333 void vvMainWindow::show(){
 334   vvMainWindowBase::show();
 335   PopupRegisterForm(true);
 336 }
 337 //------------------------------------------------------------------------------
 338 void vvMainWindow::UpdateMemoryUsage()
 339 {
 340   //  clitk::PrintMemory(true);
 341   if (clitk::GetMemoryUsageInMb() == 0) infoPanel->setMemoryInMb("NA");
 342   else infoPanel->setMemoryInMb(QString::number(clitk::GetMemoryUsageInMb())+" MiB");
 343 }
 344 //------------------------------------------------------------------------------
 345
 346
 347 //------------------------------------------------------------------------------
 348 void vvMainWindow::createRecentlyOpenedFilesMenu()
 349 {
 350     recentlyOpenedFilesMenu = new QMenu("Recently opened files...");
 351     recentlyOpenedFilesMenu->setIcon(QIcon(QString::fromUtf8(":/common/icons/open.png")));
 352     menuFile->insertMenu(actionOpen_Image_With_Time,recentlyOpenedFilesMenu);
 353     menuFile->insertSeparator(actionOpen_Image_With_Time);
 354 }
 355 //------------------------------------------------------------------------------
 356
 357
 358 //------------------------------------------------------------------------------
 359
 360 void vvMainWindow::updateRecentlyOpenedFilesMenu(const std::list<std::string> &recent_files)
 361 {
 362   if(recentlyOpenedFilesMenu==NULL){
 363     createRecentlyOpenedFilesMenu();
 364   }else{
 365     recentlyOpenedFilesMenu->clear();
 366   }
 367   for (std::list<std::string>::const_iterator i = recent_files.begin(); i!=recent_files.end(); i++) {
 368     QAction* current=new QAction(QIcon(QString::fromUtf8(":/common/icons/open.png")), i->c_str(),this);
 369     recentlyOpenedFilesMenu->addAction(current);
 370     connect(current,SIGNAL(triggered()),this,SLOT(OpenRecentImage()));
 371   }
 372 }
 373 //------------------------------------------------------------------------------
 374
 375
 376 //------------------------------------------------------------------------------
 377 void vvMainWindow::ComputeMidPosition()
 378 {
 379   bool ok;
 380   int index=GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
 381   int ref = QInputDialog::getInteger(this,"Chose reference phase","Reference phase",0,0,\
 382                                      mSlicerManagers[index]->GetImage()->GetVTKImages().size()-1,1,&ok);
 383   if (ok) {
 384     vvMidPosition midp;
 385     midp.slicer_manager = mSlicerManagers[index];
 386     midp.reference_image_index = ref;
 387     QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
 388     midp.Update();
 389     if (midp.error)
 390       QMessageBox::warning(this, "Error computing midposition image",midp.error_message.c_str());
 391     else {
 392       QFileInfo info(midp.slicer_manager->GetFileName().c_str());
 393       AddImage(midp.output,info.path().toStdString()+"/"+info.completeBaseName().toStdString()+"_midposition.mhd");
 394     }
 395     QApplication::restoreOverrideCursor();
 396   }
 397 }
 398 //------------------------------------------------------------------------------
 399
 400
 401 //------------------------------------------------------------------------------
 402 void vvMainWindow::AddContour(int image_index, vvMesh::Pointer contour, bool propagation)
 403 {
 404   QTreeWidgetItem *item = new QTreeWidgetItem();
 405   item->setData(0,Qt::UserRole,"filename.vtk");
 406   item->setData(1,Qt::UserRole,tr("contour"));
 407   QBrush brush;
 408   brush.setColor(QColor(contour->r*255,contour->g*255,contour->b*255));
 409   brush.setStyle(Qt::SolidPattern);
 410   item->setData(COLUMN_IMAGE_NAME,Qt::BackgroundRole,brush);
 411   item->setData(COLUMN_IMAGE_NAME,Qt::DisplayRole,contour->structure_name.c_str());
 412
 413   for (int j = 1; j <= 4; j++)
 414     item->setData(j,Qt::CheckStateRole,DataTree->topLevelItem(image_index)->data(j,Qt::CheckStateRole));
 415
 416   QTreePushButton* cButton = new QTreePushButton;
 417   cButton->setItem(item);
 418   cButton->setColumn(COLUMN_CLOSE_IMAGE);
 419   cButton->setToolTip(tr("close image"));
 420   cButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/exit.png")));
 421   connect(cButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
 422           this,SLOT(CloseImage(QTreeWidgetItem*, int)));
 423
 424   QTreePushButton* rButton = new QTreePushButton;
 425   rButton->setItem(item);
 426   rButton->setColumn(COLUMN_RELOAD_IMAGE);
 427   rButton->setToolTip(tr("reload image"));
 428   rButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/rotateright.png")));
 429   rButton->setEnabled(false);
 430   //Not implemented
 431   //connect(rButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
 432   //this,SLOT(ReloadImage(QTreeWidgetItem*, int)));
 433
 434   DataTree->topLevelItem(image_index)->setExpanded(1);
 435   DataTree->topLevelItem(image_index)->addChild(item);
 436   DataTree->setItemWidget(item, COLUMN_CLOSE_IMAGE, cButton);
 437   DataTree->setItemWidget(item, COLUMN_RELOAD_IMAGE, rButton);
 438   QString id = DataTree->topLevelItem(image_index)->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString();
 439   item->setData(COLUMN_IMAGE_NAME,Qt::UserRole,id.toStdString().c_str());
 440
 441   UpdateTree();
 442   mSlicerManagers[image_index]->AddContour(contour,propagation);
 443   mSlicerManagers[image_index]->Render();
 444 }
 445 //------------------------------------------------------------------------------
 446
 447
 448 //------------------------------------------------------------------------------
 449 void vvMainWindow::OpenVTKContour()
 450 {
 451   if (mSlicerManagers.size() > 0) {
 452     QString Extensions = "Images ( *.vtk *.obj)";
 453     Extensions += ";;All Files (*)";
 454     QString file = QFileDialog::getOpenFileName(this,tr("Open vtkPolyData"),mInputPathName,Extensions);
 455     if (file.isNull())
 456       return;
 457     QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
 458     int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
 459     vvMeshReader reader;
 460     reader.SetImage(mSlicerManagers[index]->GetImage());
 461     reader.SetModeToVTK();
 462     reader.SetFilename(file.toStdString());
 463     reader.Update();
 464     AddContour(index,reader.GetOutput()[0],false);
 465     QApplication::restoreOverrideCursor();
 466   }
 467 }
 468 //------------------------------------------------------------------------------
 469
 470
 471 //------------------------------------------------------------------------------
 472 void vvMainWindow::OpenDCStructContour()
 473 {
 474   if (mSlicerManagers.size() > 0) {
 475     QString Extensions = "Dicom Files ( *.dcm RS*)";
 476     Extensions += ";;All Files (*)";
 477     QString file = QFileDialog::getOpenFileName(this,tr("Merge Images"),mInputPathName,Extensions);
 478     if (file.isNull())
 479       return;
 480     int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
 481     vvMeshReader reader;
 482     reader.SetFilename(file.toStdString());
 483     vvStructSelector selector;
 484     selector.SetStructures(reader.GetROINames());
 485     if (!mSlicerManagers[index]->GetVF().IsNull())
 486       selector.EnablePropagationCheckBox();
 487     if (selector.exec()) {
 488       QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
 489       reader.SetSelectedItems(selector.getSelectedItems());
 490       reader.SetImage(mSlicerManagers[index]->GetImage());
 491       if (selector.PropagationEnabled())
 492         reader.SetPropagationVF(mSlicerManagers[index]->GetVF());
 493       reader.Update();
 494       std::vector<vvMesh::Pointer> contours=reader.GetOutput();
 495       for (std::vector<vvMesh::Pointer>::iterator i=contours.begin();
 496            i!=contours.end(); i++)
 497         AddContour(index,*i,selector.PropagationEnabled());
 498       QApplication::restoreOverrideCursor();
 499     }
 500   }
 501 }
 502 //------------------------------------------------------------------------------
 503
 504
 505 //------------------------------------------------------------------------------
 506 void vvMainWindow::ComputeDeformableRegistration()
 507 {
 508   if (mSlicerManagers.size() > 0) {
 509     int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
 510     vvDeformationDialog dialog(index,mSlicerManagers);
 511     if (dialog.exec()) {
 512       std::string base_name=itksys::SystemTools::GetFilenameWithoutExtension(mSlicerManagers[dialog.GetInputFileIndex()]->GetFileName());
 513       AddField(dialog.GetOutput(),dialog.getFieldFile(),dialog.GetInputFileIndex());
 514       WarpImage(dialog.GetSelectedSlicer(),dialog.GetReferenceFrameIndex());
 515     } else
 516       std::cout << "Error or user cancellation while computing deformation field..." << std::endl;
 517   } else QMessageBox::information(this, "Need to open image","You must open an image first.");
 518 }
 519 //------------------------------------------------------------------------------
 520
 521
 522 //------------------------------------------------------------------------------
 523 void vvMainWindow::WarpImage()
 524 {
 525   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
 526   if (!mSlicerManagers[index]->GetVF().IsNull()) {
 527     bool ok;
 528     int ref = QInputDialog::getInteger(this,"Chose reference phase","Reference phase",0,0,\
 529                                        mSlicerManagers[index]->GetImage()->GetVTKImages().size()-1,1,&ok);
 530     if (ok) {
 531       WarpImage(mSlicerManagers[index],ref);
 532     }
 533   } else
 534     QMessageBox::warning(this,tr("No vector field"),tr("Sorry, can't warp without a vector field"));
 535 }
 536 //------------------------------------------------------------------------------
 537
 538
 539 //------------------------------------------------------------------------------
 540 void vvMainWindow::WarpImage(vvSlicerManager* selected_slicer,int reference_phase)
 541 {
 542   if (!selected_slicer->GetVF().IsNull()) {
 543     QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
 544     QFileInfo info(selected_slicer->GetFileName().c_str());
 545     vvImageWarp warp(selected_slicer->GetImage(),selected_slicer->GetVF(),
 546                      reference_phase,this);
 547     if (warp.ComputeWarpedImage()) {
 548       AddImage(warp.GetWarpedImage(),info.path().toStdString()+"/"+info.completeBaseName().toStdString()+"_warped.mhd");
 549       AddImage(warp.GetDiffImage()  ,info.path().toStdString()+"/"+info.completeBaseName().toStdString()+"_diff.mhd");
 550       AddImage(warp.GetJacobianImage()  ,info.path().toStdString()+"/"+info.completeBaseName().toStdString()+"_jacobian.mhd");
 551       QApplication::restoreOverrideCursor();
 552     } else {
 553       QApplication::restoreOverrideCursor();
 554       QMessageBox::warning(this,tr("Different spacings"),tr("The vector field and image spacings must be the same in order to warp."));
 555     }
 556   } else
 557     QMessageBox::warning(this,tr("No vector field"),tr("Sorry, can't warp without a vector field."));
 558 }
 559 //------------------------------------------------------------------------------
 560
 561
 562 //------------------------------------------------------------------------------
 563 vvMainWindow::~vvMainWindow()
 564 {
 565   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
 566     if (mSlicerManagers[i] != NULL)
 567       delete mSlicerManagers[i];
 568   }
 569 }
 570 //------------------------------------------------------------------------------
 571
 572 //------------------------------------------------------------------------------
 573 QTabWidget * vvMainWindow::GetTab()
 574 {
 575   return tabWidget;
 576 }
 577 //------------------------------------------------------------------------------
 578
 579
 580 //------------------------------------------------------------------------------
 581 void vvMainWindow::MergeImages()
 582 {
 583   QString Extensions = EXTENSIONS;
 584   Extensions += ";;All Files (*)";
 585   QStringList files = QFileDialog::getOpenFileNames(this,tr("Merge Images"),mInputPathName,Extensions);
 586   if (files.isEmpty())
 587     return;
 588   mInputPathName = itksys::SystemTools::GetFilenamePath(files[0].toStdString()).c_str();
 589   std::vector<std::string> vector;
 590
 591   unsigned int currentDim = 0;
 592   std::vector<double> currentSpacing;
 593   std::vector<int> currentSize;
 594   std::vector<double> currentOrigin;
 595
 596   for (int i = 0; i < files.size(); i++) {
 597     itk::ImageIOBase::Pointer reader = itk::ImageIOFactory::CreateImageIO(
 598                                          files[i].toStdString().c_str(), itk::ImageIOFactory::ReadMode);
 599     reader->SetFileName(files[i].toStdString().c_str());
 600     reader->ReadImageInformation();
 601     if (reader)        {
 602       //NOViewWidget->hide();
 603       //NEViewWidget->hide();
 604       //SOViewWidget->hide();
 605       //SEViewWidget->hide();
 606       if (i == 0)
 607         currentDim = reader->GetNumberOfDimensions();
 608       bool IsOk = true;
 609       for (unsigned int j = 0; j < currentDim; j++) {
 610         if (i == 0) {
 611           if (j == 0) {
 612             currentSpacing.resize(currentDim);
 613             currentSize.resize(currentDim);
 614             currentOrigin.resize(currentDim);
 615           }
 616           currentOrigin[j] = reader->GetOrigin(j);
 617           currentSpacing[j] = reader->GetSpacing(j);
 618           currentSize[j] = reader->GetDimensions(j);
 619         } else if (currentDim != reader->GetNumberOfDimensions()
 620                    || currentSpacing[j] != reader->GetSpacing(j)
 621                    || currentSize[j] != (int)reader->GetDimensions(j)
 622                    || currentOrigin[j] != reader->GetOrigin(j)) {
 623           QString error = "Cannot read file (too different from others ";
 624           error += files[i].toStdString().c_str();
 625           QMessageBox::information(this,tr("Reading problem"),error);
 626           IsOk = false;
 627           break;
 628         }
 629       }
 630       if (IsOk)
 631         vector.push_back(files[i].toStdString());
 632     }
 633   }
 634   if (vector.size() > 0)
 635     LoadImages(vector, vvImageReader::MERGED);
 636 }
 637 //------------------------------------------------------------------------------
 638
 639 //------------------------------------------------------------------------------
 640 void vvMainWindow::SliceImages()
 641 {
 642   QString Extensions = EXTENSIONS;
 643   Extensions += ";;All Files (*)";
 644
 645   QStringList files = QFileDialog::getOpenFileNames(this,tr("Slice Images"),mInputPathName,Extensions);
 646   if (files.isEmpty())
 647     return;
 648   mInputPathName = itksys::SystemTools::GetFilenamePath(files[0].toStdString()).c_str();
 649   std::vector<std::string> vector;
 650   for (int i = 0; i < files.size(); i++)
 651     vector.push_back(files[i].toStdString());
