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 #include <QShortcut>
  27
  28 // VV include
  29 #include "vvMainWindow.h"
  30 #include "vvHelpDialog.h"
  31 #include "vvRegisterForm.h"
  32 #include "vvDocumentation.h"
  33 #include "vvProgressDialog.h"
  34 #include "vvQDicomSeriesSelector.h"
  35 #include "vvSlicerManager.h"
  36 #include "clitkImageCommon.h"
  37 #include "vvSlicer.h"
  38 #include "vvInteractorStyleNavigator.h"
  39 #include "vvImageWriter.h"
  40 #include "vvSegmentationDialog.h"
  41 #include "vvSurfaceViewerDialog.h"
  42 #include "vvDeformationDialog.h"
  43 #include "vvImageWarp.h"
  44 #include "vvUtils.h"
  45 #include "vvMidPosition.h"
  46 #include "vvMesh.h"
  47 #include "vvStructSelector.h"
  48 #include "vvMeshReader.h"
  49 #include "vvSaveState.h"
  50 #include "vvReadState.h"
  51 #include "clitkConfiguration.h"
  52 #include "clitkMatrix.h"
  53 #ifdef Q_OS_OSX
  54 # include "vvOSXHelper.h"
  55 #endif
  56
  57 // ITK include
  58 #include <itkImage.h>
  59 #include <itkImageFileReader.h>
  60 #include <itkByteSwapper.h>
  61 #include <itkCommand.h>
  62 #include <itkNumericSeriesFileNames.h>
  63
  64 // VTK include
  65 #include <vtkImageMapper3D.h>
  66 #include <vtkInformation.h>
  67 #include <vtkVersion.h>
  68 #include <vtkImageData.h>
  69 #include <vtkImageActor.h>
  70 #include <vtkCornerAnnotation.h>
  71 #include <vtkRenderWindow.h>
  72 #include <vtkRenderWindowInteractor.h>
  73 #include <vtkRenderer.h>
  74 #include <vtkRendererCollection.h>
  75 #include <vtkWindowToImageFilter.h>
  76 #include <vtkBMPWriter.h>
  77 #include <vtkTIFFWriter.h>
  78 #include <vtkPNMWriter.h>
  79 #include <vtkPNGWriter.h>
  80 #include <vtkJPEGWriter.h>
  81 #include <vtkGenericMovieWriter.h>
  82 #ifdef CLITK_EXPERIMENTAL
  83 #  include <vvAnimatedGIFWriter.h>
  84 #endif
  85 #ifdef VTK_USE_VIDEO_FOR_WINDOWS
  86 #  include <vtkAVIWriter.h>
  87 #endif
  88 #ifdef VTK_USE_FFMPEG_ENCODER
  89 #  include <vtkFFMPEGWriter.h>
  90 #endif
  91 #ifdef VTK_USE_MPEG2_ENCODER
  92 #  include <vtkMPEG2Writer.h>
  93 #endif
  94 #include <vtkMatrix4x4.h>
  95 #include <vtkTransform.h>
  96
  97 // Standard includes
  98 #include <iostream>
  99 #include <fstream>
 100 #include <sstream>
 101 #include <iomanip>
 102
 103 #define COLUMN_TREE 0
 104 #define COLUMN_UL_VIEW 1
 105 #define COLUMN_UR_VIEW 2
 106 #define COLUMN_DL_VIEW 3
 107 #define COLUMN_DR_VIEW 4
 108 #define COLUMN_CLOSE_IMAGE 5
 109 #define COLUMN_RELOAD_IMAGE 6
 110 #define COLUMN_IMAGE_NAME 7
 111
 112 #include <extensions.h>
 113
 114
 115 /*Data Tree values
 116 0,Qt::UserRole full filename
 117 1,Qt::CheckStateRole checkbutton UL View
 118 1,Qt::UserRole overlay, fusion or vector
 119 2,Qt::CheckStateRole checkbutton UR View
 120 3,Qt::CheckStateRole checkbutton DL View
 121 4,Qt::CheckStateRole checkbutton DR View
 122 5,0  short filename
 123 5,Qt::UserRole mSlicerManager id*/
 124
 125 //------------------------------------------------------------------------------
 126 vvMainWindow::vvMainWindow():vvMainWindowBase()
 127 {
 128   setupUi(this); // this sets up the GUI
 129
 130   //Qt::WindowFlags flags = windowFlags();
 131   //setWindowFlags(flags | Qt::WindowStaysOnTopHint);
 132
 133   mInputPathName = "";
 134   mMenuTools = menuTools;
 135   //  mMenuSegmentation = menuSegmentation;
 136   mContextMenu = &contextMenu;
 137   mMenuExperimentalTools = menuExperimental;
 138   mMainWidget = this;
 139   mCurrentTime = -1;
 140   mCurrentSelectedImageId = "";
 141   mCurrentPickedImageId = "";
 142   mCurrentPickedImageIndex = 0;
 143
 144   //Init the contextMenu
 145   this->setContextMenuPolicy(Qt::CustomContextMenu);
 146   contextActions.resize(0);
 147   QAction* actionOpen_new_image = contextMenu.addAction(QIcon(QString::fromUtf8(":/common/icons/fileopen.png")),
 148     tr("O&pen new Image"));
 149   connect(actionOpen_new_image,SIGNAL(triggered()),this,SLOT(OpenImages()));
 150   contextActions.push_back(actionOpen_new_image);
 151   contextMenu.addSeparator();
 152
 153   QAction* actionClose_Image = contextMenu.addAction(QIcon(QString::fromUtf8(":/common/icons/exit.png")),
 154     tr("Close Current Image"));
 155   connect(actionClose_Image,SIGNAL(triggered()),this,SLOT(CloseImage()));
 156   contextActions.push_back(actionClose_Image);
 157
 158   QAction* actionReload_image = contextMenu.addAction(QIcon(QString::fromUtf8(":/common/icons/rotateright.png")),
 159     tr("Reload Current Image"));
 160   connect(actionReload_image,SIGNAL(triggered()),this,SLOT(ReloadImage()));
 161   contextActions.push_back(actionReload_image);
 162
 163   QAction* actionSave_image = contextMenu.addAction(QIcon(QString::fromUtf8(":/common/icons/filesave.png")),
 164     tr("Save Current Image"));
 165   connect(actionSave_image,SIGNAL(triggered()),this,SLOT(SaveAs()));
 166   contextActions.push_back(actionSave_image);
 167
 168   QAction* actionSave_state = contextMenu.addAction(QIcon(QString::fromUtf8(":/common/icons/filesave.png")),
 169     tr("Save Current State"));
 170   connect(actionSave_state,SIGNAL(triggered()),this,SLOT(SaveCurrentState()));
 171   contextActions.push_back(actionSave_state);
 172
 173   QAction* actionRead_state = contextMenu.addAction(QIcon(QString::fromUtf8(":/common/icons/filesave.png")),
 174     tr("Read Saved State"));
 175   connect(actionRead_state,SIGNAL(triggered()),this,SLOT(ReadSavedState()));
 176   contextActions.push_back(actionRead_state);
 177
 178   contextMenu.addSeparator();
 179
 180   contextMenu.addAction(actionAdd_VF_to_current_Image);
 181   contextActions.push_back(actionAdd_VF_to_current_Image);
 182
 183   //QAction* actionAdd_Overlay_to_current_Image = menuOverlay->addAction(QIcon(QString::fromUtf8(":/common/icons/GPSup.png")),
 184   //    tr("Add overlay image to current image"));
 185   contextMenu.addAction(actionAdd_overlay_image_to_current_image);
 186   contextActions.push_back(actionAdd_overlay_image_to_current_image);
 187
 188   contextMenu.addAction(actionAdd_fusion_image);
 189   contextActions.push_back(actionAdd_fusion_image);
 190
 191 #ifdef CLITK_EXPERIMENTAL
 192   contextMenu.addAction(actionAdd_USSequence_toCT);
 193   contextActions.push_back(actionAdd_USSequence_toCT);
 194 #endif
 195
 196   contextMenu.addAction(actionAdd_wipe_image);
 197   contextActions.push_back(actionAdd_wipe_image);
 198
 199
 200   contextMenu.addSeparator();
 201   QAction* actionResetMatrix = contextMenu.addAction(QIcon(QString::fromUtf8(":/common/icons/identity.png")),
 202     tr("Reset transformation to identity"));
 203   connect(actionResetMatrix, SIGNAL(triggered()), this,SLOT(ResetTransformationToIdentity()));
 204
 205   //init the DataTree
 206   mSlicerManagers.resize(0);
 207
 208   QStringList header;
 209   header.append("");
 210   header.append("TL");
 211   header.append("TR");
 212   header.append("BL");
 213   header.append("BR");
 214   header.append("");
 215   header.append("");
 216   header.append("Name");
 217
 218   DataTree->setHeaderLabels(header);
 219   DataTree->resizeColumnToContents(COLUMN_TREE);
