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