 652   LoadImages(vector, vvImageReader::SLICED);
 653 }
 654 //------------------------------------------------------------------------------
 655
 656 //------------------------------------------------------------------------------
 657 void vvMainWindow::MergeImagesWithTime()
 658 {
 659   QString Extensions = EXTENSIONS;
 660   Extensions += ";;All Files (*)";
 661   QStringList files = QFileDialog::getOpenFileNames(this,tr("Merge Images With Time"),mInputPathName,Extensions);
 662   if (files.isEmpty())
 663     return;
 664   mInputPathName = itksys::SystemTools::GetFilenamePath(files[0].toStdString()).c_str();
 665   std::vector<std::string> vector;
 666
 667   unsigned int currentDim = 0;
 668   std::vector<double> currentSpacing;
 669   std::vector<int> currentSize;
 670   std::vector<double> currentOrigin;
 671
 672   for (int i = 0; i < files.size(); i++) {
 673     itk::ImageIOBase::Pointer reader = itk::ImageIOFactory::CreateImageIO(
 674                                          files[i].toStdString().c_str(), itk::ImageIOFactory::ReadMode);
 675     if (reader) {
 676       reader->SetFileName(files[i].toStdString().c_str());
 677       reader->ReadImageInformation();
 678       if (i == 0)
 679         currentDim = reader->GetNumberOfDimensions();
 680       bool IsOk = true;
 681       for (unsigned int j = 0; j < currentDim; j++) {
 682         if (i == 0) {
 683           if (j == 0) {
 684             currentSpacing.resize(currentDim);
 685             currentSize.resize(currentDim);
 686             currentOrigin.resize(currentDim);
 687           }
 688           currentOrigin[j] = reader->GetOrigin(j);
 689           currentSpacing[j] = reader->GetSpacing(j);
 690           currentSize[j] = reader->GetDimensions(j);
 691         } else if (currentDim != reader->GetNumberOfDimensions()
 692                    || currentSpacing[j] != reader->GetSpacing(j)
 693                    || currentSize[j] != (int)reader->GetDimensions(j)
 694                    || currentOrigin[j] != reader->GetOrigin(j)) {
 695           QString error = "Cannot read file (too different from others ";
 696           error += files[i].toStdString().c_str();
 697           QMessageBox::information(this,tr("Reading problem"),error);
 698           IsOk = false;
 699           break;
 700         }
 701       }
 702       if (IsOk)
 703         vector.push_back(files[i].toStdString());
 704     } else {
 705       QString error = "Cannot read file info for ";
 706       error += files[i].toStdString().c_str();
 707       error += "\n";
 708       error += "Maybe you're trying to open an image in an unsupported format?\n";
 709       QMessageBox::information(this,tr("Reading problem"),error);
 710     }
 711   }
 712   sort(vector.begin(),vector.end());
 713   if (vector.size() > 1)
 714     LoadImages(vector, vvImageReader::MERGEDWITHTIME);
 715   else
 716     QMessageBox::warning(this,tr("Reading problem"),"You need to select at least two images to merge images with time.\nIf you only want to open one image, please use the \"Open Image\" function.");
 717 }
 718 //------------------------------------------------------------------------------
 719
 720
 721 //------------------------------------------------------------------------------
 722 void vvMainWindow::OpenDicom()
 723 {
 724   std::vector<std::string> files;
 725
 726   std::cout << "dicomSeriesSelector " << std::endl;
 727   if (dicomSeriesSelector->exec() == QDialog::Accepted) {
 728     files = *(dicomSeriesSelector->GetFilenames());
 729     LoadImages(files, vvImageReader::DICOM);
 730   }
 731 }
 732 //------------------------------------------------------------------------------
 733
 734 //------------------------------------------------------------------------------
 735 void vvMainWindow::OpenImages()
 736 {
 737   QString Extensions = EXTENSIONS;
 738   Extensions += ";;All Files (*)";
 739
 740   QStringList files = QFileDialog::getOpenFileNames(this,tr("Load Images"),mInputPathName,Extensions);
 741   if (files.isEmpty())
 742     return;
 743   mInputPathName = itksys::SystemTools::GetFilenamePath(files[0].toStdString()).c_str();
 744   std::vector<std::string> vector;
 745   for (int i = 0; i < files.size(); i++)
 746     vector.push_back(files[i].toStdString());
 747   LoadImages(vector, vvImageReader::IMAGE);
 748 }
 749 //------------------------------------------------------------------------------
 750 void vvMainWindow::OpenRecentImage()
 751 {
 752   QAction * caller = qobject_cast<QAction*>(sender());
 753   std::vector<std::string> images;
 754   images.push_back(caller->text().toStdString());
 755   mInputPathName = itksys::SystemTools::GetFilenamePath(images[0]).c_str();
 756   LoadImages(images, vvImageReader::IMAGE);
 757 }
 758 //------------------------------------------------------------------------------
 759
 760
 761 //------------------------------------------------------------------------------
 762 void vvMainWindow::OpenImageWithTime()
 763 {
 764   QString Extensions = EXTENSIONS;
 765   Extensions += ";;All Files (*)";
 766
 767   QStringList files = QFileDialog::getOpenFileNames(this,tr("Load Images With Time"),mInputPathName,Extensions);
 768   if (files.isEmpty())
 769     return;
 770   mInputPathName = itksys::SystemTools::GetFilenamePath(files[0].toStdString()).c_str();
 771   std::vector<std::string> vector;
 772   for (int i = 0; i < files.size(); i++) {
 773     vector.push_back(files[i].toStdString());
 774   }
 775   LoadImages(vector, vvImageReader::IMAGEWITHTIME);
 776 }
 777 //------------------------------------------------------------------------------
 778
 779
 780 //------------------------------------------------------------------------------
 781 void vvMainWindow::LoadImages(std::vector<std::string> files, vvImageReader::LoadedImageType filetype)
 782 {
 783   //Separate the way to open images and dicoms
 784   int fileSize;
 785   if (filetype == vvImageReader::IMAGE || filetype == vvImageReader::IMAGEWITHTIME)
 786     fileSize = files.size();
 787   else
 788     fileSize = 1;
 789
 790   // For SLICED, we need the number of slices (ndim and #slices)
 791   std::vector<unsigned int> nSlices;
 792   nSlices.resize(files.size());
 793   std::fill(nSlices.begin(), nSlices.end(), 1);
 794   if (filetype == vvImageReader::SLICED) {
 795     for (int i = 0; i < fileSize; i++) {
 796       itk::ImageIOBase::Pointer header = clitk::readImageHeader(files[i]);
 797       QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
 798       if (!header) {
 799         nSlices[i] = 0;
 800         QString error = "Cannot open file \n";
 801         error += files[i].c_str();
 802         QMessageBox::information(this,tr("Reading problem"),error);
 803         return;
 804       }
 805       if (header->GetNumberOfDimensions() < 3) {
 806         nSlices[i] = 0;
 807         QString error = "Dimension problem. Cannot slice \n";
 808         error += files[i].c_str();
 809         QMessageBox::information(this,tr("Reading problem"),error);
 810         return;
 811       }
 812       nSlices[i] = header->GetDimensions( header->GetNumberOfDimensions()-1 );
 813     }
 814   }
 815
 816   //Only add to the list of recently opened files when a single file is opened,
 817   //to avoid polluting the list of recently opened files
 818   if (files.size() == 1) {
 819     QFileInfo finfo=tr(files[0].c_str());
 820     AddToRecentlyOpenedImages(finfo.absoluteFilePath().toStdString());
 821     updateRecentlyOpenedFilesMenu(GetRecentlyOpenedImages());
 822   }
 823   //init the progress events
 824   QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
 825   vvProgressDialog progress("Opening " + files[0],fileSize>1);
 826   qApp->processEvents();
 827
 828   int numberofsuccesulreads=0;
 829   //open images as 1 or multiples
 830   for (int i = 0; i < fileSize; i++) {
 831
 832     progress.SetText("Opening " + files[i]);
 833     progress.SetProgress(i,fileSize);
 834     qApp->processEvents();
 835
 836     for (unsigned int j = 0; j < nSlices[i]; j++) {
 837       //read the image and put it in mSlicerManagers
 838       vvSlicerManager* imageManager = new vvSlicerManager(4);
 839       qApp->processEvents();
 840
 841       bool SetImageSucceed=false;
 842
 843       // Change filename if an image with the same already exist
 844       int number = GetImageDuplicateFilenameNumber(files[i] + std::string("_slice"));
 845
 846       if (filetype == vvImageReader::IMAGE || filetype == vvImageReader::IMAGEWITHTIME || filetype == vvImageReader::SLICED)
 847         SetImageSucceed = imageManager->SetImage(files[i],filetype, number, j);
 848       else {
 849         SetImageSucceed = imageManager->SetImages(files,filetype, number);
 850       }
 851       if (!SetImageSucceed) {
 852         QApplication::restoreOverrideCursor();
 853         QString error = "Cannot open file \n";
 854         error += imageManager->GetLastError().c_str();
 855         QMessageBox::information(this,tr("Reading problem"),error);
 856         delete imageManager;
 857       } else {
 858         mSlicerManagers.push_back(imageManager);
 859
 860         //create an item in the tree with good settings
 861         QTreeWidgetItem *item = new QTreeWidgetItem();
 862         item->setData(0,Qt::UserRole,files[i].c_str());
 863         QFileInfo fileinfo(imageManager->GetFileName().c_str()); //Do not show the path
 864         item->setData(COLUMN_IMAGE_NAME,Qt::DisplayRole,fileinfo.fileName());
 865         item->setToolTip(COLUMN_IMAGE_NAME,fileinfo.absoluteFilePath());
 866         qApp->processEvents();
 867
 868         //Create the buttons for reload and close
 869         qApp->processEvents();
 870         QTreePushButton* cButton = new QTreePushButton;
 871         cButton->setItem(item);
 872         cButton->setColumn(COLUMN_CLOSE_IMAGE);
 873         cButton->setToolTip(tr("close image"));
 874         cButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/exit.png")));
 875         connect(cButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
 876                 this,SLOT(CloseImage(QTreeWidgetItem*, int)));
 877
 878         QTreePushButton* rButton = new QTreePushButton;
 879         rButton->setItem(item);
 880         rButton->setColumn(COLUMN_RELOAD_IMAGE);
 881         rButton->setToolTip(tr("reload image"));
 882         rButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/rotateright.png")));
 883         connect(rButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
 884                 this,SLOT(ReloadImage(QTreeWidgetItem*, int)));
 885
 886         DataTree->addTopLevelItem(item);
 887         DataTree->setItemWidget(item, COLUMN_CLOSE_IMAGE, cButton);
 888         DataTree->setItemWidget(item, COLUMN_RELOAD_IMAGE, rButton);
 889
 890         //set the id of the image
 891         QString id = files[i].c_str() + QString::number(mSlicerManagers.size()-1);
 892         item->setData(COLUMN_IMAGE_NAME,Qt::UserRole,id.toStdString().c_str());
 893         mSlicerManagers.back()->SetId(id.toStdString());
 894
 895         linkPanel->addImage(imageManager->GetFileName(), id.toStdString());
 896
 897         connect(mSlicerManagers.back(), SIGNAL(currentImageChanged(std::string)),
 898                 this,SLOT(CurrentImageChanged(std::string)));
 899         connect(mSlicerManagers.back(), SIGNAL(currentPickedImageChanged(std::string)),
 900                 this, SLOT(CurrentPickedImageChanged(std::string)));
 901         connect(mSlicerManagers.back(), SIGNAL(UpdatePosition(int, double, double, double, double, double, double, double)),
 902                 this,SLOT(MousePositionChanged(int,double, double, double, double, double, double, double)));
 903         connect(mSlicerManagers.back(), SIGNAL(UpdateVector(int, double, double, double, double)),
 904                 this, SLOT(VectorChanged(int,double,double,double, double)));
 905         connect(mSlicerManagers.back(), SIGNAL(UpdateOverlay(int, double, double)),
 906                 this, SLOT(OverlayChanged(int,double,double)));
 907         connect(mSlicerManagers.back(), SIGNAL(UpdateFusion(int, double)),
 908                 this, SLOT(FusionChanged(int,double)));
 909         connect(mSlicerManagers.back(), SIGNAL(UpdateWindows(int, int, int)),
 910                 this,SLOT(WindowsChanged(int, int, int)));
 911         connect(mSlicerManagers.back(), SIGNAL(WindowLevelChanged(double, double,int, int)),
 912                 this,SLOT(WindowLevelChanged(double, double, int, int)));
 913         connect(mSlicerManagers.back(), SIGNAL(UpdateSlice(int,int)),
 914                 this,SLOT(UpdateSlice(int,int)));
 915         connect(mSlicerManagers.back(), SIGNAL(UpdateTSlice(int, int)),
 916                 this,SLOT(UpdateTSlice(int, int)));
 917         connect(mSlicerManagers.back(), SIGNAL(UpdateSliceRange(int,int,int,int,int)),
 918                 this,SLOT(UpdateSliceRange(int,int,int,int,int)));
 919         connect(mSlicerManagers.back(), SIGNAL(UpdateLinkManager(std::string,int,double,double,double,int)),
 920                 this,SLOT(UpdateLinkManager(std::string,int,double,double,double,int)));
 921         connect(mSlicerManagers.back(), SIGNAL(UpdateLinkedNavigation(std::string,vvSlicerManager*,vvSlicer*)),
 922                 this,SLOT(UpdateLinkedNavigation(std::string,vvSlicerManager*,vvSlicer*)));
 923         connect(mSlicerManagers.back(), SIGNAL(ChangeImageWithIndexOffset(vvSlicerManager*,int,int)),
 924                 this,SLOT(ChangeImageWithIndexOffset(vvSlicerManager*,int,int)));
 925         connect(mSlicerManagers.back(),SIGNAL(LandmarkAdded()),landmarksPanel,SLOT(AddPoint()));
 926         InitSlicers();
 927         numberofsuccesulreads++;
 928       }
 929     }
 930   }
 931   if (numberofsuccesulreads) {
 932     NOViewWidget->show();
 933     NEViewWidget->show();
 934     SOViewWidget->show();
 935     SEViewWidget->show();
 936     UpdateTree();
 937     InitDisplay();
 938     ShowLastImage();
 939
 940     // Try to guess default WindowLevel
 941     double range[2];
 942     mSlicerManagers.back()->GetImage()->GetFirstVTKImageData()->GetScalarRange(range);
 943     if ((range[0] == 0) && (range[1] == 1)) {
 944       presetComboBox->setCurrentIndex(5);// binary
 945     } else {
 946       // TODO
 947     }
 948   }
 949   QApplication::restoreOverrideCursor();
 950 }
 951 //------------------------------------------------------------------------------
 952
 953 //------------------------------------------------------------------------------
 954 void vvMainWindow::UpdateTree()
 955 {
 956   DataTree->resizeColumnToContents(COLUMN_TREE);
 957   DataTree->resizeColumnToContents(COLUMN_UL_VIEW);
 958   DataTree->resizeColumnToContents(COLUMN_UR_VIEW);
 959   DataTree->resizeColumnToContents(COLUMN_DL_VIEW);
 960   DataTree->resizeColumnToContents(COLUMN_DR_VIEW);
 961   DataTree->resizeColumnToContents(COLUMN_IMAGE_NAME);
