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 "vvSaveState.h"
  49 #include "vvReadState.h"
  50 #include "clitkConfiguration.h"
  51
  52 // ITK include
  53 #include <itkImage.h>
  54 #include <itkImageFileReader.h>
  55 #include <itkByteSwapper.h>
  56 #include <itkCommand.h>
  57 #include <itkNumericSeriesFileNames.h>
  58
  59 // VTK include
  60 #include <vtkImageData.h>
  61 #include <vtkImageActor.h>
  62 #include <vtkCornerAnnotation.h>
  63 #include <vtkRenderWindow.h>
  64 #include <vtkRenderWindowInteractor.h>
  65 #include <vtkRenderer.h>
  66 #include <vtkRendererCollection.h>
  67 #include <vtkWindowToImageFilter.h>
  68 #include <vtkBMPWriter.h>
  69 #include <vtkTIFFWriter.h>
  70 #include <vtkPNMWriter.h>
  71 #include <vtkPNGWriter.h>
  72 #include <vtkJPEGWriter.h>
  73 #include <vtkGenericMovieWriter.h>
  74 #ifdef CLITK_EXPERIMENTAL
  75 #  include <vvAnimatedGIFWriter.h>
  76 #endif
  77 #ifdef VTK_USE_VIDEO_FOR_WINDOWS
  78 #  include <vtkAVIWriter.h>
  79 #endif
  80 #ifdef VTK_USE_FFMPEG_ENCODER
  81 #  include <vtkFFMPEGWriter.h>
  82 #endif
  83 #ifdef VTK_USE_MPEG2_ENCODER
  84 #  include <vtkMPEG2Writer.h>
  85 #endif
  86 #include <vtkMatrix4x4.h>
  87 #include <vtkTransform.h>
  88
  89 // Standard includes
  90 #include <iostream>
  91 #include <fstream>
  92 #include <sstream>
  93 #include <iomanip>
  94
  95 #define COLUMN_TREE 0
  96 #define COLUMN_UL_VIEW 1
  97 #define COLUMN_UR_VIEW 2
  98 #define COLUMN_DL_VIEW 3
  99 #define COLUMN_DR_VIEW 4
 100 #define COLUMN_CLOSE_IMAGE 5
 101 #define COLUMN_RELOAD_IMAGE 6
 102 #define COLUMN_IMAGE_NAME 7
 103
 104 #ifdef CLITK_PRIVATE_FEATURES
 105 #define EXTENSIONS "Images ( *.bmp *.png *.jpeg *.jpg *.tif *.mhd *.mha *.hdr *.vox *.his *.xdr *.SCAN *.nii *.nrrd *.nhdr *.refscan *.nii.gz *.usf *.svl)"
 106 #else
 107 #define EXTENSIONS "Images ( *.bmp *.png *.jpeg *.jpg *.tif *.mhd *.mha *.hdr *.vox *.his *.xdr *.SCAN *.nii *.nrrd *.nhdr *.refscan *.nii.gz)"
 108 #endif
 109
 110
 111 /*Data Tree values
 112 0,Qt::UserRole full filename
 113 1,Qt::CheckStateRole checkbutton UL View
 114 1,Qt::UserRole overlay, fusion or vector
 115 2,Qt::CheckStateRole checkbutton UR View
 116 3,Qt::CheckStateRole checkbutton DL View
 117 4,Qt::CheckStateRole checkbutton DR View
 118 5,0  short filename
 119 5,Qt::UserRole mSlicerManager id*/
 120
 121 //------------------------------------------------------------------------------
 122 vvMainWindow::vvMainWindow():vvMainWindowBase()
 123 {
 124   setupUi(this); // this sets up the GUI
 125
 126   mInputPathName = "";
 127   mMenuTools = menuTools;
 128   //  mMenuSegmentation = menuSegmentation;
 129   mContextMenu = &contextMenu;
 130   mMenuExperimentalTools = menuExperimental;
 131   mMainWidget = this;
 132   mCurrentTime = -1;
 133   mCurrentSelectedImageId = "";
 134   mCurrentPickedImageId = "";
 135   mCurrentPickedImageIndex = 0;
 136
 137   //Init the contextMenu
 138   this->setContextMenuPolicy(Qt::CustomContextMenu);
 139   contextActions.resize(0);
 140   QAction* actionOpen_new_image = contextMenu.addAction(QIcon(QString::fromUtf8(":/common/icons/fileopen.png")),
 141     tr("O&pen new Image"));
 142   actionOpen_new_image->setShortcut(QKeySequence(tr("Ctrl+O")));
 143   connect(actionOpen_new_image,SIGNAL(triggered()),this,SLOT(OpenImages()));
 144   contextActions.push_back(actionOpen_new_image);
 145   contextMenu.addSeparator();
 146
 147   QAction* actionClose_Image = contextMenu.addAction(QIcon(QString::fromUtf8(":/common/icons/exit.png")),
 148     tr("Close Current Image"));
 149   connect(actionClose_Image,SIGNAL(triggered()),this,SLOT(CloseImage()));
 150   contextActions.push_back(actionClose_Image);
 151
 152   QAction* actionReload_image = contextMenu.addAction(QIcon(QString::fromUtf8(":/common/icons/rotateright.png")),
 153     tr("Reload Current Image"));
 154   connect(actionReload_image,SIGNAL(triggered()),this,SLOT(ReloadImage()));
 155   contextActions.push_back(actionReload_image);
 156
 157   QAction* actionSave_image = contextMenu.addAction(QIcon(QString::fromUtf8(":/common/icons/filesave.png")),
 158     tr("Save Current Image"));
 159   connect(actionSave_image,SIGNAL(triggered()),this,SLOT(SaveAs()));
 160   contextActions.push_back(actionSave_image);
 161
 162   QAction* actionSave_state = contextMenu.addAction(QIcon(QString::fromUtf8(":/common/icons/filesave.png")),
 163     tr("Save Current State"));
 164   connect(actionSave_state,SIGNAL(triggered()),this,SLOT(SaveCurrentState()));
 165   contextActions.push_back(actionSave_state);
 166
 167   QAction* actionRead_state = contextMenu.addAction(QIcon(QString::fromUtf8(":/common/icons/filesave.png")),
 168     tr("Read Saved State"));
 169   connect(actionRead_state,SIGNAL(triggered()),this,SLOT(ReadSavedState()));
 170   contextActions.push_back(actionRead_state);
 171
 172   contextMenu.addSeparator();
 173
 174   contextMenu.addAction(actionAdd_VF_to_current_Image);
 175   contextActions.push_back(actionAdd_VF_to_current_Image);
 176
 177   //QAction* actionAdd_Overlay_to_current_Image = menuOverlay->addAction(QIcon(QString::fromUtf8(":/common/icons/GPSup.png")),
 178   //    tr("Add overlay image to current image"));
 179   contextMenu.addAction(actionAdd_overlay_image_to_current_image);
 180   contextActions.push_back(actionAdd_overlay_image_to_current_image);
 181
 182   contextMenu.addAction(actionAdd_fusion_image);
 183   contextActions.push_back(actionAdd_fusion_image);
 184
 185 #ifdef CLITK_EXPERIMENTAL
 186   contextMenu.addAction(actionAdd_USSequence_toCT);
 187   contextActions.push_back(actionAdd_USSequence_toCT);
 188 #endif
 189
 190
 191   contextMenu.addSeparator();
 192   QAction* actionResetMatrix = contextMenu.addAction(QIcon(QString::fromUtf8(":/common/icons/identity.png")),
 193     tr("Reset transformation to identity"));
 194   connect(actionResetMatrix, SIGNAL(triggered()), this,SLOT(ResetTransformationToIdentity()));
 195
 196   // TRIAL DS
 197   /*
 198   QMenu * m = new QMenu(menubar);
 199   m->setTitle("TOTO");
 200   //  m->setObjectName(QString::fromUtf8("TOTOTO"));
 201   contextMenu.addMenu(m);
 202   QAction * a = m->addAction(QIcon(QString::fromUtf8(":/common/icons/GPSup.png")),
 203   tr("BIDON"));
 204   QAction * b = m->addAction(QIcon(QString::fromUtf8(":/common/icons/GPSup.png")),
 205   tr("BIDON2"));
 206   m->addAction(a);
 207   m->addAction(b);
 208   connect(a,SIGNAL(triggered()),this,SLOT(AddFusionImage()));
 209   */
 210
 211   //init the DataTree
 212   mSlicerManagers.resize(0);
 213
 214   QStringList header;
 215   header.append("");
 216   header.append("TL");
 217   header.append("TR");
 218   header.append("BL");
 219   header.append("BR");
 220   header.append("");
 221   header.append("");
 222   header.append("Name");
 223
 224   DataTree->setHeaderLabels(header);
 225   DataTree->resizeColumnToContents(COLUMN_TREE);
 226   DataTree->resizeColumnToContents(COLUMN_UL_VIEW);
 227   DataTree->resizeColumnToContents(COLUMN_UR_VIEW);
 228   DataTree->resizeColumnToContents(COLUMN_DL_VIEW);
 229   DataTree->resizeColumnToContents(COLUMN_DR_VIEW);
 230   DataTree->resizeColumnToContents(COLUMN_CLOSE_IMAGE);
 231   DataTree->resizeColumnToContents(COLUMN_RELOAD_IMAGE);
 232   DataTree->resizeColumnToContents(COLUMN_IMAGE_NAME);
 233
 234   viewMode = 1;
 235   documentation = new vvDocumentation();
 236   help_dialog = new vvHelpDialog();
 237   dicomSeriesSelector = new vvDicomSeriesSelector();
 238
 239   inverseButton->setEnabled(0);
 240   actionAdd_overlay_image_to_current_image->setEnabled(0);
 241   actionSave_As->setEnabled(0);
 242   actionAdd_VF_to_current_Image->setEnabled(0);
 243   actionAdd_fusion_image->setEnabled(0);
 244   actionAdd_USSequence_toCT->setEnabled(0);
 245
 246   //init the sliders
 247   verticalSliders.push_back(NOVerticalSlider);
 248   verticalSliders.push_back(NEVerticalSlider);
 249   verticalSliders.push_back(SOVerticalSlider);
 250   verticalSliders.push_back(SEVerticalSlider);
 251
 252   for (int i =0; i < 4; i++)
 253     verticalSliders[i]->hide();
 254
 255   horizontalSliders.push_back(NOHorizontalSlider);
 256   horizontalSliders.push_back(NEHorizontalSlider);
 257   horizontalSliders.push_back(SOHorizontalSlider);
 258   horizontalSliders.push_back(SEHorizontalSlider);
 259
 260   for (int i =0; i < 4; i++)
 261     horizontalSliders[i]->hide();
 262
 263
 264   connect(NOVerticalSlider,SIGNAL(valueChanged(int)),this,SLOT(NOVerticalSliderChanged()));
 265   connect(NEVerticalSlider,SIGNAL(valueChanged(int)),this,SLOT(NEVerticalSliderChanged()));
 266   connect(SOVerticalSlider,SIGNAL(valueChanged(int)),this,SLOT(SOVerticalSliderChanged()));
 267   connect(SEVerticalSlider,SIGNAL(valueChanged(int)),this,SLOT(SEVerticalSliderChanged()));
 268
 269   connect(NOHorizontalSlider,SIGNAL(valueChanged(int)),this,SLOT(NOHorizontalSliderMoved()));
 270   connect(NEHorizontalSlider,SIGNAL(valueChanged(int)),this,SLOT(NEHorizontalSliderMoved()));
 271   connect(SOHorizontalSlider,SIGNAL(valueChanged(int)),this,SLOT(SOHorizontalSliderMoved()));
 272   connect(SEHorizontalSlider,SIGNAL(valueChanged(int)),this,SLOT(SEHorizontalSliderMoved()));
 273
 274   //connect everything
 275   connect(actionCompute_mid_position_image,SIGNAL(triggered()),this,SLOT(ComputeMidPosition()));
 276   connect(actionDeformable_Registration,SIGNAL(triggered()),this,SLOT(ComputeDeformableRegistration()));
 277   connect(actionWarp_image_with_vector_field,SIGNAL(triggered()),this,SLOT(WarpImage()));
 278   connect(actionLoad_images,SIGNAL(triggered()),this,SLOT(OpenImages()));
 279   connect(actionOpen_Dicom,SIGNAL(triggered()),this,SLOT(OpenDicom()));
 280   connect(actionOpen_Dicom_Struct,SIGNAL(triggered()),this,SLOT(OpenDCStructContour()));
 281   connect(actionOpen_VTK_contour,SIGNAL(triggered()),this,SLOT(OpenVTKContour()));
 282   connect(actionOpen_Multiple_Images_As_One,SIGNAL(triggered()),this,SLOT(MergeImages()));
 283   connect(actionSlice_Image_As_Multiple_Images,SIGNAL(triggered()),this,SLOT(SliceImages()));
 284   connect(actionOpen_Image_With_Time,SIGNAL(triggered()),this,SLOT(OpenImageWithTime()));
 285   connect(actionMerge_images_as_n_dim_t, SIGNAL(triggered()), this, SLOT(MergeImagesWithTime()));
 286   connect(actionSave_As,SIGNAL(triggered()),this,SLOT(SaveAs()));
 287   connect(actionSave_current_state,SIGNAL(triggered()),this,SLOT(SaveCurrentState()));
 288   connect(actionRead_saved_state,SIGNAL(triggered()),this,SLOT(ReadSavedState()));
 289   connect(actionExit,SIGNAL(triggered()),this,SLOT(close()));
 290   connect(actionAdd_VF_to_current_Image,SIGNAL(triggered()),this,SLOT(OpenField()));
 291   connect(actionAdd_fusion_image,SIGNAL(triggered()),this,SLOT(SelectFusionImage()));
 292   connect(actionAdd_overlay_image_to_current_image,SIGNAL(triggered()), this,SLOT(SelectOverlayImage()));
 293   connect(actionAdd_USSequence_toCT,SIGNAL(triggered()), this,SLOT(SelectFusionSequence()));
 294   connect(actionNavigation_Help,SIGNAL(triggered()),this,SLOT(ShowHelpDialog()));
 295   connect(actionDocumentation,SIGNAL(triggered()),this,SLOT(ShowDocumentation()));
 296   connect(actionRegister_vv,SIGNAL(triggered()),this,SLOT(PopupRegisterForm()));
 297
 298   connect(overlayPanel, SIGNAL(FusionSequenceCorrespondancesButtonPressed()), this, SLOT(SelectFusionSequenceCorrespondances()));
 299
 300
 301   ///////////////////////////////////////////////
 302   connect(actionSegmentation,SIGNAL(triggered()),this,SLOT(SegmentationOnCurrentImage()));
 303   connect(actionSurface_Viewer,SIGNAL(triggered()),this,SLOT(SurfaceViewerLaunch()));
 304   ///////////////////////////////////////////////
 305
 306   actionNorth_East_Window->setEnabled(0);
 307   actionNorth_West_Window->setEnabled(0);
 308   actionSouth_East_Window->setEnabled(0);
 309   actionSouth_West_Window->setEnabled(0);
 310
 311   connect(actionNorth_East_Window,SIGNAL(triggered()),this,SLOT(SaveNEScreenshot()));
 312   connect(actionNorth_West_Window,SIGNAL(triggered()),this,SLOT(SaveNOScreenshot()));
 313   connect(actionSouth_East_Window,SIGNAL(triggered()),this,SLOT(SaveSEScreenshot()));
 314   connect(actionSouth_West_Window,SIGNAL(triggered()),this,SLOT(SaveSOScreenshot()));
 315   connect(actionSave_all_slices,SIGNAL(triggered()),this,SLOT(SaveScreenshotAllSlices()));
 316
 317   connect(DataTree,SIGNAL(itemSelectionChanged()),this,SLOT(ImageInfoChanged()));
 318   connect(DataTree,SIGNAL(itemClicked(QTreeWidgetItem*, int)),this,
 319     SLOT(DisplayChanged(QTreeWidgetItem*, int)));
 320
 321   connect(viewButton,SIGNAL(clicked()),this, SLOT(ChangeViewMode()) );
 322   connect(windowSpinBox,SIGNAL(editingFinished()),this,SLOT(WindowLevelEdited()));
 323   connect(levelSpinBox,SIGNAL(editingFinished()),this,SLOT(WindowLevelEdited()));
 324   connect(colorMapComboBox,SIGNAL(currentIndexChanged(int)),this,SLOT(UpdateColorMap()));
 325   connect(presetComboBox,SIGNAL(currentIndexChanged(int)),this,SLOT(UpdateWindowLevel()));
 326   connect(slicingPresetComboBox, SIGNAL(currentIndexChanged(int)),this,SLOT(UpdateSlicingPreset()));
 327   connect(inverseButton,SIGNAL(clicked()),this,SLOT(SwitchWindowLevel()));
 328   connect(applyWindowLevelToAllButton,SIGNAL(clicked()),this,SLOT(ApplyWindowLevelToAllImages()));
 329
 330   connect(this,SIGNAL(customContextMenuRequested(QPoint)),this,SLOT(ShowContextMenu(QPoint)));
 331
 332   connect(linkPanel,SIGNAL(addLink(QString,QString,bool)),this,SLOT(AddLink(QString,QString,bool)));
 333   connect(linkPanel,SIGNAL(removeLink(QString,QString)),this,SLOT(RemoveLink(QString,QString)));
 334   connect(overlayPanel,SIGNAL(VFPropertyUpdated(int,int,int,int,double,double,double)),this,SLOT(SetVFProperty(int,int,int,int,double,double,double)));
 335   connect(overlayPanel,SIGNAL(OverlayPropertyUpdated(int,int,double,double)),
 336     this,SLOT(SetOverlayProperty(int,int,double,double)));
 337   connect(overlayPanel,SIGNAL(FusionPropertyUpdated(int,int,int,double,double, bool)),
 338     this,SLOT(SetFusionProperty(int,int,int,double,double, bool)));
 339   connect(landmarksPanel,SIGNAL(UpdateRenderWindows()),this,SLOT(UpdateRenderWindows()));
 340   connect(landmarksPanel,SIGNAL(SelectedPointChanged()),this,SLOT(GoToLandmark()));
 341
 342   connect(overlayPanel,SIGNAL(FusionSequencePropertyUpdated(int, bool, unsigned int, bool)),
 343     this,SLOT(SetFusionSequenceProperty(int, bool,unsigned int, bool)));
 344
 345
 346   playMode = 0;//pause
 347   mFrameRate = 10;
 348   playButton->setEnabled(0);
 349   frameRateLabel->setEnabled(0);
 350   frameRateSpinBox->setEnabled(0);
 351   connect(playButton, SIGNAL(clicked()),this,SLOT(PlayPause()));
 352   connect(frameRateSpinBox, SIGNAL(valueChanged(int)),this,SLOT(ChangeFrameRate(int)));
 353
 354   goToCursorPushButton->setEnabled(0);
 355   connect(goToCursorPushButton, SIGNAL(clicked()),this,SLOT(GoToCursor()));
 356
 357   NOViewWidget->hide();
 358   NEViewWidget->hide();
 359   SOViewWidget->hide();
 360   SEViewWidget->hide();
 361
 362   //Recently opened files
 363   std::list<std::string> recent_files = GetRecentlyOpenedImages();
 364   recentlyOpenedFilesMenu=NULL;
 365   if ( !recent_files.empty() ) {
 366     createRecentlyOpenedFilesMenu();
 367     updateRecentlyOpenedFilesMenu(recent_files);
 368   }
 369
 370   // Adding all new tools (insertion in the menu)
 371   vvToolManager::GetInstance()->InsertToolsInMenu(this);
 372   vvToolManager::GetInstance()->EnableToolsInMenu(this, false);
 373
 374   if (!CLITK_EXPERIMENTAL)
 375     menuExperimental->menuAction()->setVisible(false);
 376
 377
 378   QTimer * timerMemory = new QTimer(this);
 379   //timerMemory->setInterval(5);
 380   connect(timerMemory, SIGNAL(timeout()), this, SLOT(UpdateMemoryUsage()));
 381   timerMemory->start(2000);
 382
 383 }
 384 //------------------------------------------------------------------------------
 385 void vvMainWindow::show()
 386 {
 387   vvMainWindowBase::show();
 388   PopupRegisterForm(true);
 389 }
 390 //------------------------------------------------------------------------------
 391 void vvMainWindow::UpdateMemoryUsage()
 392 {
 393   //  clitk::PrintMemory(true);
 394   if (clitk::GetMemoryUsageInMb() == 0) infoPanel->setMemoryInMb("NA");
 395   else infoPanel->setMemoryInMb(QString::number(clitk::GetMemoryUsageInMb())+" MiB");
 396 }
 397 //------------------------------------------------------------------------------
 398
 399
 400 //------------------------------------------------------------------------------
 401 void vvMainWindow::createRecentlyOpenedFilesMenu()
 402 {
 403   recentlyOpenedFilesMenu = new QMenu("Recently opened files...");
 404   recentlyOpenedFilesMenu->setIcon(QIcon(QString::fromUtf8(":/common/icons/open.png")));
 405   menuFile->insertMenu(actionOpen_Image_With_Time,recentlyOpenedFilesMenu);
 406   menuFile->insertSeparator(actionOpen_Image_With_Time);
 407 }
 408 //------------------------------------------------------------------------------
 409
 410
 411 //------------------------------------------------------------------------------
 412
 413 void vvMainWindow::updateRecentlyOpenedFilesMenu(const std::list<std::string> &recent_files)
 414 {
 415   if(recentlyOpenedFilesMenu==NULL) {
 416     createRecentlyOpenedFilesMenu();
 417   } else {
 418     recentlyOpenedFilesMenu->clear();
 419   }
 420   for (std::list<std::string>::const_iterator i = recent_files.begin(); i!=recent_files.end(); i++) {
 421     QAction* current=new QAction(QIcon(QString::fromUtf8(":/common/icons/open.png")), i->c_str(),this);
 422     recentlyOpenedFilesMenu->addAction(current);
 423     connect(current,SIGNAL(triggered()),this,SLOT(OpenRecentImage()));
 424   }
 425 }
 426 //------------------------------------------------------------------------------
 427
 428
 429 //------------------------------------------------------------------------------
 430 void vvMainWindow::ComputeMidPosition()
 431 {
 432   bool ok;
 433   int index=GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
 434   int ref = QInputDialog::getInteger(this,"Chose reference phase","Reference phase",0,0,\
 435     mSlicerManagers[index]->GetImage()->GetVTKImages().size()-1,1,&ok);
 436   if (ok) {
 437     vvMidPosition midp;
 438     midp.slicer_manager = mSlicerManagers[index];
 439     midp.reference_image_index = ref;
 440     QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
 441     midp.Update();
 442     if (midp.error)
 443       QMessageBox::warning(this, "Error computing midposition image",midp.error_message.c_str());
 444     else {
 445       QFileInfo info(midp.slicer_manager->GetFileName().c_str());
 446       AddImage(midp.output,info.path().toStdString()+"/"+info.completeBaseName().toStdString()+"_midposition.mhd");
 447     }
 448     QApplication::restoreOverrideCursor();
 449   }
 450 }
 451 //------------------------------------------------------------------------------
 452
 453
 454 //------------------------------------------------------------------------------
 455 void vvMainWindow::AddContour(int image_index, vvMesh::Pointer contour, bool propagation)
 456 {
 457   QTreeWidgetItem *item = new QTreeWidgetItem();
 458   item->setData(0,Qt::UserRole,"filename.vtk");
 459   item->setData(1,Qt::UserRole,tr("contour"));
 460   QBrush brush;
 461   brush.setColor(QColor(contour->r*255,contour->g*255,contour->b*255));
 462   brush.setStyle(Qt::SolidPattern);
 463   item->setData(COLUMN_IMAGE_NAME,Qt::BackgroundRole,brush);
