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