 962   DataTree->resizeColumnToContents(COLUMN_CLOSE_IMAGE);
 963   DataTree->resizeColumnToContents(COLUMN_RELOAD_IMAGE);
 964 }
 965 //------------------------------------------------------------------------------
 966
 967 //------------------------------------------------------------------------------
 968 void vvMainWindow::CurrentImageChanged(std::string id)
 969 {
 970   if (id == mCurrentSelectedImageId) return; // Do nothing
 971   int selected = 0;
 972   for (int i = 0; i < DataTree->topLevelItemCount(); i++) {
 973     if (DataTree->topLevelItem(i)->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString().toStdString() == id) {
 974       selected = i;
 975     } else {
 976       DataTree->topLevelItem(i)->setSelected(0);
 977     }
 978     for (int child = 0; child < DataTree->topLevelItem(i)->childCount(); child++)
 979       DataTree->topLevelItem(i)->child(child)->setSelected(0);
 980
 981   }
 982   DataTree->topLevelItem(selected)->setSelected(1);
 983   mCurrentSelectedImageId = id;
 984   emit SelectedImageHasChanged(mSlicerManagers[selected]);
 985 }
 986 //------------------------------------------------------------------------------
 987
 988 //------------------------------------------------------------------------------
 989 void vvMainWindow::CurrentPickedImageChanged(std::string id)
 990 {
 991   if (id == mCurrentPickedImageId) return; // Do nothing
 992   int selected = 0;
 993   for (int i = 0; i < DataTree->topLevelItemCount(); i++) {
 994     if (DataTree->topLevelItem(i)->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString().toStdString() == id) {
 995       selected = i;
 996     } else {
 997       DataTree->topLevelItem(i)->setSelected(0);
 998     }
 999     for (int child = 0; child < DataTree->topLevelItem(i)->childCount(); child++)
1000       DataTree->topLevelItem(i)->child(child)->setSelected(0);
1001
1002   }
1003   DataTree->topLevelItem(selected)->setSelected(1);
1004   mCurrentPickedImageId = id;
1005   mCurrentPickedImageIndex = selected;
1006 }
1007 //------------------------------------------------------------------------------
1008
1009 //------------------------------------------------------------------------------
1010 void vvMainWindow::ImageInfoChanged()
1011 {
1012   contextActions[6]->setEnabled(1);
1013   contextActions[5]->setEnabled(1);
1014   actionSave_As->setEnabled(1);
1015   actionAdd_VF_to_current_Image->setEnabled(1);
1016   actionAdd_fusion_image->setEnabled(1);
1017   actionNorth_East_Window->setEnabled(1);
1018   actionNorth_West_Window->setEnabled(1);
1019   actionSouth_East_Window->setEnabled(1);
1020   actionSouth_West_Window->setEnabled(1);
1021   vvToolManager::GetInstance()->EnableToolsInMenu(this, true);
1022   inverseButton->setEnabled(1);
1023
1024   goToCursorPushButton->setEnabled(1);
1025
1026   if (DataTree->selectedItems().size()) {
1027     int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1028
1029     colorMapComboBox->setEnabled(1);
1030     for (int i = 0; i < DataTree->topLevelItem(index)->childCount(); i++) {
1031       if (DataTree->topLevelItem(index)->child(i)->data(1,Qt::UserRole).toString() == "overlay" ||
1032           DataTree->topLevelItem(index)->child(i)->data(1,Qt::UserRole).toString() == "fusion") {
1033         colorMapComboBox->setEnabled(0);
1034         break;
1035       }
1036     }
1037
1038     std::vector<double> origin;
1039     std::vector<double> inputSpacing;
1040     std::vector<int> inputSize;
1041     std::vector<double> sizeMM;
1042     vtkSmartPointer<vtkMatrix4x4> transformation;
1043     int dimension=0;
1044     QString pixelType;
1045     QString inputSizeInBytes;
1046     QString image = DataTree->selectedItems()[0]->data(COLUMN_IMAGE_NAME,Qt::DisplayRole).toString();
1047
1048     if (mSlicerManagers[index]->GetSlicer(0)->GetImage()->GetVTKImages().size() > 1 || playMode == 1) {
1049       playButton->setEnabled(1);
1050       frameRateLabel->setEnabled(1);
1051       frameRateSpinBox->setEnabled(1);
1052     } else {
1053       playButton->setEnabled(0);
1054       frameRateLabel->setEnabled(0);
1055       frameRateSpinBox->setEnabled(0);
1056     }
1057
1058     //read image header
1059     int NPixel = 1;
1060
1061     vvImage::Pointer imageSelected;
1062     if (DataTree->topLevelItem(index) == DataTree->selectedItems()[0]) {
1063       imageSelected = mSlicerManagers[index]->GetSlicer(0)->GetImage();
1064       dimension = imageSelected->GetNumberOfDimensions();
1065       origin.resize(dimension);
1066       inputSpacing.resize(dimension);
1067       inputSize.resize(dimension);
1068       sizeMM.resize(dimension);
1069       pixelType = mSlicerManagers[index]->GetImage()->GetScalarTypeAsITKString().c_str();
1070       for (int i = 0; i < dimension; i++) {
1071         origin[i] = imageSelected->GetOrigin()[i];
1072         inputSpacing[i] = imageSelected->GetSpacing()[i];
1073         inputSize[i] = imageSelected->GetSize()[i];
1074         sizeMM[i] = inputSize[i]*inputSpacing[i];
1075         NPixel *= inputSize[i];
1076       }
1077       inputSizeInBytes = GetSizeInBytes(imageSelected->GetActualMemorySize()*1000);
1078     } else if (DataTree->selectedItems()[0]->data(1,Qt::UserRole).toString() == "vector") {
1079       imageSelected = mSlicerManagers[index]->GetSlicer(0)->GetVF();
1080       dimension = imageSelected->GetNumberOfDimensions();
1081       origin.resize(dimension);
1082       inputSpacing.resize(dimension);
1083       inputSize.resize(dimension);
1084       sizeMM.resize(dimension);
1085       pixelType = mSlicerManagers[index]->GetVF()->GetScalarTypeAsITKString().c_str();
1086       for (int i = 0; i < dimension; i++) {
1087         origin[i] = imageSelected->GetOrigin()[i];
1088         inputSpacing[i] = imageSelected->GetSpacing()[i];
1089         inputSize[i] = imageSelected->GetSize()[i];
1090         sizeMM[i] = inputSize[i]*inputSpacing[i];
1091         NPixel *= inputSize[i];
1092       }
1093       inputSizeInBytes = GetSizeInBytes(imageSelected->GetActualMemorySize()*1000);
1094     } else if (DataTree->selectedItems()[0]->data(1,Qt::UserRole).toString() == "overlay") {
1095       imageSelected = mSlicerManagers[index]->GetSlicer(0)->GetOverlay();
1096       dimension = imageSelected->GetNumberOfDimensions();
1097       origin.resize(dimension);
1098       inputSpacing.resize(dimension);
1099       inputSize.resize(dimension);
1100       sizeMM.resize(dimension);
1101       pixelType = mSlicerManagers[index]->GetImage()->GetScalarTypeAsITKString().c_str();
1102       for (int i = 0; i < dimension; i++) {
1103         origin[i] = imageSelected->GetOrigin()[i];
1104         inputSpacing[i] = imageSelected->GetSpacing()[i];
1105         inputSize[i] = imageSelected->GetSize()[i];
1106         sizeMM[i] = inputSize[i]*inputSpacing[i];
1107         NPixel *= inputSize[i];
1108       }
1109       inputSizeInBytes = GetSizeInBytes(imageSelected->GetActualMemorySize()*1000);
1110     } else if (DataTree->selectedItems()[0]->data(1,Qt::UserRole).toString() == "fusion") {
1111       imageSelected = mSlicerManagers[index]->GetSlicer(0)->GetFusion();
1112       dimension = imageSelected->GetNumberOfDimensions();
1113       origin.resize(dimension);
1114       inputSpacing.resize(dimension);
1115       inputSize.resize(dimension);
1116       sizeMM.resize(dimension);
1117       pixelType = mSlicerManagers[index]->GetImage()->GetScalarTypeAsITKString().c_str();
1118       for (int i = 0; i < dimension; i++) {
1119         origin[i] = imageSelected->GetOrigin()[i];
1120         inputSpacing[i] = imageSelected->GetSpacing()[i];
1121         inputSize[i] = imageSelected->GetSize()[i];
1122         sizeMM[i] = inputSize[i]*inputSpacing[i];
1123         NPixel *= inputSize[i];
1124       }
1125       inputSizeInBytes = GetSizeInBytes(imageSelected->GetActualMemorySize()*1000);
1126     }
1127
1128     QString dim = QString::number(dimension) + " (";
1129     dim += pixelType + ")";
1130
1131     infoPanel->setFileName(image);
1132     infoPanel->setDimension(dim);
1133     infoPanel->setSizePixel(GetVectorIntAsString(inputSize));
1134     infoPanel->setSizeMM(GetVectorDoubleAsString(sizeMM));
1135     infoPanel->setOrigin(GetVectorDoubleAsString(origin));
1136     infoPanel->setSpacing(GetVectorDoubleAsString(inputSpacing));
1137     infoPanel->setNPixel(QString::number(NPixel)+" ("+inputSizeInBytes+")");
1138     transformation = imageSelected->GetTransform()->GetMatrix();
1139     infoPanel->setTransformation(Get4x4MatrixDoubleAsString(transformation));
1140
1141     landmarksPanel->SetCurrentLandmarks(mSlicerManagers[index]->GetLandmarks(),
1142                                         mSlicerManagers[index]->GetSlicer(0)->GetImage()->GetVTKImages().size());
1143     landmarksPanel->SetCurrentPath(mInputPathName.toStdString());
1144     landmarksPanel->SetCurrentImage(mSlicerManagers[index]->GetFileName().c_str());
1145
1146     overlayPanel->getCurrentImageName(mSlicerManagers[index]->GetFileName().c_str());
1147     for (int i = 0; i < 4; i++) {
1148       if (DataTree->selectedItems()[0]->data(i+1,Qt::CheckStateRole).toInt() > 0 || i == 3) {
1149         mSlicerManagers[index]->UpdateInfoOnCursorPosition(i);
1150         break;
1151       }
1152     }
1153     windowSpinBox->setValue(mSlicerManagers[index]->GetColorWindow());
1154     levelSpinBox->setValue(mSlicerManagers[index]->GetColorLevel());
1155     presetComboBox->setCurrentIndex(mSlicerManagers[index]->GetPreset());
1156     colorMapComboBox->setCurrentIndex(mSlicerManagers[index]->GetColorMap());
1157
1158     infoPanel->setFileName(image);
1159     infoPanel->setDimension(dim);
1160     infoPanel->setSizePixel(GetVectorIntAsString(inputSize));
1161     infoPanel->setSizeMM(GetVectorDoubleAsString(sizeMM));
1162     infoPanel->setOrigin(GetVectorDoubleAsString(origin));
1163     infoPanel->setSpacing(GetVectorDoubleAsString(inputSpacing));
1164     infoPanel->setNPixel(QString::number(NPixel)+" ("+inputSizeInBytes+")");
1165
1166     landmarksPanel->SetCurrentLandmarks(mSlicerManagers[index]->GetLandmarks(),
1167                                         mSlicerManagers[index]->GetSlicer(0)->GetImage()->GetVTKImages().size());
1168     landmarksPanel->SetCurrentPath(mInputPathName.toStdString());
1169     landmarksPanel->SetCurrentImage(mSlicerManagers[index]->GetFileName().c_str());
1170
1171     overlayPanel->getCurrentImageName(mSlicerManagers[index]->GetFileName().c_str());
1172     for (int i = 0; i < 4; i++) {
1173       if (DataTree->selectedItems()[0]->data(i+1,Qt::CheckStateRole).toInt() > 0 || i == 3) {
1174         mSlicerManagers[index]->UpdateInfoOnCursorPosition(i);
1175         break;
1176       }
1177     }
1178     windowSpinBox->setValue(mSlicerManagers[index]->GetColorWindow());
1179     levelSpinBox->setValue(mSlicerManagers[index]->GetColorLevel());
1180     presetComboBox->setCurrentIndex(mSlicerManagers[index]->GetPreset());
1181     colorMapComboBox->setCurrentIndex(mSlicerManagers[index]->GetColorMap());
1182
1183     if (mSlicerManagers[index]->GetSlicer(0)->GetVF()) {
1184       overlayPanel->getVFName(mSlicerManagers[index]->GetVFName().c_str());
1185       overlayPanel->getVFProperty(mSlicerManagers[index]->GetSlicer(0)->GetVFSubSampling(),
1186                                   mSlicerManagers[index]->GetSlicer(0)->GetVFScale(),
1187                                   mSlicerManagers[index]->GetSlicer(0)->GetVFLog());
1188     } else {
1189       overlayPanel->getVFName(mSlicerManagers[index]->GetVFName().c_str());
1190       overlayPanel->getVFProperty(-1,-1,-1);
1191     }
1192     if (mSlicerManagers[index]->GetSlicer(0)->GetOverlay()) {
1193       overlayPanel->getOverlayName(mSlicerManagers[index]->GetOverlayName().c_str());
1194       overlayPanel->getOverlayProperty(mSlicerManagers[index]->GetOverlayColor());
1195     } else {
1196       overlayPanel->getOverlayName(mSlicerManagers[index]->GetOverlayName().c_str());
1197       overlayPanel->getOverlayProperty(-1);
1198     }
1199     if (mSlicerManagers[index]->GetSlicer(0)->GetFusion()) {
1200       overlayPanel->getFusionName(mSlicerManagers[index]->GetFusionName().c_str());
1201       overlayPanel->getFusionProperty(mSlicerManagers[index]->GetFusionOpacity(),
1202                                       mSlicerManagers[index]->GetFusionColorMap(),
1203                                       mSlicerManagers[index]->GetFusionWindow(),
1204                                       mSlicerManagers[index]->GetFusionLevel());
1205     } else {
1206       overlayPanel->getFusionName(mSlicerManagers[index]->GetFusionName().c_str());
1207       overlayPanel->getFusionProperty(-1, -1,-1,-1);
1208     }
1209   }
1210 }
1211 //------------------------------------------------------------------------------
1212
1213 //------------------------------------------------------------------------------
1214 void vvMainWindow::ShowDocumentation()
1215 {
1216   documentation->show();
1217 }
1218 //------------------------------------------------------------------------------
1219
1220 //------------------------------------------------------------------------------
1221 void vvMainWindow::PopupRegisterForm(bool checkCanPush)
1222 {
1223   vvRegisterForm* registerForm = new vvRegisterForm(QUrl("http://www.creatis.insa-lyon.fr/~dsarrut/vvregister/write.php"), getVVSettingsPath(), getSettingsOptionFormat());
1224   if(!checkCanPush){
1225     registerForm->show();
1226   }else{
1227     if(registerForm->canPush()){
1228       registerForm->show();
1229       registerForm->acquitPushed();//too bad if there is not internet connection anymore.
1230     }
1231   }
1232 }
1233 //------------------------------------------------------------------------------
1234
1235 //------------------------------------------------------------------------------
1236 void vvMainWindow::ShowHelpDialog()
1237 {
1238   help_dialog->show();
1239 }
1240 //------------------------------------------------------------------------------
1241
1242 //------------------------------------------------------------------------------
1243 void vvMainWindow::ChangeViewMode()
1244 {
1245   QList<int> size;
1246   if (viewMode == 1) {
1247     viewMode = 0;
1248     size.push_back(1);
1249     size.push_back(0);
1250     splitter_3->setSizes(size);
1251     OSplitter->setSizes(size);
1252     DataTree->setColumnHidden(2,1);
1253     DataTree->setColumnHidden(3,1);
1254     DataTree->setColumnHidden(4,1);
1255   } else {
1256     viewMode = 1;
1257     size.push_back(1);
1258     size.push_back(1);
1259     splitter_3->setSizes(size);
1260     OSplitter->setSizes(size);
1261     DataTree->setColumnHidden(2,0);
1262     DataTree->setColumnHidden(3,0);
1263     DataTree->setColumnHidden(4,0);
1264   }
1265   UpdateRenderWindows();
1266   /*
1267   ** I don't know why but for both resized QVTKWidget we also need to render
1268   ** the associated Slicer to redraw crosses.