 464   item->setData(COLUMN_IMAGE_NAME,Qt::DisplayRole,contour->structure_name.c_str());
 465
 466   for (int j = 1; j <= 4; j++)
 467     item->setData(j,Qt::CheckStateRole,DataTree->topLevelItem(image_index)->data(j,Qt::CheckStateRole));
 468
 469   QTreePushButton* cButton = new QTreePushButton;
 470   cButton->setItem(item);
 471   cButton->setColumn(COLUMN_CLOSE_IMAGE);
 472   cButton->setToolTip(tr("close image"));
 473   cButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/exit.png")));
 474   connect(cButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
 475     this,SLOT(CloseImage(QTreeWidgetItem*, int)));
 476
 477   QTreePushButton* rButton = new QTreePushButton;
 478   rButton->setItem(item);
 479   rButton->setColumn(COLUMN_RELOAD_IMAGE);
 480   rButton->setToolTip(tr("reload image"));
 481   rButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/rotateright.png")));
 482   rButton->setEnabled(false);
 483   //Not implemented
 484   //connect(rButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
 485   //this,SLOT(ReloadImage(QTreeWidgetItem*, int)));
 486
 487   DataTree->topLevelItem(image_index)->setExpanded(1);
 488   DataTree->topLevelItem(image_index)->addChild(item);
 489   DataTree->setItemWidget(item, COLUMN_CLOSE_IMAGE, cButton);
 490   DataTree->setItemWidget(item, COLUMN_RELOAD_IMAGE, rButton);
 491   QString id = DataTree->topLevelItem(image_index)->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString();
 492   item->setData(COLUMN_IMAGE_NAME,Qt::UserRole,id.toStdString().c_str());
 493
 494   UpdateTree();
 495   mSlicerManagers[image_index]->AddContour(contour,propagation);
 496   mSlicerManagers[image_index]->Render();
 497 }
 498 //------------------------------------------------------------------------------
 499
 500
 501 //------------------------------------------------------------------------------
 502 void vvMainWindow::OpenVTKContour()
 503 {
 504   if (mSlicerManagers.size() > 0) {
 505     QString Extensions = "Images ( *.vtk *.obj)";
 506     Extensions += ";;All Files (*)";
 507     QString file = QFileDialog::getOpenFileName(this,tr("Open vtkPolyData"),mInputPathName,Extensions);
 508     if (file.isNull())
 509       return;
 510     QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
 511     int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
 512     vvMeshReader reader;
 513     reader.SetImage(mSlicerManagers[index]->GetImage());
 514     reader.SetModeToVTK();
 515     reader.SetFilename(file.toStdString());
 516     reader.Update();
 517     AddContour(index,reader.GetOutput()[0],false);
 518     QApplication::restoreOverrideCursor();
 519   }
 520 }
 521 //------------------------------------------------------------------------------
 522
 523
 524 //------------------------------------------------------------------------------
 525 void vvMainWindow::AddDCStructContour(int index, QString file)
 526 {
 527   vvMeshReader reader;
 528   reader.SetFilename(file.toStdString());
 529   vvStructSelector selector;
 530   selector.SetStructures(reader.GetROINames());
 531   if (!mSlicerManagers[index]->GetVF().IsNull())
 532     selector.EnablePropagationCheckBox();
 533   if (selector.exec()) {
 534     QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
 535     reader.SetSelectedItems(selector.getSelectedItems());
 536     reader.SetImage(mSlicerManagers[index]->GetImage());
 537     if (selector.PropagationEnabled())
 538       reader.SetPropagationVF(mSlicerManagers[index]->GetVF());
 539     reader.Update();
 540     std::vector<vvMesh::Pointer> contours=reader.GetOutput();
 541     for (std::vector<vvMesh::Pointer>::iterator i=contours.begin();
 542       i!=contours.end(); i++)
 543       AddContour(index,*i,selector.PropagationEnabled());
 544     QApplication::restoreOverrideCursor();
 545   }
 546 }
 547
 548 //------------------------------------------------------------------------------
 549 void vvMainWindow::OpenDCStructContour()
 550 {
 551   if (mSlicerManagers.size() > 0) {
 552     QString Extensions = "Dicom Files ( *.dcm RS*)";
 553     Extensions += ";;All Files (*)";
 554     QString file = QFileDialog::getOpenFileName(this,tr("Merge Images"),mInputPathName,Extensions);
 555     if (file.isNull())
 556       return;
 557     int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
 558     AddDCStructContour(index, file);
 559   }
 560 }
 561 //------------------------------------------------------------------------------
 562
 563
 564 //------------------------------------------------------------------------------
 565 void vvMainWindow::ComputeDeformableRegistration()
 566 {
 567   if (mSlicerManagers.size() > 0) {
 568     int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
 569     vvDeformationDialog dialog(index,mSlicerManagers);
 570     if (dialog.exec()) {
 571       std::string base_name=itksys::SystemTools::GetFilenameWithoutExtension(mSlicerManagers[dialog.GetInputFileIndex()]->GetFileName());
 572       AddField(dialog.GetOutput(),dialog.getFieldFile(),dialog.GetInputFileIndex());
 573       WarpImage(dialog.GetSelectedSlicer(),dialog.GetReferenceFrameIndex());
 574     } else
 575       std::cout << "Error or user cancellation while computing deformation field..." << std::endl;
 576   } else QMessageBox::information(this, "Need to open image","You must open an image first.");
 577 }
 578 //------------------------------------------------------------------------------
 579
 580
 581 //------------------------------------------------------------------------------
 582 void vvMainWindow::WarpImage()
 583 {
 584   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
 585   if (!mSlicerManagers[index]->GetVF().IsNull()) {
 586     bool ok;
 587     int ref = QInputDialog::getInteger(this,"Chose reference phase","Reference phase",0,0,\
 588       mSlicerManagers[index]->GetImage()->GetVTKImages().size()-1,1,&ok);
 589     if (ok) {
 590       WarpImage(mSlicerManagers[index],ref);
 591     }
 592   } else
 593     QMessageBox::warning(this,tr("No vector field"),tr("Sorry, can't warp without a vector field"));
 594 }
 595 //------------------------------------------------------------------------------
 596
 597
 598 //------------------------------------------------------------------------------
 599 void vvMainWindow::WarpImage(vvSlicerManager* selected_slicer,int reference_phase)
 600 {
 601   if (!selected_slicer->GetVF().IsNull()) {
 602     QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
 603     QFileInfo info(selected_slicer->GetFileName().c_str());
 604     vvImageWarp warp(selected_slicer->GetImage(),selected_slicer->GetVF(),
 605       reference_phase,this);
 606     if (warp.ComputeWarpedImage()) {
 607       AddImage(warp.GetWarpedImage(),info.path().toStdString()+"/"+info.completeBaseName().toStdString()+"_warped.mhd");
 608       AddImage(warp.GetDiffImage()  ,info.path().toStdString()+"/"+info.completeBaseName().toStdString()+"_diff.mhd");
 609       AddImage(warp.GetJacobianImage()  ,info.path().toStdString()+"/"+info.completeBaseName().toStdString()+"_jacobian.mhd");
 610       QApplication::restoreOverrideCursor();
 611     } else {
 612       QApplication::restoreOverrideCursor();
 613       QMessageBox::warning(this,tr("Different spacings"),tr("The vector field and image spacings must be the same in order to warp."));
 614     }
 615   } else
 616     QMessageBox::warning(this,tr("No vector field"),tr("Sorry, can't warp without a vector field."));
 617 }
 618 //------------------------------------------------------------------------------
 619
 620
 621 //------------------------------------------------------------------------------
 622 vvMainWindow::~vvMainWindow()
 623 {
 624   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
 625     if (mSlicerManagers[i] != NULL)
 626       delete mSlicerManagers[i];
 627   }
 628 }
 629 //------------------------------------------------------------------------------
 630
 631 //------------------------------------------------------------------------------
 632 QTabWidget * vvMainWindow::GetTab()
 633 {
 634   return tabWidget;
 635 }
 636 //------------------------------------------------------------------------------
 637
 638
 639 //------------------------------------------------------------------------------
 640 void vvMainWindow::MergeImages()
 641 {
 642   QString Extensions = EXTENSIONS;
 643   Extensions += ";;All Files (*)";
 644   QStringList files = QFileDialog::getOpenFileNames(this,tr("Merge Images"),mInputPathName,Extensions);
 645   if (files.isEmpty())
 646     return;
 647   mInputPathName = itksys::SystemTools::GetFilenamePath(files[0].toStdString()).c_str();
 648   std::vector<std::string> vector;
 649
 650   unsigned int currentDim = 0;
 651   std::vector<double> currentSpacing;
 652   std::vector<int> currentSize;
 653   std::vector<double> currentOrigin;
 654
 655   for (int i = 0; i < files.size(); i++) {
 656     itk::ImageIOBase::Pointer reader = itk::ImageIOFactory::CreateImageIO(
 657       files[i].toStdString().c_str(), itk::ImageIOFactory::ReadMode);
 658     reader->SetFileName(files[i].toStdString().c_str());
 659     reader->ReadImageInformation();
 660     if (reader)        {
 661       //NOViewWidget->hide();
 662       //NEViewWidget->hide();
 663       //SOViewWidget->hide();
 664       //SEViewWidget->hide();
 665       if (i == 0)
 666         currentDim = reader->GetNumberOfDimensions();
 667       bool IsOk = true;
 668       for (unsigned int j = 0; j < currentDim; j++) {
 669         if (i == 0) {
 670           if (j == 0) {
 671             currentSpacing.resize(currentDim);
 672             currentSize.resize(currentDim);
 673             currentOrigin.resize(currentDim);
 674           }
 675           currentOrigin[j] = reader->GetOrigin(j);
 676           currentSpacing[j] = reader->GetSpacing(j);
 677           currentSize[j] = reader->GetDimensions(j);
 678         } else if (currentDim != reader->GetNumberOfDimensions()
 679           || currentSpacing[j] != reader->GetSpacing(j)
 680           || currentSize[j] != (int)reader->GetDimensions(j)
 681           || currentOrigin[j] != reader->GetOrigin(j)) {
 682             QString error = "Cannot read file (too different from others ";
 683             error += files[i].toStdString().c_str();
 684             QMessageBox::information(this,tr("Reading problem"),error);
 685             IsOk = false;
 686             break;
 687         }
 688       }
 689       if (IsOk)
 690         vector.push_back(files[i].toStdString());
 691     }
 692   }
 693   if (vector.size() > 0)
 694     LoadImages(vector, vvImageReader::MERGED);
 695 }
 696 //------------------------------------------------------------------------------
 697
 698 //------------------------------------------------------------------------------
 699 void vvMainWindow::SliceImages()
 700 {
 701   QString Extensions = EXTENSIONS;
 702   Extensions += ";;All Files (*)";
 703
 704   QStringList files = QFileDialog::getOpenFileNames(this,tr("Slice Images"),mInputPathName,Extensions);
 705   if (files.isEmpty())
 706     return;
 707   mInputPathName = itksys::SystemTools::GetFilenamePath(files[0].toStdString()).c_str();
 708   std::vector<std::string> vector;
 709   for (int i = 0; i < files.size(); i++)
 710     vector.push_back(files[i].toStdString());
 711   LoadImages(vector, vvImageReader::SLICED);
 712 }
 713 //------------------------------------------------------------------------------
 714
 715 //------------------------------------------------------------------------------
 716 void vvMainWindow::MergeImagesWithTime()
 717 {
 718   QString Extensions = EXTENSIONS;
 719   Extensions += ";;All Files (*)";
 720   QStringList files = QFileDialog::getOpenFileNames(this,tr("Merge Images With Time"),mInputPathName,Extensions);
 721   if (files.isEmpty())
 722     return;
 723   mInputPathName = itksys::SystemTools::GetFilenamePath(files[0].toStdString()).c_str();
 724   std::vector<std::string> vector;
 725
 726   for (int i = 0; i < files.size(); i++)
 727     vector.push_back(files[i].toStdString());
 728   sort(vector.begin(),vector.end());
 729   if (vector.size() > 1)
 730     LoadImages(vector, vvImageReader::MERGEDWITHTIME);
 731   else
 732     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.");
 733 }
 734 //------------------------------------------------------------------------------
 735
 736
 737 //------------------------------------------------------------------------------
 738 void vvMainWindow::OpenDicom()
 739 {
 740   std::vector<std::string> files;
 741
 742   std::cout << "dicomSeriesSelector " << std::endl;
 743   if (dicomSeriesSelector->exec() == QDialog::Accepted) {
 744     files = *(dicomSeriesSelector->GetFilenames());
 745     LoadImages(files, vvImageReader::DICOM);
 746   }
 747 }
 748 //------------------------------------------------------------------------------
 749
 750 //------------------------------------------------------------------------------
 751 void vvMainWindow::OpenImages()
 752 {
 753   QString Extensions = EXTENSIONS;
 754   Extensions += ";;All Files (*)";
 755
 756   QStringList files = QFileDialog::getOpenFileNames(this,tr("Load Images"),mInputPathName,Extensions);
 757   if (files.isEmpty())
 758     return;
 759   mInputPathName = itksys::SystemTools::GetFilenamePath(files[0].toStdString()).c_str();
 760   std::vector<std::string> vector;
 761   for (int i = 0; i < files.size(); i++)
 762     vector.push_back(files[i].toStdString());
 763   LoadImages(vector, vvImageReader::IMAGE);
 764 }
 765 //------------------------------------------------------------------------------
 766 void vvMainWindow::OpenRecentImage()
 767 {
 768   QAction * caller = qobject_cast<QAction*>(sender());
 769   std::vector<std::string> images;
 770   images.push_back(caller->text().toStdString());
 771   mInputPathName = itksys::SystemTools::GetFilenamePath(images[0]).c_str();
 772   LoadImages(images, vvImageReader::IMAGE);
 773 }
 774 //------------------------------------------------------------------------------
 775
 776
 777 //------------------------------------------------------------------------------
 778 void vvMainWindow::OpenImageWithTime()
 779 {
 780   QString Extensions = EXTENSIONS;
 781   Extensions += ";;All Files (*)";
 782
 783   QStringList files = QFileDialog::getOpenFileNames(this,tr("Load Images With Time"),mInputPathName,Extensions);
 784   if (files.isEmpty())
 785     return;
 786   mInputPathName = itksys::SystemTools::GetFilenamePath(files[0].toStdString()).c_str();
 787   std::vector<std::string> vector;
 788   for (int i = 0; i < files.size(); i++) {
 789     vector.push_back(files[i].toStdString());
 790   }
 791   LoadImages(vector, vvImageReader::IMAGEWITHTIME);
 792 }
 793 //------------------------------------------------------------------------------
 794
 795
 796 //------------------------------------------------------------------------------
 797 void vvMainWindow::LoadImages(std::vector<std::string> files, vvImageReader::LoadedImageType filetype)
 798 {
 799   //Separate the way to open images and dicoms
 800   int fileSize;
 801   if (filetype == vvImageReader::IMAGE || filetype == vvImageReader::IMAGEWITHTIME)
 802     fileSize = files.size();
 803   else
 804     fileSize = 1;
 805
 806   // For SLICED, we need the number of slices (ndim and #slices)
 807   std::vector<unsigned int> nSlices;
 808   nSlices.resize(files.size());
 809   std::fill(nSlices.begin(), nSlices.end(), 1);
 810   if (filetype == vvImageReader::SLICED) {
 811     for (int i = 0; i < fileSize; i++) {
 812       itk::ImageIOBase::Pointer header = clitk::readImageHeader(files[i]);
 813       QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
 814       if (!header) {
 815         nSlices[i] = 0;
 816         QString error = "Cannot open file \n";
 817         error += files[i].c_str();
 818         QMessageBox::information(this,tr("Reading problem"),error);
 819         return;
 820       }
 821       if (header->GetNumberOfDimensions() < 3) {
 822         nSlices[i] = 0;
 823         QString error = "Dimension problem. Cannot slice \n";
 824         error += files[i].c_str();
 825         QMessageBox::information(this,tr("Reading problem"),error);
 826         return;
 827       }
 828       nSlices[i] = header->GetDimensions( header->GetNumberOfDimensions()-1 );
 829     }
 830   }
 831
 832   //Only add to the list of recently opened files when a single file is opened,
 833   //to avoid polluting the list of recently opened files
 834   if (files.size() == 1) {
 835     QFileInfo finfo=tr(files[0].c_str());
 836     AddToRecentlyOpenedImages(finfo.absoluteFilePath().toStdString());
 837     updateRecentlyOpenedFilesMenu(GetRecentlyOpenedImages());
 838   }
 839   //init the progress events
 840   QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
 841   vvProgressDialog progress("Opening " + files[0],fileSize>1);
 842   qApp->processEvents();
 843
 844   int numberofsuccesulreads=0;
 845   //open images as 1 or multiples
 846   for (int i = 0; i < fileSize; i++) {
 847     progress.SetText("Opening " + files[i]);
 848     progress.SetProgress(i,fileSize);
 849     qApp->processEvents();
 850
 851     for (unsigned int j = 0; j < nSlices[i]; j++) {
 852       //read the image and put it in mSlicerManagers
 853       vvSlicerManager* imageManager = new vvSlicerManager(4);
 854       qApp->processEvents();
 855
 856       bool SetImageSucceed=false;
 857
 858       // Change filename if an image with the same already exist
 859       int number = GetImageDuplicateFilenameNumber(files[i] + std::string("_slice"));
 860
 861       if (filetype == vvImageReader::IMAGE || filetype == vvImageReader::IMAGEWITHTIME || filetype == vvImageReader::SLICED)
 862         SetImageSucceed = imageManager->SetImage(files[i],filetype, number, j);
 863       else {
 864         SetImageSucceed = imageManager->SetImages(files,filetype, number);
 865       }
 866
 867       if (!SetImageSucceed) {
 868         QApplication::restoreOverrideCursor();
 869         QString error = "Cannot open file \n";
 870         error += imageManager->GetLastError().c_str();
 871         QMessageBox::information(this,tr("Reading problem"),error);
 872         delete imageManager;
 873       } else {
 874         mSlicerManagers.push_back(imageManager);
 875
 876         //create an item in the tree with good settings
 877         QTreeWidgetItem *item = new QTreeWidgetItem();
 878         item->setData(0,Qt::UserRole,files[i].c_str());
 879         QFileInfo fileinfo(imageManager->GetFileName().c_str()); //Do not show the path
 880         item->setData(COLUMN_IMAGE_NAME,Qt::DisplayRole,fileinfo.fileName());
 881         item->setData(1,Qt::UserRole,tr("image"));
 882         item->setToolTip(COLUMN_IMAGE_NAME, imageManager->GetListOfAbsoluteFilePathInOneString("image").c_str());
 883         qApp->processEvents();
 884
 885         //Create the buttons for reload and close
 886         qApp->processEvents();
 887         QTreePushButton* cButton = new QTreePushButton;
 888         cButton->setItem(item);
 889         cButton->setColumn(COLUMN_CLOSE_IMAGE);
 890         cButton->setToolTip(tr("close image"));
 891         cButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/exit.png")));
 892         connect(cButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
 893           this,SLOT(CloseImage(QTreeWidgetItem*, int)));
 894