 220   DataTree->resizeColumnToContents(COLUMN_UL_VIEW);
 221   DataTree->resizeColumnToContents(COLUMN_UR_VIEW);
 222   DataTree->resizeColumnToContents(COLUMN_DL_VIEW);
 223   DataTree->resizeColumnToContents(COLUMN_DR_VIEW);
 224   DataTree->resizeColumnToContents(COLUMN_CLOSE_IMAGE);
 225   DataTree->resizeColumnToContents(COLUMN_RELOAD_IMAGE);
 226   DataTree->resizeColumnToContents(COLUMN_IMAGE_NAME);
 227
 228   viewMode = 1;
 229   documentation = new vvDocumentation();
 230   help_dialog = new vvHelpDialog();
 231   dicomSeriesSelector = new vvDicomSeriesSelector();
 232
 233   inverseButton->setEnabled(0);
 234   actionAdd_overlay_image_to_current_image->setEnabled(0);
 235   actionSave_As->setEnabled(0);
 236   actionAdd_VF_to_current_Image->setEnabled(0);
 237   actionAdd_fusion_image->setEnabled(0);
 238   actionAdd_USSequence_toCT->setEnabled(0);
 239   actionAdd_wipe_image->setEnabled(0);
 240
 241   //init the sliders
 242   verticalSliders.push_back(NOVerticalSlider);
 243   verticalSliders.push_back(NEVerticalSlider);
 244   verticalSliders.push_back(SOVerticalSlider);
 245   verticalSliders.push_back(SEVerticalSlider);
 246
 247   for (int i =0; i < 4; i++)
 248     verticalSliders[i]->hide();
 249
 250   horizontalSliders.push_back(NOHorizontalSlider);
 251   horizontalSliders.push_back(NEHorizontalSlider);
 252   horizontalSliders.push_back(SOHorizontalSlider);
 253   horizontalSliders.push_back(SEHorizontalSlider);
 254
 255   for (int i =0; i < 4; i++)
 256     horizontalSliders[i]->hide();
 257
 258
 259   connect(NOVerticalSlider,SIGNAL(valueChanged(int)),this,SLOT(NOVerticalSliderChanged()));
 260   connect(NEVerticalSlider,SIGNAL(valueChanged(int)),this,SLOT(NEVerticalSliderChanged()));
 261   connect(SOVerticalSlider,SIGNAL(valueChanged(int)),this,SLOT(SOVerticalSliderChanged()));
 262   connect(SEVerticalSlider,SIGNAL(valueChanged(int)),this,SLOT(SEVerticalSliderChanged()));
 263
 264   connect(NOHorizontalSlider,SIGNAL(valueChanged(int)),this,SLOT(NOHorizontalSliderMoved()));
 265   connect(NEHorizontalSlider,SIGNAL(valueChanged(int)),this,SLOT(NEHorizontalSliderMoved()));
 266   connect(SOHorizontalSlider,SIGNAL(valueChanged(int)),this,SLOT(SOHorizontalSliderMoved()));
 267   connect(SEHorizontalSlider,SIGNAL(valueChanged(int)),this,SLOT(SEHorizontalSliderMoved()));
 268
 269   //connect everything
 270   connect(actionCompute_mid_position_image,SIGNAL(triggered()),this,SLOT(ComputeMidPosition()));
 271   connect(actionDeformable_Registration,SIGNAL(triggered()),this,SLOT(ComputeDeformableRegistration()));
 272   connect(actionWarp_image_with_vector_field,SIGNAL(triggered()),this,SLOT(WarpImage()));
 273   connect(actionLoad_images,SIGNAL(triggered()),this,SLOT(OpenImages()));
 274   connect(actionOpen_Dicom,SIGNAL(triggered()),this,SLOT(OpenDicom()));
 275   //  connect(actionOpen_Dicom_Struct,SIGNAL(triggered()),this,SLOT(OpenDCStructContour()));
 276   connect(actionOpen_VTK_contour,SIGNAL(triggered()),this,SLOT(OpenVTKContour()));
 277   connect(actionOpen_Multiple_Images_As_One,SIGNAL(triggered()),this,SLOT(MergeImages()));
 278   connect(actionSlice_Image_As_Multiple_Images,SIGNAL(triggered()),this,SLOT(SliceImages()));
 279   connect(actionOpen_Image_With_Time,SIGNAL(triggered()),this,SLOT(OpenImageWithTime()));
 280   connect(actionMerge_images_as_n_dim_t, SIGNAL(triggered()), this, SLOT(MergeImagesWithTime()));
 281   connect(actionSave_As,SIGNAL(triggered()),this,SLOT(SaveAs()));
 282   connect(actionSave_current_state,SIGNAL(triggered()),this,SLOT(SaveCurrentState()));
 283   connect(actionRead_saved_state,SIGNAL(triggered()),this,SLOT(ReadSavedState()));
 284   connect(actionExit,SIGNAL(triggered()),this,SLOT(close()));
 285   connect(actionAdd_VF_to_current_Image,SIGNAL(triggered()),this,SLOT(OpenField()));
 286   connect(actionAdd_wipe_image,SIGNAL(triggered()),this,SLOT(SelectWipeImage()));
 287   connect(actionAdd_fusion_image,SIGNAL(triggered()),this,SLOT(SelectFusionImage()));
 288   connect(actionAdd_overlay_image_to_current_image,SIGNAL(triggered()), this,SLOT(SelectOverlayImage()));
 289   connect(actionAdd_USSequence_toCT,SIGNAL(triggered()), this,SLOT(SelectFusionSequence()));
 290   connect(actionNavigation_Help,SIGNAL(triggered()),this,SLOT(ShowHelpDialog()));
 291
 292   QShortcut *shortcutHelp = new QShortcut(QKeySequence(QKeySequence::HelpContents),this);
 293   shortcutHelp->setContext(Qt::ApplicationShortcut);
 294   QObject::connect(shortcutHelp, SIGNAL(activated()), this, SLOT(ShowHelpDialog()));
 295
 296   connect(actionDocumentation,SIGNAL(triggered()),this,SLOT(ShowDocumentation()));
 297   connect(actionRegister_vv,SIGNAL(triggered()),this,SLOT(PopupRegisterForm()));
 298
 299   connect(overlayPanel, SIGNAL(FusionSequenceCorrespondancesButtonPressed()), this, SLOT(SelectFusionSequenceCorrespondances()));
 300
 301
 302   ///////////////////////////////////////////////
 303   connect(actionSegmentation,SIGNAL(triggered()),this,SLOT(SegmentationOnCurrentImage()));
 304   connect(actionSurface_Viewer,SIGNAL(triggered()),this,SLOT(SurfaceViewerLaunch()));
 305   ///////////////////////////////////////////////
 306
 307   actionNorth_East_Window->setEnabled(0);
 308   actionNorth_West_Window->setEnabled(0);
 309   actionSouth_East_Window->setEnabled(0);
 310   actionSouth_West_Window->setEnabled(0);
 311
 312   connect(actionNorth_East_Window,SIGNAL(triggered()),this,SLOT(SaveNEScreenshot()));
 313   connect(actionNorth_West_Window,SIGNAL(triggered()),this,SLOT(SaveNOScreenshot()));
 314   connect(actionSouth_East_Window,SIGNAL(triggered()),this,SLOT(SaveSEScreenshot()));
 315   connect(actionSouth_West_Window,SIGNAL(triggered()),this,SLOT(SaveSOScreenshot()));
 316   connect(actionSave_all_slices,SIGNAL(triggered()),this,SLOT(SaveScreenshotAllSlices()));
 317
 318   connect(DataTree,SIGNAL(itemSelectionChanged()),this,SLOT(ImageInfoChanged()));
 319   connect(DataTree,SIGNAL(itemClicked(QTreeWidgetItem*, int)),this,
 320     SLOT(DisplayChanged(QTreeWidgetItem*, int)));
 321
 322   connect(viewButton,SIGNAL(clicked()),this, SLOT(ChangeViewMode()) );
 323   connect(windowSpinBox,SIGNAL(editingFinished()),this,SLOT(WindowLevelEdited()));
 324   connect(levelSpinBox,SIGNAL(editingFinished()),this,SLOT(WindowLevelEdited()));
 325   connect(colorMapComboBox,SIGNAL(currentIndexChanged(int)),this,SLOT(UpdateColorMap()));
 326   connect(presetComboBox,SIGNAL(currentIndexChanged(int)),this,SLOT(UpdateWindowLevel()));
 327   connect(slicingPresetComboBox, SIGNAL(currentIndexChanged(int)),this,SLOT(UpdateSlicingPreset()));
 328   connect(inverseButton,SIGNAL(clicked()),this,SLOT(SwitchWindowLevel()));
 329   connect(applyWindowLevelToAllButton,SIGNAL(clicked()),this,SLOT(ApplyWindowLevelToAllImages()));
 330
 331   connect(this,SIGNAL(customContextMenuRequested(QPoint)),this,SLOT(ShowContextMenu(QPoint)));
 332
 333   connect(linkPanel,SIGNAL(addLink(QString,QString,bool)),this,SLOT(AddLink(QString,QString,bool)));
 334   connect(linkPanel,SIGNAL(removeLink(QString,QString)),this,SLOT(RemoveLink(QString,QString)));