1269   */
1270   for (unsigned int i = 0; i < mSlicerManagers.size(); i++)
1271   {
1272     if (DataTree->topLevelItem(i)->data(COLUMN_UL_VIEW,Qt::CheckStateRole).toInt() > 1)
1273       mSlicerManagers[i]->GetSlicer(0)->Render();
1274     if (DataTree->topLevelItem(i)->data(COLUMN_DL_VIEW,Qt::CheckStateRole).toInt() > 1)
1275       mSlicerManagers[i]->GetSlicer(2)->Render();
1276   }
1277 }
1278 //------------------------------------------------------------------------------
1279
1280 //------------------------------------------------------------------------------
1281 QString vvMainWindow::GetSizeInBytes(unsigned long size)
1282 {
1283   QString result = "";// QString::number(size);
1284   //result += " bytes (";
1285   if (size > 1000000000) {
1286     size /= 1000000000;
1287     result += QString::number(size);
1288     result += "Gb";//)";
1289   } else if (size > 1000000) {
1290     size /= 1000000;
1291     result += QString::number(size);
1292     result += "Mb";//)";
1293   } else if (size > 1000) {
1294     size /= 1000;
1295     result += QString::number(size);
1296     result += "kb";//)";
1297   }
1298   return result;
1299 }
1300 //------------------------------------------------------------------------------
1301
1302 //------------------------------------------------------------------------------
1303 QString vvMainWindow::Get4x4MatrixDoubleAsString(vtkSmartPointer<vtkMatrix4x4> matrix)
1304 {
1305   std::ostringstream strmatrix;
1306
1307   for (unsigned int i = 0; i < 4; i++) {
1308     for (unsigned int j = 0; j < 4; j++) {
1309       strmatrix.flags(ios::showpos);
1310       strmatrix.width(10);
1311       strmatrix.precision(3);
1312       strmatrix.setf(ios::fixed,ios::floatfield);
1313       strmatrix.fill(' ');
1314       strmatrix << std::left << matrix->GetElement(i, j);
1315       //strmatrix.width(10);
1316       strmatrix << " ";
1317     }
1318     strmatrix << std::endl;
1319   }
1320   QString result = strmatrix.str().c_str();
1321   return result;
1322 }
1323 //------------------------------------------------------------------------------
1324
1325 //------------------------------------------------------------------------------
1326 QString vvMainWindow::GetVectorDoubleAsString(std::vector<double> vectorDouble)
1327 {
1328   QString result;
1329   for (unsigned int i= 0; i < vectorDouble.size(); i++) {
1330     if (i != 0)
1331       result += " ";
1332     result += QString::number(vectorDouble[i]);
1333   }
1334   return result;
1335 }
1336 //------------------------------------------------------------------------------
1337
1338 //------------------------------------------------------------------------------
1339 QString vvMainWindow::GetVectorIntAsString(std::vector<int> vectorInt)
1340 {
1341   QString result;
1342   for (unsigned int i= 0; i < vectorInt.size(); i++) {
1343     if (i != 0)
1344       result += " ";
1345     result += QString::number(vectorInt[i]);
1346   }
1347   return result;
1348 }
1349 //------------------------------------------------------------------------------
1350
1351 //------------------------------------------------------------------------------
1352 int vvMainWindow::GetSlicerIndexFromItem(QTreeWidgetItem* item)
1353 {
1354   QString id = item->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString();
1355   for (int i = 0; i < DataTree->topLevelItemCount(); i++) {
1356     if (DataTree->topLevelItem(i)->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString() == id)
1357       return i;
1358   }
1359   return -1;
1360 }
1361 //------------------------------------------------------------------------------
1362
1363 //------------------------------------------------------------------------------
1364 QTreeWidgetItem* vvMainWindow::GetItemFromSlicerManager(vvSlicerManager* sm)
1365 {
1366   QString id = sm->GetId().c_str();
1367   for (int i = 0; i < DataTree->topLevelItemCount(); i++) {
1368     if (DataTree->topLevelItem(i)->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString() == id)
1369       return DataTree->topLevelItem(i);
1370   }
1371   return NULL;
1372 }
1373 //------------------------------------------------------------------------------
1374
1375 //------------------------------------------------------------------------------
1376 void vvMainWindow::DisplayChanged(QTreeWidgetItem *clicked_item, int column)
1377 {
1378   int index = GetSlicerIndexFromItem(clicked_item);
1379   if ( column >= COLUMN_CLOSE_IMAGE || column <= 0)
1380     return;
1381   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
1382     //Trick to avoid redoing twice the job for a key (sr)
1383     mSlicerManagers[i]->GetSlicer(column-1)->GetRenderWindow()-> GetInteractor()->SetKeySym("Crap");
1384
1385     QTreeWidgetItem* current_row=DataTree->topLevelItem(i);
1386     if (DataTree->topLevelItem(index) == current_row) {
1387       vvSlicer* clicked_slicer=mSlicerManagers[i]->GetSlicer(column-1);
1388       if (current_row == clicked_item) {
1389         //If we just activated a slicer
1390         if (current_row->data(column,Qt::CheckStateRole).toInt() > 0) {
1391           mSlicerManagers[i]->UpdateSlicer(column-1,clicked_item->data(column,Qt::CheckStateRole).toInt());
1392           mSlicerManagers[i]->UpdateInfoOnCursorPosition(column-1);
1393           DisplaySliders(i,column-1);
1394           std::map<std::string,int> overlay_counts;
1395           for (int child = 0; child < current_row->childCount(); child++) {
1396             std::string overlay_type =
1397               current_row->child(child)->data(1,Qt::UserRole).toString().toStdString();
1398             overlay_counts[overlay_type]++;
1399             current_row->child(child)->setData(column,Qt::CheckStateRole,
1400                                                current_row->data(column,Qt::CheckStateRole));
1401             clicked_slicer->SetActorVisibility(overlay_type,overlay_counts[overlay_type]-1,true);
1402           }
1403         } else { //We don't allow simply desactivating a slicer
1404           clicked_item->setData(column,Qt::CheckStateRole,2);
1405           return;
1406         }
1407       }
1408       //if we clicked on the vector(or overlay) and not the image
1409       else {
1410         if (clicked_item->data(column,Qt::CheckStateRole).toInt()) {
1411           current_row->setData(column,Qt::CheckStateRole,2);
1412           mSlicerManagers[i]->UpdateSlicer(column-1,2);
1413           mSlicerManagers[i]->UpdateInfoOnCursorPosition(column-1);
1414           DisplaySliders(i,column-1);
1415         }
1416         int vis = clicked_item->data(column,Qt::CheckStateRole).toInt();
1417         std::string overlay_type = clicked_item->data(1,Qt::UserRole).toString().toStdString();
1418         int overlay_index=0;
1419         for (int child = 0; child < current_row->childCount(); child++) {
1420           if (current_row->child(child)->data(1,Qt::UserRole).toString().toStdString() == overlay_type)
1421             overlay_index++;
1422           if (current_row->child(child) == clicked_item) break;
1423         }
1424         clicked_slicer->SetActorVisibility(
1425           clicked_item->data(1,Qt::UserRole).toString().toStdString(), overlay_index-1,vis);
1426       }
1427     } else if (current_row->data(column,Qt::CheckStateRole).toInt() > 0) {
1428       current_row->setData(column,Qt::CheckStateRole,0);
1429       mSlicerManagers[i]->UpdateSlicer(column-1,0);
1430       std::map<std::string,int> overlay_counts;
1431       for (int child = 0; child < current_row->childCount(); child++) {
1432         std::string overlay_type =
1433           current_row->child(child)->data(1,Qt::UserRole).toString().toStdString();
1434         overlay_counts[overlay_type]++;
1435         current_row->child(child)->setData(column,Qt::CheckStateRole,0);
1436         vvSlicer * current_slicer=mSlicerManagers[i]->GetSlicer(column-1);
1437         current_slicer->SetActorVisibility(overlay_type,overlay_counts[overlay_type]-1,false);
1438       }
1439     }
1440     //mSlicerManagers[i]->SetColorMap(-1);
1441     mSlicerManagers[i]->SetColorMap();
1442   }
1443   mSlicerManagers[index]->GetSlicer(column-1)->Render();
1444 }
1445 //------------------------------------------------------------------------------
1446
1447 void vvMainWindow::InitSlicers()
1448 {
1449   if (mSlicerManagers.size()) {
1450     mSlicerManagers.back()->GenerateDefaultLookupTable();
1451
1452     mSlicerManagers.back()->SetSlicerWindow(0,NOViewWidget->GetRenderWindow());
1453     mSlicerManagers.back()->SetSlicerWindow(1,NEViewWidget->GetRenderWindow());
1454     mSlicerManagers.back()->SetSlicerWindow(2,SOViewWidget->GetRenderWindow());
1455     mSlicerManagers.back()->SetSlicerWindow(3,SEViewWidget->GetRenderWindow());
1456   }
1457 }
1458
1459 //------------------------------------------------------------------------------
1460 void vvMainWindow::InitDisplay()
1461 {
1462   if (mSlicerManagers.size()) {
1463     //BE CAREFUL : this is absolutely necessary to set the interactor style
1464     //in order to have the same style instanciation for all SlicerManagers in
1465     // a same window
1466     for (int j = 0; j < 4; j++) {
1467       vvInteractorStyleNavigator* style = vvInteractorStyleNavigator::New();
1468       style->SetAutoAdjustCameraClippingRange(1);
1469       bool AlreadySelected = false;
1470       for (int i = 0; i < DataTree->topLevelItemCount(); i++) {
1471         mSlicerManagers[i]->SetInteractorStyleNavigator(j,style);
1472
1473         //select the image only if previous are not selected
1474         if (DataTree->topLevelItem(i)->data(j+1,Qt::CheckStateRole).toInt() > 1) {
1475           mSlicerManagers[i]->UpdateSlicer(j,1);
1476           AlreadySelected = true;
1477         } else if (i == DataTree->topLevelItemCount()-1 && !AlreadySelected) {
1478           if (DataTree->selectedItems().size() == 0)
1479             DataTree->topLevelItem(i)->setSelected(1);
1480           DataTree->topLevelItem(i)->setData(j+1,Qt::CheckStateRole,2);
1481           mSlicerManagers[i]->UpdateSlicer(j,1);
1482           DisplaySliders(i,j);
1483         } else {
1484           DataTree->topLevelItem(i)->setData(j+1,Qt::CheckStateRole,0);
1485           mSlicerManagers[i]->UpdateSlicer(j,0);
1486         }
1487       }
1488       style->Delete();
1489     }
1490   }
1491 }
1492 //------------------------------------------------------------------------------
1493
1494 //------------------------------------------------------------------------------
1495 void vvMainWindow::DisplaySliders(int slicer, int window)
1496 {
1497   int range[2];
1498   mSlicerManagers[slicer]->GetSlicer(window)->GetSliceRange(range);
1499   int position = mSlicerManagers[slicer]->GetSlicer(window)->GetSlice();
1500
1501   int tRange[2];
1502   tRange[0] = 0;
1503   tRange[1] = mSlicerManagers[slicer]->GetSlicer(window)->GetTMax();
1504   int tPosition = mSlicerManagers[slicer]->GetSlicer(window)->GetTSlice();
1505   bool showHorizontal = false;
1506   bool showVertical = false;
1507   if (mSlicerManagers[slicer]->GetSlicer(window)->GetImage()->GetNumberOfDimensions() > 3
1508       || (mSlicerManagers[slicer]->GetSlicer(window)->GetImage()->GetNumberOfDimensions() > 2
1509           && mSlicerManagers[slicer]->GetType() != vvImageReader::IMAGEWITHTIME
1510           && mSlicerManagers[slicer]->GetType() != vvImageReader::MERGEDWITHTIME))
1511     showVertical = true;
1512   if (mSlicerManagers[slicer]->GetSlicer(window)->GetImage()->GetNumberOfDimensions() > 3
1513       || mSlicerManagers[slicer]->GetType() == vvImageReader::IMAGEWITHTIME
1514       || mSlicerManagers[slicer]->GetType() == vvImageReader::MERGEDWITHTIME)
1515     showHorizontal = true;
1516
1517   if (showVertical)
1518     verticalSliders[window]->show();
1519   else
1520     verticalSliders[window]->hide();
1521   verticalSliders[window]->setRange(range[0],range[1]);
1522   verticalSliders[window]->setValue(position);
1523
1524   if (showHorizontal)
1525     horizontalSliders[window]->show();
1526   else
1527     horizontalSliders[window]->hide();
1528   horizontalSliders[window]->setRange(tRange[0],tRange[1]);
1529   horizontalSliders[window]->setValue(tPosition);
1530 }
1531 //------------------------------------------------------------------------------
1532
1533 //------------------------------------------------------------------------------
1534 void vvMainWindow::CloseImage(QTreeWidgetItem* item, int column)
1535 {
1536   int index = GetSlicerIndexFromItem(item);
1537
1538   if (DataTree->topLevelItem(index) != item) {
1539     QString warning = "Do you really want to close the overlay : ";
1540     warning += item->data(COLUMN_IMAGE_NAME,Qt::DisplayRole).toString();
1541     QMessageBox msgBox(QMessageBox::Warning, tr("Close Overlay"),
1542                        warning, 0, this);
1543     msgBox.addButton(tr("Close"), QMessageBox::AcceptRole);
1544     msgBox.addButton(tr("Cancel"), QMessageBox::RejectRole);
1545     if (msgBox.exec() == QMessageBox::AcceptRole) {
1546       std::string overlay_type=item->data(1,Qt::UserRole).toString().toStdString();
1547       int overlay_index=0;
1548       for (int child = 0; child < DataTree->topLevelItem(index)->childCount(); child++) {
1549         if (DataTree->topLevelItem(index)->\
1550             child(child)->data(1,Qt::UserRole).toString().toStdString() == overlay_type)
1551           overlay_index++;
1552         if (DataTree->topLevelItem(index)->child(child) == item) break;
1553       }
1554       mSlicerManagers[index]->RemoveActor(overlay_type, overlay_index-1);
1555       mSlicerManagers[index]->SetColorMap(0);
1556       DataTree->topLevelItem(index)->takeChild(DataTree->topLevelItem(index)->indexOfChild(item));
1557       mSlicerManagers[index]->Render();
1558     }
1559   } else if (DataTree->topLevelItemCount() <= 1) {
1560     QString warning = "Do you really want to close the image : ";
1561     warning += item->data(COLUMN_IMAGE_NAME,Qt::DisplayRole).toString();
1562     warning += "\nThis is the last image, you're about to close vv !!!";
1563     QMessageBox msgBox(QMessageBox::Warning, tr("Close Image"),
1564                        warning, 0, this);
1565     msgBox.addButton(tr("Close vv"), QMessageBox::AcceptRole);
1566     msgBox.addButton(tr("Cancel"), QMessageBox::RejectRole);
1567     if (msgBox.exec() == QMessageBox::AcceptRole) {
1568       this->close();
1569     }
1570   } else {
1571     QString warning = "Do you really want to close the image : ";
1572     warning += item->data(COLUMN_IMAGE_NAME,Qt::DisplayRole).toString();
1573     QMessageBox msgBox(QMessageBox::Warning, tr("Close Image"),
1574                        warning, 0, this);
1575     msgBox.addButton(tr("Close"), QMessageBox::AcceptRole);
1576     msgBox.addButton(tr("Cancel"), QMessageBox::RejectRole);
1577     if (msgBox.exec() == QMessageBox::AcceptRole) {
1578
1579       // Tell tools that we close an image