 895         QTreePushButton* rButton = new QTreePushButton;
 896         rButton->setItem(item);
 897         rButton->setColumn(COLUMN_RELOAD_IMAGE);
 898         rButton->setToolTip(tr("reload image"));
 899         rButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/rotateright.png")));
 900         connect(rButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
 901           this,SLOT(ReloadImage(QTreeWidgetItem*, int)));
 902
 903         DataTree->addTopLevelItem(item);
 904         DataTree->setItemWidget(item, COLUMN_CLOSE_IMAGE, cButton);
 905         DataTree->setItemWidget(item, COLUMN_RELOAD_IMAGE, rButton);
 906
 907         //set the id of the image
 908         QString id = QDir::current().absoluteFilePath(files[i].c_str()) + QString::number(mSlicerManagers.size()-1);
 909         item->setData(COLUMN_IMAGE_NAME,Qt::UserRole,id.toStdString().c_str());
 910         mSlicerManagers.back()->SetId(id.toStdString());
 911
 912         linkPanel->addImage(imageManager->GetFileName(), id.toStdString());
 913
 914         connect(mSlicerManagers.back(), SIGNAL(currentImageChanged(std::string)),
 915           this,SLOT(CurrentImageChanged(std::string)));
 916         connect(mSlicerManagers.back(), SIGNAL(currentPickedImageChanged(std::string)),
 917           this, SLOT(CurrentPickedImageChanged(std::string)));
 918         connect(mSlicerManagers.back(), SIGNAL(UpdatePosition(int, double, double, double, double, double, double, double)),
 919           this,SLOT(MousePositionChanged(int,double, double, double, double, double, double, double)));
 920         connect(mSlicerManagers.back(), SIGNAL(UpdateVector(int, double, double, double, double)),
 921           this, SLOT(VectorChanged(int,double,double,double, double)));
 922         connect(mSlicerManagers.back(), SIGNAL(UpdateOverlay(int, double, double)),
 923           this, SLOT(OverlayChanged(int,double,double)));
 924         connect(mSlicerManagers.back(), SIGNAL(UpdateFusion(int, double)),
 925           this, SLOT(FusionChanged(int,double)));
 926         connect(mSlicerManagers.back(), SIGNAL(WindowLevelChanged()),
 927           this,SLOT(WindowLevelChanged()));
 928         connect(mSlicerManagers.back(), SIGNAL(UpdateSlice(int,int)),
 929           this,SLOT(UpdateSlice(int,int)));
 930         connect(mSlicerManagers.back(), SIGNAL(UpdateTSlice(int, int, int)),
 931           this,SLOT(UpdateTSlice(int, int, int)));
 932         connect(mSlicerManagers.back(), SIGNAL(UpdateTSlice(int, int, int)),
 933           this,SLOT(ImageInfoChanged()));
 934         connect(mSlicerManagers.back(), SIGNAL(UpdateSliceRange(int,int,int,int,int)),
 935           this,SLOT(UpdateSliceRange(int,int,int,int,int)));
 936         connect(mSlicerManagers.back(), SIGNAL(UpdateLinkManager(std::string,int,double,double,double,int)),
 937           this,SLOT(UpdateLinkManager(std::string,int,double,double,double,int)));
 938         connect(mSlicerManagers.back(), SIGNAL(UpdateLinkedNavigation(std::string,vvSlicerManager*,vvSlicer*)),
 939           this,SLOT(UpdateLinkedNavigation(std::string,vvSlicerManager*,vvSlicer*)));
 940         connect(mSlicerManagers.back(), SIGNAL(ChangeImageWithIndexOffset(vvSlicerManager*,int,int)),
 941           this,SLOT(ChangeImageWithIndexOffset(vvSlicerManager*,int,int)));
 942         connect(mSlicerManagers.back(),SIGNAL(LandmarkAdded()),landmarksPanel,SLOT(AddPoint()));
 943
 944         InitSlicers();
 945         numberofsuccesulreads++;
 946       }
 947     }
 948   }
 949   if (numberofsuccesulreads) {
 950     NOViewWidget->show();
 951     NEViewWidget->show();
 952     SOViewWidget->show();
 953     SEViewWidget->show();
 954     UpdateTree();
 955     InitDisplay();
 956     ShowLastImage();
 957
 958     // Try to guess default WindowLevel
 959     double range[2];
 960     mSlicerManagers.back()->GetImage()->GetFirstVTKImageData()->GetScalarRange(range);
 961     if ((range[0] == 0) && (range[1] == 1)) {
 962       presetComboBox->setCurrentIndex(WL_BINARY);// binary
 963     } else {
 964       // TODO
 965     }
 966   }
 967   QApplication::restoreOverrideCursor();
 968 }
 969 //------------------------------------------------------------------------------
 970
 971 //------------------------------------------------------------------------------
 972 void vvMainWindow::UpdateTree()
 973 {
 974   DataTree->resizeColumnToContents(COLUMN_TREE);
 975   DataTree->resizeColumnToContents(COLUMN_UL_VIEW);
 976   DataTree->resizeColumnToContents(COLUMN_UR_VIEW);
 977   DataTree->resizeColumnToContents(COLUMN_DL_VIEW);
 978   DataTree->resizeColumnToContents(COLUMN_DR_VIEW);
 979   DataTree->resizeColumnToContents(COLUMN_IMAGE_NAME);
 980   DataTree->resizeColumnToContents(COLUMN_CLOSE_IMAGE);
 981   DataTree->resizeColumnToContents(COLUMN_RELOAD_IMAGE);
 982 }
 983 //------------------------------------------------------------------------------
 984
 985 //------------------------------------------------------------------------------
 986 void vvMainWindow::CurrentImageChanged(std::string id)
 987 {
 988   if (id == mCurrentSelectedImageId) return; // Do nothing
 989   int selected = 0;
 990   for (int i = 0; i < DataTree->topLevelItemCount(); i++) {
 991     if (DataTree->topLevelItem(i)->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString().toStdString() == id) {
 992       selected = i;
 993     } else {
 994       DataTree->topLevelItem(i)->setSelected(0);
 995     }
 996     for (int child = 0; child < DataTree->topLevelItem(i)->childCount(); child++)
 997       DataTree->topLevelItem(i)->child(child)->setSelected(0);
 998
 999   }
1000   DataTree->topLevelItem(selected)->setSelected(1);
1001   mCurrentSelectedImageId = id;
1002
1003   landmarksPanel->SetCurrentLandmarks(mSlicerManagers[selected]->GetLandmarks(),
1004                                       mSlicerManagers[selected]->GetTSlice());
1005   landmarksPanel->SetCurrentPath(mInputPathName.toStdString());
1006   landmarksPanel->SetCurrentImage(mSlicerManagers[selected]->GetFileName().c_str());
1007
1008   emit SelectedImageHasChanged(mSlicerManagers[selected]);
1009 }
1010 //------------------------------------------------------------------------------
1011
1012 //------------------------------------------------------------------------------
1013 void vvMainWindow::CurrentPickedImageChanged(std::string id)
1014 {
1015   if (id == mCurrentPickedImageId) return; // Do nothing
1016   int selected = 0;
1017   for (int i = 0; i < DataTree->topLevelItemCount(); i++) {
1018     if (DataTree->topLevelItem(i)->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString().toStdString() == id) {
1019       selected = i;
1020     } else {
1021       DataTree->topLevelItem(i)->setSelected(0);
1022     }
1023     for (int child = 0; child < DataTree->topLevelItem(i)->childCount(); child++)
1024       DataTree->topLevelItem(i)->child(child)->setSelected(0);
1025
1026   }
1027   DataTree->topLevelItem(selected)->setSelected(1);
1028   mCurrentPickedImageId = id;
1029   mCurrentPickedImageIndex = selected;
1030 }
1031 //------------------------------------------------------------------------------
1032
1033 //------------------------------------------------------------------------------
1034 void vvMainWindow::ImageInfoChanged()
1035 {
1036   contextActions[6]->setEnabled(1);
1037   contextActions[5]->setEnabled(1);
1038   actionSave_As->setEnabled(1);
1039   actionAdd_VF_to_current_Image->setEnabled(1);
1040   actionAdd_fusion_image->setEnabled(1);
1041   actionAdd_overlay_image_to_current_image->setEnabled(1);
1042   actionAdd_USSequence_toCT->setEnabled(1);
1043   actionNorth_East_Window->setEnabled(1);
1044   actionNorth_West_Window->setEnabled(1);
1045   actionSouth_East_Window->setEnabled(1);
1046   actionSouth_West_Window->setEnabled(1);
1047   vvToolManager::GetInstance()->EnableToolsInMenu(this, true);
1048   inverseButton->setEnabled(1);
1049
1050   goToCursorPushButton->setEnabled(1);
1051
1052   if (DataTree->selectedItems().size()) {
1053     int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1054
1055     colorMapComboBox->setEnabled(1);
1056     for (int i = 0; i < DataTree->topLevelItem(index)->childCount(); i++) {
1057       if (DataTree->topLevelItem(index)->child(i)->data(1,Qt::UserRole).toString() == "overlay" ||
1058         DataTree->topLevelItem(index)->child(i)->data(1,Qt::UserRole).toString() == "fusion" ||
1059         DataTree->topLevelItem(index)->child(i)->data(1,Qt::UserRole).toString() == "fusionSequence") {
1060           colorMapComboBox->setEnabled(0);
1061           break;
1062       }
1063     }
1064
1065     std::vector<double> origin;
1066     std::vector<double> inputSpacing;
1067     std::vector<int> inputSize;
1068     std::vector<double> sizeMM;
1069     vtkSmartPointer<vtkMatrix4x4> transformation;
1070     int dimension=0;
1071     QString pixelType;
1072     QString inputSizeInBytes;
1073     QString image = DataTree->selectedItems()[0]->data(COLUMN_IMAGE_NAME,Qt::DisplayRole).toString();
1074
1075     int nframes = mSlicerManagers[index]->GetSlicer(0)->GetTMax();
1076
1077     if (nframes > 1 || playMode == 1) {
1078       playButton->setEnabled(1);
1079       frameRateLabel->setEnabled(1);
1080       frameRateSpinBox->setEnabled(1);
1081     } else {
1082       playButton->setEnabled(0);
1083       frameRateLabel->setEnabled(0);
1084       frameRateSpinBox->setEnabled(0);
1085     }
1086
1087     //read image header
1088     int NPixel = 1;
1089
1090     int tSlice = 0;
1091     vvImage::Pointer imageSelected;
1092     if (DataTree->topLevelItem(index) == DataTree->selectedItems()[0]) {
1093       imageSelected = mSlicerManagers[index]->GetSlicer(0)->GetImage();
1094       tSlice = mSlicerManagers[index]->GetSlicer(0)->GetTSlice();
1095     } else if (DataTree->selectedItems()[0]->data(1,Qt::UserRole).toString() == "vector") {
1096       imageSelected = mSlicerManagers[index]->GetSlicer(0)->GetVF();
1097       tSlice = mSlicerManagers[index]->GetSlicer(0)->GetOverlayTSlice();
1098     } else if (DataTree->selectedItems()[0]->data(1,Qt::UserRole).toString() == "overlay") {
1099       imageSelected = mSlicerManagers[index]->GetSlicer(0)->GetOverlay();
1100       tSlice = mSlicerManagers[index]->GetSlicer(0)->GetOverlayTSlice();
1101     } else if (DataTree->selectedItems()[0]->data(1,Qt::UserRole).toString() == "fusion") {
1102       imageSelected = mSlicerManagers[index]->GetSlicer(0)->GetFusion();
1103       tSlice = mSlicerManagers[index]->GetSlicer(0)->GetFusionTSlice();
1104     }
1105     else if (DataTree->selectedItems()[0]->data(1,Qt::UserRole).toString() == "fusionSequence") {
1106       imageSelected = mSlicerManagers[index]->GetSlicer(0)->GetFusion();
1107       tSlice = mSlicerManagers[index]->GetSlicer(0)->GetFusionTSlice();
1108     }
1109     else if (DataTree->selectedItems()[0]->data(1,Qt::UserRole).toString() == "contour") {
1110       imageSelected = mSlicerManagers[index]->GetSlicer(0)->GetImage();
1111       tSlice = mSlicerManagers[index]->GetSlicer(0)->GetTSlice();
1112     }
1113     else {
1114       imageSelected = mSlicerManagers[index]->GetSlicer(0)->GetImage();
1115       tSlice = mSlicerManagers[index]->GetSlicer(0)->GetTSlice();
1116     }
1117
1118     dimension = imageSelected->GetNumberOfDimensions();
1119     origin.resize(dimension);
1120     inputSpacing.resize(dimension);
1121     inputSize.resize(dimension);
1122     sizeMM.resize(dimension);
1123     pixelType = mSlicerManagers[index]->GetImage()->GetScalarTypeAsITKString().c_str();
1124     for (int i = 0; i < dimension; i++) {
1125       origin[i] = imageSelected->GetOrigin()[i];
1126       inputSpacing[i] = imageSelected->GetSpacing()[i];
1127       inputSize[i] = imageSelected->GetSize()[i];
1128       sizeMM[i] = inputSize[i]*inputSpacing[i];
1129       NPixel *= inputSize[i];
1130     }
1131     inputSizeInBytes = GetSizeInBytes(imageSelected->GetActualMemorySize()*1000);
1132
1133     QString dim = QString::number(dimension) + " (";
1134     dim += pixelType + ")";
1135
1136     infoPanel->setFileName(image);
1137     infoPanel->setDimension(dim);
1138     infoPanel->setSizePixel(GetVectorIntAsString(inputSize));
1139     infoPanel->setSizeMM(GetVectorDoubleAsString(sizeMM));
1140     infoPanel->setOrigin(GetVectorDoubleAsString(origin));
1141     infoPanel->setSpacing(GetVectorDoubleAsString(inputSpacing));
1142     infoPanel->setNPixel(QString::number(NPixel)+" ("+inputSizeInBytes+")");
1143
1144     transformation = imageSelected->GetTransform()[tSlice]->GetMatrix();
1145     infoPanel->setTransformation(Get4x4MatrixDoubleAsString(transformation));
1146
1147     landmarksPanel->SetCurrentLandmarks(mSlicerManagers[index]->GetLandmarks(),
1148                                         mSlicerManagers[index]->GetTSlice());
1149     landmarksPanel->SetCurrentPath(mInputPathName.toStdString());
1150     landmarksPanel->SetCurrentImage(mSlicerManagers[index]->GetFileName().c_str());
1151
1152     overlayPanel->getCurrentImageName(mSlicerManagers[index]->GetFileName().c_str());
1153     for (int i = 0; i < 4; i++) {
1154       if (DataTree->selectedItems()[0]->data(i+1,Qt::CheckStateRole).toInt() > 0 || i == 3) {
1155         mSlicerManagers[index]->UpdateInfoOnCursorPosition(i);
1156         break;
1157       }
1158     }
1159
1160 //     infoPanel->setFileName(image);
1161 //     infoPanel->setDimension(dim);
1162 //     infoPanel->setSizePixel(GetVectorIntAsString(inputSize));
1163 //     infoPanel->setSizeMM(GetVectorDoubleAsString(sizeMM));
1164 //     infoPanel->setOrigin(GetVectorDoubleAsString(origin));
1165 //     infoPanel->setSpacing(GetVectorDoubleAsString(inputSpacing));
1166 //     infoPanel->setNPixel(QString::number(NPixel)+" ("+inputSizeInBytes+")");
1167 //
1168 //     landmarksPanel->SetCurrentLandmarks(mSlicerManagers[index]->GetLandmarks(),
1169 //                                         mSlicerManagers[index]->GetTSlice());
1170 //     landmarksPanel->SetCurrentPath(mInputPathName.toStdString());
1171 //     landmarksPanel->SetCurrentImage(mSlicerManagers[index]->GetFileName().c_str());
1172 //
1173 //     overlayPanel->getCurrentImageName(mSlicerManagers[index]->GetFileName().c_str());
1174 //     for (int i = 0; i < 4; i++) {
1175 //       if (DataTree->selectedItems()[0]->data(i+1,Qt::CheckStateRole).toInt() > 0 || i == 3) {
1176 //         mSlicerManagers[index]->UpdateInfoOnCursorPosition(i);
1177 //         break;
1178 //       }
1179 //     }
1180     WindowLevelChanged();
1181
1182     slicingPresetComboBox->setCurrentIndex(mSlicerManagers[index]->GetSlicingPreset());
1183
1184     if (mSlicerManagers[index]->GetSlicer(0)->GetVF()) {
1185       overlayPanel->getVFName(mSlicerManagers[index]->GetVFName().c_str());
1186       overlayPanel->getVFProperty(mSlicerManagers[index]->GetSlicer(0)->GetVFSubSampling(),
1187         mSlicerManagers[index]->GetSlicer(0)->GetVFScale(),
1188         mSlicerManagers[index]->GetSlicer(0)->GetVFLog());
1189     } else {
1190       overlayPanel->getVFName(mSlicerManagers[index]->GetVFName().c_str());
1191       overlayPanel->getVFProperty(-1,-1,-1);
1192     }
1193     if (mSlicerManagers[index]->GetSlicer(0)->GetOverlay()) {
1194       overlayPanel->getOverlayName(mSlicerManagers[index]->GetOverlayName().c_str());
1195     } else {
1196       overlayPanel->getOverlayName(mSlicerManagers[index]->GetOverlayName().c_str());
1197     }
1198
1199     if (mSlicerManagers[index]->GetSlicer(0)->GetFusion()) {
1200       overlayPanel->getFusionName(mSlicerManagers[index]->GetFusionName().c_str());
1201     } else {
1202       overlayPanel->getFusionName(mSlicerManagers[index]->GetFusionName().c_str());
1203     }
1204   }
1205 }
1206 //------------------------------------------------------------------------------
1207
1208 //------------------------------------------------------------------------------
1209 void vvMainWindow::ShowDocumentation()
1210 {
1211   documentation->show();
1212 }
1213 //------------------------------------------------------------------------------
1214
1215 //------------------------------------------------------------------------------
1216 void vvMainWindow::PopupRegisterForm(bool checkCanPush)
1217 {
1218   vvRegisterForm* registerForm = new vvRegisterForm(QUrl("http://www.creatis.insa-lyon.fr/~dsarrut/vvregister/write.php"), getVVSettingsPath(), getSettingsOptionFormat());
1219   if(!checkCanPush) {
1220     registerForm->show();
1221   } else {
1222     if(registerForm->canPush()) {
1223       registerForm->show();
1224       registerForm->acquitPushed();//too bad if there is not internet connection anymore.
1225     }
1226   }
1227 }
1228 //------------------------------------------------------------------------------
1229
1230 //------------------------------------------------------------------------------
1231 void vvMainWindow::ShowHelpDialog()
1232 {
1233   help_dialog->show();
1234 }
1235 //------------------------------------------------------------------------------
1236
1237 //------------------------------------------------------------------------------
1238 void vvMainWindow::ChangeViewMode()
1239 {
1240   typedef struct _SIZE{
1241     QSplitter* splitter;
1242     QList<int> size1, size2;
1243     int cols[3];
1244   }SplitterSize;
1245   SplitterSize sizes[4];
1246   sizes[0].splitter = OSplitter;
1247   sizes[0].size1.push_back(1);
1248   sizes[0].size1.push_back(0);
1249   sizes[0].size2.push_back(1);
1250   sizes[0].size2.push_back(0);
1251   sizes[0].cols[0] = 2;
1252   sizes[0].cols[1] = 3;
1253   sizes[0].cols[2] = 4;
1254
1255   sizes[1].splitter = ESplitter;
1256   sizes[1].size1.push_back(0);
1257   sizes[1].size1.push_back(1);
1258   sizes[1].size2.push_back(1);
1259   sizes[1].size2.push_back(0);
1260   sizes[1].cols[0] = 1;
1261   sizes[1].cols[1] = 3;
1262   sizes[1].cols[2] = 4;
1263
1264   sizes[2].splitter = OSplitter;
1265   sizes[2].size1.push_back(1);
1266   sizes[2].size1.push_back(0);
1267   sizes[2].size2.push_back(0);
1268   sizes[2].size2.push_back(1);
1269   sizes[2].cols[0] = 1;
1270   sizes[2].cols[1] = 2;
1271   sizes[2].cols[2] = 4;
1272
1273   sizes[3].splitter = ESplitter;
1274   sizes[3].size1.push_back(0);
1275   sizes[3].size1.push_back(1);
1276   sizes[3].size2.push_back(0);
1277   sizes[3].size2.push_back(1);
1278   sizes[3].cols[0] = 1;
1279   sizes[3].cols[1] = 2;
1280   sizes[3].cols[2] = 3;
1281
1282   int slicer = mSlicerManagers[mCurrentPickedImageIndex]->GetSelectedSlicer();
1283   if (viewMode == 1) {
1284     if (slicer >= 0) {
1285       viewMode = 0;
1286       splitter_3->setSizes(sizes[slicer].size1);
1287       sizes[slicer].splitter->setSizes(sizes[slicer].size2);
1288       DataTree->setColumnHidden(sizes[slicer].cols[0],1);
1289       DataTree->setColumnHidden(sizes[slicer].cols[1],1);
1290       DataTree->setColumnHidden(sizes[slicer].cols[2],1);
1291     }
1292   } else {
1293     QList<int> size;
1294     if (slicer >= 0) {
1295       viewMode = 1;
1296       size.push_back(1);
1297       size.push_back(1);
1298       splitter_3->setSizes(size);
1299       sizes[slicer].splitter->setSizes(size);
1300       DataTree->setColumnHidden(sizes[slicer].cols[0],0);
1301       DataTree->setColumnHidden(sizes[slicer].cols[1],0);
1302       DataTree->setColumnHidden(sizes[slicer].cols[2],0);
1303     }
1304   }
1305   UpdateRenderWindows();
1306   /*
1307   ** I don't know why but for both resized QVTKWidget we also need to render
1308   ** the associated Slicer to redraw crosses.