 335   connect(overlayPanel,SIGNAL(VFPropertyUpdated(int,int,int,int,double,double,double)),this,SLOT(SetVFProperty(int,int,int,int,double,double,double)));
 336   connect(overlayPanel,SIGNAL(OverlayPropertyUpdated(int,int,double,double)),
 337     this,SLOT(SetOverlayProperty(int,int,double,double)));
 338   connect(overlayPanel,SIGNAL(FusionPropertyUpdated(int,int,int,double,double, bool)),
 339     this,SLOT(SetFusionProperty(int,int,int,double,double, bool)));
 340   connect(landmarksPanel,SIGNAL(UpdateRenderWindows()),this,SLOT(UpdateRenderWindows()));
 341   connect(landmarksPanel,SIGNAL(SelectedPointChanged()),this,SLOT(GoToLandmark()));
 342
 343   connect(overlayPanel,SIGNAL(FusionSequencePropertyUpdated(int, bool, unsigned int, bool)),
 344     this,SLOT(SetFusionSequenceProperty(int, bool,unsigned int, bool)));
 345
 346
 347   playMode = 0;//pause
 348   mFrameRate = 10;
 349   playButton->setEnabled(0);
 350   frameRateLabel->setEnabled(0);
 351   frameRateSpinBox->setEnabled(0);
 352   connect(playButton, SIGNAL(clicked()),this,SLOT(PlayPause()));
 353   connect(frameRateSpinBox, SIGNAL(valueChanged(int)),this,SLOT(ChangeFrameRate(int)));
 354
 355   goToCursorPushButton->setEnabled(0);
 356   connect(goToCursorPushButton, SIGNAL(clicked()),this,SLOT(GoToCursor()));
 357
 358   NOViewWidget->hide();
 359   NEViewWidget->hide();
 360   SOViewWidget->hide();
 361   SEViewWidget->hide();
 362
 363 #ifdef Q_OS_OSX
 364   disableGLHiDPI(NOViewWidget->winId());
 365   disableGLHiDPI(NEViewWidget->winId());
 366   disableGLHiDPI(SOViewWidget->winId());
 367   disableGLHiDPI(SEViewWidget->winId());
 368 #endif
 369
 370   //Recently opened files
 371   std::list<std::string> recent_files = GetRecentlyOpenedImages();
 372   recentlyOpenedFilesMenu=NULL;
 373   if ( !recent_files.empty() ) {
 374     createRecentlyOpenedFilesMenu();
 375     updateRecentlyOpenedFilesMenu(recent_files);
 376   }
 377
 378   // Adding all new tools (insertion in the menu)
 379   vvToolManager::GetInstance()->InsertToolsInMenu(this);
 380   vvToolManager::GetInstance()->EnableToolsInMenu(this, false);
 381
 382 //#ifndef CLITK_EXPERIMENTAL
 383 //#define CLITK_EXPERIMENTAL 0
 384 //#endif
 385 #ifdef CLITK_EXPERIMENTAL
 386   if (!CLITK_EXPERIMENTAL)
 387     menuExperimental->menuAction()->setVisible(false);
 388 #endif
 389
 390   QTimer * timerMemory = new QTimer(this);
 391   //timerMemory->setInterval(5);
 392   connect(timerMemory, SIGNAL(timeout()), this, SLOT(UpdateMemoryUsage()));
 393   timerMemory->start(2000);
 394 }
 395
 396 //------------------------------------------------------------------------------
 397 void vvMainWindow::show()
 398 {
 399   vvMainWindowBase::show();
 400   PopupRegisterForm(true);
 401 }
 402 //------------------------------------------------------------------------------
 403 void vvMainWindow::UpdateMemoryUsage()
 404 {
 405   //  clitk::PrintMemory(true);
 406   if (clitk::GetMemoryUsageInMb() == 0) infoPanel->setMemoryInMb("NA");
 407   else infoPanel->setMemoryInMb(QString::number(clitk::GetMemoryUsageInMb())+" MiB");
 408 }
 409 //------------------------------------------------------------------------------
 410
 411
 412 //------------------------------------------------------------------------------
 413 void vvMainWindow::createRecentlyOpenedFilesMenu()
 414 {
 415   recentlyOpenedFilesMenu = new QMenu("Recently opened files...");
 416   recentlyOpenedFilesMenu->setIcon(QIcon(QString::fromUtf8(":/common/icons/open.png")));
 417   menuFile->insertMenu(actionOpen_Image_With_Time,recentlyOpenedFilesMenu);
 418   menuFile->insertSeparator(actionOpen_Image_With_Time);
 419 }
 420 //------------------------------------------------------------------------------
 421
 422
 423 //------------------------------------------------------------------------------
 424
 425 void vvMainWindow::updateRecentlyOpenedFilesMenu(const std::list<std::string> &recent_files)
 426 {
 427   if(recentlyOpenedFilesMenu==NULL) {
 428     createRecentlyOpenedFilesMenu();
 429   } else {
 430     recentlyOpenedFilesMenu->clear();
 431   }
 432   for (std::list<std::string>::const_iterator i = recent_files.begin(); i!=recent_files.end(); i++) {
 433     QAction* current=new QAction(QIcon(QString::fromUtf8(":/common/icons/open.png")), i->c_str(),this);
 434     recentlyOpenedFilesMenu->addAction(current);
 435     connect(current,SIGNAL(triggered()),this,SLOT(OpenRecentImage()));
 436   }
 437 }
 438 //------------------------------------------------------------------------------
 439
 440
 441 //------------------------------------------------------------------------------
 442 void vvMainWindow::ComputeMidPosition()
 443 {
 444   bool ok;
 445   int index=GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
 446   int ref = QInputDialog::getInt(this,"Chose reference phase","Reference phase",0,0,\
 447 mSlicerManagers[index]->GetImage()->GetVTKImages().size()-1,1,&ok);
 448   if (ok) {
 449     vvMidPosition midp;
 450     midp.slicer_manager = mSlicerManagers[index];
 451     midp.reference_image_index = ref;
 452     QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
 453     midp.Update();
 454     if (midp.error)
 455       QMessageBox::warning(this, "Error computing midposition image",midp.error_message.c_str());
 456     else {
 457       QFileInfo info(midp.slicer_manager->GetFileName().c_str());
 458       AddImage(midp.output,info.path().toStdString()+"/"+info.completeBaseName().toStdString()+"_midposition.mhd");
 459     }
 460     QApplication::restoreOverrideCursor();
 461   }
 462 }
 463 //------------------------------------------------------------------------------
 464
 465
 466 //------------------------------------------------------------------------------
 467 void vvMainWindow::AddContour(int image_index, vvMesh::Pointer contour, bool propagation)
 468 {
 469   QTreeWidgetItem *item = new QTreeWidgetItem();
 470   item->setData(0,Qt::UserRole,"filename.vtk");
 471   item->setData(1,Qt::UserRole,tr("contour"));
 472   QBrush brush;
 473   brush.setColor(QColor(contour->r*255,contour->g*255,contour->b*255));
 474   brush.setStyle(Qt::SolidPattern);
 475   item->setData(COLUMN_IMAGE_NAME,Qt::BackgroundRole,brush);
 476   item->setData(COLUMN_IMAGE_NAME,Qt::DisplayRole,contour->structure_name.c_str());
 477
 478   for (int j = 1; j <= 4; j++)
 479     item->setData(j,Qt::CheckStateRole,DataTree->topLevelItem(image_index)->data(j,Qt::CheckStateRole));
 480
 481   QTreePushButton* cButton = new QTreePushButton;
 482   cButton->setItem(item);
 483   cButton->setColumn(COLUMN_CLOSE_IMAGE);
 484   cButton->setToolTip(tr("close image"));
 485   cButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/exit.png")));
 486   connect(cButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
 487     this,SLOT(CloseImage(QTreeWidgetItem*, int)));
 488
 489   QTreePushButton* rButton = new QTreePushButton;
 490   rButton->setItem(item);
 491   rButton->setColumn(COLUMN_RELOAD_IMAGE);
 492   rButton->setToolTip(tr("reload image"));