1580       emit AnImageIsBeingClosed(mSlicerManagers[index]);
1581
1582       std::vector<vvSlicerManager*>::iterator Manageriter = mSlicerManagers.begin();
1583       DataTree->takeTopLevelItem(index);
1584       for (int i = 0; i < index; i++) {
1585         Manageriter++;
1586       }
1587       linkPanel->removeImage(index);
1588       mSlicerManagers[index]->RemoveActors();
1589       delete mSlicerManagers[index];
1590       mSlicerManagers.erase(Manageriter);
1591
1592       //
1593       InitDisplay();
1594     }
1595   }
1596   ImageInfoChanged();
1597 }
1598 //------------------------------------------------------------------------------
1599
1600 //------------------------------------------------------------------------------
1601 void vvMainWindow::ReloadImage(QTreeWidgetItem* item, int column)
1602 {
1603   // int index = GetSlicerIndexFromItem(item);
1604   //   QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
1605   //   if (item->data(1,Qt::UserRole).toString() == "vector")
1606   //     mSlicerManagers[index]->ReloadVF();
1607   //   else
1608   //     mSlicerManagers[index]->Reload();
1609
1610   //   QApplication::restoreOverrideCursor();
1611   int index = GetSlicerIndexFromItem(item);
1612   QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
1613   QString role=item->data(1,Qt::UserRole).toString();
1614   if ( role == "vector")
1615     mSlicerManagers[index]->ReloadVF();
1616   else if (role == "overlay")
1617     mSlicerManagers[index]->ReloadOverlay();
1618   else if (role == "fusion")
1619     mSlicerManagers[index]->ReloadFusion();
1620   else
1621     mSlicerManagers[index]->Reload();
1622
1623   // Update view and info
1624   ImageInfoChanged();
1625   mSlicerManagers[index]->Render();
1626   QApplication::restoreOverrideCursor();
1627 }
1628 //------------------------------------------------------------------------------
1629
1630 //------------------------------------------------------------------------------
1631 void vvMainWindow::MousePositionChanged(int visibility,double x, double y, double z, double X, double Y, double Z , double value)
1632 {
1633   infoPanel->setCurrentInfo(visibility,x,y,z,X,Y,Z,value);
1634 }
1635 //------------------------------------------------------------------------------
1636
1637 //------------------------------------------------------------------------------
1638 void vvMainWindow::VectorChanged(int visibility,double x, double y, double z, double value)
1639 {
1640   overlayPanel->getCurrentVectorInfo(visibility,x,y,z,value);
1641 }
1642 //------------------------------------------------------------------------------
1643
1644 //------------------------------------------------------------------------------
1645 void vvMainWindow::OverlayChanged(int visibility, double valueOver, double valueRef)
1646 {
1647   overlayPanel->getCurrentOverlayInfo(visibility,valueOver, valueRef);
1648 }
1649 //------------------------------------------------------------------------------
1650
1651 //------------------------------------------------------------------------------
1652 void vvMainWindow::FusionChanged(int visibility, double value)
1653 {
1654   overlayPanel->getCurrentFusionInfo(visibility,value);
1655 }
1656 //------------------------------------------------------------------------------
1657
1658 //------------------------------------------------------------------------------
1659 void vvMainWindow::WindowsChanged(int window, int view, int slice)
1660 {
1661   infoPanel->setViews(window, view, slice);
1662 }
1663 //------------------------------------------------------------------------------
1664
1665 //------------------------------------------------------------------------------
1666 void vvMainWindow::WindowLevelChanged(double window, double level,int preset,int colormap)
1667 {
1668   windowSpinBox->setValue(window);
1669   levelSpinBox->setValue(level);
1670   colorMapComboBox->setCurrentIndex(colormap);
1671   presetComboBox->setCurrentIndex(preset);
1672 }
1673 //------------------------------------------------------------------------------
1674
1675 //------------------------------------------------------------------------------
1676 void vvMainWindow::WindowLevelEdited()
1677 {
1678   presetComboBox->setCurrentIndex(6);
1679   UpdateWindowLevel();
1680 }
1681 //------------------------------------------------------------------------------
1682
1683 //------------------------------------------------------------------------------
1684 void vvMainWindow::UpdateWindowLevel()
1685 {
1686   if (DataTree->selectedItems().size()) {
1687     if (presetComboBox->currentIndex() == 7) //For ventilation
1688       colorMapComboBox->setCurrentIndex(5);
1689     int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1690     mSlicerManagers[index]->SetColorWindow(windowSpinBox->value());
1691     mSlicerManagers[index]->SetColorLevel(levelSpinBox->value());
1692     mSlicerManagers[index]->SetPreset(presetComboBox->currentIndex());
1693     mSlicerManagers[index]->Render();
1694     windowSpinBox->setValue(mSlicerManagers[index]->GetColorWindow());
1695     levelSpinBox->setValue(mSlicerManagers[index]->GetColorLevel());
1696   }
1697 }
1698 //------------------------------------------------------------------------------
1699
1700 //------------------------------------------------------------------------------
1701 void vvMainWindow::UpdateColorMap()
1702 {
1703   if (DataTree->selectedItems().size()) {
1704     int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1705     mSlicerManagers[index]->SetColorMap(colorMapComboBox->currentIndex());
1706     mSlicerManagers[index]->Render();
1707   }
1708 }
1709 //------------------------------------------------------------------------------
1710 void vvMainWindow::SwitchWindowLevel()
1711 {
1712   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1713   int window = mSlicerManagers[index]->GetColorWindow();
1714   presetComboBox->setCurrentIndex(6);
1715   windowSpinBox->setValue(-window);
1716   UpdateWindowLevel();
1717 }
1718 //------------------------------------------------------------------------------
1719
1720 //------------------------------------------------------------------------------
1721 void vvMainWindow::ApplyWindowLevelToAllImages()
1722 {
1723   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
1724     if (mSlicerManagers[i] == NULL)
1725       continue;
1726     mSlicerManagers[i]->SetColorWindow(windowSpinBox->value());
1727     mSlicerManagers[i]->SetColorLevel(levelSpinBox->value());
1728     mSlicerManagers[i]->SetPreset(6);
1729     mSlicerManagers[i]->Render();
1730   }
1731 }
1732 //------------------------------------------------------------------------------
1733
1734 //------------------------------------------------------------------------------
1735 void vvMainWindow::UpdateLinkManager(std::string id, int slicer, double x, double y, double z, int temps)
1736 {
1737   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
1738     if (mSlicerManagers[i]->GetId() == id) {
1739       //mSlicerManagers[i]->SetTSlice(temps);
1740       mSlicerManagers[i]->GetSlicer(slicer)->SetCurrentPosition(x,y,z,temps);
1741       mSlicerManagers[i]->UpdateViews(0,slicer);
1742       break;
1743     }
1744   }
1745 }
1746 //------------------------------------------------------------------------------
1747
1748 //------------------------------------------------------------------------------
1749 void vvMainWindow::UpdateLinkedNavigation(std::string id, vvSlicerManager * sm, vvSlicer* refSlicer)
1750 {
1751   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
1752     if (id == mSlicerManagers[i]->GetId()) {
1753       mSlicerManagers[i]->UpdateLinkedNavigation(refSlicer);
1754     }
1755   }
1756 }
1757 //------------------------------------------------------------------------------
1758
1759 //------------------------------------------------------------------------------
1760 void vvMainWindow::ShowContextMenu(QPoint point)
1761 {
1762   if (!DataTree->selectedItems().size()) {
1763     contextActions[1]->setEnabled(0);
1764     contextActions[2]->setEnabled(0);
1765     contextActions[3]->setEnabled(0);
1766     contextActions[4]->setEnabled(0);
1767     contextActions[5]->setEnabled(0);
1768     contextActions[6]->setEnabled(0);
1769   } else {
1770     int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1771     contextActions[1]->setEnabled(1);
1772     contextActions[2]->setEnabled(
1773       DataTree->itemWidget(DataTree->selectedItems()[0],
1774                            COLUMN_RELOAD_IMAGE)->isEnabled());
1775     contextActions[3]->setEnabled(1);
1776     contextActions[5]->setEnabled(1);
1777     contextActions[6]->setEnabled(1);
1778
1779     if (mSlicerManagers[index]->GetDimension() < 3)
1780       contextActions[4]->setEnabled(0);
1781     else
1782       contextActions[4]->setEnabled(1);
1783   }
1784   contextMenu.exec(QCursor::pos());
1785 }
1786 //------------------------------------------------------------------------------
1787
1788 //------------------------------------------------------------------------------
1789 void vvMainWindow::CloseImage()
1790 {
1791   CloseImage(DataTree->selectedItems()[0],0);
1792 }
1793 //------------------------------------------------------------------------------
1794
1795 //------------------------------------------------------------------------------
1796 void vvMainWindow::ReloadImage()
1797 {
1798   ReloadImage(DataTree->selectedItems()[0],0);
1799 }
1800 //------------------------------------------------------------------------------
1801
1802 //------------------------------------------------------------------------------
1803 void vvMainWindow::SelectOverlayImage()
1804 {
1805   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1806
1807   //check if one overlay image is added
1808   for (int child = 0; child < DataTree->topLevelItem(index)->childCount(); child++)
1809     if (DataTree->topLevelItem(index)->child(child)->data(1,Qt::UserRole).toString() == "overlay") {
1810       QString error = "Cannot add more than one compared image\n";
1811       error += "Please remove first ";
1812       error += DataTree->topLevelItem(index)->child(child)->data(COLUMN_IMAGE_NAME,Qt::DisplayRole).toString();
1813       QMessageBox::information(this,tr("Problem adding compared image !"),error);
1814       return;
1815     }
1816
1817   QString Extensions = EXTENSIONS;
1818   Extensions += ";;All Files (*)";
1819   QString file = QFileDialog::getOpenFileName(this,tr("Load Overlay image"),mInputPathName,Extensions);
1820   if (!file.isEmpty())
1821     AddOverlayImage(index,file);
1822 }
1823 //------------------------------------------------------------------------------
1824
1825 //------------------------------------------------------------------------------
1826 void vvMainWindow::AddOverlayImage(int index, QString file)
1827 {
1828
1829   mInputPathName = itksys::SystemTools::GetFilenamePath(file.toStdString()).c_str();
1830   itk::ImageIOBase::Pointer reader = itk::ImageIOFactory::CreateImageIO(
1831                                        file.toStdString().c_str(), itk::ImageIOFactory::ReadMode);
1832   reader->SetFileName(file.toStdString().c_str());
1833   reader->ReadImageInformation();
1834   std::string component = reader->GetComponentTypeAsString(reader->GetComponentType());
1835   int dimension = reader->GetNumberOfDimensions();
1836   QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
1837   vvProgressDialog progress("Opening " + file.toStdString());
1838   qApp->processEvents();
1839
1840   std::string filename = itksys::SystemTools::GetFilenameWithoutExtension(file.toStdString()).c_str();
1841   if (mSlicerManagers[index]->SetOverlay(file.toStdString(),dimension, component)) {
1842     //create an item in the tree with good settings
1843     QTreeWidgetItem *item = new QTreeWidgetItem();
1844     item->setData(0,Qt::UserRole,file.toStdString().c_str());
1845     item->setData(1,Qt::UserRole,tr("overlay"));
1846     QFileInfo fileinfo(file); //Do not show the path
1847     item->setData(COLUMN_IMAGE_NAME,Qt::DisplayRole,fileinfo.fileName());
1848     item->setToolTip(COLUMN_IMAGE_NAME,fileinfo.absoluteFilePath());
1849     qApp->processEvents();
1850
1851     for (int j = 1; j <= 4; j++) {
1852       item->setData(j,Qt::CheckStateRole,DataTree->topLevelItem(index)->data(j,Qt::CheckStateRole));
1853       mSlicerManagers[index]->GetSlicer(j-1)->SetActorVisibility("overlay",0,
1854           DataTree->topLevelItem(index)->data(j,Qt::CheckStateRole).toInt());
1855     }
1856
1857     //Create the buttons for reload and close
1858     qApp->processEvents();
1859     QTreePushButton* cButton = new QTreePushButton;
1860     cButton->setItem(item);
1861     cButton->setColumn(COLUMN_CLOSE_IMAGE);
1862     cButton->setToolTip(tr("close image"));
1863     cButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/exit.png")));
1864     connect(cButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
1865             this,SLOT(CloseImage(QTreeWidgetItem*, int)));
1866
1867     QTreePushButton* rButton = new QTreePushButton;
1868     rButton->setItem(item);
1869     rButton->setColumn(COLUMN_RELOAD_IMAGE);
1870     rButton->setToolTip(tr("reload image"));
1871     rButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/rotateright.png")));
1872     connect(rButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
1873             this,SLOT(ReloadImage(QTreeWidgetItem*, int)));
1874
1875     DataTree->topLevelItem(index)->setExpanded(1);
1876     DataTree->topLevelItem(index)->addChild(item);
1877     DataTree->setItemWidget(item, COLUMN_CLOSE_IMAGE, cButton);
1878     DataTree->setItemWidget(item, COLUMN_RELOAD_IMAGE, rButton);
1879
1880     //set the id of the image
1881     QString id = DataTree->topLevelItem(index)->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString();
1882     item->setData(COLUMN_IMAGE_NAME,Qt::UserRole,id.toStdString().c_str());
1883     UpdateTree();
1884     qApp->processEvents();
1885     ImageInfoChanged();
1886     QApplication::restoreOverrideCursor();
1887   } else {
1888     QApplication::restoreOverrideCursor();
1889     QString error = "Cannot import the new image.\n";
1890     error += mSlicerManagers[index]->GetLastError().c_str();
1891     QMessageBox::information(this,tr("Problem reading image !"),error);
1892   }
1893 }
1894 //------------------------------------------------------------------------------
1895
1896
1897 //------------------------------------------------------------------------------
1898 void vvMainWindow::AddROI(int index, QString file)
1899 {
1900   /*
1901   // Get slice manager
1902
1903   // Load image
1904
1905   vvImageReader * mReader = new vvImageReader;
1906   mReader->SetInputFilename(filename.toStdString());
1907   mReader->Update(IMAGE);
1908   if (mReader->GetLastError().size() != 0) {
1909     std::cerr << "Error while reading " << filename.toStdString() << std::endl;