1309   */
1310   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
1311     //     if (DataTree->topLevelItem(i)->data(COLUMN_UL_VIEW,Qt::CheckStateRole).toInt() > 1)
1312     mSlicerManagers[i]->GetSlicer(0)->Render();
1313     mSlicerManagers[i]->GetSlicer(1)->Render();
1314     //     if (DataTree->topLevelItem(i)->data(COLUMN_DL_VIEW,Qt::CheckStateRole).toInt() > 1)
1315     mSlicerManagers[i]->GetSlicer(2)->Render();
1316     mSlicerManagers[i]->GetSlicer(3)->Render();
1317   }
1318 }
1319 //------------------------------------------------------------------------------
1320
1321 //------------------------------------------------------------------------------
1322 QString vvMainWindow::GetSizeInBytes(unsigned long size)
1323 {
1324   QString result = "";// QString::number(size);
1325   //result += " bytes (";
1326   if (size > 1000000000) {
1327     size /= 1000000000;
1328     result += QString::number(size);
1329     result += "Gb";//)";
1330   } else if (size > 1000000) {
1331     size /= 1000000;
1332     result += QString::number(size);
1333     result += "Mb";//)";
1334   } else if (size > 1000) {
1335     size /= 1000;
1336     result += QString::number(size);
1337     result += "kb";//)";
1338   }
1339   return result;
1340 }
1341 //------------------------------------------------------------------------------
1342
1343 //------------------------------------------------------------------------------
1344 QString vvMainWindow::Get4x4MatrixDoubleAsString(vtkSmartPointer<vtkMatrix4x4> matrix, const int precision)
1345 {
1346   std::ostringstream strmatrix;
1347
1348   // Figure out the number of digits of the integer part of the largest absolute value
1349   // for each column
1350   unsigned width[4];
1351   for (unsigned int j = 0; j < 4; j++){
1352     double absmax = 0.;
1353     for (unsigned int i = 0; i < 4; i++)
1354       absmax = std::max(absmax, vnl_math_abs(matrix->GetElement(i, j)));
1355     unsigned ndigits = (unsigned)std::max(0.,std::log10(absmax))+1;
1356     width[j] = precision+ndigits+3;
1357   }
1358
1359   // Output with correct width, aligned to the right
1360   for (unsigned int i = 0; i < 4; i++) {
1361     for (unsigned int j = 0; j < 4; j++) {
1362       strmatrix.setf(ios::fixed,ios::floatfield);
1363       strmatrix.precision(precision);
1364       strmatrix.fill(' ');
1365       strmatrix.width(width[j]);
1366       strmatrix << std::right << matrix->GetElement(i, j);
1367     }
1368     strmatrix << std::endl;
1369   }
1370   QString result = strmatrix.str().c_str();
1371   return result;
1372 }
1373 //------------------------------------------------------------------------------
1374
1375 //------------------------------------------------------------------------------
1376 QString vvMainWindow::GetVectorDoubleAsString(std::vector<double> vectorDouble)
1377 {
1378   QString result;
1379   for (unsigned int i= 0; i < vectorDouble.size(); i++) {
1380     if (i != 0)
1381       result += " ";
1382     result += QString::number(vectorDouble[i]);
1383   }
1384   return result;
1385 }
1386 //------------------------------------------------------------------------------
1387
1388 //------------------------------------------------------------------------------
1389 QString vvMainWindow::GetVectorIntAsString(std::vector<int> vectorInt)
1390 {
1391   QString result;
1392   for (unsigned int i= 0; i < vectorInt.size(); i++) {
1393     if (i != 0)
1394       result += " ";
1395     result += QString::number(vectorInt[i]);
1396   }
1397   return result;
1398 }
1399 //------------------------------------------------------------------------------
1400
1401 //------------------------------------------------------------------------------
1402 //this actually returns the SlicerManager index!
1403 int vvMainWindow::GetSlicerIndexFromItem(QTreeWidgetItem* item)
1404 {
1405   QString id = item->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString();
1406   for (int i = 0; i < DataTree->topLevelItemCount(); i++) {
1407     if (DataTree->topLevelItem(i)->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString() == id)
1408       return i;
1409   }
1410   return -1;
1411 }
1412 //------------------------------------------------------------------------------
1413
1414 //------------------------------------------------------------------------------
1415 QTreeWidgetItem* vvMainWindow::GetItemFromSlicerManager(vvSlicerManager* sm)
1416 {
1417   QString id = sm->GetId().c_str();
1418   for (int i = 0; i < DataTree->topLevelItemCount(); i++) {
1419     if (DataTree->topLevelItem(i)->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString() == id)
1420       return DataTree->topLevelItem(i);
1421   }
1422   return NULL;
1423 }
1424 //------------------------------------------------------------------------------
1425
1426 //------------------------------------------------------------------------------
1427 void vvMainWindow::DisplayChanged(QTreeWidgetItem *clickedItem, int column)
1428 {
1429   if ( column >= COLUMN_CLOSE_IMAGE || column <= 0)
1430     return;
1431
1432   // Get parent information (might be the same item)
1433   int slicerManagerIndex = GetSlicerIndexFromItem(clickedItem);
1434   QTreeWidgetItem* clickedParentItem = DataTree->topLevelItem(slicerManagerIndex);
1435   vvSlicer* clickedSlicer = mSlicerManagers[slicerManagerIndex]->GetSlicer(column-1);
1436
1437   // Go over the complete item tree (only 2 levels, parents and children)
1438   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
1439     // Trick to avoid redoing twice the job for a key (sr)
1440     mSlicerManagers[i]->GetSlicer(column-1)->GetRenderWindow()->GetInteractor()->SetKeySym("Crap");
1441
1442     QTreeWidgetItem* currentParentItem = DataTree->topLevelItem(i);
1443     if(currentParentItem != clickedParentItem) {
1444       // Not the branch of the clicked item, uncheck all
1445
1446       // Parent
1447       currentParentItem->setData(column,Qt::CheckStateRole, 0);
1448       mSlicerManagers[i]->UpdateSlicer(column-1, false);
1449
1450       // Children
1451       for (int iChild = 0; iChild < currentParentItem->childCount(); iChild++) {
1452         currentParentItem->child(iChild)->setData(column,Qt::CheckStateRole, 0);
1453       }
1454     }
1455     else {
1456       // Branch of the clicked one: get check status from actor visibility in slicer
1457       // and toggle the clicked one
1458
1459       // Parent
1460       bool vis = clickedSlicer->GetActorVisibility("image", 0);
1461       bool draw = clickedSlicer->GetRenderer()->GetDraw();
1462
1463       // Update slicer (after getting visibility)
1464       mSlicerManagers[slicerManagerIndex]->UpdateSlicer(column-1, true);
1465       mSlicerManagers[slicerManagerIndex]->UpdateInfoOnCursorPosition(column-1);
1466       DisplaySliders(slicerManagerIndex, column-1);
1467       if(clickedParentItem == clickedItem) {
1468         // Toggle
1469         vis = !draw || !vis;
1470       }
1471       clickedSlicer->SetActorVisibility("image", 0, vis);
1472       clickedParentItem->setData(column, Qt::CheckStateRole, vis?2:0);
1473
1474       // Children
1475       std::map<std::string, int> actorTypeCounts;
1476       for (int iChild = 0; iChild < clickedParentItem->childCount(); iChild++) {
1477         QTreeWidgetItem* currentChildItem = clickedParentItem->child(iChild);
1478         std::string actorType = currentChildItem->data(1,Qt::UserRole).toString().toStdString();
1479         vis = clickedSlicer->GetActorVisibility(actorType, actorTypeCounts[actorType]);
1480         if(currentChildItem == clickedItem) {
1481           // Toggle or force visibility if it was not on this branch so far
1482           vis = !draw || !vis;
1483           clickedSlicer->SetActorVisibility(actorType, actorTypeCounts[actorType], vis);
1484         }
1485         currentChildItem->setData(column, Qt::CheckStateRole, vis?2:0);
1486         actorTypeCounts[actorType]++;
1487       }
1488     }
1489   }
1490
1491   clickedSlicer->Render();
1492 }
1493 //------------------------------------------------------------------------------
1494
1495 void vvMainWindow::InitSlicers()
1496 {
1497   if (mSlicerManagers.size()) {
1498     mSlicerManagers.back()->GenerateDefaultLookupTable();
1499
1500     mSlicerManagers.back()->SetSlicerWindow(0,NOViewWidget->GetRenderWindow());
1501     mSlicerManagers.back()->SetSlicerWindow(1,NEViewWidget->GetRenderWindow());
1502     mSlicerManagers.back()->SetSlicerWindow(2,SOViewWidget->GetRenderWindow());
1503     mSlicerManagers.back()->SetSlicerWindow(3,SEViewWidget->GetRenderWindow());
1504   }
1505 }
1506
1507 //------------------------------------------------------------------------------
1508 void vvMainWindow::InitDisplay()
1509 {
1510   if (mSlicerManagers.size()) {
1511     //BE CAREFUL : this is absolutely necessary to set the interactor style
1512     //in order to have the same style instanciation for all SlicerManagers in
1513     // a same window
1514     for (int j = 0; j < 4; j++) {
1515       vvInteractorStyleNavigator* style = vvInteractorStyleNavigator::New();
1516       style->SetAutoAdjustCameraClippingRange(1);
1517       bool AlreadySelected = false;
1518       for (int i = 0; i < DataTree->topLevelItemCount(); i++) {
1519         mSlicerManagers[i]->SetInteractorStyleNavigator(j,style);
1520
1521         //select the image only if previous are not selected
1522         if (DataTree->topLevelItem(i)->data(j+1,Qt::CheckStateRole).toInt() > 1) {
1523           mSlicerManagers[i]->UpdateSlicer(j,1);
1524           AlreadySelected = true;
1525         } else if (i == DataTree->topLevelItemCount()-1 && !AlreadySelected) {
1526           if (DataTree->selectedItems().size() == 0)
1527             DataTree->topLevelItem(i)->setSelected(1);
1528           DataTree->topLevelItem(i)->setData(j+1,Qt::CheckStateRole,2);
1529           mSlicerManagers[i]->UpdateSlicer(j,1);
1530           DisplaySliders(i,j);
1531         } else {
1532           DataTree->topLevelItem(i)->setData(j+1,Qt::CheckStateRole,0);
1533           mSlicerManagers[i]->UpdateSlicer(j,0);
1534         }
1535       }
1536       style->Delete();
1537     }
1538   }
1539 }
1540 //------------------------------------------------------------------------------
1541
1542 //------------------------------------------------------------------------------
1543 void vvMainWindow::DisplaySliders(int slicer, int window)
1544 {
1545   if(!mSlicerManagers[slicer]->GetSlicer(window)->GetRenderer()->GetDraw())
1546     return;
1547
1548   int range[2];
1549   mSlicerManagers[slicer]->GetSlicer(window)->GetSliceRange(range);
1550   int position = mSlicerManagers[slicer]->GetSlicer(window)->GetSlice();
1551   if (range[1]>0)
1552     verticalSliders[window]->show();
1553   else
1554     verticalSliders[window]->hide();
1555   verticalSliders[window]->setRange(range[0],range[1]);
1556   verticalSliders[window]->setValue(position);
1557
1558   int tRange[2];
1559   tRange[0] = 0;
1560   tRange[1] = mSlicerManagers[slicer]->GetSlicer(window)->GetTMax();
1561   if (tRange[1]>0)
1562     horizontalSliders[window]->show();
1563   else
1564     horizontalSliders[window]->hide();
1565   horizontalSliders[window]->setRange(tRange[0],tRange[1]);
1566   int tPosition = mSlicerManagers[slicer]->GetSlicer(window)->GetMaxCurrentTSlice();
1567   horizontalSliders[window]->setValue(tPosition);
1568 }
1569 //------------------------------------------------------------------------------
1570
1571 //------------------------------------------------------------------------------
1572 void vvMainWindow::CloseImage(QTreeWidgetItem* item, int column)
1573 {
1574   int index = GetSlicerIndexFromItem(item);
1575
1576   if (DataTree->topLevelItem(index) != item) {
1577     QString warning = "Do you really want to close the overlay : ";
1578     warning += item->data(COLUMN_IMAGE_NAME,Qt::DisplayRole).toString();
1579     QMessageBox msgBox(QMessageBox::Warning, tr("Close Overlay"),
1580       warning, 0, this);
1581     msgBox.addButton(tr("Close"), QMessageBox::AcceptRole);
1582     msgBox.addButton(tr("Cancel"), QMessageBox::RejectRole);
1583     if (msgBox.exec() == QMessageBox::AcceptRole) {
1584       std::string overlay_type=item->data(1,Qt::UserRole).toString().toStdString();
1585       int overlay_index=0;
1586       for (int child = 0; child < DataTree->topLevelItem(index)->childCount(); child++) {
1587         if (DataTree->topLevelItem(index)->\
1588           child(child)->data(1,Qt::UserRole).toString().toStdString() == overlay_type)
1589           overlay_index++;
1590         if (DataTree->topLevelItem(index)->child(child) == item) break;
1591       }
1592       if (overlay_type=="fusionSequence") {
1593         //removing the overlay sequence in a fusion sequence visualization mode
1594         //reset the transforms
1595         overlayPanel->getFusionSequenceProperty(-1, false, 0, false);
1596
1597         //unlink and untie the slicer managers
1598         RemoveLink(mSlicerManagers[index]->GetId().c_str(), mSlicerManagers[mSlicerManagers[index]->GetFusionSequenceIndexOfLinkedManager()]->GetId().c_str());
1599         mSlicerManagers[index]->SetFusionSequenceInvolvmentCode(-1);
1600         mSlicerManagers[mSlicerManagers[index]->GetFusionSequenceIndexOfLinkedManager()]->SetFusionSequenceInvolvmentCode(-1);
1601         for (unsigned i=0 ; i<4 ; i++) {
1602             mSlicerManagers[index]->GetSlicer(i)->SetFusionSequenceCode(-1);
1603             mSlicerManagers[mSlicerManagers[index]->GetFusionSequenceIndexOfLinkedManager()]->GetSlicer(i)->SetFusionSequenceCode(-1);
1604         }
1605
1606       }
1607       mSlicerManagers[index]->RemoveActor(overlay_type, overlay_index-1);
1608       mSlicerManagers[index]->SetColorMap(0);
1609       DataTree->topLevelItem(index)->takeChild(DataTree->topLevelItem(index)->indexOfChild(item));
1610       mSlicerManagers[index]->Render();
1611     }
1612   } else if (DataTree->topLevelItemCount() <= 1) {
1613     QString warning = "Do you really want to close the image : ";
1614     warning += item->data(COLUMN_IMAGE_NAME,Qt::DisplayRole).toString();
1615     warning += "\nThis is the last image, you're about to close vv !!!";
1616     QMessageBox msgBox(QMessageBox::Warning, tr("Close Image"),
1617       warning, 0, this);
1618     msgBox.addButton(tr("Close vv"), QMessageBox::AcceptRole);
1619     msgBox.addButton(tr("Cancel"), QMessageBox::RejectRole);
1620     if (msgBox.exec() == QMessageBox::AcceptRole) {
1621       this->close();
1622     }
1623   } else {
1624     QString warning = "Do you really want to close the image : ";
1625     warning += item->data(COLUMN_IMAGE_NAME,Qt::DisplayRole).toString();
1626     QMessageBox msgBox(QMessageBox::Warning, tr("Close Image"),
1627       warning, 0, this);
1628     msgBox.addButton(tr("Close"), QMessageBox::AcceptRole);
1629     msgBox.addButton(tr("Cancel"), QMessageBox::RejectRole);
1630     if (msgBox.exec() == QMessageBox::AcceptRole) {
1631
1632       // Tell tools that we close an image
1633       emit AnImageIsBeingClosed(mSlicerManagers[index]);
1634
1635       std::vector<vvSlicerManager*>::iterator Manageriter = mSlicerManagers.begin();
1636       DataTree->takeTopLevelItem(index);
1637       for (int i = 0; i < index; i++) {
1638         Manageriter++;
1639       }
1640       //if the slicer manager was involved in a fusion sequence visualization...
1641       if ( mSlicerManagers[index]->IsInvolvedInFusionSequence() ) {
1642         //reset the transforms
1643         overlayPanel->getFusionSequenceProperty(-1, false, 0, false);
1644
1645         //unlink and untie the slicer managers
1646         RemoveLink(mSlicerManagers[index]->GetId().c_str(), mSlicerManagers[mSlicerManagers[index]->GetFusionSequenceIndexOfLinkedManager()]->GetId().c_str());
1647         mSlicerManagers[index]->SetFusionSequenceInvolvmentCode(-1);
1648         mSlicerManagers[mSlicerManagers[index]->GetFusionSequenceIndexOfLinkedManager()]->SetFusionSequenceInvolvmentCode(-1);
1649         for (unsigned i=0 ; i<4 ; i++) {
1650             mSlicerManagers[index]->GetSlicer(i)->SetFusionSequenceCode(-1);
1651             mSlicerManagers[mSlicerManagers[index]->GetFusionSequenceIndexOfLinkedManager()]->GetSlicer(i)->SetFusionSequenceCode(-1);
1652         }
1653
1654         //TODO: also remove the image overlaid with the main sequence, as it is becoming invalid...
1655         //this shall be done by calling this->CloseImage() with the correct index;...
1656       }
1657
1658       linkPanel->removeImage(index);
1659       mSlicerManagers[index]->RemoveActors();
1660
1661       //remove the slicer manager
1662       delete mSlicerManagers[index];
1663       mSlicerManagers.erase(Manageriter);
1664
1665       //
1666       InitDisplay();
1667     }
1668   }
1669   ImageInfoChanged();
1670 }
1671 //------------------------------------------------------------------------------
1672
1673 //------------------------------------------------------------------------------
1674 void vvMainWindow::ReloadImage(QTreeWidgetItem* item, int column)
1675 {
1676   // int index = GetSlicerIndexFromItem(item);
1677   //   QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
1678   //   if (item->data(1,Qt::UserRole).toString() == "vector")
1679   //     mSlicerManagers[index]->ReloadVF();
1680   //   else
1681   //     mSlicerManagers[index]->Reload();
1682
1683   //   QApplication::restoreOverrideCursor();
1684   int index = GetSlicerIndexFromItem(item);
1685   QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
1686   QString role=item->data(1,Qt::UserRole).toString();
1687   if ( role == "vector") {
1688     mSlicerManagers[index]->ReloadVF();
1689   }
1690   else if (role == "overlay") {
1691     mSlicerManagers[index]->ReloadOverlay();
1692   }
1693   else if (role == "fusion") {
1694     mSlicerManagers[index]->ReloadFusion();
1695   }
1696   else if (role == "fusionSequence") {
1697     //both versions of the secondary sequence must be updated.
1698     mSlicerManagers[index]->ReloadFusionSequence();
1699     mSlicerManagers[mSlicerManagers[index]->GetFusionSequenceIndexOfLinkedManager()]->Reload();
1700   }
1701   else {
1702     mSlicerManagers[index]->Reload();
1703     //if we update the secondary sequence, then the overlay of the main sequence should also be updated
1704     if (mSlicerManagers[index]->IsSecondarySequenceOfFusionSequence()) mSlicerManagers[mSlicerManagers[index]->GetFusionSequenceIndexOfLinkedManager()]->ReloadFusionSequence();
1705   }
1706   // Update view and info
1707   ImageInfoChanged();
1708   mSlicerManagers[index]->Render();
1709   QApplication::restoreOverrideCursor();
1710 }
1711 //------------------------------------------------------------------------------
1712
1713 //------------------------------------------------------------------------------
1714 void vvMainWindow::MousePositionChanged(int visibility,double x, double y, double z, double X, double Y, double Z , double value)
1715 {
1716   infoPanel->setCurrentInfo(visibility,x,y,z,X,Y,Z,value);
1717 }
1718 //------------------------------------------------------------------------------
1719
1720 //------------------------------------------------------------------------------
1721 void vvMainWindow::VectorChanged(int visibility,double x, double y, double z, double value)
1722 {
1723   overlayPanel->getCurrentVectorInfo(visibility,x,y,z,value);
1724 }
1725 //------------------------------------------------------------------------------
1726
1727 //------------------------------------------------------------------------------
1728 void vvMainWindow::OverlayChanged(int visibility, double valueOver, double valueRef)
1729 {
1730   overlayPanel->getCurrentOverlayInfo(visibility,valueOver, valueRef);
1731 }
1732 //------------------------------------------------------------------------------
1733
1734 //------------------------------------------------------------------------------
1735 void vvMainWindow::FusionChanged(int visibility, double value)
1736 {
1737   overlayPanel->getCurrentFusionInfo(visibility,value);
1738 }
1739 //------------------------------------------------------------------------------
1740
1741 //------------------------------------------------------------------------------
1742 //called when AddOverlayImage, AddFusionSequence
1743 //or when UpdateWindowLevel() is called ; when slicerManager emits WindowLevelChanged
1744 //when ImageInfoChanged() is called
1745 void vvMainWindow::WindowLevelChanged()
1746 {
1747   // Base image
1748   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1749   if(index==-1) return;
1750   windowSpinBox->setValue(mSlicerManagers[index]->GetColorWindow());
1751   levelSpinBox->setValue(mSlicerManagers[index]->GetColorLevel());
1752   colorMapComboBox->setCurrentIndex(mSlicerManagers[index]->GetColorMap());
1753   presetComboBox->setCurrentIndex(mSlicerManagers[index]->GetPreset());
1754
1755   // Overlay image
1756   if (mSlicerManagers[index]->GetSlicer(0)->GetOverlay())
1757     overlayPanel->getOverlayProperty(mSlicerManagers[index]->GetOverlayColor(),
1758     mSlicerManagers[index]->GetLinkOverlayWindowLevel(),
1759     mSlicerManagers[index]->GetOverlayColorWindow(),
1760     mSlicerManagers[index]->GetOverlayColorLevel());
1761   else
1762     overlayPanel->getOverlayProperty(-1,0,0.,0.);
1763
1764   // Fusion & SequenceFusion image
1765   if (mSlicerManagers[index]->GetSlicer(0)->GetFusion()) {
1766     overlayPanel->getFusionProperty(mSlicerManagers[index]->GetFusionOpacity(),
1767       mSlicerManagers[index]->GetFusionThresholdOpacity(),
1768       mSlicerManagers[index]->GetFusionColorMap(),
1769       mSlicerManagers[index]->GetFusionWindow(),
1770       mSlicerManagers[index]->GetFusionLevel());
1771     if (mSlicerManagers[index]->IsMainSequenceOfFusionSequence()) {
1772       overlayPanel->getFusionSequenceProperty(mSlicerManagers[index]->GetFusionSequenceFrameIndex(),
1773         mSlicerManagers[index]->GetFusionSequenceSpatialSyncFlag(),
1774         mSlicerManagers[index]->GetFusionSequenceNbFrames(),
1775         mSlicerManagers[index]->GetFusionSequenceTemporalSyncFlag());
1776     }
1777   }
1778   else if ( mSlicerManagers[index]->IsSecondarySequenceOfFusionSequence() ) {
1779     //if the image is involved in a fusion sequence, preserve the overlay panel!