 493   rButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/rotateright.png")));
 494   rButton->setEnabled(false);
 495   //Not implemented
 496   //connect(rButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
 497   //this,SLOT(ReloadImage(QTreeWidgetItem*, int)));
 498
 499   DataTree->topLevelItem(image_index)->setExpanded(1);
 500   DataTree->topLevelItem(image_index)->addChild(item);
 501   DataTree->setItemWidget(item, COLUMN_CLOSE_IMAGE, cButton);
 502   DataTree->setItemWidget(item, COLUMN_RELOAD_IMAGE, rButton);
 503   QString id = DataTree->topLevelItem(image_index)->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString();
 504   item->setData(COLUMN_IMAGE_NAME,Qt::UserRole,id.toStdString().c_str());
 505
 506   UpdateTree();
 507   mSlicerManagers[image_index]->AddContour(contour,propagation);
 508   mSlicerManagers[image_index]->Render();
 509 }
 510 //------------------------------------------------------------------------------
 511
 512
 513 //------------------------------------------------------------------------------
 514 void vvMainWindow::OpenVTKContour()
 515 {
 516   if (mSlicerManagers.size() > 0) {
 517     QString Extensions = "Images ( *.vtk *.obj)";
 518     Extensions += ";;All Files (*)";
 519     QString file = QFileDialog::getOpenFileName(this,tr("Open vtkPolyData"),mInputPathName,Extensions);
 520     if (file.isNull())
 521       return;
 522     QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
 523     int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
 524     vvMeshReader reader;
 525     reader.SetImage(mSlicerManagers[index]->GetImage());
 526     reader.SetModeToVTK();
 527     reader.SetFilename(file.toStdString());
 528     reader.Update();
 529     AddContour(index,reader.GetOutput()[0],false);
 530     QApplication::restoreOverrideCursor();
 531   }
 532 }
 533 //------------------------------------------------------------------------------
 534
 535
 536 //------------------------------------------------------------------------------
 537 void vvMainWindow::AddDCStructContour(int index, QString file)
 538 {
 539   vvMeshReader reader;
 540   reader.SetFilename(file.toStdString());
 541   vvStructSelector selector;
 542   selector.SetStructures(reader.GetROINames());
 543   if (!mSlicerManagers[index]->GetVF().IsNull())
 544     selector.EnablePropagationCheckBox();
 545   if (selector.exec()) {
 546     QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
 547     reader.SetSelectedItems(selector.getSelectedItems());
 548     reader.SetImage(mSlicerManagers[index]->GetImage());
 549     if (selector.PropagationEnabled())
 550       reader.SetPropagationVF(mSlicerManagers[index]->GetVF());
 551     reader.Update();
 552     std::vector<vvMesh::Pointer> contours=reader.GetOutput();
 553     for (std::vector<vvMesh::Pointer>::iterator i=contours.begin();
 554       i!=contours.end(); i++)
 555       AddContour(index,*i,selector.PropagationEnabled());
 556     QApplication::restoreOverrideCursor();
 557   }
 558 }
 559
 560 //------------------------------------------------------------------------------
 561 void vvMainWindow::OpenDCStructContour()
 562 {
 563   if (mSlicerManagers.size() > 0) {
 564     QString Extensions = "Dicom Files ( *.dcm RS*)";
 565     Extensions += ";;All Files (*)";
 566     QString file = QFileDialog::getOpenFileName(this,tr("Merge Images"),mInputPathName,Extensions);
 567     if (file.isNull())
 568       return;
 569     int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
 570     AddDCStructContour(index, file);
 571   }
 572 }
 573 //------------------------------------------------------------------------------
 574
 575
 576 //------------------------------------------------------------------------------
 577 void vvMainWindow::ComputeDeformableRegistration()
 578 {
 579   if (mSlicerManagers.size() > 0) {
 580     int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
 581     vvDeformationDialog dialog(index,mSlicerManagers);
 582     if (dialog.exec()) {
 583       std::string base_name=itksys::SystemTools::GetFilenameWithoutExtension(mSlicerManagers[dialog.GetInputFileIndex()]->GetFileName());
 584       AddField(dialog.GetOutput(),dialog.getFieldFile(),dialog.GetInputFileIndex());
 585       WarpImage(dialog.GetSelectedSlicer(),dialog.GetReferenceFrameIndex());
 586     } else
 587       std::cout << "Error or user cancellation while computing deformation field..." << std::endl;
 588   } else QMessageBox::information(this, "Need to open image","You must open an image first.");
 589 }
 590 //------------------------------------------------------------------------------
 591
 592
 593 //------------------------------------------------------------------------------
 594 void vvMainWindow::WarpImage()
 595 {
 596   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
 597   if (!mSlicerManagers[index]->GetVF().IsNull()) {
 598     bool ok;
 599     int ref = QInputDialog::getInt(this,"Chose reference phase","Reference phase",0,0,\
 600       mSlicerManagers[index]->GetImage()->GetVTKImages().size()-1,1,&ok);
 601     if (ok) {
 602       WarpImage(mSlicerManagers[index],ref);
 603     }
 604   } else
 605     QMessageBox::warning(this,tr("No vector field"),tr("Sorry, can't warp without a vector field"));
 606 }
 607 //------------------------------------------------------------------------------
 608
 609
 610 //------------------------------------------------------------------------------
 611 void vvMainWindow::WarpImage(vvSlicerManager* selected_slicer,int reference_phase)
 612 {
 613   if (!selected_slicer->GetVF().IsNull()) {
 614     QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
 615     QFileInfo info(selected_slicer->GetFileName().c_str());
 616     vvImageWarp warp(selected_slicer->GetImage(),selected_slicer->GetVF(),
 617       reference_phase,this);
 618     if (warp.ComputeWarpedImage()) {
 619       AddImage(warp.GetWarpedImage(),info.path().toStdString()+"/"+info.completeBaseName().toStdString()+"_warped.mhd");
 620       AddImage(warp.GetDiffImage()  ,info.path().toStdString()+"/"+info.completeBaseName().toStdString()+"_diff.mhd");
 621       AddImage(warp.GetJacobianImage()  ,info.path().toStdString()+"/"+info.completeBaseName().toStdString()+"_jacobian.mhd");
 622       QApplication::restoreOverrideCursor();
 623     } else {
 624       QApplication::restoreOverrideCursor();
 625       QMessageBox::warning(this,tr("Different spacings"),tr("The vector field and image spacings must be the same in order to warp."));
 626     }
 627   } else
 628     QMessageBox::warning(this,tr("No vector field"),tr("Sorry, can't warp without a vector field."));
 629 }
 630 //------------------------------------------------------------------------------
 631
 632
 633 //------------------------------------------------------------------------------
 634 vvMainWindow::~vvMainWindow()
 635 {
 636   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
 637     if (mSlicerManagers[i] != NULL)
 638       delete mSlicerManagers[i];
 639   }
 640   delete documentation;
 641   delete help_dialog;