1910     QString error = "Cannot open file \n";
1911     error += mReader->GetLastError().c_str();
1912     QMessageBox::information(this,tr("Reading problem"),error);
1913     delete mReader;
1914     return;
1915   }
1916   vvImage::Pointer roi = mReader->GetOutput();
1917
1918   // Create roi in new tool
1919   vvToolStructureSetManager::AddImage(mCurrentSlicerManager, roi);
1920   */
1921 }
1922 //------------------------------------------------------------------------------
1923
1924 //------------------------------------------------------------------------------
1925 void vvMainWindow::SelectFusionImage()
1926 {
1927   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1928
1929   //check if one fusion image is added
1930   for (int child = 0; child < DataTree->topLevelItem(index)->childCount(); child++)
1931     if (DataTree->topLevelItem(index)->child(child)->data(1,Qt::UserRole).toString() == "fusion") {
1932       QString error = "Cannot add more than one fusion image\n";
1933       error += "Please remove first ";
1934       error += DataTree->topLevelItem(index)->child(child)->data(COLUMN_IMAGE_NAME,Qt::DisplayRole).toString();
1935       QMessageBox::information(this,tr("Problem adding fusion image !"),error);
1936       return;
1937     }
1938
1939   QString Extensions = EXTENSIONS;
1940   Extensions += ";;All Files (*)";
1941   QString file = QFileDialog::getOpenFileName(this,tr("Load Fusion image"),mInputPathName,Extensions);
1942   if (!file.isEmpty())
1943     AddFusionImage(index,file);
1944 }
1945 //------------------------------------------------------------------------------
1946
1947 //------------------------------------------------------------------------------
1948 void vvMainWindow::AddFusionImage(int index, QString file)
1949 {
1950   mInputPathName = itksys::SystemTools::GetFilenamePath(file.toStdString()).c_str();
1951   itk::ImageIOBase::Pointer reader = itk::ImageIOFactory::CreateImageIO(
1952                                        file.toStdString().c_str(), itk::ImageIOFactory::ReadMode);
1953   reader->SetFileName(file.toStdString().c_str());
1954   reader->ReadImageInformation();
1955   std::string component = reader->GetComponentTypeAsString(reader->GetComponentType());
1956   if (reader) {
1957     QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
1958     vvProgressDialog progress("Opening fusion");
1959     qApp->processEvents();
1960
1961     std::string filename = itksys::SystemTools::GetFilenameWithoutExtension(file.toStdString()).c_str();
1962     if (mSlicerManagers[index]->SetFusion(file.toStdString(),
1963                                           reader->GetNumberOfDimensions(), component)) {
1964       //create an item in the tree with good settings
1965       QTreeWidgetItem *item = new QTreeWidgetItem();
1966       item->setData(0,Qt::UserRole,file.toStdString().c_str());
1967       item->setData(1,Qt::UserRole,tr("fusion"));
1968       QFileInfo fileinfo(filename.c_str()); //Do not show the path
1969       item->setData(COLUMN_IMAGE_NAME,Qt::DisplayRole,fileinfo.fileName());
1970       item->setToolTip(COLUMN_IMAGE_NAME,fileinfo.absoluteFilePath());
1971       qApp->processEvents();
1972
1973       for (int j = 1; j <= 4; j++) {
1974         item->setData(j,Qt::CheckStateRole,DataTree->topLevelItem(index)->data(j,Qt::CheckStateRole));
1975         mSlicerManagers[index]->GetSlicer(j-1)->SetActorVisibility("fusion",0,
1976             DataTree->topLevelItem(index)->data(j,Qt::CheckStateRole).toInt());
1977       }
1978
1979       //Create the buttons for reload and close
1980       qApp->processEvents();
1981       QTreePushButton* cButton = new QTreePushButton;
1982       cButton->setItem(item);
1983       cButton->setColumn(COLUMN_CLOSE_IMAGE);
1984       cButton->setToolTip(tr("close image"));
1985       cButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/exit.png")));
1986       connect(cButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
1987               this,SLOT(CloseImage(QTreeWidgetItem*, int)));
1988
1989       QTreePushButton* rButton = new QTreePushButton;
1990       rButton->setItem(item);
1991       rButton->setColumn(COLUMN_RELOAD_IMAGE);
1992       rButton->setToolTip(tr("reload image"));
1993       rButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/rotateright.png")));
1994       connect(rButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
1995               this,SLOT(ReloadImage(QTreeWidgetItem*, int)));
1996
1997       DataTree->topLevelItem(index)->setExpanded(1);
1998       DataTree->topLevelItem(index)->addChild(item);
1999       DataTree->setItemWidget(item, COLUMN_CLOSE_IMAGE, cButton);
2000       DataTree->setItemWidget(item, COLUMN_RELOAD_IMAGE, rButton);
2001
2002       //set the id of the image
2003       QString id = DataTree->topLevelItem(index)->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString();
2004       item->setData(COLUMN_IMAGE_NAME,Qt::UserRole,id.toStdString().c_str());
2005       UpdateTree();
2006       qApp->processEvents();
2007       ImageInfoChanged();
2008       QApplication::restoreOverrideCursor();
2009     } else {
2010       QApplication::restoreOverrideCursor();
2011       QString error = "Cannot import the new image.\n";
2012       error += mSlicerManagers[index]->GetLastError().c_str();
2013       QMessageBox::information(this,tr("Problem reading image !"),error);
2014     }
2015   } else {
2016     QString error = "Cannot import the new image.\n";
2017     QMessageBox::information(this,tr("Problem reading image !"),error);
2018   }
2019 }
2020 //------------------------------------------------------------------------------
2021
2022
2023 //------------------------------------------------------------------------------
2024 void vvMainWindow::OpenField()
2025 {
2026   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2027   //check if a vector field has already been added
2028   for (int child = 0; child < DataTree->topLevelItem(index)->childCount(); child++)
2029     if (DataTree->topLevelItem(index)->child(child)->data(1,Qt::UserRole).toString() == "vector") {
2030       QString error = "Cannot add more than one vector field\n";
2031       error += "Please remove first ";
2032       error += DataTree->topLevelItem(index)->child(child)->data(COLUMN_IMAGE_NAME,Qt::DisplayRole).toString();
2033       QMessageBox::information(this,tr("Problem adding vector field!"),error);
2034       return;
2035     }
2036
2037   QString Extensions = "Images ( *.mhd)";
2038   Extensions += ";;Images ( *.vf)";
2039   QString file = QFileDialog::getOpenFileName(this,tr("Load deformation field"),mInputPathName,Extensions);
2040   if (!file.isEmpty())
2041     AddField(file,index);
2042 }
2043 //------------------------------------------------------------------------------
2044
2045
2046 //------------------------------------------------------------------------------
2047 void vvMainWindow::AddFieldEntry(QString filename,int index,bool from_disk)
2048 {
2049   //create an item in the tree with good settings
2050   QTreeWidgetItem *item = new QTreeWidgetItem();
2051   item->setData(0,Qt::UserRole,filename.toStdString().c_str());
2052   item->setData(1,Qt::UserRole,tr("vector"));
2053   QFileInfo fileinfo(filename); //Do not show the path
2054   item->setData(COLUMN_IMAGE_NAME,Qt::DisplayRole,fileinfo.fileName());
2055   item->setToolTip(COLUMN_IMAGE_NAME,fileinfo.absoluteFilePath());
2056   qApp->processEvents();
2057
2058   for (int j = 1; j <= 4; j++) {
2059     item->setData(j,Qt::CheckStateRole,DataTree->topLevelItem(index)->data(j,Qt::CheckStateRole));
2060     mSlicerManagers[index]->GetSlicer(j-1)->SetActorVisibility("vector",0,
2061         DataTree->topLevelItem(index)->data(j,Qt::CheckStateRole).toInt());
2062   }
2063
2064   //Create the buttons for reload and close
2065   qApp->processEvents();
2066   QTreePushButton* cButton = new QTreePushButton;
2067   cButton->setItem(item);
2068   cButton->setColumn(COLUMN_CLOSE_IMAGE);
2069   cButton->setToolTip(tr("close vector field"));
2070   cButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/exit.png")));
2071   connect(cButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
2072           this,SLOT(CloseImage(QTreeWidgetItem*, int)));
2073
2074   QTreePushButton* rButton = new QTreePushButton;
2075   rButton->setItem(item);
2076   rButton->setColumn(COLUMN_RELOAD_IMAGE);
2077   rButton->setToolTip(tr("reload vector field"));
2078   rButton->setEnabled(from_disk);
2079   rButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/rotateright.png")));
2080   connect(rButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
2081           this,SLOT(ReloadImage(QTreeWidgetItem*, int)));
2082
2083   DataTree->topLevelItem(index)->setExpanded(1);
2084   DataTree->topLevelItem(index)->addChild(item);
2085   DataTree->setItemWidget(item, COLUMN_RELOAD_IMAGE, rButton);
2086   DataTree->setItemWidget(item, COLUMN_CLOSE_IMAGE, cButton);
2087
2088   //set the id of the image
2089   QString id = DataTree->topLevelItem(index)->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString();
2090   item->setData(COLUMN_IMAGE_NAME,Qt::UserRole,id.toStdString().c_str());
2091   UpdateTree();
2092   qApp->processEvents();
2093   ImageInfoChanged();
2094   QApplication::restoreOverrideCursor();
2095 }
2096 //------------------------------------------------------------------------------
2097
2098
2099 //------------------------------------------------------------------------------
2100 void vvMainWindow::AddField(vvImage::Pointer vf,QString file,int index)
2101 {
2102   QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
2103   vvSlicerManager* imageManager = mSlicerManagers[index];
2104   if (imageManager->SetVF(vf,file.toStdString())) {
2105     AddFieldEntry(file,index,false);
2106   } else {
2107     QString error = "Cannot import the vector field for this image.\n";
2108     error += imageManager->GetLastError().c_str();
2109     QMessageBox::information(this,tr("Problem reading VF !"),error);
2110   }
2111   QApplication::restoreOverrideCursor();
2112 }
2113 //------------------------------------------------------------------------------
2114
2115
2116 //------------------------------------------------------------------------------
2117 void vvMainWindow::AddField(QString file,int index)
2118 {
2119   if (QFile::exists(file)) {
2120     mInputPathName = itksys::SystemTools::GetFilenamePath(file.toStdString()).c_str();
2121
2122     //init the progress events
2123     QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
2124     vvProgressDialog progress("Opening " + file.toStdString());
2125     qApp->processEvents();
2126
2127     //read the vector and put it in the current mSlicerManager
2128     vvSlicerManager* imageManager = mSlicerManagers[index];
2129     qApp->processEvents();
2130
2131     std::string filename = itksys::SystemTools::GetFilenameWithoutExtension(file.toStdString()).c_str();
2132     if (imageManager->SetVF(file.toStdString())) {
2133       imageManager->Render();
2134       AddFieldEntry(file,index,true);
2135     } else {
2136       QApplication::restoreOverrideCursor();
2137       QString error = "Cannot import the vector field for this image.\n";
2138       error += imageManager->GetLastError().c_str();
2139       QMessageBox::information(this,tr("Problem reading VF !"),error);
2140     }
2141   } else
2142     QMessageBox::information(this,tr("Problem reading VF !"),"File doesn't exist!");
2143
2144 }
2145 //------------------------------------------------------------------------------
2146
2147
2148 //------------------------------------------------------------------------------
2149 void vvMainWindow::SetVFProperty(int subsampling, int scale, int log, int width, double r, double g, double b)
2150 {
2151   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2152   if (mSlicerManagers[index]->GetSlicer(0)->GetVF()) {
2153     for (int i = 0; i < 4; i++) {
2154       mSlicerManagers[index]->GetSlicer(i)->SetVFSubSampling(subsampling);
2155       mSlicerManagers[index]->GetSlicer(i)->SetVFScale(scale);
2156       mSlicerManagers[index]->GetSlicer(i)->SetVFWidth(width);
2157       mSlicerManagers[index]->GetSlicer(i)->SetVFColor(r,g,b);
2158       if (log > 0)
2159         mSlicerManagers[index]->GetSlicer(i)->SetVFLog(1);
2160       else
2161         mSlicerManagers[index]->GetSlicer(i)->SetVFLog(0);
2162     }
2163   }
2164 }
2165 //------------------------------------------------------------------------------
2166
2167
2168 //------------------------------------------------------------------------------
2169 void vvMainWindow::SetOverlayProperty(int color)
2170 {
2171   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2172   if (mSlicerManagers[index]->GetSlicer(0)->GetOverlay()) {
2173     mSlicerManagers[index]->SetOverlayColor(color);
2174     mSlicerManagers[index]->SetColorMap(0);
2175     mSlicerManagers[index]->Render();
2176   }
2177 }
2178 //------------------------------------------------------------------------------
2179
2180 //------------------------------------------------------------------------------
2181 void vvMainWindow::SetFusionProperty(int opacity, int colormap,double window, double level)
2182 {
2183   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2184   if (mSlicerManagers[index]->GetSlicer(0)->GetFusion()) {
2185     mSlicerManagers[index]->SetFusionOpacity(opacity);
2186     mSlicerManagers[index]->SetFusionColorMap(colormap);
2187     mSlicerManagers[index]->SetFusionWindow(window);
2188     mSlicerManagers[index]->SetFusionLevel(level);
2189     mSlicerManagers[index]->SetColorMap(0);
2190     mSlicerManagers[index]->Render();
2191   }
2192 }
2193 //------------------------------------------------------------------------------
2194
2195 //------------------------------------------------------------------------------
2196 void vvMainWindow::SaveAs()
2197 {
2198   if (DataTree->selectedItems()[0]->data(1,Qt::UserRole).toString() == "vector") {
2199     QMessageBox::warning(this,tr("Unsupported type"),tr("Sorry, saving a vector field is unsupported for the moment"));
2200     return;
2201   }
2202
2203   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2204   int dimension = mSlicerManagers[index]->GetDimension();
2205   QStringList OutputListeFormat;
2206   OutputListeFormat.clear();
2207   if (dimension == 1) {
2208     OutputListeFormat.push_back(".mhd");
2209   }
2210   if (dimension == 2) {
2211     OutputListeFormat.push_back(".bmp");
2212     OutputListeFormat.push_back(".png");
2213     OutputListeFormat.push_back(".jpeg");
2214     OutputListeFormat.push_back(".tif");
2215     OutputListeFormat.push_back(".mhd");
2216     OutputListeFormat.push_back(".hdr");
2217     OutputListeFormat.push_back(".vox");
2218   } else if (dimension == 3) {
2219     OutputListeFormat.push_back(".mhd");
2220     OutputListeFormat.push_back(".hdr");
2221     OutputListeFormat.push_back(".vox");