1780     int ind = mSlicerManagers[index]->GetFusionSequenceIndexOfLinkedManager();
1781     overlayPanel->getFusionProperty(mSlicerManagers[ind]->GetFusionOpacity(),
1782       mSlicerManagers[ind]->GetFusionThresholdOpacity(),
1783       mSlicerManagers[ind]->GetFusionColorMap(),
1784       mSlicerManagers[ind]->GetFusionWindow(),
1785       mSlicerManagers[ind]->GetFusionLevel());
1786     overlayPanel->getFusionSequenceProperty(mSlicerManagers[ind]->GetFusionSequenceFrameIndex(),
1787       mSlicerManagers[ind]->GetFusionSequenceSpatialSyncFlag(),
1788       mSlicerManagers[ind]->GetFusionSequenceNbFrames(),
1789       mSlicerManagers[ind]->GetFusionSequenceTemporalSyncFlag());
1790   }
1791   else
1792   {
1793     overlayPanel->getFusionProperty(-1, -1, -1, -1, -1);
1794     overlayPanel->getFusionSequenceProperty(-1, false, 0, false);
1795   }
1796 }
1797 //------------------------------------------------------------------------------
1798
1799 //------------------------------------------------------------------------------
1800 void vvMainWindow::WindowLevelEdited()
1801 {
1802   presetComboBox->setCurrentIndex(WL_USER);
1803   UpdateWindowLevel();
1804 }
1805 //------------------------------------------------------------------------------
1806
1807 //------------------------------------------------------------------------------
1808 void vvMainWindow::SetWindowLevel(double w, double l)
1809 {
1810   windowSpinBox->setValue(w);
1811   levelSpinBox->setValue(l);
1812   presetComboBox->setCurrentIndex(WL_USER);
1813   colorMapComboBox->setCurrentIndex(0);
1814   UpdateWindowLevel();
1815 }
1816 //------------------------------------------------------------------------------
1817
1818 //------------------------------------------------------------------------------
1819 void vvMainWindow::UpdateWindowLevel()
1820 {
1821   if (DataTree->selectedItems().size()) {
1822     if (presetComboBox->currentIndex() == WL_VENTILATION) //For ventilation
1823       colorMapComboBox->setCurrentIndex(5);
1824     int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1825     mSlicerManagers[index]->SetColorWindow(windowSpinBox->value());
1826     mSlicerManagers[index]->SetColorLevel(levelSpinBox->value());
1827     mSlicerManagers[index]->SetPreset(presetComboBox->currentIndex());
1828     mSlicerManagers[index]->Render();
1829     WindowLevelChanged();
1830   }
1831 }
1832 //------------------------------------------------------------------------------
1833
1834 //------------------------------------------------------------------------------
1835 void vvMainWindow::UpdateSlicingPreset()
1836 {
1837   if (DataTree->selectedItems().size()) {
1838     int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1839     mSlicerManagers[index]->SetSlicingPreset(vvSlicerManager::SlicingPresetType(slicingPresetComboBox->currentIndex()));
1840   }
1841 }
1842 //------------------------------------------------------------------------------
1843
1844 //------------------------------------------------------------------------------
1845 void vvMainWindow::UpdateColorMap()
1846 {
1847   if (DataTree->selectedItems().size()) {
1848     int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1849     mSlicerManagers[index]->SetColorMap(colorMapComboBox->currentIndex());
1850     mSlicerManagers[index]->Render();
1851   }
1852 }
1853 //------------------------------------------------------------------------------
1854 void vvMainWindow::SwitchWindowLevel()
1855 {
1856   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1857   int window = mSlicerManagers[index]->GetColorWindow();
1858   presetComboBox->setCurrentIndex(WL_USER);
1859   windowSpinBox->setValue(-window);
1860   UpdateWindowLevel();
1861 }
1862 //------------------------------------------------------------------------------
1863
1864 //------------------------------------------------------------------------------
1865 void vvMainWindow::ApplyWindowLevelToAllImages()
1866 {
1867   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1868   if(index==-1) return;
1869   double window = mSlicerManagers[index]->GetColorWindow();
1870   double level = mSlicerManagers[index]->GetColorLevel();
1871
1872   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
1873     if (mSlicerManagers[i] == NULL)
1874       continue;
1875     mSlicerManagers[i]->SetColorWindow(window);
1876     mSlicerManagers[i]->SetColorLevel(level);
1877     mSlicerManagers[i]->SetPreset(WL_USER);
1878     mSlicerManagers[i]->Render();
1879   }
1880 }
1881 //------------------------------------------------------------------------------
1882
1883 //------------------------------------------------------------------------------
1884 void vvMainWindow::ApplyWindowToSetOfImages(double window, unsigned int indexMin, unsigned int indexMax)
1885 {
1886   for (unsigned int i = indexMin; i <= indexMax && i < mSlicerManagers.size(); i++) {
1887     if (mSlicerManagers[i] == NULL)
1888       continue;
1889     mSlicerManagers[i]->SetColorWindow(window);
1890     mSlicerManagers[i]->SetPreset(WL_USER);
1891     mSlicerManagers[i]->Render();
1892   }
1893 }
1894 //------------------------------------------------------------------------------
1895
1896 //------------------------------------------------------------------------------
1897 void vvMainWindow::ApplyLevelToSetOfImages(double level, unsigned int indexMin, unsigned int indexMax)
1898 {
1899   for (unsigned int i = indexMin; i <= indexMax && i < mSlicerManagers.size(); i++) {
1900     if (mSlicerManagers[i] == NULL)
1901       continue;
1902     mSlicerManagers[i]->SetColorLevel(level);
1903     mSlicerManagers[i]->SetPreset(WL_USER);
1904     mSlicerManagers[i]->Render();
1905   }
1906 }
1907 //------------------------------------------------------------------------------
1908
1909 //------------------------------------------------------------------------------
1910 void vvMainWindow::UpdateLinkManager(std::string id, int slicer, double x, double y, double z, int temps)
1911 {
1912   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
1913     if (mSlicerManagers[i]->GetId() == id) {
1914       mSlicerManagers[i]->GetSlicer(slicer)->SetCurrentPosition(x,y,z,temps);
1915       mSlicerManagers[i]->UpdateViews(0,slicer);
1916       break;
1917     }
1918   }
1919 }
1920 //------------------------------------------------------------------------------
1921
1922 //------------------------------------------------------------------------------
1923 void vvMainWindow::UpdateLinkedNavigation(std::string id, vvSlicerManager * sm, vvSlicer* refSlicer)
1924 {
1925   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
1926     if (id == mSlicerManagers[i]->GetId()) {
1927       mSlicerManagers[i]->UpdateLinkedNavigation(refSlicer);
1928     }
1929   }
1930 }
1931 //------------------------------------------------------------------------------
1932
1933 //------------------------------------------------------------------------------
1934 void vvMainWindow::ShowContextMenu(QPoint point)
1935 {
1936   if (!DataTree->selectedItems().size()) {
1937     contextActions[1]->setEnabled(0);
1938     contextActions[2]->setEnabled(0);
1939     contextActions[3]->setEnabled(0);
1940     contextActions[4]->setEnabled(0);
1941     contextActions[5]->setEnabled(0);
1942     contextActions[6]->setEnabled(0);
1943   } else {
1944     int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1945     contextActions[1]->setEnabled(1);
1946     contextActions[2]->setEnabled(
1947       DataTree->itemWidget(DataTree->selectedItems()[0],
1948       COLUMN_RELOAD_IMAGE)->isEnabled());
1949     contextActions[3]->setEnabled(1);
1950     contextActions[5]->setEnabled(1);
1951     contextActions[6]->setEnabled(1);
1952
1953     if (mSlicerManagers[index]->GetDimension() < 3)
1954       contextActions[4]->setEnabled(0);
1955     else
1956       contextActions[4]->setEnabled(1);
1957   }
1958   contextMenu.exec(QCursor::pos());
1959 }
1960 //------------------------------------------------------------------------------
1961
1962 //------------------------------------------------------------------------------
1963 void vvMainWindow::CloseImage()
1964 {
1965   CloseImage(DataTree->selectedItems()[0],0);
1966 }
1967 //------------------------------------------------------------------------------
1968
1969 //------------------------------------------------------------------------------
1970 void vvMainWindow::ReloadImage()
1971 {
1972   ReloadImage(DataTree->selectedItems()[0],0);
1973 }
1974 //------------------------------------------------------------------------------
1975
1976 //------------------------------------------------------------------------------
1977 void vvMainWindow::SelectOverlayImage()
1978 {
1979   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1980
1981   //check if one overlay image is added
1982   for (int child = 0; child < DataTree->topLevelItem(index)->childCount(); child++)
1983     if (DataTree->topLevelItem(index)->child(child)->data(1,Qt::UserRole).toString() == "overlay") {
1984       QString error = "Cannot add more than one compared image\n";
1985       error += "Please remove first ";
1986       error += DataTree->topLevelItem(index)->child(child)->data(COLUMN_IMAGE_NAME,Qt::DisplayRole).toString();
1987       QMessageBox::information(this,tr("Problem adding compared image !"),error);
1988       return;
1989     }
1990
1991     QString Extensions = EXTENSIONS;
1992     Extensions += ";;All Files (*)";
1993     QStringList files = QFileDialog::getOpenFileNames(this,tr("Load Overlay image"),mInputPathName,Extensions);
1994     if (files.isEmpty())
1995       return;
1996
1997     std::vector<std::string> vecFileNames;
1998     for (int i = 0; i < files.size(); i++) {
1999       vecFileNames.push_back(files[i].toStdString());
2000     }
2001     AddOverlayImage(index,vecFileNames,vvImageReader::IMAGE);
2002 }
2003 //------------------------------------------------------------------------------
2004
2005 //------------------------------------------------------------------------------
2006 void vvMainWindow::AddOverlayImage(int index, std::vector<std::string> fileNames, vvImageReader::LoadedImageType type)
2007 {
2008   QString file(fileNames[0].c_str());
2009   if (QFile::exists(file))
2010   {
2011     mInputPathName = itksys::SystemTools::GetFilenamePath(file.toStdString()).c_str();
2012     itk::ImageIOBase::Pointer reader = itk::ImageIOFactory::CreateImageIO(
2013       file.toStdString().c_str(), itk::ImageIOFactory::ReadMode);
2014     reader->SetFileName(fileNames[0].c_str());
2015     reader->ReadImageInformation();
2016     std::string component = reader->GetComponentTypeAsString(reader->GetComponentType());
2017     int dimension = reader->GetNumberOfDimensions();
2018     QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
2019     vvProgressDialog progress("Opening " + file.toStdString());
2020     qApp->processEvents();
2021
2022     std::string filename = itksys::SystemTools::GetFilenameWithoutExtension(file.toStdString()).c_str();
2023     if (mSlicerManagers[index]->SetOverlay(fileNames,dimension, component,type)) {
2024       //create an item in the tree with good settings
2025       QTreeWidgetItem *item = new QTreeWidgetItem();
2026       item->setData(0,Qt::UserRole,file.toStdString().c_str());
2027       item->setData(1,Qt::UserRole,tr("overlay"));
2028       QFileInfo fileinfo(file); //Do not show the path
2029       item->setData(COLUMN_IMAGE_NAME,Qt::DisplayRole,fileinfo.fileName());
2030       item->setToolTip(COLUMN_IMAGE_NAME, mSlicerManagers[index]->GetListOfAbsoluteFilePathInOneString("overlay").c_str());
2031       qApp->processEvents();
2032
2033       for (int j = 1; j <= 4; j++) {
2034         item->setData(j,Qt::CheckStateRole,DataTree->topLevelItem(index)->data(j,Qt::CheckStateRole));
2035       }
2036
2037       //Create the buttons for reload and close
2038       qApp->processEvents();
2039       QTreePushButton* cButton = new QTreePushButton;
2040       cButton->setItem(item);
2041       cButton->setColumn(COLUMN_CLOSE_IMAGE);
2042       cButton->setToolTip(tr("close image"));
2043       cButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/exit.png")));
2044       connect(cButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
2045         this,SLOT(CloseImage(QTreeWidgetItem*, int)));
2046
2047       QTreePushButton* rButton = new QTreePushButton;
2048       rButton->setItem(item);
2049       rButton->setColumn(COLUMN_RELOAD_IMAGE);
2050       rButton->setToolTip(tr("reload image"));
2051       rButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/rotateright.png")));
2052       connect(rButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
2053         this,SLOT(ReloadImage(QTreeWidgetItem*, int)));
2054
2055       DataTree->topLevelItem(index)->setExpanded(1);
2056       DataTree->topLevelItem(index)->addChild(item);
2057       DataTree->setItemWidget(item, COLUMN_CLOSE_IMAGE, cButton);
2058       DataTree->setItemWidget(item, COLUMN_RELOAD_IMAGE, rButton);
2059
2060       //set the id of the image
2061       QString id = DataTree->topLevelItem(index)->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString();
2062       item->setData(COLUMN_IMAGE_NAME,Qt::UserRole,id.toStdString().c_str());
2063       UpdateTree();
2064       qApp->processEvents();
2065       ImageInfoChanged();
2066       QApplication::restoreOverrideCursor();
2067
2068       // Update the display to update, e.g., the sliders
2069       for(int i=0; i<4; i++)
2070         DisplaySliders(index, i);
2071     } else {
2072       QApplication::restoreOverrideCursor();
2073       QString error = "Cannot import the new image.\n";
2074       error += mSlicerManagers[index]->GetLastError().c_str();
2075       QMessageBox::information(this,tr("Problem reading image !"),error);
2076     }
2077     WindowLevelChanged();
2078   }
2079   else
2080     QMessageBox::information(this,tr("Problem reading Overlay !"),"File doesn't exist!");
2081 }
2082 //------------------------------------------------------------------------------
2083
2084
2085 //------------------------------------------------------------------------------
2086 void vvMainWindow::AddROI(int index, QString file)
2087 {
2088   /*
2089   // Get slice manager
2090
2091   // Load image
2092
2093   vvImageReader * mReader = new vvImageReader;
2094   mReader->SetInputFilename(filename.toStdString());
2095   mReader->Update(IMAGE);
2096   if (mReader->GetLastError().size() != 0) {
2097   std::cerr << "Error while reading " << filename.toStdString() << std::endl;
2098   QString error = "Cannot open file \n";
2099   error += mReader->GetLastError().c_str();
2100   QMessageBox::information(this,tr("Reading problem"),error);
2101   delete mReader;
2102   return;
2103   }
2104   vvImage::Pointer roi = mReader->GetOutput();
2105
2106   // Create roi in new tool
2107   vvToolStructureSetManager::AddImage(mCurrentSlicerManager, roi);
2108   */
2109 }
2110 //------------------------------------------------------------------------------
2111
2112 //------------------------------------------------------------------------------
2113 void vvMainWindow::SelectFusionImage()
2114 {
2115   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2116
2117   //check if one fusion image is added
2118   for (int child = 0; child < DataTree->topLevelItem(index)->childCount(); child++)
2119     if ( (DataTree->topLevelItem(index)->child(child)->data(1,Qt::UserRole).toString() == "fusion") ||
2120       (DataTree->topLevelItem(index)->child(child)->data(1,Qt::UserRole).toString() == "fusionSequence") ) {
2121         QString error = "Cannot add more than one fusion image\n";
2122         error += "Please remove first ";
2123         error += DataTree->topLevelItem(index)->child(child)->data(COLUMN_IMAGE_NAME,Qt::DisplayRole).toString();
2124         QMessageBox::information(this,tr("Problem adding fusion image !"),error);
2125         return;
2126     }
2127
2128     QString Extensions = EXTENSIONS;
2129     Extensions += ";;All Files (*)";
2130     QString file = QFileDialog::getOpenFileName(this,tr("Load Fusion image"),mInputPathName,Extensions);
2131     if (!file.isEmpty())
2132       AddFusionImage(index,file);
2133 }
2134 //------------------------------------------------------------------------------
2135
2136 //------------------------------------------------------------------------------
2137 void vvMainWindow::ResetTransformationToIdentity()
2138 {
2139   std::string actorType = DataTree->selectedItems()[0]->data(1,Qt::UserRole).toString().toStdString();
2140   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2141   mSlicerManagers[index]->ResetTransformationToIdentity(actorType);
2142   ImageInfoChanged();
2143 }
2144 //------------------------------------------------------------------------------
2145
2146 //------------------------------------------------------------------------------
2147 void vvMainWindow::AddFusionImage(int index, QString file)
2148 {
2149   if (QFile::exists(file))
2150   {
2151     mInputPathName = itksys::SystemTools::GetFilenamePath(file.toStdString()).c_str();
2152     itk::ImageIOBase::Pointer reader = itk::ImageIOFactory::CreateImageIO(
2153       file.toStdString().c_str(), itk::ImageIOFactory::ReadMode);
2154     reader->SetFileName(file.toStdString().c_str());
2155     reader->ReadImageInformation();
2156     std::string component = reader->GetComponentTypeAsString(reader->GetComponentType());
2157     if (reader) {
2158       QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
2159       vvProgressDialog progress("Opening fusion");
2160       qApp->processEvents();
2161
2162       std::string filename = itksys::SystemTools::GetFilenameWithoutExtension(file.toStdString()).c_str();
2163       if (mSlicerManagers[index]->SetFusion(file.toStdString(),
2164         reader->GetNumberOfDimensions(), component)) {
2165           //create an item in the tree with good settings
2166           QTreeWidgetItem *item = new QTreeWidgetItem();
2167           item->setData(0,Qt::UserRole,file.toStdString().c_str());
2168           item->setData(1,Qt::UserRole,tr("fusion"));
2169           QFileInfo fileinfo(filename.c_str()); //Do not show the path
2170           item->setData(COLUMN_IMAGE_NAME,Qt::DisplayRole,fileinfo.fileName());
2171           item->setToolTip(COLUMN_IMAGE_NAME, mSlicerManagers[index]->GetListOfAbsoluteFilePathInOneString("fusion").c_str());
2172           qApp->processEvents();
2173
2174           for (int j = 1; j <= 4; j++) {
2175             item->setData(j,Qt::CheckStateRole,DataTree->topLevelItem(index)->data(j,Qt::CheckStateRole));
2176           }
2177
2178           //Create the buttons for reload and close
2179           qApp->processEvents();
2180           QTreePushButton* cButton = new QTreePushButton;
2181           cButton->setItem(item);
2182           cButton->setColumn(COLUMN_CLOSE_IMAGE);
2183           cButton->setToolTip(tr("close image"));
2184           cButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/exit.png")));
2185           connect(cButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
2186             this,SLOT(CloseImage(QTreeWidgetItem*, int)));
2187
2188           QTreePushButton* rButton = new QTreePushButton;
2189           rButton->setItem(item);
2190           rButton->setColumn(COLUMN_RELOAD_IMAGE);
2191           rButton->setToolTip(tr("reload image"));
2192           rButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/rotateright.png")));
2193           connect(rButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
2194             this,SLOT(ReloadImage(QTreeWidgetItem*, int)));
2195
2196           DataTree->topLevelItem(index)->setExpanded(1);
2197           DataTree->topLevelItem(index)->addChild(item);
2198           DataTree->setItemWidget(item, COLUMN_CLOSE_IMAGE, cButton);
2199           DataTree->setItemWidget(item, COLUMN_RELOAD_IMAGE, rButton);
2200
2201           //set the id of the image
2202           QString id = DataTree->topLevelItem(index)->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString();
2203           item->setData(COLUMN_IMAGE_NAME,Qt::UserRole,id.toStdString().c_str());
2204           UpdateTree();
2205           qApp->processEvents();
2206           ImageInfoChanged();
2207           QApplication::restoreOverrideCursor();
2208       } else {
2209         QApplication::restoreOverrideCursor();
2210         QString error = "Cannot import the new image.\n";
2211         error += mSlicerManagers[index]->GetLastError().c_str();
2212         QMessageBox::information(this,tr("Problem reading image !"),error);
2213       }
2214     } else {
2215       QString error = "Cannot import the new image.\n";
2216       QMessageBox::information(this,tr("Problem reading image !"),error);
2217     }
2218   }
2219   else
2220     QMessageBox::information(this,tr("Problem reading Fusion !"),"File doesn't exist!");
2221 }
2222 //------------------------------------------------------------------------------
2223 //------------------------------------------------------------------------------
2224 void vvMainWindow::AddLandmarks(int index, std::vector<std::string> files)
2225 {
2226     if (!landmarksPanel->LoadFromFile(files))
2227       QMessageBox::information(this,tr("Problem reading Landmarks !"),"File doesn't exist!");
2228
2229     landmarksPanel->SetCurrentPath(mInputPathName.toStdString());
2230     landmarksPanel->SetCurrentImage(mSlicerManagers[index]->GetFileName().c_str());
2231 }
2232
2233 //------------------------------------------------------------------------------
2234 void vvMainWindow::OpenField()
2235 {
2236   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2237   //check if a vector field has already been added
2238   for (int child = 0; child < DataTree->topLevelItem(index)->childCount(); child++)
2239     if (DataTree->topLevelItem(index)->child(child)->data(1,Qt::UserRole).toString() == "vector") {
2240       QString error = "Cannot add more than one vector field\n";
2241       error += "Please remove first ";
2242       error += DataTree->topLevelItem(index)->child(child)->data(COLUMN_IMAGE_NAME,Qt::DisplayRole).toString();
2243       QMessageBox::information(this,tr("Problem adding vector field!"),error);
2244       return;
2245     }
2246
2247     QString Extensions = "Images ( *.mhd)";
2248     Extensions += ";;Images ( *.mha)";