 642   delete dicomSeriesSelector;
 643 }
 644 //------------------------------------------------------------------------------
 645
 646 //------------------------------------------------------------------------------
 647 QTabWidget * vvMainWindow::GetTab()
 648 {
 649   return tabWidget;
 650 }
 651 //------------------------------------------------------------------------------
 652
 653
 654 //------------------------------------------------------------------------------
 655 void vvMainWindow::MergeImages()
 656 {
 657   QString Extensions = EXTENSIONS;
 658   Extensions += ";;All Files (*)";
 659   QStringList files = QFileDialog::getOpenFileNames(this,tr("Merge Images"),mInputPathName,Extensions);
 660   if (files.isEmpty())
 661     return;
 662   mInputPathName = itksys::SystemTools::GetFilenamePath(files[0].toStdString()).c_str();
 663   std::vector<std::string> vector;
 664
 665   unsigned int currentDim = 0;
 666   std::vector<double> currentSpacing;
 667   std::vector<int> currentSize;
 668   std::vector<double> currentOrigin;
 669
 670   for (int i = 0; i < files.size(); i++) {
 671     itk::ImageIOBase::Pointer reader = itk::ImageIOFactory::CreateImageIO(
 672       files[i].toStdString().c_str(), itk::ImageIOFactory::ReadMode);
 673     reader->SetFileName(files[i].toStdString().c_str());
 674     reader->ReadImageInformation();
 675     if (reader)        {
 676       //NOViewWidget->hide();
 677       //NEViewWidget->hide();
 678       //SOViewWidget->hide();
 679       //SEViewWidget->hide();
 680       if (i == 0)
 681         currentDim = reader->GetNumberOfDimensions();
 682       bool IsOk = true;
 683       for (unsigned int j = 0; j < currentDim; j++) {
 684         if (i == 0) {
 685           if (j == 0) {
 686             currentSpacing.resize(currentDim);
 687             currentSize.resize(currentDim);
 688             currentOrigin.resize(currentDim);
 689           }
 690           currentOrigin[j] = reader->GetOrigin(j);
 691           currentSpacing[j] = reader->GetSpacing(j);
 692           currentSize[j] = reader->GetDimensions(j);
 693         } else if (currentDim != reader->GetNumberOfDimensions()
 694           || currentSpacing[j] != reader->GetSpacing(j)
 695           || currentSize[j] != (int)reader->GetDimensions(j)
 696           || currentOrigin[j] != reader->GetOrigin(j)) {
 697             QString error = "Cannot read file (too different from others ";
 698             error += files[i].toStdString().c_str();
 699             QMessageBox::information(this,tr("Reading problem"),error);
 700             IsOk = false;
 701             break;
 702         }
 703       }
 704       if (IsOk)
 705         vector.push_back(files[i].toStdString());
 706     }
 707   }
 708   if (vector.size() > 0)
 709     LoadImages(vector, vvImageReader::MERGED);
 710 }
 711 //------------------------------------------------------------------------------
 712
 713 //------------------------------------------------------------------------------
 714 void vvMainWindow::SliceImages()
 715 {
 716   QString Extensions = EXTENSIONS;
 717   Extensions += ";;All Files (*)";
 718
 719   QStringList files = QFileDialog::getOpenFileNames(this,tr("Slice Images"),mInputPathName,Extensions);
 720   if (files.isEmpty())
 721     return;
 722   mInputPathName = itksys::SystemTools::GetFilenamePath(files[0].toStdString()).c_str();
 723   std::vector<std::string> vector;
 724   for (int i = 0; i < files.size(); i++)
 725     vector.push_back(files[i].toStdString());
 726   LoadImages(vector, vvImageReader::SLICED);
 727 }
 728 //------------------------------------------------------------------------------
 729
 730 //------------------------------------------------------------------------------
 731 void vvMainWindow::MergeImagesWithTime()
 732 {
 733   QString Extensions = EXTENSIONS;
 734   Extensions += ";;All Files (*)";
 735   QStringList files = QFileDialog::getOpenFileNames(this,tr("Merge Images With Time"),mInputPathName,Extensions);
 736   if (files.isEmpty())
 737     return;
 738   mInputPathName = itksys::SystemTools::GetFilenamePath(files[0].toStdString()).c_str();
 739   std::vector<std::string> vector;
 740
 741   for (int i = 0; i < files.size(); i++)
 742     vector.push_back(files[i].toStdString());
 743   sort(vector.begin(),vector.end());
 744   if (vector.size() > 1)
 745     LoadImages(vector, vvImageReader::MERGEDWITHTIME);
 746   else
 747     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.");
 748 }
 749 //------------------------------------------------------------------------------
 750
 751
 752 //------------------------------------------------------------------------------
 753 void vvMainWindow::OpenDicom()
 754 {
 755   std::vector<std::string> files;
 756
 757   //std::cout << "dicomSeriesSelector " << std::endl;
 758   if (dicomSeriesSelector->exec() == QDialog::Accepted) {
 759     files = *(dicomSeriesSelector->GetFilenames());
 760     LoadImages(files, vvImageReader::DICOM);
 761   }
 762 }
 763 //------------------------------------------------------------------------------
 764
 765 //------------------------------------------------------------------------------
 766 void vvMainWindow::OpenImages()
 767 {
 768   QString Extensions = EXTENSIONS;
 769   Extensions += ";;All Files (*)";
 770
 771   QStringList files = QFileDialog::getOpenFileNames(this,tr("Load Images"),mInputPathName,Extensions);
 772   if (files.isEmpty())
 773     return;
 774   mInputPathName = itksys::SystemTools::GetFilenamePath(files[0].toStdString()).c_str();
 775   std::vector<std::string> vector;
 776   for (int i = 0; i < files.size(); i++)
 777     vector.push_back(files[i].toStdString());
 778   LoadImages(vector, vvImageReader::IMAGE);
 779 }
 780 //------------------------------------------------------------------------------
 781 void vvMainWindow::OpenRecentImage()
 782 {
 783   QAction * caller = qobject_cast<QAction*>(sender());
 784   std::vector<std::string> images;
 785   images.push_back(caller->text().toStdString());
 786   mInputPathName = itksys::SystemTools::GetFilenamePath(images[0]).c_str();
 787   LoadImages(images, vvImageReader::IMAGE);
 788 }
 789 //------------------------------------------------------------------------------
 790
 791
 792 //------------------------------------------------------------------------------
 793 void vvMainWindow::OpenImageWithTime()
 794 {
 795   QString Extensions = EXTENSIONS;
 796   Extensions += ";;All Files (*)";
 797
 798   QStringList files = QFileDialog::getOpenFileNames(this,tr("Load Images With Time"),mInputPathName,Extensions);
 799   if (files.isEmpty())
 800     return;
 801   mInputPathName = itksys::SystemTools::GetFilenamePath(files[0].toStdString()).c_str();
 802   std::vector<std::string> vector;
 803   for (int i = 0; i < files.size(); i++) {
 804     vector.push_back(files[i].toStdString());
 805   }
 806   LoadImages(vector, vvImageReader::IMAGEWITHTIME);
 807 }
 808 //------------------------------------------------------------------------------
 809
 810