2222   } else if (dimension == 4) {
2223     OutputListeFormat.push_back(".mhd");
2224   }
2225   QString Extensions = "AllFiles(*.*)";
2226   for (int i = 0; i < OutputListeFormat.count(); i++) {
2227     Extensions += ";;Images ( *";
2228     Extensions += OutputListeFormat[i];
2229     Extensions += ")";
2230   }
2231   QString fileName = QFileDialog::getSaveFileName(this,
2232                      tr("Save As"),
2233                      mSlicerManagers[index]->GetFileName().c_str(),
2234                      Extensions);
2235   if (!fileName.isEmpty()) {
2236     std::string fileformat = itksys::SystemTools::GetFilenameLastExtension(fileName.toStdString());
2237     if (OutputListeFormat.contains(
2238           fileformat.c_str())) {
2239       QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
2240       std::string action = "Saving";
2241       vvProgressDialog progress("Saving "+fileName.toStdString());
2242       qApp->processEvents();
2243       vvImageWriter::Pointer writer = vvImageWriter::New();
2244       writer->SetOutputFileName(fileName.toStdString());
2245       writer->SetInput(mSlicerManagers[index]->GetImage());
2246       writer->Update();
2247       QApplication::restoreOverrideCursor();
2248       if (writer->GetLastError().size()) {
2249         QString error = "Saving did not succeed\n";
2250         error += writer->GetLastError().c_str();
2251         QMessageBox::information(this,tr("Saving Problem"),error);
2252         SaveAs();
2253       }
2254     } else {
2255       QString error = fileformat.c_str();
2256       if (error.isEmpty())
2257         error += "no file format specified !";
2258       else
2259         error += " format unknown !!!\n";
2260       QMessageBox::information(this,tr("Saving Problem"),error);
2261       SaveAs();
2262     }
2263   }
2264 }
2265 //------------------------------------------------------------------------------
2266
2267
2268 //------------------------------------------------------------------------------
2269 void vvMainWindow::AddLink(QString image1,QString image2)
2270 {
2271   unsigned int sm1 = 0;
2272   unsigned int sm2 = 0;
2273
2274   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
2275     if (image1.toStdString() == mSlicerManagers[i]->GetId()) {
2276       mSlicerManagers[i]->AddLink(image2.toStdString());
2277       sm1 = i;
2278     }
2279     if (image2.toStdString() == mSlicerManagers[i]->GetId()) {
2280       mSlicerManagers[i]->AddLink(image1.toStdString());
2281       sm2 = i;
2282     }
2283   }
2284
2285   if (linkPanel->isLinkAll())   {
2286     emit UpdateLinkedNavigation(mSlicerManagers[sm1]->GetId(), mSlicerManagers[mCurrentPickedImageIndex], mSlicerManagers[mCurrentPickedImageIndex]->GetSlicer(0));
2287     emit UpdateLinkedNavigation(mSlicerManagers[sm2]->GetId(), mSlicerManagers[mCurrentPickedImageIndex], mSlicerManagers[mCurrentPickedImageIndex]->GetSlicer(0));
2288   }
2289   else {
2290     emit UpdateLinkedNavigation(mSlicerManagers[sm2]->GetId(), mSlicerManagers[sm1], mSlicerManagers[sm1]->GetSlicer(0));
2291   }
2292 }
2293
2294 //------------------------------------------------------------------------------
2295
2296
2297 //------------------------------------------------------------------------------
2298 void vvMainWindow::RemoveLink(QString image1,QString image2)
2299 {
2300   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
2301     if (image1.toStdString() == mSlicerManagers[i]->GetId()) {
2302       mSlicerManagers[i]->RemoveLink(image2.toStdString());
2303     }
2304     if (image2.toStdString() == mSlicerManagers[i]->GetId()) {
2305       mSlicerManagers[i]->RemoveLink(image1.toStdString());
2306     }
2307   }
2308 }
2309 //------------------------------------------------------------------------------
2310
2311 //------------------------------------------------------------------------------
2312 void vvMainWindow::ChangeImageWithIndexOffset(vvSlicerManager *sm, int slicer, int offset)
2313 {
2314   int index = 0;
2315   while(sm != mSlicerManagers[index])
2316     index++;
2317   index = (index+offset) % mSlicerManagers.size();
2318
2319   QTreeWidgetItem* item = GetItemFromSlicerManager(mSlicerManagers[index]);
2320   //CurrentImageChanged(mSlicerManagers[index]->GetId()); //select new image
2321   item->setData(slicer+1,Qt::CheckStateRole,2);         //change checkbox
2322   DisplayChanged(item,slicer+1);
2323 }
2324 //------------------------------------------------------------------------------
2325
2326 void vvMainWindow::HorizontalSliderMoved(int value,int column, int slicer_index)
2327 {
2328   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
2329     if (DataTree->topLevelItem(i)->data(column,Qt::CheckStateRole).toInt() > 1) {
2330       for (int j = 0; j < 4; j++) {
2331         mSlicerManagers[i]->SetTSliceInSlicer(value,j);
2332         //if (mSlicerManagers[i]->GetSlicer(j)->GetImageActor()->GetVisibility())
2333         //UpdateTSlice(j,value);
2334       }
2335       mSlicerManagers[i]->GetSlicer(slicer_index)->Render();
2336       break;
2337     }
2338   }
2339 }
2340 //------------------------------------------------------------------------------
2341
2342
2343 //------------------------------------------------------------------------------
2344 void vvMainWindow::NOHorizontalSliderMoved()
2345 {
2346   // if (mCurrentTime == NOHorizontalSlider->value()) return;
2347   HorizontalSliderMoved(NOHorizontalSlider->value(),COLUMN_UL_VIEW,0);
2348 //  mCurrentTime = NOHorizontalSlider->value();
2349 }
2350 //------------------------------------------------------------------------------
2351
2352
2353 //------------------------------------------------------------------------------
2354 void vvMainWindow::NEHorizontalSliderMoved()
2355 {
2356   // if (mCurrentTime == NEHorizontalSlider->value()) return;
2357   HorizontalSliderMoved(NEHorizontalSlider->value(),COLUMN_UR_VIEW,1);
2358 //  mCurrentTime = NEHorizontalSlider->value();
2359 }
2360 //------------------------------------------------------------------------------
2361
2362
2363 //------------------------------------------------------------------------------
2364 void vvMainWindow::SOHorizontalSliderMoved()
2365 {
2366   // if (mCurrentTime == SOHorizontalSlider->value()) return;
2367   HorizontalSliderMoved(SOHorizontalSlider->value(),COLUMN_DL_VIEW,2);
2368   // mCurrentTime = SOHorizontalSlider->value();
2369 }
2370 //------------------------------------------------------------------------------
2371
2372
2373 //------------------------------------------------------------------------------
2374 void vvMainWindow::SEHorizontalSliderMoved()
2375 {
2376   // if (mCurrentTime == SEHorizontalSlider->value()) return;
2377   HorizontalSliderMoved(SEHorizontalSlider->value(),COLUMN_DR_VIEW,3);
2378   // mCurrentTime = SEHorizontalSlider->value();
2379 }
2380 //------------------------------------------------------------------------------
2381
2382 //------------------------------------------------------------------------------
2383 void vvMainWindow::NOVerticalSliderChanged()
2384 {
2385   static int value=-1;
2386   if (value == NOVerticalSlider->value()) return;
2387   else value = NOVerticalSlider->value();
2388   //  int value = NOVerticalSlider->value();
2389   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
2390     if (DataTree->topLevelItem(i)->data(COLUMN_UL_VIEW,Qt::CheckStateRole).toInt() > 1) {
2391       if (mSlicerManagers[i]->GetSlicer(0)->GetSlice() != value) {
2392         mSlicerManagers[i]->GetSlicer(0)->SetSlice(value);
2393         mSlicerManagers[i]->VerticalSliderHasChanged(0, value);
2394
2395         // If nor Update/Render -> slider not work
2396         // only render = ok navigation, but for contour Update needed but slower ?
2397
2398         mSlicerManagers[i]->UpdateSlice(0);  // <-- DS add this. Not too much update ? YES. but needed for ImageContour ...
2399         //mSlicerManagers[i]->GetSlicer(0)->Render(); // <-- DS add this, needed for contour, seems ok ? not too slow ?
2400       }
2401       break;
2402     }
2403   }
2404 }
2405 //------------------------------------------------------------------------------
2406
2407
2408 //------------------------------------------------------------------------------
2409 void vvMainWindow::NEVerticalSliderChanged()
2410 {
2411   static int value=-1;
2412   if (value == NEVerticalSlider->value()) return;
2413   else value = NEVerticalSlider->value();
2414   //  int value = NEVerticalSlider->value();
2415   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
2416     if (DataTree->topLevelItem(i)->data(COLUMN_UR_VIEW,Qt::CheckStateRole).toInt() > 1) {
2417       if (mSlicerManagers[i]->GetSlicer(1)->GetSlice() != value) {
2418         mSlicerManagers[i]->GetSlicer(1)->SetSlice(value);
2419         mSlicerManagers[i]->VerticalSliderHasChanged(1, value);
2420         mSlicerManagers[i]->UpdateSlice(1);
2421         //mSlicerManagers[i]->GetSlicer(1)->Render(); // <-- DS add this, needed for contour, seems ok ? not too slow ?
2422       }
2423       break;
2424     }
2425   }
2426 }
2427 //------------------------------------------------------------------------------
2428
2429
2430 //------------------------------------------------------------------------------
2431 void vvMainWindow::SOVerticalSliderChanged()
2432 {
2433   static int value=-1;
2434   if (value == SOVerticalSlider->value()) return;
2435   else value = SOVerticalSlider->value();
2436   //int value = SOVerticalSlider->value();
2437   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
2438     if (DataTree->topLevelItem(i)->data(COLUMN_DL_VIEW,Qt::CheckStateRole).toInt() > 1) {
2439       if (mSlicerManagers[i]->GetSlicer(2)->GetSlice() != value) {
2440         mSlicerManagers[i]->GetSlicer(2)->SetSlice(value);
2441         mSlicerManagers[i]->VerticalSliderHasChanged(2, value);
2442         mSlicerManagers[i]->UpdateSlice(2);
2443         //mSlicerManagers[i]->GetSlicer(2)->Render(); // <-- DS add this, needed for contour, seems ok ? not too slow ?
2444       }
2445       // else { DD("avoid SOVerticalSlider slicer update"); }
2446       break;
2447     }
2448   }
2449 }
2450 //------------------------------------------------------------------------------
2451
2452
2453 //------------------------------------------------------------------------------
2454 void vvMainWindow::SEVerticalSliderChanged()
2455 {
2456   static int value=-1;
2457   if (value == SEVerticalSlider->value()) return;
2458   else value = SEVerticalSlider->value();
2459   // int value = SEVerticalSlider->value();
2460   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
2461     if (DataTree->topLevelItem(i)->data(COLUMN_DR_VIEW,Qt::CheckStateRole).toInt() > 1) {
2462       if (mSlicerManagers[i]->GetSlicer(3)->GetSlice() != value) {
2463         mSlicerManagers[i]->GetSlicer(3)->SetSlice(value);
2464         mSlicerManagers[i]->VerticalSliderHasChanged(3, value);
2465         mSlicerManagers[i]->UpdateSlice(3);
2466         //mSlicerManagers[i]->GetSlicer(3)->Render(); // <-- DS add this, needed for contour, seems ok ? not too slow ?
2467       }
2468       break;
2469     }
2470   }
2471 }
2472 //------------------------------------------------------------------------------
2473
2474
2475 //------------------------------------------------------------------------------
2476 void vvMainWindow::UpdateSlice(int slicer, int slice)
2477 {
2478   // DD("vvMainWindow::UpdateSlice");
2479 //   DD(slicer);
2480 //   DD(slice);
2481   if (slicer == 0) {
2482     //    if (slice != NOVerticalSlider->value())
2483     NOVerticalSlider->setValue(slice);
2484   } else {
2485     if (slicer == 1)
2486       NEVerticalSlider->setValue(slice);
2487     else {
2488       if (slicer == 2)
2489         SOVerticalSlider->setValue(slice);
2490       else {
2491         if (slicer == 3)
2492           SEVerticalSlider->setValue(slice);
2493       }
2494     }
2495   }
2496   // DD("vvMainWindow:UpdateSlice END");
2497 }
2498 //------------------------------------------------------------------------------
2499
2500
2501 //------------------------------------------------------------------------------
2502 void vvMainWindow::UpdateTSlice(int slicer, int slice)
2503 {
2504   switch (slicer) {
2505   case 0:
2506     NOHorizontalSlider->setValue(slice);
2507     break;
2508   case 1:
2509     NEHorizontalSlider->setValue(slice);
2510     break;
2511   case 2:
2512     SOHorizontalSlider->setValue(slice);
2513     break;
2514   case 3:
2515     SEHorizontalSlider->setValue(slice);
2516     break;
2517   }
2518 }
2519 //------------------------------------------------------------------------------
2520
2521
2522 //------------------------------------------------------------------------------
2523 void vvMainWindow::UpdateSliceRange(int slicer, int min, int max, int tmin, int tmax)
2524 {
2525   int position = int((min+max)/2);
2526   int tPosition = int((tmin+tmax)/2);
2527   if (slicer == 0) {
2528     NOVerticalSlider->setValue(position);
2529     NOVerticalSlider->setRange(min,max);
2530     NOHorizontalSlider->setRange(tmin,tmax);
2531     NOHorizontalSlider->setValue(tPosition);
2532   } else if (slicer == 1) {
2533     NEVerticalSlider->setValue(position);
2534     NEVerticalSlider->setRange(min,max);
2535     NEHorizontalSlider->setRange(tmin,tmax);
2536     NEHorizontalSlider->setValue(tPosition);
2537   } else if (slicer == 2) {
2538     SOVerticalSlider->setValue(position);
2539     SOVerticalSlider->setRange(min,max);
2540     SOHorizontalSlider->setRange(tmin,tmax);
2541     SOHorizontalSlider->setValue(tPosition);
2542   } else if (slicer == 3) {
2543     SEVerticalSlider->setValue(position);
2544     SEVerticalSlider->setRange(min,max);
2545     SEHorizontalSlider->setRange(tmin,tmax);
2546     SEHorizontalSlider->setValue(tPosition);
2547   }
2548 }
2549 //------------------------------------------------------------------------------
2550
2551
2552 //------------------------------------------------------------------------------
2553 void vvMainWindow::SaveNOScreenshot()
2554 {
2555   SaveScreenshot(NOViewWidget);
2556 }
2557 //------------------------------------------------------------------------------
2558
2559
2560 //------------------------------------------------------------------------------
2561 void vvMainWindow::SaveNEScreenshot()
2562 {
2563   SaveScreenshot(NEViewWidget);
2564 }
2565 //------------------------------------------------------------------------------
2566
2567
2568 //------------------------------------------------------------------------------
2569 void vvMainWindow::SaveSOScreenshot()
2570 {
2571   SaveScreenshot(SOViewWidget);
2572 }
2573 //------------------------------------------------------------------------------
2574
2575
2576 //------------------------------------------------------------------------------
2577 void vvMainWindow::SaveSEScreenshot()
2578 {
2579   SaveScreenshot(SEViewWidget);
2580 }