2249     Extensions += ";;VF Images ( *.vf)";
2250     Extensions += ";;nii Images ( *.nii)";
2251     Extensions += ";;nrrd Images ( *.nrrd)";
2252     Extensions += ";;nhdr Images ( *.nhdr)";
2253     Extensions += ";;All Files (*)";
2254     QString file = QFileDialog::getOpenFileName(this,tr("Load deformation field"),mInputPathName,Extensions);
2255     if (!file.isEmpty())
2256       AddField(file,index);
2257 }
2258 //------------------------------------------------------------------------------
2259
2260
2261 //------------------------------------------------------------------------------
2262 void vvMainWindow::AddFieldEntry(QString filename,int index,bool from_disk)
2263 {
2264   //create an item in the tree with good settings
2265   QTreeWidgetItem *item = new QTreeWidgetItem();
2266   item->setData(0,Qt::UserRole,filename.toStdString().c_str());
2267   item->setData(1,Qt::UserRole,tr("vector"));
2268   QFileInfo fileinfo(filename); //Do not show the path
2269   item->setData(COLUMN_IMAGE_NAME,Qt::DisplayRole,fileinfo.fileName());
2270   item->setToolTip(COLUMN_IMAGE_NAME, mSlicerManagers[index]->GetListOfAbsoluteFilePathInOneString("vector").c_str());
2271   qApp->processEvents();
2272
2273   for (int j = 1; j <= 4; j++) {
2274     item->setData(j,Qt::CheckStateRole,DataTree->topLevelItem(index)->data(j,Qt::CheckStateRole));
2275   }
2276
2277   //Create the buttons for reload and close
2278   qApp->processEvents();
2279   QTreePushButton* cButton = new QTreePushButton;
2280   cButton->setItem(item);
2281   cButton->setColumn(COLUMN_CLOSE_IMAGE);
2282   cButton->setToolTip(tr("close vector field"));
2283   cButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/exit.png")));
2284   connect(cButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
2285     this,SLOT(CloseImage(QTreeWidgetItem*, int)));
2286
2287   QTreePushButton* rButton = new QTreePushButton;
2288   rButton->setItem(item);
2289   rButton->setColumn(COLUMN_RELOAD_IMAGE);
2290   rButton->setToolTip(tr("reload vector field"));
2291   rButton->setEnabled(from_disk);
2292   rButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/rotateright.png")));
2293   connect(rButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
2294     this,SLOT(ReloadImage(QTreeWidgetItem*, int)));
2295
2296   DataTree->topLevelItem(index)->setExpanded(1);
2297   DataTree->topLevelItem(index)->addChild(item);
2298   DataTree->setItemWidget(item, COLUMN_RELOAD_IMAGE, rButton);
2299   DataTree->setItemWidget(item, COLUMN_CLOSE_IMAGE, cButton);
2300
2301   //set the id of the image
2302   QString id = DataTree->topLevelItem(index)->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString();
2303   item->setData(COLUMN_IMAGE_NAME,Qt::UserRole,id.toStdString().c_str());
2304   UpdateTree();
2305   qApp->processEvents();
2306   ImageInfoChanged();
2307   QApplication::restoreOverrideCursor();
2308 }
2309 //------------------------------------------------------------------------------
2310
2311
2312 //------------------------------------------------------------------------------
2313 void vvMainWindow::AddField(vvImage::Pointer vf,QString file,int index)
2314 {
2315   QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
2316   vvSlicerManager* imageManager = mSlicerManagers[index];
2317   if (imageManager->SetVF(vf,file.toStdString())) {
2318     AddFieldEntry(file,index,false);
2319   } else {
2320     QString error = "Cannot import the vector field for this image.\n";
2321     error += imageManager->GetLastError().c_str();
2322     QMessageBox::information(this,tr("Problem reading VF !"),error);
2323   }
2324   QApplication::restoreOverrideCursor();
2325 }
2326 //------------------------------------------------------------------------------
2327
2328
2329 //------------------------------------------------------------------------------
2330 void vvMainWindow::AddField(QString file,int index)
2331 {
2332   if (QFile::exists(file)) {
2333     mInputPathName = itksys::SystemTools::GetFilenamePath(file.toStdString()).c_str();
2334
2335     //init the progress events
2336     QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
2337     vvProgressDialog progress("Opening " + file.toStdString());
2338     qApp->processEvents();
2339
2340     //read the vector and put it in the current mSlicerManager
2341     vvSlicerManager* imageManager = mSlicerManagers[index];
2342     qApp->processEvents();
2343
2344     std::string filename = itksys::SystemTools::GetFilenameWithoutExtension(file.toStdString()).c_str();
2345     if (imageManager->SetVF(file.toStdString())) {
2346       imageManager->Render();
2347       AddFieldEntry(file,index,true);
2348     } else {
2349       QApplication::restoreOverrideCursor();
2350       QString error = "Cannot import the vector field for this image.\n";
2351       error += imageManager->GetLastError().c_str();
2352       QMessageBox::information(this,tr("Problem reading VF !"),error);
2353     }
2354   } else
2355     QMessageBox::information(this,tr("Problem reading VF !"),"File doesn't exist!");
2356
2357 }
2358 //------------------------------------------------------------------------------
2359
2360
2361 //------------------------------------------------------------------------------
2362 void vvMainWindow::SetVFProperty(int subsampling, int scale, int log, int width, double r, double g, double b)
2363 {
2364   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2365   if (mSlicerManagers[index]->GetSlicer(0)->GetVF()) {
2366     for (int i = 0; i < 4; i++) {
2367       mSlicerManagers[index]->GetSlicer(i)->SetVFSubSampling(subsampling);
2368       mSlicerManagers[index]->GetSlicer(i)->SetVFScale(scale);
2369       mSlicerManagers[index]->GetSlicer(i)->SetVFWidth(width);
2370       mSlicerManagers[index]->GetSlicer(i)->SetVFColor(r,g,b);
2371       if (log > 0)
2372         mSlicerManagers[index]->GetSlicer(i)->SetVFLog(1);
2373       else
2374         mSlicerManagers[index]->GetSlicer(i)->SetVFLog(0);
2375     }
2376   }
2377 }
2378 //------------------------------------------------------------------------------
2379
2380
2381 //------------------------------------------------------------------------------
2382 void vvMainWindow::SetOverlayProperty(int color, int linked, double window, double level)
2383 {
2384   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2385   if (mSlicerManagers[index]->GetSlicer(0)->GetOverlay()) {
2386     mSlicerManagers[index]->SetOverlayColor(color);
2387     mSlicerManagers[index]->SetColorMap(0);
2388     mSlicerManagers[index]->SetLinkOverlayWindowLevel(linked);
2389     mSlicerManagers[index]->SetOverlayColorWindow(window);
2390     mSlicerManagers[index]->SetOverlayColorLevel(level);
2391     mSlicerManagers[index]->Render();
2392   }
2393 }
2394 //------------------------------------------------------------------------------
2395
2396 //------------------------------------------------------------------------------
2397 void vvMainWindow::SetFusionProperty(int opacity, int thresOpacity, int colormap,double window, double level, bool showLegend)
2398 {
2399   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2400   if (mSlicerManagers[index]->GetSlicer(0)->GetFusion()) {
2401     mSlicerManagers[index]->SetFusionColorMap(colormap);
2402     mSlicerManagers[index]->SetFusionOpacity(opacity);
2403     mSlicerManagers[index]->SetFusionThresholdOpacity(thresOpacity);
2404     mSlicerManagers[index]->SetFusionWindow(window);
2405     mSlicerManagers[index]->SetFusionLevel(level);
2406     mSlicerManagers[index]->SetFusionShowLegend(showLegend);
2407     mSlicerManagers[index]->SetColorMap(0);
2408     mSlicerManagers[index]->Render();
2409   }
2410 }
2411 //------------------------------------------------------------------------------
2412
2413
2414 //------------------------------------------------------------------------------
2415 void vvMainWindow::SelectFusionSequence()
2416 {
2417   //get the index of the slicer manager of the main sequence (CT)
2418   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2419   //check if one overlay image is already associated
2420   for (int child = 0; child < DataTree->topLevelItem(index)->childCount(); child++)
2421     if ( (DataTree->topLevelItem(index)->child(child)->data(1,Qt::UserRole).toString() == "fusion") ||
2422       (DataTree->topLevelItem(index)->child(child)->data(1,Qt::UserRole).toString() == "fusionSequence") ) {
2423         QString error = "Cannot add more than one compared image\n";
2424         error += "Please remove first ";
2425         error += DataTree->topLevelItem(index)->child(child)->data(COLUMN_IMAGE_NAME,Qt::DisplayRole).toString();
2426         QMessageBox::information(this,tr("Problem adding compared image !"),error);
2427         return;
2428     }
2429
2430     QString Extensions = EXTENSIONS;
2431     Extensions += ";;All Files (*)";
2432     QStringList files = QFileDialog::getOpenFileNames(this,tr("Load Overlay image sequence"),mInputPathName,Extensions);
2433     if (files.isEmpty())
2434       return;
2435
2436     std::vector<std::string> vecFileNames;
2437     for (int i = 0; i < files.size(); i++) {
2438       vecFileNames.push_back(files[i].toStdString());
2439     }
2440
2441     //associate the secondary sequence (US) to the main one
2442     AddFusionSequence(index,vecFileNames,vvImageReader::MERGEDWITHTIME);
2443 }
2444 //------------------------------------------------------------------------------
2445
2446
2447 //------------------------------------------------------------------------------
2448 void vvMainWindow::SelectFusionSequenceCorrespondances() {
2449
2450   //make sure the index is right?
2451   //in the end, I should attach the temporal data to the right sequence!
2452   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2453   //in case the other sequence got selected, make sure we select the primary sequence
2454   if ( (!mSlicerManagers[index]->GetSlicer(0)->GetFusion()) && mSlicerManagers[index]->GetFusionSequenceIndexOfLinkedManager()>=0 ) {
2455     index = mSlicerManagers[index]->GetFusionSequenceIndexOfLinkedManager();
2456   }
2457
2458   //open a dialog box to find a file
2459   //QString Extensions = EXTENSIONS;
2460   QString Extensions = ";;All Files (*)";
2461   QString fileName = QFileDialog::getOpenFileName(this,tr("Load respiratory signal for fused sequence"),mInputPathName,Extensions);
2462   if (fileName.isNull())
2463     return;
2464
2465   //read it as a vector of values
2466   vnl_vector<double> tmpVect;
2467
2468   std::ifstream file;
2469   file.open(fileName.toStdString().c_str());
2470   tmpVect.read_ascii(file);
2471   file.close();
2472
2473   //if compatible with the fused image sequence (number of entries = nb of entries in main sequence + nb of entries in joint sequence), enable the temporalSync
2474   bool signalOK = true;
2475   unsigned nbFrameMain = mSlicerManagers[index]->GetImage()->GetTransform().size();
2476   unsigned nbFrameSecondary = mSlicerManagers[index]->GetFusionSequenceNbFrames();
2477
2478   std::vector<unsigned> temporalCorrespondances;
2479   if ( tmpVect.size() == nbFrameMain + nbFrameSecondary ) {
2480     for (unsigned i=0 ; i<tmpVect.size() ; i++) {
2481       if (i<nbFrameMain) { //first part of the file: i -> index in secondary seq.
2482         if ( tmpVect(i)<nbFrameSecondary ) temporalCorrespondances.push_back(tmpVect(i));
2483         else { signalOK=false; break; } //pointing outside the secondary sequence...
2484       }
2485       else { //first part of the file -> index in secondary seq.
2486         if ( tmpVect(i)<nbFrameMain ) temporalCorrespondances.push_back(tmpVect(i));
2487         else { signalOK=false; break; } //pointing outside the secondary sequence...
2488       }
2489     }
2490   }
2491   else {signalOK=false;}
2492   if (!signalOK) {//else, send a message to signal the failure...
2493     QString error = "The provided temporal correspondances is invalid - check tooltip.\n";
2494     error += "Ignoring file: " + fileName;
2495     QMessageBox::information(this,tr("Problem adding temporal correspondances!"),error);
2496     return;
2497   }
2498   else {
2499     //for convenience, associate this sequence to both the current slicer manager, and to the linked one
2500     mSlicerManagers[index]->SetFusionSequenceCorrespondances(temporalCorrespondances);
2501     mSlicerManagers[ mSlicerManagers[index]->GetFusionSequenceIndexOfLinkedManager() ]->SetFusionSequenceCorrespondances(temporalCorrespondances);
2502     overlayPanel->enableFusionSequenceTemporalSync();
2503   }
2504
2505 }
2506 //------------------------------------------------------------------------------
2507
2508
2509 //------------------------------------------------------------------------------
2510 //when this function is called index is the slicer manager index corresponding to the main sequence (CT)
2511 //the files behind fileNames points to the data for the secondary sequence
2512 void vvMainWindow::AddFusionSequence(int index, std::vector<std::string> fileNames, vvImageReader::LoadedImageType type)
2513 {
2514   QString file(fileNames[0].c_str());
2515   if (QFile::exists(file))
2516   {
2517     mInputPathName = itksys::SystemTools::GetFilenamePath(file.toStdString()).c_str();
2518     itk::ImageIOBase::Pointer reader = itk::ImageIOFactory::CreateImageIO(
2519       file.toStdString().c_str(), itk::ImageIOFactory::ReadMode);
2520     reader->SetFileName(fileNames[0].c_str());
2521     reader->ReadImageInformation();
2522     std::string component = reader->GetComponentTypeAsString(reader->GetComponentType());
2523     int dimension = reader->GetNumberOfDimensions();
2524     QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
2525     vvProgressDialog progress("Opening " + file.toStdString());
2526     qApp->processEvents();
2527
2528     std::string filename = itksys::SystemTools::GetFilenameWithoutExtension(file.toStdString()).c_str();
2529
2530     if (mSlicerManagers[index]->SetFusionSequence(fileNames,dimension, component,type)) {
2531       //create an item in the tree with good settings
2532       QTreeWidgetItem *item = new QTreeWidgetItem();
2533       item->setData(0,Qt::UserRole,file.toStdString().c_str());
2534       item->setData(1,Qt::UserRole,tr("fusionSequence"));
2535
2536       QFileInfo fileinfo(file); //Do not show the path
2537       item->setData(COLUMN_IMAGE_NAME,Qt::DisplayRole,fileinfo.fileName());
2538       item->setToolTip(COLUMN_IMAGE_NAME, mSlicerManagers[index]->GetListOfAbsoluteFilePathInOneString("fusionSequence").c_str());
2539       qApp->processEvents();
2540       for (int j = 1; j <= 4; j++) {
2541         item->setData(j,Qt::CheckStateRole,DataTree->topLevelItem(index)->data(j,Qt::CheckStateRole));
2542       }
2543
2544       //Create the buttons for reload and close
2545       qApp->processEvents();
2546       QTreePushButton* cButton = new QTreePushButton;
2547       cButton->setItem(item);
2548       cButton->setColumn(COLUMN_CLOSE_IMAGE);
2549       cButton->setToolTip(tr("close image"));
2550       cButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/exit.png")));
2551       connect(cButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
2552         this,SLOT(CloseImage(QTreeWidgetItem*, int)));
2553
2554       QTreePushButton* rButton = new QTreePushButton;
2555       rButton->setItem(item);
2556       rButton->setColumn(COLUMN_RELOAD_IMAGE);
2557       rButton->setToolTip(tr("reload image"));
2558       rButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/rotateright.png")));
2559       connect(rButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
2560         this,SLOT(ReloadImage(QTreeWidgetItem*, int)));
2561
2562       DataTree->topLevelItem(index)->setExpanded(1);
2563       DataTree->topLevelItem(index)->addChild(item);
2564       DataTree->setItemWidget(item, COLUMN_CLOSE_IMAGE, cButton);
2565       DataTree->setItemWidget(item, COLUMN_RELOAD_IMAGE, rButton);
2566
2567       //store the original transform matrix
2568       int indexParent = GetSlicerIndexFromItem( DataTree->topLevelItem(index) );
2569       mSlicerManagers[indexParent]->SetFusionSequenceMainTransformMatrix( mSlicerManagers[indexParent]->GetSlicer(0)->GetImage()->GetTransform()[0]->GetMatrix() );
2570
2571       //set the id of the image
2572       QString id = DataTree->topLevelItem(index)->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString();
2573       item->setData(COLUMN_IMAGE_NAME,Qt::UserRole,id.toStdString().c_str());
2574       UpdateTree();
2575       qApp->processEvents();
2576
2577       //ImageInfoChanged();
2578
2579       QApplication::restoreOverrideCursor();
2580       // Update the display to update, e.g., the sliders
2581       for(int i=0; i<4; i++)
2582         DisplaySliders(index, i);
2583
2584
2585       //This loads the secondary sequence (US) as an independent sequence
2586       LoadImages(fileNames, type);
2587       //reset the transforms to identiy
2588       for (unsigned i=0 ; i<mSlicerManagers.back()->GetImage()->GetTransform().size() ; i++) {
2589         mSlicerManagers.back()->GetImage()->GetTransform()[i]->Identity();
2590         mSlicerManagers.back()->GetImage()->GetTransform()[i]->Update();
2591       }
2592
2593       //automatically link both images...
2594       AddLink(mSlicerManagers[indexParent]->GetId().c_str(), mSlicerManagers.back()->GetId().c_str(), false);
2595
2596       //tie the main and secondary sequences by raising flags and informing each another of their respective SlicerManager indices
2597       mSlicerManagers[indexParent]->SetFusionSequenceIndexOfLinkedManager(mSlicerManagers.size()-1);
2598       mSlicerManagers[indexParent]->SetFusionSequenceInvolvmentCode(0); //main sequence
2599       mSlicerManagers.back()->SetFusionSequenceIndexOfLinkedManager(indexParent);
2600       mSlicerManagers.back()->SetFusionSequenceInvolvmentCode(1); //secondary sequence
2601       for (unsigned i=0 ; i<4 ; i++) {
2602         mSlicerManagers.back()->GetSlicer(i)->SetFusionSequenceCode(1); //flag the slicers of the secondary sequence
2603       }
2604
2605     } else {
2606       QApplication::restoreOverrideCursor();
2607       QString error = "Cannot import the new image.\n";
2608       error += mSlicerManagers[index]->GetLastError().c_str();
2609       QMessageBox::information(this,tr("Problem reading image !"),error);
2610     }
2611     //WindowLevelChanged();
2612     ImageInfoChanged(); //this internally calls WindowLevelChanged...
2613   }
2614   else {
2615     QMessageBox::information(this,tr("Problem reading fusion sequence !"),"File doesn't exist!");
2616     return;
2617   }
2618
2619 }
2620 //------------------------------------------------------------------------------
2621
2622
2623 //------------------------------------------------------------------------------
2624 //fusionSequenceFrameIndex and fusionSequenceNbFrames are relative to the secondary sequence (US)
2625 void vvMainWindow::SetFusionSequenceProperty(int fusionSequenceFrameIndex, bool spatialSyncFlag, unsigned int fusionSequenceNbFrames, bool temporalSyncFlag)
2626 {
2627   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2628
2629   if (!mSlicerManagers[index]->IsInvolvedInFusionSequence()) return;
2630
2631   //check if the focus moved to the linked sequence, and in this case, select the master sequence instead
2632   if (!mSlicerManagers[index]->IsMainSequenceOfFusionSequence()) {
2633     index = mSlicerManagers[index]->GetFusionSequenceIndexOfLinkedManager();
2634   }
2635   int secondaryIndex = mSlicerManagers[index]->GetFusionSequenceIndexOfLinkedManager();
2636   if (secondaryIndex==-1) return; //this should never happen
2637   if ( (!mSlicerManagers[index]->IsMainSequenceOfFusionSequence()) ||
2638     (!mSlicerManagers[secondaryIndex]->IsSecondarySequenceOfFusionSequence()) )
2639   {return;} //this should never happen, raise an exception?
2640
2641   if (mSlicerManagers[index]->GetSlicer(0)->GetFusion()) {
2642
2643     //First, if the spatialSync button is unchecked, then reposition the parent sequence (CT) in its original coordinate frame
2644     if ( (!spatialSyncFlag) && (mSlicerManagers[index]->GetFusionSequenceSpatialSyncFlag()) ) {
2645       for ( unsigned i=0 ; i<mSlicerManagers[index]->GetSlicer(0)->GetImage()->GetTransform().size() ; i++ ) {
2646         mSlicerManagers[index]->GetSlicer(0)->GetImage()->GetTransform()[i]->SetMatrix( mSlicerManagers[index]->GetFusionSequenceMainTransformMatrix() );
2647         mSlicerManagers[index]->GetSlicer(0)->GetImage()->GetTransform()[i]->Update();
2648       }
2649
2650       for (int i=0; i<mSlicerManagers[index]->GetNumberOfSlicers(); i++) {
2651         mSlicerManagers[index]->GetSlicer(i)->ForceUpdateDisplayExtent();
2652         mSlicerManagers[index]->GetSlicer(i)->Render();
2653       }
2654     }
2655
2656     //then, update the property values in the slicer manager
2657     mSlicerManagers[index]->SetFusionSequenceLength(fusionSequenceNbFrames);
2658     mSlicerManagers[index]->SetFusionSequenceSpatialSyncFlag(spatialSyncFlag);
2659     mSlicerManagers[index]->SetFusionSequenceTemporalSyncFlag(temporalSyncFlag);
2660     mSlicerManagers[index]->SetFusionSequenceFrameIndex(fusionSequenceFrameIndex);
2661
2662     //select the right frame of the US sequence
2663     mSlicerManagers[index]->SetFusionSequenceTSlice(fusionSequenceFrameIndex); //here, I should only update the overlayed sequence
2664     mSlicerManagers[secondaryIndex]->SetTSlice(fusionSequenceFrameIndex, false); //this should update the secondary sequence (individual version)
2665
2666     //update the horizontal sliders of the main window
2667     overlayPanel->updateFusionSequenceSliderValueFromWindow(fusionSequenceFrameIndex, false);
2668
2669     if (spatialSyncFlag) { //reslice the CT
2670
2671       if (temporalSyncFlag) { //do the temporal synchronisation
2672         int mainSequenceFrameIndex=0;
2673         //estimate the TSlice to set to the CT
2674         unsigned nbFramesMain = mSlicerManagers[index]->GetImage()->GetTransform().size();
2675         mainSequenceFrameIndex = mSlicerManagers[index]->GetFusionSequenceCorrespondances()[ nbFramesMain + fusionSequenceFrameIndex];
2676         //and set it!
2677         mSlicerManagers[index]->SetTSlice(mainSequenceFrameIndex, false);
2678         //warning, there is a loopback, and modification of the TSlice in main sequence forces an update of the TSlice in secondary, etc...