 811 //------------------------------------------------------------------------------
 812 void vvMainWindow::LoadImages(std::vector<std::string> files, vvImageReader::LoadedImageType filetype)
 813 {
 814   //Separate the way to open images and dicoms
 815   int fileSize;
 816   if (filetype == vvImageReader::IMAGE || filetype == vvImageReader::IMAGEWITHTIME)
 817     fileSize = files.size();
 818   else
 819     fileSize = 1;
 820
 821   // For SLICED, we need the number of slices (ndim and #slices)
 822   std::vector<unsigned int> nSlices;
 823   nSlices.resize(files.size());
 824   std::fill(nSlices.begin(), nSlices.end(), 1);
 825   if (filetype == vvImageReader::SLICED) {
 826     for (int i = 0; i < fileSize; i++) {
 827       itk::ImageIOBase::Pointer header = clitk::readImageHeader(files[i]);
 828       QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
 829       if (!header) {
 830         nSlices[i] = 0;
 831         QString error = "Cannot open file \n";
 832         error += files[i].c_str();
 833         QMessageBox::information(this,tr("Reading problem"),error);
 834         return;
 835       }
 836       if (header->GetNumberOfDimensions() < 3) {
 837         nSlices[i] = 0;
 838         QString error = "Dimension problem. Cannot slice \n";
 839         error += files[i].c_str();
 840         QMessageBox::information(this,tr("Reading problem"),error);
 841         return;
 842       }
 843       nSlices[i] = header->GetDimensions( header->GetNumberOfDimensions()-1 );
 844     }
 845   }
 846
 847   //Only add to the list of recently opened files when a single file is opened,
 848   //to avoid polluting the list of recently opened files
 849   if (files.size() == 1) {
 850     QFileInfo finfo=tr(files[0].c_str());
 851     AddToRecentlyOpenedImages(finfo.absoluteFilePath().toStdString());
 852     updateRecentlyOpenedFilesMenu(GetRecentlyOpenedImages());
 853   }
 854   //init the progress events
 855   QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
 856   vvProgressDialog progress("Opening " + files[0],fileSize>1);
 857   qApp->processEvents();
 858
 859   int numberofsuccesulreads=0;
 860   //open images as 1 or multiples
 861   for (int i = 0; i < fileSize; i++) {
 862     progress.SetText("Opening " + files[i]);
 863     progress.SetProgress(i,fileSize);
 864     qApp->processEvents();
 865
 866     for (unsigned int j = 0; j < nSlices[i]; j++) {
 867       //read the image and put it in mSlicerManagers
 868       vvSlicerManager* imageManager = new vvSlicerManager(4);
 869       qApp->processEvents();
 870
 871       bool SetImageSucceed=false;
 872
 873       // Change filename if an image with the same already exist
 874       int number = GetImageDuplicateFilenameNumber(files[i] + std::string("_slice"));
 875
 876       if (filetype == vvImageReader::IMAGE || filetype == vvImageReader::IMAGEWITHTIME || filetype == vvImageReader::SLICED) {
 877         SetImageSucceed = imageManager->SetImage(files[i],filetype, number, j);
 878       } else {
 879         SetImageSucceed = imageManager->SetImages(files,filetype, number);
 880       }
 881       if (!SetImageSucceed) {
 882         QApplication::restoreOverrideCursor();
 883         QString error = "Cannot open file \n";
 884         error += imageManager->GetLastError().c_str();
 885         QMessageBox::information(this,tr("Reading problem"),error);
 886         delete imageManager;
 887       } else {
 888
 889         mSlicerManagers.push_back(imageManager);
 890
 891         //create an item in the tree with good settings
 892         QTreeWidgetItem *item = new QTreeWidgetItem();
 893         item->setData(0,Qt::UserRole,files[i].c_str());
 894         QFileInfo fileinfo(imageManager->GetFileName().c_str()); //Do not show the path
 895         item->setData(COLUMN_IMAGE_NAME,Qt::DisplayRole,fileinfo.fileName());
 896         item->setData(1,Qt::UserRole,tr("image"));
 897         item->setToolTip(COLUMN_IMAGE_NAME, imageManager->GetListOfAbsoluteFilePathInOneString("image").c_str());
 898         qApp->processEvents();
 899
 900         //Create the buttons for reload and close
 901         qApp->processEvents();
 902         QTreePushButton* cButton = new QTreePushButton;
 903         cButton->setItem(item);
 904         cButton->setColumn(COLUMN_CLOSE_IMAGE);
 905         cButton->setToolTip(tr("close image"));
 906         cButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/exit.png")));
 907         connect(cButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
 908           this,SLOT(CloseImage(QTreeWidgetItem*, int)));
 909
 910         QTreePushButton* rButton = new QTreePushButton;
 911         rButton->setItem(item);
 912         rButton->setColumn(COLUMN_RELOAD_IMAGE);
 913         rButton->setToolTip(tr("reload image"));
 914         rButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/rotateright.png")));
 915         connect(rButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
 916           this,SLOT(ReloadImage(QTreeWidgetItem*, int)));
 917
 918         DataTree->addTopLevelItem(item);
 919         DataTree->setItemWidget(item, COLUMN_CLOSE_IMAGE, cButton);
 920         DataTree->setItemWidget(item, COLUMN_RELOAD_IMAGE, rButton);
 921
 922         //set the id of the image
 923         QString id = QDir::current().absoluteFilePath(files[i].c_str()) + QString::number(mSlicerManagers.size()-1);
 924         item->setData(COLUMN_IMAGE_NAME,Qt::UserRole,id.toStdString().c_str());
 925         mSlicerManagers.back()->SetId(id.toStdString());
 926
 927         linkPanel->addImage(imageManager->GetFileName(), id.toStdString());
 928
 929         connect(mSlicerManagers.back(), SIGNAL(currentImageChanged(std::string)),
 930           this,SLOT(CurrentImageChanged(std::string)));
 931         connect(mSlicerManagers.back(), SIGNAL(currentPickedImageChanged(std::string)),
 932           this, SLOT(CurrentPickedImageChanged(std::string)));
 933         connect(mSlicerManagers.back(), SIGNAL(UpdatePosition(int, double, double, double, double, double, double, double)),
 934           this,SLOT(MousePositionChanged(int,double, double, double, double, double, double, double)));
 935         connect(mSlicerManagers.back(), SIGNAL(UpdateVector(int, double, double, double, double)),
 936           this, SLOT(VectorChanged(int,double,double,double, double)));
 937         connect(mSlicerManagers.back(), SIGNAL(UpdateOverlay(int, double, double)),
 938           this, SLOT(OverlayChanged(int,double,double)));
 939         connect(mSlicerManagers.back(), SIGNAL(UpdateFusion(int, double)),
 940           this, SLOT(FusionChanged(int,double)));
 941         connect(mSlicerManagers.back(), SIGNAL(WindowLevelChanged()),
 942           this,SLOT(WindowLevelChanged()));
 943         connect(mSlicerManagers.back(), SIGNAL(UpdateSlice(int,int)),
 944           this,SLOT(UpdateSlice(int,int)));
 945         connect(mSlicerManagers.back(), SIGNAL(UpdateTSlice(int, int, int)),
 946           this,SLOT(UpdateTSlice(int, int, int)));
 947         connect(mSlicerManagers.back(), SIGNAL(UpdateTSlice(int, int, int)),