2581 //------------------------------------------------------------------------------
2582
2583
2584 //------------------------------------------------------------------------------
2585 void vvMainWindow::SaveScreenshot(QVTKWidget *widget)
2586 {
2587   QString Extensions = "Images( *.png);;";
2588   Extensions += "Images( *.jpg);;";
2589   Extensions += "Images( *.bmp);;";
2590   Extensions += "Images( *.tif);;";
2591   Extensions += "Images( *.ppm)";
2592 #ifdef VTK_USE_FFMPEG_ENCODER
2593   Extensions += "Images( *.avi)";
2594 #endif
2595 #ifdef VTK_USE_MPEG2_ENCODER
2596   Extensions += "Images( *.mpg)";
2597 #endif
2598
2599   int smIndex=GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2600   QString fileName = QFileDialog::getSaveFileName(this,
2601                      tr("Save As"),
2602                      itksys::SystemTools::GetFilenamePath(mSlicerManagers[smIndex]->GetFileName()).c_str(),
2603                      Extensions);
2604
2605   if (!fileName.isEmpty()) {
2606     vtkSmartPointer<vtkWindowToImageFilter> w2i = vtkSmartPointer<vtkWindowToImageFilter>::New();
2607     w2i->SetInput(widget->GetRenderWindow());
2608     w2i->Update();
2609     vtkImageData *image = w2i->GetOutput();
2610
2611     const char *ext = fileName.toStdString().c_str() + strlen(fileName.toStdString().c_str()) - 4;
2612     if (!strcmp(ext, ".bmp")) {
2613       vtkBMPWriter *bmp = vtkBMPWriter::New();
2614       bmp->SetInput(image);
2615       bmp->SetFileName(fileName.toStdString().c_str());
2616       bmp->Write();
2617       bmp->Delete();
2618     } else if (!strcmp(ext, ".tif")) {
2619       vtkTIFFWriter *tif = vtkTIFFWriter::New();
2620       tif->SetInput(image);
2621       tif->SetFileName(fileName.toStdString().c_str());
2622       tif->Write();
2623       tif->Delete();
2624     } else if (!strcmp(ext, ".ppm")) {
2625       vtkPNMWriter *pnm = vtkPNMWriter::New();
2626       pnm->SetInput(image);
2627       pnm->SetFileName(fileName.toStdString().c_str());
2628       pnm->Write();
2629       pnm->Delete();
2630     } else if (!strcmp(ext, ".png")) {
2631       vtkPNGWriter *png = vtkPNGWriter::New();
2632       png->SetInput(image);
2633       png->SetFileName(fileName.toStdString().c_str());
2634       png->Write();
2635       png->Delete();
2636     } else if (!strcmp(ext, ".jpg")) {
2637       vtkJPEGWriter *jpg = vtkJPEGWriter::New();
2638       jpg->SetInput(image);
2639       jpg->SetFileName(fileName.toStdString().c_str());
2640       jpg->Write();
2641       jpg->Delete();
2642 #ifdef VTK_USE_FFMPEG_ENCODER
2643     } else if (!strcmp(ext, ".avi")) {
2644       vtkFFMPEGWriter *mpg = vtkFFMPEGWriter::New();
2645       mpg->SetInput(image);
2646       mpg->SetFileName(fileName.toStdString().c_str());
2647       mpg->SetQuality(2);
2648       mpg->SetRate(5);
2649       mpg->Start();
2650
2651       vvImage * vvImg = mSlicerManagers[smIndex]->GetImage();
2652       int nSlice = vvImg->GetVTKImages().size();
2653       for(int i=0; i<nSlice; i++)
2654       {
2655         mSlicerManagers[smIndex]->SetNextTSlice(0);
2656         vtkSmartPointer<vtkWindowToImageFilter> w2i = vtkSmartPointer<vtkWindowToImageFilter>::New();
2657         w2i->SetInput(widget->GetRenderWindow());
2658         w2i->Update();
2659         mpg->SetInput(w2i->GetOutput());
2660         mpg->Write();
2661       }
2662       mpg->End();
2663       mpg->Delete();
2664 #endif
2665 #ifdef VTK_USE_MPEG2_ENCODER
2666     } else if (!strcmp(ext, ".mpg")) {
2667       vtkMPEG2Writer *mpg = vtkMPEG2Writer::New();
2668       mpg->SetInput(image);
2669       mpg->SetFileName(fileName.toStdString().c_str());
2670       mpg->Start();
2671
2672       vvImage * vvImg = mSlicerManagers[smIndex]->GetImage();
2673       int nSlice = vvImg->GetVTKImages().size();
2674       for(int i=0; i<nSlice; i++)
2675       {
2676         mSlicerManagers[smIndex]->SetNextTSlice(0);
2677         vtkSmartPointer<vtkWindowToImageFilter> w2i = vtkSmartPointer<vtkWindowToImageFilter>::New();
2678         w2i->SetInput(widget->GetRenderWindow());
2679         w2i->Update();
2680         mpg->SetInput(w2i->GetOutput());
2681         mpg->Write();
2682       }
2683       mpg->End();
2684       mpg->Delete();
2685 #endif
2686     } else {
2687       QMessageBox::information(this,tr("Problem saving screenshot !"),tr("Cannot save image.\nPlease set a file extension !!!"));
2688     }
2689   }
2690 }
2691 //------------------------------------------------------------------------------
2692
2693
2694 //------------------------------------------------------------------------------
2695 void vvMainWindow::GoToCursor()
2696 {
2697   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2698   for (int column = 1; column < 5; column++) {
2699     if (DataTree->selectedItems()[0]->data(column,Qt::CheckStateRole).toInt() > 1) {
2700       double* cursorPos = mSlicerManagers[index]->GetSlicer(column-1)->GetCursorPosition();
2701       mSlicerManagers[index]->GetSlicer(column-1)->SetCurrentPosition(
2702         cursorPos[0],cursorPos[1],cursorPos[2],cursorPos[3]);
2703       mSlicerManagers[index]->UpdateViews(1,column-1);
2704       mSlicerManagers[index]->UpdateLinked(column-1);
2705       break;
2706     }
2707   }
2708 }
2709 //------------------------------------------------------------------------------
2710
2711 //------------------------------------------------------------------------------
2712 void vvMainWindow::PlayPause()
2713 {
2714   if (playMode) {
2715     playMode = 0;
2716     playButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/player_play.png")));
2717     ImageInfoChanged();
2718     return;
2719   } else {
2720     int image_number=DataTree->topLevelItemCount();
2721     bool has_temporal;
2722     for (int i=0; i<image_number; i++)
2723       if (mSlicerManagers[i]->GetImage()->GetVTKImages().size() > 1) {
2724         has_temporal=true;
2725         break;
2726       }
2727     if (has_temporal) {
2728       playMode = 1;
2729       playButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/player_pause.png")));
2730       QTimer::singleShot(1000/mFrameRate, this, SLOT(PlayNext()));
2731     }
2732   }
2733 }
2734 //------------------------------------------------------------------------------
2735
2736 //------------------------------------------------------------------------------
2737 void vvMainWindow::PlayNext()
2738 {
2739   if (playMode && !this->isHidden()) {
2740     int image_number=DataTree->topLevelItemCount();
2741     ///Only play one slicer per SM, and only if the SM is being displayed
2742     for (int i=0; i<image_number; i++)
2743       for (int j=0; j<4; j++)
2744         if (mSlicerManagers[i]->GetImage()->GetVTKImages().size() > 1 &&
2745             DataTree->topLevelItem(i)->data(j+1,Qt::CheckStateRole).toInt() > 0) {
2746           mSlicerManagers[i]->SetNextTSlice(j);
2747           break;
2748         }
2749     QTimer::singleShot(1000/mFrameRate, this, SLOT(PlayNext()));
2750   }
2751 }
2752 //------------------------------------------------------------------------------
2753
2754 void vvMainWindow::ShowLastImage()
2755 {
2756   if (mSlicerManagers.size() > 1) {
2757     QTreeWidgetItem * item=DataTree->topLevelItem(DataTree->topLevelItemCount()-1);
2758     CurrentImageChanged(mSlicerManagers.back()->GetId()); //select new image
2759     item->setData(1,Qt::CheckStateRole,2); //show the new image in the first panel
2760     DisplayChanged(item,1);
2761   }
2762 }
2763
2764 //------------------------------------------------------------------------------
2765 void vvMainWindow::UpdateRenderWindows()
2766 {
2767   if (NOViewWidget->GetRenderWindow()) NOViewWidget->GetRenderWindow()->Render();
2768   if (NEViewWidget->GetRenderWindow()) NEViewWidget->GetRenderWindow()->Render();
2769   if (SOViewWidget->GetRenderWindow()) SOViewWidget->GetRenderWindow()->Render();
2770   if (SEViewWidget->GetRenderWindow()) SEViewWidget->GetRenderWindow()->Render();
2771 }
2772 //------------------------------------------------------------------------------
2773
2774 //------------------------------------------------------------------------------
2775 void vvMainWindow::SegmentationOnCurrentImage()
2776 {
2777   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2778
2779   vvSegmentationDialog segmentation;
2780   segmentation.SetImage(mSlicerManagers[index]->GetSlicer(0)->GetImage());
2781   segmentation.exec();
2782 }
2783 //------------------------------------------------------------------------------
2784
2785 void vvMainWindow::SurfaceViewerLaunch()
2786 {
2787   vvSurfaceViewerDialog surfaceViewer;
2788   surfaceViewer.exec();
2789 }
2790 //------------------------------------------------------------------------------
2791
2792
2793 //------------------------------------------------------------------------------
2794 int vvMainWindow::GetImageDuplicateFilenameNumber(std::string filename)
2795 {
2796   int number=0;
2797   for(unsigned int l=0; l<mSlicerManagers.size(); l++) {
2798     vvSlicerManager * v = mSlicerManagers[l];
2799     if (v->GetBaseFileName() ==
2800         vtksys::SystemTools::GetFilenameName(vtksys::SystemTools::GetFilenameWithoutLastExtension(filename))) {
2801       number = std::max(number, v->GetBaseFileNameNumber()+1);
2802     }
2803   }
2804   return number;
2805 }
2806 //------------------------------------------------------------------------------
2807
2808
2809 //------------------------------------------------------------------------------
2810 vvSlicerManager* vvMainWindow::AddImage(vvImage::Pointer image,std::string filename)
2811 {
2812   // Change filename if another image exist with the same name
2813   int number = GetImageDuplicateFilenameNumber(filename);
2814
2815   // Create new SliceManager
2816   vvSlicerManager* slicer_manager = new vvSlicerManager(4);
2817   slicer_manager->SetImage(image);//, IMAGE, number);
2818   //  filename = filename+"_"+clitk::toString(number);
2819   slicer_manager->SetFilename(filename, number);
2820   mSlicerManagers.push_back(slicer_manager);
2821
2822   //create an item in the tree with good settings
2823   QTreeWidgetItem *item = new QTreeWidgetItem();
2824   item->setData(0,Qt::UserRole,slicer_manager->GetFileName().c_str());//files[i].c_str());
2825   item->setData(COLUMN_IMAGE_NAME,Qt::DisplayRole,slicer_manager->GetFileName().c_str());//filename.c_str());
2826   qApp->processEvents();
2827
2828   for (int j = 1; j <= 4; j++) item->setData(j,Qt::CheckStateRole,1);
2829
2830   //Create the buttons for reload and close
2831   qApp->processEvents();
2832   QTreePushButton* cButton = new QTreePushButton;
2833   cButton->setItem(item);
2834   cButton->setColumn(COLUMN_CLOSE_IMAGE);
2835   cButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/exit.png")));
2836   connect(cButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
2837           this,SLOT(CloseImage(QTreeWidgetItem*, int)));
2838
2839   QTreePushButton* rButton = new QTreePushButton;
2840   rButton->setItem(item);
2841   rButton->setColumn(COLUMN_RELOAD_IMAGE);
2842   rButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/rotateright.png")));
2843   rButton->setEnabled(0);
2844   connect(rButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
2845           this,SLOT(ReloadImage(QTreeWidgetItem*, int)));
2846
2847   DataTree->addTopLevelItem(item);
2848   DataTree->setItemWidget(item, COLUMN_CLOSE_IMAGE, cButton);
2849   DataTree->setItemWidget(item, COLUMN_RELOAD_IMAGE, rButton);
2850
2851   //set the id of the image
2852   QString id = slicer_manager->GetFileName().c_str() + QString::number(mSlicerManagers.size()-1);
2853   item->setData(COLUMN_IMAGE_NAME,Qt::UserRole,id.toStdString().c_str());
2854   mSlicerManagers.back()->SetId(id.toStdString());
2855
2856   linkPanel->addImage(slicer_manager->GetFileName().c_str()// filename
2857                       , id.toStdString());
2858
2859   connect(mSlicerManagers.back(), SIGNAL(currentImageChanged(std::string)),
2860           this, SLOT(CurrentImageChanged(std::string)));
2861   connect(mSlicerManagers.back(), SIGNAL(currentPickedImageChanged(std::string)),
2862           this, SLOT(CurrentPickedImageChanged(std::string)));
2863   connect(mSlicerManagers.back(), SIGNAL(UpdatePosition(int, double, double, double, double, double, double, double)),
2864           this, SLOT(MousePositionChanged(int,double, double, double, double, double, double, double)));
2865   connect(mSlicerManagers.back(), SIGNAL(UpdateVector(int, double, double, double, double)),
2866           this, SLOT(VectorChanged(int,double,double,double, double)));
2867   connect(mSlicerManagers.back(), SIGNAL(UpdateOverlay(int, double, double)),
2868           this, SLOT(OverlayChanged(int,double,double)));
2869   connect(mSlicerManagers.back(), SIGNAL(UpdateFusion(int, double)),
2870           this, SLOT(FusionChanged(int,double)));
2871   connect(mSlicerManagers.back(), SIGNAL(UpdateWindows(int, int, int)),
2872           this,SLOT(WindowsChanged(int, int, int)));
2873   connect(mSlicerManagers.back(), SIGNAL(WindowLevelChanged(double, double,int, int)),
2874           this,SLOT(WindowLevelChanged(double, double, int, int)));
2875   connect(mSlicerManagers.back(), SIGNAL(UpdateSlice(int,int)),
2876           this,SLOT(UpdateSlice(int,int)));
2877   connect(mSlicerManagers.back(), SIGNAL(UpdateTSlice(int, int)),
2878           this,SLOT(UpdateTSlice(int, int)));
2879   connect(mSlicerManagers.back(), SIGNAL(UpdateSliceRange(int,int,int,int,int)),
2880           this,SLOT(UpdateSliceRange(int,int,int,int,int)));
2881   connect(mSlicerManagers.back(), SIGNAL(UpdateLinkManager(std::string,int,double,double,double,int)),
2882           this,SLOT(UpdateLinkManager(std::string,int,double,double,double,int)));
2883   connect(mSlicerManagers.back(), SIGNAL(UpdateLinkedNavigation(std::string,vvSlicerManager*,vvSlicer*)),
2884           this,SLOT(UpdateLinkedNavigation(std::string,vvSlicerManager*,vvSlicer*)));
2885   connect(mSlicerManagers.back(), SIGNAL(ChangeImageWithIndexOffset(vvSlicerManager*,int,int)),
2886           this,SLOT(ChangeImageWithIndexOffset(vvSlicerManager*,int,int)));
2887   connect(mSlicerManagers.back(), SIGNAL(LandmarkAdded()),landmarksPanel,SLOT(AddPoint()));
2888   UpdateTree();
2889   qApp->processEvents();
2890   InitSlicers();
2891   ShowLastImage();
2892   InitDisplay();
2893   qApp->processEvents();
2894
2895   // End
2896   ImageInfoChanged();
2897   return slicer_manager;
2898 }
2899 //------------------------------------------------------------------------------
2900
2901
2902 //------------------------------------------------------------------------------
2903 void vvMainWindow::UpdateCurrentSlicer()
2904 {
2905   int index = -1;
2906   if (DataTree->selectedItems().size() > 0) {
2907     index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2908   }
2909   mSlicerManagerCurrentIndex = index;
2910 }
2911 //------------------------------------------------------------------------------
2912