2679       }
2680
2681
2682       //Set the transform matrix of the parent sequence (typically CT / 4DCT)
2683       vtkSmartPointer<vtkMatrix4x4> tmpMat = vtkSmartPointer<vtkMatrix4x4>::New();
2684       vtkMatrix4x4::Invert( mSlicerManagers[index]->GetFusionSequenceInitialTransformMatrixAtFrame(fusionSequenceFrameIndex), tmpMat );
2685       for ( unsigned i=0 ; i<mSlicerManagers[index]->GetSlicer(0)->GetImage()->GetTransform().size() ; i++ ) {
2686         mSlicerManagers[index]->GetSlicer(0)->GetImage()->GetTransform()[i]->SetMatrix( mSlicerManagers[index]->GetFusionSequenceMainTransformMatrix() );
2687         mSlicerManagers[index]->GetSlicer(0)->GetImage()->GetTransform()[i]->PreMultiply();
2688         mSlicerManagers[index]->GetSlicer(0)->GetImage()->GetTransform()[i]->Concatenate( tmpMat );
2689         mSlicerManagers[index]->GetSlicer(0)->GetImage()->GetTransform()[i]->Update();
2690       }
2691
2692       for (int i=0; i<mSlicerManagers[index]->GetNumberOfSlicers(); i++) {
2693         mSlicerManagers[index]->GetSlicer(i)->ForceUpdateDisplayExtent();
2694         mSlicerManagers[index]->GetSlicer(i)->Render();
2695       }
2696
2697     }
2698
2699   }
2700 }
2701 //------------------------------------------------------------------------------
2702
2703
2704 //------------------------------------------------------------------------------
2705 void vvMainWindow::SaveAs()
2706 {
2707   if (DataTree->selectedItems()[0]->data(1,Qt::UserRole).toString() == "vector") {
2708     QMessageBox::warning(this,tr("Unsupported type"),tr("Sorry, saving a vector field is unsupported for the moment"));
2709     return;
2710   }
2711
2712   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2713   int dimension = mSlicerManagers[index]->GetDimension();
2714   QStringList OutputListeFormat;
2715   OutputListeFormat.clear();
2716   if (dimension == 1) {
2717     OutputListeFormat.push_back(".mhd");
2718     OutputListeFormat.push_back(".mha");
2719   }
2720   if (dimension == 2) {
2721     OutputListeFormat.push_back(".bmp");
2722     OutputListeFormat.push_back(".png");
2723     OutputListeFormat.push_back(".jpeg");
2724     OutputListeFormat.push_back(".tif");
2725     OutputListeFormat.push_back(".mhd");
2726     OutputListeFormat.push_back(".mha");
2727     OutputListeFormat.push_back(".hdr");
2728     OutputListeFormat.push_back(".vox");
2729   } else if (dimension == 3) {
2730     OutputListeFormat.push_back(".mhd");
2731     OutputListeFormat.push_back(".mha");
2732     OutputListeFormat.push_back(".nii");
2733     OutputListeFormat.push_back(".nrrd");
2734     OutputListeFormat.push_back(".nhdr");
2735     OutputListeFormat.push_back(".hdr");
2736     OutputListeFormat.push_back(".vox");
2737   } else if (dimension == 4) {
2738     OutputListeFormat.push_back(".mhd");
2739     OutputListeFormat.push_back(".mha");
2740     OutputListeFormat.push_back(".nii");
2741     OutputListeFormat.push_back(".nrrd");
2742     OutputListeFormat.push_back(".nhdr");
2743   }
2744   QString Extensions = "AllFiles(*.*)";
2745   for (int i = 0; i < OutputListeFormat.count(); i++) {
2746     Extensions += ";;Images ( *";
2747     Extensions += OutputListeFormat[i];
2748     Extensions += ")";
2749   }
2750   QString fileName = QFileDialog::getSaveFileName(this,
2751     tr("Save As"),
2752     mSlicerManagers[index]->GetFileName().c_str(),
2753     Extensions);
2754   if (!fileName.isEmpty()) {
2755     std::string fileformat = itksys::SystemTools::GetFilenameLastExtension(fileName.toStdString());
2756     if (OutputListeFormat.contains(
2757       fileformat.c_str())) {
2758         QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
2759         std::string action = "Saving";
2760         vvProgressDialog progress("Saving "+fileName.toStdString());
2761         qApp->processEvents();
2762         vvImageWriter::Pointer writer = vvImageWriter::New();
2763         writer->SetOutputFileName(fileName.toStdString());
2764         writer->SetInput(mSlicerManagers[index]->GetImage());
2765
2766         // Check on transform and prompt user
2767         writer->SetSaveTransform(false);
2768         bool bId = true;
2769         for(int i=0; i<4; i++)
2770           for(int j=0; j<4; j++) {
2771             // TODO SR and BP: check on the list of transforms and not the first only
2772             double elt = mSlicerManagers[index]->GetImage()->GetTransform()[0]->GetMatrix()->GetElement(i,j);
2773             if(i==j && elt!=1.)
2774               bId = false;
2775             if(i!=j && elt!=0.)
2776               bId = false;
2777           }
2778           if( !bId ) {
2779             QString warning = "The image has an associated linear transform. Do you want to save it along?";
2780             QMessageBox msgBox(QMessageBox::Warning, tr("Save transform"), warning, 0, this);
2781             msgBox.addButton(tr("Yes"), QMessageBox::AcceptRole);
2782             msgBox.addButton(tr("No"), QMessageBox::RejectRole);
2783             if (msgBox.exec() == QMessageBox::AcceptRole)
2784               writer->SetSaveTransform(true);
2785           }
2786
2787           writer->Update();
2788           QApplication::restoreOverrideCursor();
2789           if (writer->GetLastError().size()) {
2790             QString error = "Saving did not succeed\n";
2791             error += writer->GetLastError().c_str();
2792             QMessageBox::information(this,tr("Saving Problem"),error);
2793             SaveAs();
2794           }
2795     } else {
2796       QString error = fileformat.c_str();
2797       if (error.isEmpty())
2798         error += "no file format specified !";
2799       else
2800         error += " format unknown !!!\n";
2801       QMessageBox::information(this,tr("Saving Problem"),error);
2802       SaveAs();
2803     }
2804   }
2805 }
2806 //------------------------------------------------------------------------------
2807
2808 //------------------------------------------------------------------------------
2809 void vvMainWindow::SaveCurrentState()
2810 {
2811   QString Extensions = "XML Files(*.xml)";
2812   QString fileName = QFileDialog::getSaveFileName(this,
2813     tr("Save Current Window State"),
2814     "",
2815     Extensions);
2816
2817   SaveCurrentStateAs(fileName.toStdString());
2818 }
2819 //------------------------------------------------------------------------------
2820
2821 //------------------------------------------------------------------------------
2822 void vvMainWindow::SaveCurrentStateAs(const std::string& stateFile)
2823 {
2824   vvSaveState save_state;
2825   save_state.Run(this, stateFile);
2826 }
2827
2828 //------------------------------------------------------------------------------
2829 void vvMainWindow::ReadSavedState()
2830 {
2831   QString Extensions = "XML Files(*.xml)";
2832   QString fileName = QFileDialog::getOpenFileName(this,
2833     tr("Load Window State"),
2834     "",
2835     Extensions);
2836
2837   ReadSavedStateFile(fileName.toStdString());
2838 }
2839 //------------------------------------------------------------------------------
2840
2841 //------------------------------------------------------------------------------
2842 void vvMainWindow::ReadSavedStateFile(const std::string& stateFile)
2843 {
2844   vvReadState read_state;
2845   read_state.Run(this, stateFile);
2846 }
2847 //------------------------------------------------------------------------------
2848
2849 //------------------------------------------------------------------------------
2850 void vvMainWindow::LinkAllImages()
2851 {
2852   linkPanel->linkAll();
2853 }
2854
2855 //------------------------------------------------------------------------------
2856 void vvMainWindow::AddLink(QString image1,QString image2,bool fromPanel)
2857 {
2858   if (!fromPanel) {
2859     // delegate to linkPanel if call came from elsewhere...
2860     linkPanel->addLinkFromIds(image1, image2);
2861     return;
2862   }
2863
2864   unsigned int sm1 = 0;
2865   unsigned int sm2 = 0;
2866
2867   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
2868     if (image1.toStdString() == mSlicerManagers[i]->GetId()) {
2869       mSlicerManagers[i]->AddLink(image2.toStdString());
2870       sm1 = i;
2871     }
2872     if (image2.toStdString() == mSlicerManagers[i]->GetId()) {
2873       mSlicerManagers[i]->AddLink(image1.toStdString());
2874       sm2 = i;
2875     }
2876   }
2877
2878   if (linkPanel->isLinkAll())   {
2879     emit UpdateLinkedNavigation(mSlicerManagers[sm1]->GetId(), mSlicerManagers[mCurrentPickedImageIndex], mSlicerManagers[mCurrentPickedImageIndex]->GetSlicer(0));
2880     emit UpdateLinkedNavigation(mSlicerManagers[sm2]->GetId(), mSlicerManagers[mCurrentPickedImageIndex], mSlicerManagers[mCurrentPickedImageIndex]->GetSlicer(0));
2881   } else {
2882     emit UpdateLinkedNavigation(mSlicerManagers[sm2]->GetId(), mSlicerManagers[sm1], mSlicerManagers[sm1]->GetSlicer(0));
2883   }
2884 }
2885
2886 //------------------------------------------------------------------------------
2887
2888
2889 //------------------------------------------------------------------------------
2890 void vvMainWindow::RemoveLink(QString image1,QString image2)
2891 {
2892   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
2893     if (image1.toStdString() == mSlicerManagers[i]->GetId()) {
2894       mSlicerManagers[i]->RemoveLink(image2.toStdString());
2895     }
2896     if (image2.toStdString() == mSlicerManagers[i]->GetId()) {
2897       mSlicerManagers[i]->RemoveLink(image1.toStdString());
2898     }
2899   }
2900 }
2901 //------------------------------------------------------------------------------
2902
2903 //------------------------------------------------------------------------------
2904 void vvMainWindow::ChangeImageWithIndexOffset(vvSlicerManager *sm, int slicer, int offset)
2905 {
2906   if(mSlicerManagers.size()==1)
2907     return;
2908
2909   int index = 0;
2910   while(sm != mSlicerManagers[index])
2911     index++;
2912   index = (index+offset+mSlicerManagers.size()) % mSlicerManagers.size();
2913
2914   QTreeWidgetItem* item = GetItemFromSlicerManager(mSlicerManagers[index]);
2915   item->setData(slicer+1,Qt::CheckStateRole,2);         //change checkbox
2916   CurrentImageChanged(mSlicerManagers[index]->GetId()); //select new image
2917   DisplayChanged(item,slicer+1);
2918 }
2919 //------------------------------------------------------------------------------
2920 void vvMainWindow::HorizontalSliderMoved(int value,int column, int slicer_index)
2921 {
2922   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
2923     if (DataTree->topLevelItem(i)->data(column,Qt::CheckStateRole).toInt() > 1) {
2924       //i is the SlicerManager that is in charge of this slicer.
2925       if (mSlicerManagers[i]->IsInvolvedInFusionSequence()) {
2926         //if the slicerManager is involved in a fusionSequence as the secondary sequence, then update the slider position in the overlay panel and everything accordingly
2927         if (mSlicerManagers[i]->IsSecondarySequenceOfFusionSequence()) {
2928           overlayPanel->updateFusionSequenceSliderValueFromWindow(value, true);
2929         }
2930         else { //if this is the primary sequence that has been modified
2931           if (mSlicerManagers[i]->GetFusionSequenceTemporalSyncFlag()) {
2932             //WARNING: for some obscure reason, there are problems when accessing mSlicerManagers[mSlicerManagers[i]->GetFusionSequenceIndexOfLinkedManager()]->GetFusionSequenceFrameIndex();
2933
2934             int estimatedValue=0;
2935             //estimate a corresponding time index for the secondary (US) sequence, and update it accordingly.
2936             estimatedValue = mSlicerManagers[i]->GetFusionSequenceCorrespondances()[ value ];
2937             //TODO: at the moment, there is a loop in TSlice modifications
2938             //modifying sequence 1 causes seq 2 to update, which in turns update seq1...
2939             //I disable control on seq1 at the moment.
2940             //overlayPanel->updateFusionSequenceSliderValueFromWindow(estimatedValue, true);
2941           }
2942         }
2943       }
2944
2945       for (int j = 0; j < 4; j++) {
2946         mSlicerManagers[i]->SetTSliceInSlicer(value,j);
2947       }
2948       mSlicerManagers[i]->GetSlicer(slicer_index)->Render();
2949       break;
2950     }
2951   }
2952 }
2953 //------------------------------------------------------------------------------
2954
2955
2956 //------------------------------------------------------------------------------
2957 void vvMainWindow::NOHorizontalSliderMoved()
2958 {
2959   // if (mCurrentTime == NOHorizontalSlider->value()) return;
2960   HorizontalSliderMoved(NOHorizontalSlider->value(),COLUMN_UL_VIEW,0);
2961   //  mCurrentTime = NOHorizontalSlider->value();
2962 }
2963 //------------------------------------------------------------------------------
2964
2965
2966 //------------------------------------------------------------------------------
2967 void vvMainWindow::NEHorizontalSliderMoved()
2968 {
2969   // if (mCurrentTime == NEHorizontalSlider->value()) return;
2970   HorizontalSliderMoved(NEHorizontalSlider->value(),COLUMN_UR_VIEW,1);
2971   //  mCurrentTime = NEHorizontalSlider->value();
2972 }
2973 //------------------------------------------------------------------------------
2974
2975
2976 //------------------------------------------------------------------------------
2977 void vvMainWindow::SOHorizontalSliderMoved()
2978 {
2979   // if (mCurrentTime == SOHorizontalSlider->value()) return;
2980   HorizontalSliderMoved(SOHorizontalSlider->value(),COLUMN_DL_VIEW,2);
2981   // mCurrentTime = SOHorizontalSlider->value();
2982 }
2983 //------------------------------------------------------------------------------
2984
2985
2986 //------------------------------------------------------------------------------
2987 void vvMainWindow::SEHorizontalSliderMoved()
2988 {
2989   // if (mCurrentTime == SEHorizontalSlider->value()) return;
2990   HorizontalSliderMoved(SEHorizontalSlider->value(),COLUMN_DR_VIEW,3);
2991   // mCurrentTime = SEHorizontalSlider->value();
2992 }
2993 //------------------------------------------------------------------------------
2994
2995 //------------------------------------------------------------------------------
2996 void vvMainWindow::NOVerticalSliderChanged()
2997 {
2998   static int value=-1;
2999   if (value == NOVerticalSlider->value()) return;
3000   else value = NOVerticalSlider->value();
3001   //  int value = NOVerticalSlider->value();
3002   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
3003     if (DataTree->topLevelItem(i)->data(COLUMN_UL_VIEW,Qt::CheckStateRole).toInt() > 1) {
3004       if (mSlicerManagers[i]->GetSlicer(0)->GetSlice() != value) {
3005         mSlicerManagers[i]->GetSlicer(0)->SetSlice(value);
3006         mSlicerManagers[i]->VerticalSliderHasChanged(0, value);
3007
3008         // If nor Update/Render -> slider not work
3009         // only render = ok navigation, but for contour Update needed but slower ?
3010
3011         mSlicerManagers[i]->UpdateSlice(0);  // <-- DS add this. Not too much update ? YES. but needed for ImageContour ...
3012         //mSlicerManagers[i]->GetSlicer(0)->Render(); // <-- DS add this, needed for contour, seems ok ? not too slow ?
3013       }
3014       break;
3015     }
3016   }
3017 }
3018 //------------------------------------------------------------------------------
3019
3020
3021 //------------------------------------------------------------------------------
3022 void vvMainWindow::NEVerticalSliderChanged()
3023 {
3024   static int value=-1;
3025   if (value == NEVerticalSlider->value()) return;
3026   else value = NEVerticalSlider->value();
3027   //  int value = NEVerticalSlider->value();
3028   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
3029     if (DataTree->topLevelItem(i)->data(COLUMN_UR_VIEW,Qt::CheckStateRole).toInt() > 1) {
3030       if (mSlicerManagers[i]->GetSlicer(1)->GetSlice() != value) {
3031         mSlicerManagers[i]->GetSlicer(1)->SetSlice(value);
3032         mSlicerManagers[i]->VerticalSliderHasChanged(1, value);
3033         mSlicerManagers[i]->UpdateSlice(1);
3034         //mSlicerManagers[i]->GetSlicer(1)->Render(); // <-- DS add this, needed for contour, seems ok ? not too slow ?
3035       }
3036       break;
3037     }
3038   }
3039 }
3040 //------------------------------------------------------------------------------
3041
3042
3043 //------------------------------------------------------------------------------
3044 void vvMainWindow::SOVerticalSliderChanged()
3045 {
3046   static int value=-1;
3047   if (value == SOVerticalSlider->value()) return;
3048   else value = SOVerticalSlider->value();
3049   //int value = SOVerticalSlider->value();
3050   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
3051     if (DataTree->topLevelItem(i)->data(COLUMN_DL_VIEW,Qt::CheckStateRole).toInt() > 1) {
3052       if (mSlicerManagers[i]->GetSlicer(2)->GetSlice() != value) {
3053         mSlicerManagers[i]->GetSlicer(2)->SetSlice(value);
3054         mSlicerManagers[i]->VerticalSliderHasChanged(2, value);
3055         mSlicerManagers[i]->UpdateSlice(2);
3056         //mSlicerManagers[i]->GetSlicer(2)->Render(); // <-- DS add this, needed for contour, seems ok ? not too slow ?
3057       }
3058       // else { DD("avoid SOVerticalSlider slicer update"); }
3059       break;
3060     }
3061   }
3062 }
3063 //------------------------------------------------------------------------------
3064
3065
3066 //------------------------------------------------------------------------------
3067 void vvMainWindow::SEVerticalSliderChanged()
3068 {
3069   static int value=-1;
3070   if (value == SEVerticalSlider->value()) return;
3071   else value = SEVerticalSlider->value();
3072   // int value = SEVerticalSlider->value();
3073   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
3074     if (DataTree->topLevelItem(i)->data(COLUMN_DR_VIEW,Qt::CheckStateRole).toInt() > 1) {
3075       if (mSlicerManagers[i]->GetSlicer(3)->GetSlice() != value) {
3076         mSlicerManagers[i]->GetSlicer(3)->SetSlice(value);
3077         mSlicerManagers[i]->VerticalSliderHasChanged(3, value);
3078         mSlicerManagers[i]->UpdateSlice(3);
3079         //mSlicerManagers[i]->GetSlicer(3)->Render(); // <-- DS add this, needed for contour, seems ok ? not too slow ?