 948           this,SLOT(ImageInfoChanged()));
 949         connect(mSlicerManagers.back(), SIGNAL(UpdateSliceRange(int,int,int,int,int)),
 950           this,SLOT(UpdateSliceRange(int,int,int,int,int)));
 951         connect(mSlicerManagers.back(), SIGNAL(UpdateLinkManager(std::string,int,double,double,double,int)),
 952           this,SLOT(UpdateLinkManager(std::string,int,double,double,double,int)));
 953         connect(mSlicerManagers.back(), SIGNAL(UpdateLinkedNavigation(std::string,vvSlicerManager*,vvSlicer*)),
 954           this,SLOT(UpdateLinkedNavigation(std::string,vvSlicerManager*,vvSlicer*)));
 955         connect(mSlicerManagers.back(), SIGNAL(ChangeImageWithIndexOffset(vvSlicerManager*,int,int)),
 956           this,SLOT(ChangeImageWithIndexOffset(vvSlicerManager*,int,int)));
 957         connect(mSlicerManagers.back(),SIGNAL(LandmarkAdded()),landmarksPanel,SLOT(AddPoint()));
 958         InitSlicers();
 959         numberofsuccesulreads++;
 960       }
 961     }
 962   }
 963
 964   if (numberofsuccesulreads) {
 965     NOViewWidget->show();
 966     NEViewWidget->show();
 967     SOViewWidget->show();
 968     SEViewWidget->show();
 969     UpdateTree();
 970     InitDisplay();
 971     ShowLastImage();
 972
 973     // Try to guess default WindowLevel
 974     double range[2];
 975     mSlicerManagers.back()->GetImage()->GetFirstVTKImageData()->GetScalarRange(range);
 976     if ((range[0] == 0) && (range[1] == 1)) {
 977       presetComboBox->setCurrentIndex(WL_BINARY);// binary
 978     } else {
 979       // TODO
 980     }
 981   }
 982   QApplication::restoreOverrideCursor();
 983 }
 984 //------------------------------------------------------------------------------
 985
 986 //------------------------------------------------------------------------------
 987 void vvMainWindow::UpdateTree()
 988 {
 989   DataTree->resizeColumnToContents(COLUMN_TREE);
 990   DataTree->resizeColumnToContents(COLUMN_UL_VIEW);
 991   DataTree->resizeColumnToContents(COLUMN_UR_VIEW);
 992   DataTree->resizeColumnToContents(COLUMN_DL_VIEW);
 993   DataTree->resizeColumnToContents(COLUMN_DR_VIEW);
 994   DataTree->resizeColumnToContents(COLUMN_IMAGE_NAME);
 995   DataTree->resizeColumnToContents(COLUMN_CLOSE_IMAGE);
 996   DataTree->resizeColumnToContents(COLUMN_RELOAD_IMAGE);
 997 }
 998 //------------------------------------------------------------------------------
 999
1000 //------------------------------------------------------------------------------
1001 void vvMainWindow::CurrentImageChanged(std::string id)
1002 {
1003   if (id == mCurrentSelectedImageId) return; // Do nothing
1004   int selected = 0;
1005   for (int i = 0; i < DataTree->topLevelItemCount(); i++) {
1006     if (DataTree->topLevelItem(i)->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString().toStdString() == id) {
1007       selected = i;
1008     } else {
1009       DataTree->topLevelItem(i)->setSelected(0);
1010     }
1011     for (int child = 0; child < DataTree->topLevelItem(i)->childCount(); child++)
1012       DataTree->topLevelItem(i)->child(child)->setSelected(0);
1013
1014   }
1015   DataTree->topLevelItem(selected)->setSelected(1);
1016   mCurrentSelectedImageId = id;
1017
1018   landmarksPanel->SetCurrentLandmarks(mSlicerManagers[selected]->GetLandmarks(),
1019                                       mSlicerManagers[selected]->GetTSlice());
1020   landmarksPanel->SetCurrentPath(mInputPathName.toStdString());
1021   landmarksPanel->SetCurrentImage(mSlicerManagers[selected]->GetFileName().c_str());
1022
1023   emit SelectedImageHasChanged(mSlicerManagers[selected]);
1024 }
1025 //------------------------------------------------------------------------------
1026
1027 //------------------------------------------------------------------------------
1028 void vvMainWindow::CurrentPickedImageChanged(std::string id)
1029 {
1030   if (id == mCurrentPickedImageId) return; // Do nothing
1031   int selected = 0;
1032   for (int i = 0; i < DataTree->topLevelItemCount(); i++) {
1033     if (DataTree->topLevelItem(i)->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString().toStdString() == id) {
1034       selected = i;
1035     } else {
1036       DataTree->topLevelItem(i)->setSelected(0);
1037     }
1038     for (int child = 0; child < DataTree->topLevelItem(i)->childCount(); child++)
1039       DataTree->topLevelItem(i)->child(child)->setSelected(0);
1040
1041   }
1042   DataTree->topLevelItem(selected)->setSelected(1);
1043   mCurrentPickedImageId = id;
1044   mCurrentPickedImageIndex = selected;
1045 }
1046 //------------------------------------------------------------------------------
1047
1048 //------------------------------------------------------------------------------
1049 void vvMainWindow::ImageInfoChanged()
1050 {
1051   contextActions[6]->setEnabled(1);
1052   contextActions[5]->setEnabled(1);
1053   actionSave_As->setEnabled(1);
1054   actionAdd_VF_to_current_Image->setEnabled(1);
1055   actionAdd_fusion_image->setEnabled(1);
1056   actionAdd_wipe_image->setEnabled(1);
1057   actionAdd_overlay_image_to_current_image->setEnabled(1);
1058   actionAdd_USSequence_toCT->setEnabled(1);
1059   actionNorth_East_Window->setEnabled(1);
1060   actionNorth_West_Window->setEnabled(1);
1061   actionSouth_East_Window->setEnabled(1);
1062   actionSouth_West_Window->setEnabled(1);
1063   vvToolManager::GetInstance()->EnableToolsInMenu(this, true);
1064   inverseButton->setEnabled(1);
1065
1066   goToCursorPushButton->setEnabled(1);
1067
1068   if (DataTree->selectedItems().size()) {
1069     int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1070
1071     colorMapComboBox->setEnabled(1);
1072     for (int i = 0; i < DataTree->topLevelItem(index)->childCount(); i++) {
1073       if (DataTree->topLevelItem(index)->child(i)->data(1,Qt::UserRole).toString() == "overlay" ||
1074         DataTree->topLevelItem(index)->child(i)->data(1,Qt::UserRole).toString() == "fusion" ||
1075         DataTree->topLevelItem(index)->child(i)->data(1,Qt::UserRole).toString() == "fusionSequence") {
1076           colorMapComboBox->setEnabled(0);
1077           break;
1078       }
1079     }
1080
1081     std::vector<double> origin;
1082     std::vector<double> inputSpacing;
1083     std::vector<int> inputSize;
1084     std::vector<double> sizeMM;
1085     vtkSmartPointer<vtkMatrix4x4> transformation;
1086     int dimension=0;
1087     QString pixelType;
1088     QString inputSizeInBytes;
1089     QString image = DataTree->selectedItems()[0]->data(COLUMN_IMAGE_NAME,Qt::DisplayRole).toString();
1090
1091     int nframes = mSlicerManagers[index]->GetSlicer(0)->GetTMax();
1092
1093     if (nframes > 1 || playMode == 1) {
1094       playButton->setEnabled(1);
1095       frameRateLabel->setEnabled(1);
1096       frameRateSpinBox->setEnabled(1);
1097     } else {
1098       playButton->setEnabled(0);
1099       frameRateLabel->setEnabled(0);
1100       frameRateSpinBox->setEnabled(0);
1101     }
1102
1103     //read image header
1104     int NPixel = 1;
1105
1106     int tSlice = 0;