3080       }
3081       break;
3082     }
3083   }
3084 }
3085 //------------------------------------------------------------------------------
3086
3087
3088 //------------------------------------------------------------------------------
3089 void vvMainWindow::UpdateSlice(int slicer, int slice)
3090 {
3091   // DD("vvMainWindow::UpdateSlice");
3092   //   DD(slicer);
3093   //   DD(slice);
3094   if (slicer == 0) {
3095     //    if (slice != NOVerticalSlider->value())
3096     NOVerticalSlider->setValue(slice);
3097   } else {
3098     if (slicer == 1)
3099       NEVerticalSlider->setValue(slice);
3100     else {
3101       if (slicer == 2)
3102         SOVerticalSlider->setValue(slice);
3103       else {
3104         if (slicer == 3)
3105           SEVerticalSlider->setValue(slice);
3106       }
3107     }
3108   }
3109   // DD("vvMainWindow:UpdateSlice END");
3110 }
3111 //------------------------------------------------------------------------------
3112
3113
3114 //------------------------------------------------------------------------------
3115 void vvMainWindow::UpdateTSlice(int slicer, int slice, int code)
3116 {
3117   //FusionSequence: the slider value should be updated for slicers which show the same sequence as requested
3118   bool doUpdate=false;
3119   if (code==-1) doUpdate=true;
3120   else {
3121     for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
3122       if (DataTree->topLevelItem(i)->data(slicer+1,Qt::CheckStateRole).toInt() > 1) {
3123         //i is the active SlicerManager
3124         if (mSlicerManagers[i]->GetFusionSequenceInvolvmentCode()==code) doUpdate=true;
3125         break;
3126       }
3127     }
3128   }
3129   if (!doUpdate) return;
3130
3131   switch (slicer) {
3132   case 0:
3133     if (NOHorizontalSlider->value()==slice) return;
3134     NOHorizontalSlider->setValue(slice);
3135     break;
3136   case 1:
3137     if (NEHorizontalSlider->value()==slice) return;
3138     NEHorizontalSlider->setValue(slice);
3139     break;
3140   case 2:
3141     if (SOHorizontalSlider->value()==slice) return;
3142     SOHorizontalSlider->setValue(slice);
3143     break;
3144   case 3:
3145     if (SEHorizontalSlider->value()==slice) return;
3146     SEHorizontalSlider->setValue(slice);
3147     break;
3148   }
3149 }
3150 //------------------------------------------------------------------------------
3151
3152
3153 //------------------------------------------------------------------------------
3154 void vvMainWindow::UpdateSliceRange(int slicer, int min, int max, int tmin, int tmax)
3155 {
3156   //int position = int((min+max)/2);
3157   int position = mSlicerManagers[mCurrentPickedImageIndex]->GetSlicer(slicer)->GetSlice();
3158   if (slicer == 0) {
3159     NOVerticalSlider->setRange(min,max);
3160     NOHorizontalSlider->setRange(tmin,tmax);
3161     NOVerticalSlider->setValue(position);
3162   } else if (slicer == 1) {
3163     NEVerticalSlider->setRange(min,max);
3164     NEHorizontalSlider->setRange(tmin,tmax);
3165     NEVerticalSlider->setValue(position);
3166   } else if (slicer == 2) {
3167     SOVerticalSlider->setRange(min,max);
3168     SOHorizontalSlider->setRange(tmin,tmax);
3169     SOVerticalSlider->setValue(position);
3170   } else if (slicer == 3) {
3171     SEVerticalSlider->setRange(min,max);
3172     SEHorizontalSlider->setRange(tmin,tmax);
3173     SEVerticalSlider->setValue(position);
3174   }
3175 }
3176 //------------------------------------------------------------------------------
3177
3178
3179 //------------------------------------------------------------------------------
3180 void vvMainWindow::SaveNOScreenshot()
3181 {
3182   SaveScreenshot(NOViewWidget);
3183 }
3184 //------------------------------------------------------------------------------
3185
3186
3187 //------------------------------------------------------------------------------
3188 void vvMainWindow::SaveNEScreenshot()
3189 {
3190   SaveScreenshot(NEViewWidget);
3191 }
3192 //------------------------------------------------------------------------------
3193
3194
3195 //------------------------------------------------------------------------------
3196 void vvMainWindow::SaveSOScreenshot()
3197 {
3198   SaveScreenshot(SOViewWidget);
3199 }
3200 //------------------------------------------------------------------------------
3201
3202
3203 //------------------------------------------------------------------------------
3204 void vvMainWindow::SaveSEScreenshot()
3205 {
3206   SaveScreenshot(SEViewWidget);
3207 }
3208 //------------------------------------------------------------------------------
3209
3210
3211 //------------------------------------------------------------------------------
3212 void vvMainWindow::SaveScreenshotAllSlices()
3213 {
3214   QVTKWidget *widget = NOViewWidget;
3215
3216   int index = 0;// GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
3217   vvSlicerManager * SM = mSlicerManagers[index];
3218   vvImage * image = SM->GetImage();
3219   vvSlicer * slicer = SM->GetSlicer(0);
3220   int orientation = slicer->GetOrientation();
3221   int nbSlices = image->GetSize()[orientation];
3222   vtkSmartPointer<vtkRenderWindow>  renderWindow = widget->GetRenderWindow();
3223
3224   // Select filename base
3225   QString filename = QFileDialog::getSaveFileName(this,
3226     tr("Save As (filename will be completed by slice number)"),
3227     itksys::SystemTools::GetFilenamePath(mSlicerManagers[index]->GetFileName()).c_str(),
3228     "Images( *.png);;Images( *.jpg)");
3229
3230   // Loop on slices
3231   for(int i=0; i<nbSlices; i++) {
3232     // Change the slice
3233     slicer->SetSlice(i); // -> change the slice of the current slicer
3234     SM->UpdateSlice(0); // --> this one emit UpdateSlice
3235     QCoreApplication::flush(); // -> needed to force display of contours
3236
3237     // Screenshot
3238     vtkSmartPointer<vtkWindowToImageFilter> windowToImageFilter = vtkSmartPointer<vtkWindowToImageFilter>::New();
3239     windowToImageFilter->SetInput(renderWindow);
3240     windowToImageFilter->SetMagnification(1);
3241     windowToImageFilter->SetInputBufferTypeToRGBA(); //also record the alpha (transparency) channel
3242     windowToImageFilter->Update();
3243
3244     vtkSmartPointer<vtkPNGWriter> writer = vtkSmartPointer<vtkPNGWriter>::New();
3245     std::string fn = itksys::SystemTools::GetFilenameWithoutLastExtension(filename.toStdString());
3246     std::string num = clitk::toString(i);
3247     if (i<10) num = "0"+num;
3248     if (i<100) num = "0"+num;
3249     if (i<1000) num = "0"+num;
3250
3251     fn = itksys::SystemTools::GetFilenamePath(filename.toStdString()) + "/"+ fn
3252       + "_" + num + itksys::SystemTools::GetFilenameLastExtension(filename.toStdString());
3253     writer->SetFileName(fn.c_str());
3254     writer->SetInput(windowToImageFilter->GetOutput());
3255     writer->Write();
3256   }
3257 }
3258 //------------------------------------------------------------------------------
3259
3260
3261 //------------------------------------------------------------------------------
3262 void vvMainWindow::SaveScreenshot(QVTKWidget *widget)
3263 {
3264   QString Extensions = "Images( *.png);;";
3265   Extensions += "Images( *.jpg);;";
3266   Extensions += "Images( *.bmp);;";
3267   Extensions += "Images( *.tif);;";
3268   Extensions += "Images( *.ppm)";
3269 #if defined(VTK_USE_FFMPEG_ENCODER) || defined(VTK_USE_VIDEO_FOR_WINDOWS)
3270   Extensions += ";;Video( *.avi)";
3271 #endif
3272 #ifdef VTK_USE_MPEG2_ENCODER
3273   Extensions += ";;Video( *.mpg)";
3274 #endif
3275 #ifdef CLITK_EXPERIMENTAL
3276   Extensions += ";;Video( *.gif)";
3277 #endif
3278
3279   int smIndex=GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
3280   QString fileName = QFileDialog::getSaveFileName(this,
3281     tr("Save As"),
3282     itksys::SystemTools::GetFilenamePath(mSlicerManagers[smIndex]->GetFileName()).c_str(),
3283     Extensions);
3284
3285   if (!fileName.isEmpty()) {
3286     vtkSmartPointer<vtkWindowToImageFilter> w2i = vtkSmartPointer<vtkWindowToImageFilter>::New();
3287     w2i->SetInput(widget->GetRenderWindow());
3288     w2i->Update();
3289     vtkImageData *image = w2i->GetOutput();
3290
3291     std::string ext(itksys::SystemTools::GetFilenameLastExtension(fileName.toStdString()));
3292
3293     // Image
3294     vtkImageWriter *imgwriter = NULL;
3295     if (ext==".bmp")
3296       imgwriter = vtkBMPWriter::New();
3297     else if (ext==".tif")
3298       imgwriter = vtkTIFFWriter::New();
3299     else if (ext==".ppm")
3300       imgwriter = vtkPNMWriter::New();
3301     else if (ext==".png")
3302       imgwriter = vtkPNGWriter::New();
3303     else if (ext==".jpg")
3304       imgwriter = vtkJPEGWriter::New();
3305
3306     // Snapshot image if not null
3307     if(imgwriter!=NULL) {
3308       imgwriter->SetInput(image);
3309       imgwriter->SetFileName(fileName.toStdString().c_str());
3310       imgwriter->Write();
3311       return;
3312     }
3313
3314     // Video
3315     vtkGenericMovieWriter *vidwriter = NULL;
3316 #if CLITK_EXPERIMENTAL == 1
3317     if (ext==".gif") {
3318       vvAnimatedGIFWriter *gif = vvAnimatedGIFWriter::New();
3319       vidwriter = gif;
3320
3321       // FPS
3322       bool ok;
3323       int fps = QInputDialog::getInteger(this, tr("Number of frames per second"),
3324         tr("FPS:"), 5, 0, 1000, 1, &ok);
3325       if(ok)
3326         gif->SetRate(fps);
3327
3328       // Loops
3329       int loops = QInputDialog::getInteger(this, tr("Loops"),
3330         tr("Number of loops (0 means infinite):"), 0, 0, 1000000000, 1, &ok);
3331       if(ok)
3332         gif->SetLoops(loops);
3333
3334       // Dithering
3335       QString msg = "Would you like to activate dithering?";
3336       QMessageBox msgBox(QMessageBox::Question, tr("Dithering"),msg, 0, this);
3337       msgBox.addButton(tr("Yes"), QMessageBox::AcceptRole);
3338       msgBox.addButton(tr("No"), QMessageBox::RejectRole);
3339       gif->SetDither(msgBox.exec() == QMessageBox::AcceptRole);
3340     }
3341 #endif
3342 #ifdef VTK_USE_VIDEO_FOR_WINDOWS
3343     if (ext==".avi") {
3344       vtkAVIWriter *mpg = vtkAVIWriter::New();
3345       vidwriter = mpg;
3346       mpg->SetQuality(2);
3347       bool ok;
3348       int fps = QInputDialog::getInteger(this, tr("Number of frames per second"),
3349         tr("FPS:"), 5, 0, 1024, 1, &ok);
3350       if(!ok)
3351         fps = 5;
3352       mpg->SetRate(fps);
3353     }
3354 #endif
3355 #ifdef VTK_USE_FFMPEG_ENCODER
3356     if (ext==".avi") {
3357       vtkFFMPEGWriter *mpg = vtkFFMPEGWriter::New();
3358       vidwriter = mpg;
3359       mpg->SetQuality(2);
3360       bool ok;
3361       int fps = QInputDialog::getInteger(this, tr("Number of frames per second"),
3362         tr("FPS:"), 5, 0, 1024, 1, &ok);
3363       if(!ok)
3364         fps = 5;
3365       mpg->SetRate(fps);
3366       mpg->SetBitRateTolerance(int(ceil(12.0*1024*1024/fps)));
3367     }
3368 #endif
3369 #ifdef VTK_USE_MPEG2_ENCODER
3370     if (ext==".mpg") {
3371       vtkMPEG2Writer *mpg = vtkMPEG2Writer::New();
3372       vidwriter = mpg;
3373     }
3374 #endif
3375
3376     // Take video if not null
3377     if(vidwriter!=NULL){
3378       vidwriter->SetInput(image);
3379       vidwriter->SetFileName(fileName.toStdString().c_str());
3380       vidwriter->Start();
3381       int nSlice = mSlicerManagers[smIndex]->GetSlicer(0)->GetTMax();
3382       for(int i=0; i<=nSlice; i++) {
3383         mSlicerManagers[smIndex]->SetNextTSlice(0);
3384         vtkSmartPointer<vtkWindowToImageFilter> w2i = vtkSmartPointer<vtkWindowToImageFilter>::New();
3385         w2i->SetInput(widget->GetRenderWindow());
3386         w2i->Update();
3387         vidwriter->SetInput(w2i->GetOutput());
3388         vidwriter->Write();
3389       }
3390       vidwriter->End();
3391       vidwriter->Delete();
3392       return;
3393     }
3394
3395     QMessageBox::information(this,tr("Problem saving screenshot !"),tr("Cannot save image.\nPlease set a file extension !!!"));
3396   }
3397 }
3398 //------------------------------------------------------------------------------
3399
3400
3401 //------------------------------------------------------------------------------
3402 void vvMainWindow::GoToCursor()
3403 {
3404   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
3405   for (int column = 1; column < 5; column++) {
3406     if (DataTree->selectedItems()[0]->data(column,Qt::CheckStateRole).toInt() > 1) {
3407       double* cursorPos = mSlicerManagers[index]->GetSlicer(column-1)->GetCursorPosition();
3408       mSlicerManagers[index]->GetSlicer(column-1)->SetCurrentPosition(
3409         cursorPos[0],cursorPos[1],cursorPos[2],cursorPos[3]);
3410       mSlicerManagers[index]->UpdateViews(1,column-1);
3411       mSlicerManagers[index]->UpdateLinked(column-1);
3412       break;
3413     }
3414   }
3415 }
3416 //------------------------------------------------------------------------------
3417
3418 //------------------------------------------------------------------------------
3419 void vvMainWindow::GoToLandmark()
3420 {
3421   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
3422   for (int column = 1; column < 5; column++) {
3423     if (DataTree->selectedItems()[0]->data(column,Qt::CheckStateRole).toInt() > 1) {
3424       double* cursorPos = landmarksPanel->GetSelectedPoint();
3425       mSlicerManagers[index]->GetSlicer(column-1)->SetCurrentPosition(
3426         cursorPos[0],cursorPos[1],cursorPos[2],cursorPos[3]);
3427       mSlicerManagers[index]->UpdateViews(1,column-1);
3428       mSlicerManagers[index]->UpdateLinked(column-1);
3429       break;
3430     }
3431   }
3432 }
3433 //------------------------------------------------------------------------------
3434
3435 //------------------------------------------------------------------------------
3436 void vvMainWindow::PlayPause()
3437 {
3438   if (playMode) {
3439     playMode = 0;
3440     playButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/player_play.png")));
3441     ImageInfoChanged();
3442     return;
3443   } else {
3444     int image_number=DataTree->topLevelItemCount();
3445     bool has_temporal;
3446     for (int i=0; i<image_number; i++)
3447       if (mSlicerManagers[i]->GetSlicer(0)->GetTMax() > 0) {
3448         has_temporal=true;
3449         break;
3450       }
3451       if (has_temporal) {
3452         playMode = 1;
3453         playButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/player_pause.png")));
3454         QTimer::singleShot(1000/mFrameRate, this, SLOT(PlayNext()));
3455       }
3456   }
3457 }
3458 //------------------------------------------------------------------------------
3459
3460 //------------------------------------------------------------------------------
3461 void vvMainWindow::PlayNext()
3462 {
3463   if (playMode && !this->isHidden()) {
3464     int image_number=DataTree->topLevelItemCount();
3465     ///Only play one slicer per SM, and only if the SM is being displayed
3466     for (int i=0; i<image_number; i++)
3467       for (int j=0; j<4; j++)
3468         if (mSlicerManagers[i]->GetSlicer(0)->GetTMax() > 0 &&
3469           DataTree->topLevelItem(i)->data(j+1,Qt::CheckStateRole).toInt() > 0) {
3470             mSlicerManagers[i]->SetNextTSlice(j);
3471             break;
3472         }
3473         QTimer::singleShot(1000/mFrameRate, this, SLOT(PlayNext()));
3474   }
3475 }
3476 //------------------------------------------------------------------------------
3477
3478 void vvMainWindow::ShowLastImage()
3479 {
3480   if (mSlicerManagers.size() > 1) {
3481     QTreeWidgetItem * item=DataTree->topLevelItem(DataTree->topLevelItemCount()-1);
3482     CurrentImageChanged(mSlicerManagers.back()->GetId()); //select new image
3483     item->setData(1,Qt::CheckStateRole,2); //show the new image in the first panel
3484     DisplayChanged(item,1);
3485   }
3486 }
3487
3488 //------------------------------------------------------------------------------
3489 void vvMainWindow::UpdateRenderWindows()
3490 {
3491   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
3492     mSlicerManagers[i]->GetSlicer(0)->UpdateLandmarks();
3493     mSlicerManagers[i]->GetSlicer(1)->UpdateLandmarks();
3494     mSlicerManagers[i]->GetSlicer(2)->UpdateLandmarks();
3495     mSlicerManagers[i]->GetSlicer(3)->UpdateLandmarks();
3496   }
3497   if (NOViewWidget->GetRenderWindow()) NOViewWidget->GetRenderWindow()->Render();
3498   if (NEViewWidget->GetRenderWindow()) NEViewWidget->GetRenderWindow()->Render();
3499   if (SOViewWidget->GetRenderWindow()) SOViewWidget->GetRenderWindow()->Render();
3500   if (SEViewWidget->GetRenderWindow()) SEViewWidget->GetRenderWindow()->Render();
3501 }
3502 //------------------------------------------------------------------------------
3503
3504 //------------------------------------------------------------------------------
3505 void vvMainWindow::SegmentationOnCurrentImage()
3506 {
3507   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
3508
3509   vvSegmentationDialog segmentation;
3510   segmentation.SetImage(mSlicerManagers[index]->GetSlicer(0)->GetImage());
3511   segmentation.exec();
3512 }
3513 //------------------------------------------------------------------------------
3514
3515 void vvMainWindow::SurfaceViewerLaunch()
3516 {
3517   vvSurfaceViewerDialog surfaceViewer;
3518   surfaceViewer.exec();
3519 }
3520 //------------------------------------------------------------------------------
3521
3522
3523 //------------------------------------------------------------------------------
3524 int vvMainWindow::GetImageDuplicateFilenameNumber(std::string filename)
3525 {
3526   int number=0;
3527   for(unsigned int l=0; l<mSlicerManagers.size(); l++) {
3528     vvSlicerManager * v = mSlicerManagers[l];
3529     if (v->GetBaseFileName() ==
3530       vtksys::SystemTools::GetFilenameName(vtksys::SystemTools::GetFilenameWithoutLastExtension(filename))) {
3531         number = std::max(number, v->GetBaseFileNameNumber()+1);
3532     }
3533   }
3534   return number;
3535 }
3536 //------------------------------------------------------------------------------
3537
3538
3539 //------------------------------------------------------------------------------
3540 vvSlicerManager* vvMainWindow::AddImage(vvImage::Pointer image,std::string filename)
3541 {
3542   // Change filename if another image exist with the same name
3543   int number = GetImageDuplicateFilenameNumber(filename);
3544
3545   // Create new SliceManager
3546   vvSlicerManager* slicer_manager = new vvSlicerManager(4);
3547   slicer_manager->SetImage(image);//, IMAGE, number);
3548   //  filename = filename+"_"+clitk::toString(number);
3549   slicer_manager->SetFilename(filename, number);
3550   mSlicerManagers.push_back(slicer_manager);
3551
3552   //create an item in the tree with good settings
3553   QTreeWidgetItem *item = new QTreeWidgetItem();
3554   item->setData(0,Qt::UserRole,slicer_manager->GetFileName().c_str());//files[i].c_str());
3555   item->setData(1,Qt::UserRole,tr("image"));
3556   item->setData(COLUMN_IMAGE_NAME,Qt::DisplayRole,slicer_manager->GetFileName().c_str());//filename.c_str());
3557   qApp->processEvents();
3558
3559   for (int j = 1; j <= 4; j++) item->setData(j,Qt::CheckStateRole,1);
3560
3561   //Create the buttons for reload and close
3562   qApp->processEvents();
3563   QTreePushButton* cButton = new QTreePushButton;
3564   cButton->setItem(item);
3565   cButton->setColumn(COLUMN_CLOSE_IMAGE);
3566   cButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/exit.png")));
3567   connect(cButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
3568     this,SLOT(CloseImage(QTreeWidgetItem*, int)));
3569
3570   QTreePushButton* rButton = new QTreePushButton;
3571   rButton->setItem(item);
3572   rButton->setColumn(COLUMN_RELOAD_IMAGE);
3573   rButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/rotateright.png")));
3574   rButton->setEnabled(0);
3575   connect(rButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
3576     this,SLOT(ReloadImage(QTreeWidgetItem*, int)));
3577
3578   DataTree->addTopLevelItem(item);
3579   DataTree->setItemWidget(item, COLUMN_CLOSE_IMAGE, cButton);
3580   DataTree->setItemWidget(item, COLUMN_RELOAD_IMAGE, rButton);
3581
3582   //set the id of the image
3583   QString id = QDir::current().absoluteFilePath(slicer_manager->GetFileName().c_str()) + QString::number(mSlicerManagers.size()-1);
3584   item->setData(COLUMN_IMAGE_NAME,Qt::UserRole,id.toStdString().c_str());
3585   mSlicerManagers.back()->SetId(id.toStdString());
3586
3587   linkPanel->addImage(slicer_manager->GetFileName().c_str()// filename
3588     , id.toStdString());
3589
3590   connect(mSlicerManagers.back(), SIGNAL(currentImageChanged(std::string)),
3591     this, SLOT(CurrentImageChanged(std::string)));
3592   connect(mSlicerManagers.back(), SIGNAL(currentPickedImageChanged(std::string)),
3593     this, SLOT(CurrentPickedImageChanged(std::string)));
3594   connect(mSlicerManagers.back(), SIGNAL(UpdatePosition(int, double, double, double, double, double, double, double)),
3595     this, SLOT(MousePositionChanged(int,double, double, double, double, double, double, double)));
3596   connect(mSlicerManagers.back(), SIGNAL(UpdateVector(int, double, double, double, double)),
3597     this, SLOT(VectorChanged(int,double,double,double, double)));
3598   connect(mSlicerManagers.back(), SIGNAL(UpdateOverlay(int, double, double)),
3599     this, SLOT(OverlayChanged(int,double,double)));
3600   connect(mSlicerManagers.back(), SIGNAL(UpdateFusion(int, double)),
3601     this, SLOT(FusionChanged(int,double)));
3602   //connect(mSlicerManagers.back(), SIGNAL(UpdateFusionSequence(int, bool, unsigned int)),
3603   //  this, SLOT(FusionSequenceChanged(int, bool, unsigned int)));
3604   connect(mSlicerManagers.back(), SIGNAL(WindowLevelChanged()),
3605     this,SLOT(WindowLevelChanged()));
3606   connect(mSlicerManagers.back(), SIGNAL(UpdateSlice(int,int)),
3607     this,SLOT(UpdateSlice(int,int)));
3608   connect(mSlicerManagers.back(), SIGNAL(UpdateTSlice(int, int, int)),
3609     this,SLOT(UpdateTSlice(int, int, int)));
3610   connect(mSlicerManagers.back(), SIGNAL(UpdateTSlice(int, int, int)),
3611     this,SLOT(ImageInfoChanged()));
3612   connect(mSlicerManagers.back(), SIGNAL(UpdateSliceRange(int,int,int,int,int)),
3613     this,SLOT(UpdateSliceRange(int,int,int,int,int)));
3614   connect(mSlicerManagers.back(), SIGNAL(UpdateLinkManager(std::string,int,double,double,double,int)),
3615     this,SLOT(UpdateLinkManager(std::string,int,double,double,double,int)));
3616   connect(mSlicerManagers.back(), SIGNAL(UpdateLinkedNavigation(std::string,vvSlicerManager*,vvSlicer*)),
3617     this,SLOT(UpdateLinkedNavigation(std::string,vvSlicerManager*,vvSlicer*)));
3618   connect(mSlicerManagers.back(), SIGNAL(ChangeImageWithIndexOffset(vvSlicerManager*,int,int)),
3619     this,SLOT(ChangeImageWithIndexOffset(vvSlicerManager*,int,int)));
3620   connect(mSlicerManagers.back(), SIGNAL(LandmarkAdded()),landmarksPanel,SLOT(AddPoint()));
3621
3622
3623   UpdateTree();
3624   qApp->processEvents();
3625   InitSlicers();
3626   ShowLastImage();
3627   InitDisplay();
3628   qApp->processEvents();
3629
3630   // End
3631   ImageInfoChanged();
3632   return slicer_manager;
3633 }
3634 //------------------------------------------------------------------------------
3635
3636
3637 //------------------------------------------------------------------------------
3638 void vvMainWindow::UpdateCurrentSlicer()
3639 {
3640   int index = -1;
3641   if (DataTree->selectedItems().size() > 0) {
3642     index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
3643   }
3644   mSlicerManagerCurrentIndex = index;
3645 }
3646 //------------------------------------------------------------------------------
3647