1107     vvImage::Pointer imageSelected;
1108     if (DataTree->topLevelItem(index) == DataTree->selectedItems()[0]) {
1109       imageSelected = mSlicerManagers[index]->GetSlicer(0)->GetImage();
1110       tSlice = mSlicerManagers[index]->GetSlicer(0)->GetTSlice();
1111     } else if (DataTree->selectedItems()[0]->data(1,Qt::UserRole).toString() == "vector") {
1112       imageSelected = mSlicerManagers[index]->GetSlicer(0)->GetVF();
1113       tSlice = mSlicerManagers[index]->GetSlicer(0)->GetOverlayTSlice();
1114     } else if (DataTree->selectedItems()[0]->data(1,Qt::UserRole).toString() == "overlay") {
1115       imageSelected = mSlicerManagers[index]->GetSlicer(0)->GetOverlay();
1116       tSlice = mSlicerManagers[index]->GetSlicer(0)->GetOverlayTSlice();
1117     } else if (DataTree->selectedItems()[0]->data(1,Qt::UserRole).toString() == "fusion") {
1118       imageSelected = mSlicerManagers[index]->GetSlicer(0)->GetFusion();
1119       tSlice = mSlicerManagers[index]->GetSlicer(0)->GetFusionTSlice();
1120     }
1121     else if (DataTree->selectedItems()[0]->data(1,Qt::UserRole).toString() == "fusionSequence") {
1122       imageSelected = mSlicerManagers[index]->GetSlicer(0)->GetFusion();
1123       tSlice = mSlicerManagers[index]->GetSlicer(0)->GetFusionTSlice();
1124     }
1125     else if (DataTree->selectedItems()[0]->data(1,Qt::UserRole).toString() == "contour") {
1126       imageSelected = mSlicerManagers[index]->GetSlicer(0)->GetImage();
1127       tSlice = mSlicerManagers[index]->GetSlicer(0)->GetTSlice();
1128     }
1129     else {
1130       imageSelected = mSlicerManagers[index]->GetSlicer(0)->GetImage();
1131       tSlice = mSlicerManagers[index]->GetSlicer(0)->GetTSlice();
1132     }
1133
1134     dimension = imageSelected->GetNumberOfDimensions();
1135     origin.resize(dimension);
1136     inputSpacing.resize(dimension);
1137     inputSize.resize(dimension);
1138     sizeMM.resize(dimension);
1139     pixelType = mSlicerManagers[index]->GetImage()->GetScalarTypeAsITKString().c_str();
1140     for (int i = 0; i < dimension; i++) {
1141       origin[i] = imageSelected->GetOrigin()[i];
1142       inputSpacing[i] = imageSelected->GetSpacing()[i];
1143       inputSize[i] = imageSelected->GetSize()[i];
1144       sizeMM[i] = inputSize[i]*inputSpacing[i];
1145       NPixel *= inputSize[i];
1146     }
1147     inputSizeInBytes = GetSizeInBytes(imageSelected->GetActualMemorySize()*1000);
1148
1149     QString dim = QString::number(dimension) + " (";
1150     dim += pixelType + ")";
1151
1152     infoPanel->setFileName(image);
1153     std::string creationImageTimeValue("No creation time");
1154     itk::ExposeMetaData< std::string > (*imageSelected->GetFirstMetaDataDictionary(), "creationImageTime", creationImageTimeValue);
1155     infoPanel->setImageCreationTime(QString(creationImageTimeValue.c_str()));
1156     infoPanel->setDimension(dim);
1157     infoPanel->setSizePixel(GetVectorIntAsString(inputSize));
1158     infoPanel->setSizeMM(GetVectorDoubleAsString(sizeMM));
1159     infoPanel->setOrigin(GetVectorDoubleAsString(origin));
1160     infoPanel->setSpacing(GetVectorDoubleAsString(inputSpacing));
1161     infoPanel->setNPixel(QString::number(NPixel)+" ("+inputSizeInBytes+")");
1162
1163     transformation = imageSelected->GetTransform()[tSlice]->GetMatrix();
1164     infoPanel->setTransformation(clitk::Get4x4MatrixDoubleAsString(transformation).c_str());
1165
1166     landmarksPanel->SetCurrentLandmarks(mSlicerManagers[index]->GetLandmarks(),
1167                                         mSlicerManagers[index]->GetTSlice());
1168     landmarksPanel->SetCurrentPath(mInputPathName.toStdString());
1169     landmarksPanel->SetCurrentImage(mSlicerManagers[index]->GetFileName().c_str());
1170
1171     overlayPanel->getCurrentImageName(mSlicerManagers[index]->GetFileName().c_str());
1172     for (int i = 0; i < 4; i++) {
1173       if (DataTree->selectedItems()[0]->data(i+1,Qt::CheckStateRole).toInt() > 0 || i == 3) {
1174         mSlicerManagers[index]->UpdateInfoOnCursorPosition(i);
1175         break;
1176       }
1177     }
1178
1179 //     infoPanel->setFileName(image);
1180 //     infoPanel->setDimension(dim);
1181 //     infoPanel->setSizePixel(GetVectorIntAsString(inputSize));
1182 //     infoPanel->setSizeMM(GetVectorDoubleAsString(sizeMM));
1183 //     infoPanel->setOrigin(GetVectorDoubleAsString(origin));
1184 //     infoPanel->setSpacing(GetVectorDoubleAsString(inputSpacing));
1185 //     infoPanel->setNPixel(QString::number(NPixel)+" ("+inputSizeInBytes+")");
1186 //
1187 //     landmarksPanel->SetCurrentLandmarks(mSlicerManagers[index]->GetLandmarks(),
1188 //                                         mSlicerManagers[index]->GetTSlice());
1189 //     landmarksPanel->SetCurrentPath(mInputPathName.toStdString());
1190 //     landmarksPanel->SetCurrentImage(mSlicerManagers[index]->GetFileName().c_str());
1191 //
1192 //     overlayPanel->getCurrentImageName(mSlicerManagers[index]->GetFileName().c_str());
1193 //     for (int i = 0; i < 4; i++) {
1194 //       if (DataTree->selectedItems()[0]->data(i+1,Qt::CheckStateRole).toInt() > 0 || i == 3) {
1195 //         mSlicerManagers[index]->UpdateInfoOnCursorPosition(i);
1196 //         break;
1197 //       }
1198 //     }
1199     WindowLevelChanged();
1200
1201     slicingPresetComboBox->setCurrentIndex(mSlicerManagers[index]->GetSlicingPreset());
1202
1203     if (mSlicerManagers[index]->GetSlicer(0)->GetVF()) {
1204       overlayPanel->getVFName(mSlicerManagers[index]->GetVFName().c_str());
1205       overlayPanel->getVFProperty(mSlicerManagers[index]->GetSlicer(0)->GetVFSubSampling(),
1206         mSlicerManagers[index]->GetSlicer(0)->GetVFScale(),
1207         mSlicerManagers[index]->GetSlicer(0)->GetVFLog());
1208     } else {
1209       overlayPanel->getVFName(mSlicerManagers[index]->GetVFName().c_str());
1210       overlayPanel->getVFProperty(-1,-1,-1);
1211     }
1212     if (mSlicerManagers[index]->GetSlicer(0)->GetOverlay()) {
1213       overlayPanel->getOverlayName(mSlicerManagers[index]->GetOverlayName().c_str());
1214     } else {
1215       overlayPanel->getOverlayName(mSlicerManagers[index]->GetOverlayName().c_str());
1216     }
1217
1218     if (mSlicerManagers[index]->GetSlicer(0)->GetFusion()) {
1219       overlayPanel->getFusionName(mSlicerManagers[index]->GetFusionName().c_str());
1220     } else {
1221       overlayPanel->getFusionName(mSlicerManagers[index]->GetFusionName().c_str());
1222     }
1223   }
1224 }
1225 //------------------------------------------------------------------------------
1226
1227 //------------------------------------------------------------------------------
1228 void vvMainWindow::ShowDocumentation()
1229 {
1230   documentation->show();
1231 }
1232 //------------------------------------------------------------------------------
1233
1234 //------------------------------------------------------------------------------
1235 void vvMainWindow::PopupRegisterForm(bool checkCanPush)
1236 {
1237   vvRegisterForm* registerForm = new vvRegisterForm(QUrl("http://www.creatis.insa-lyon.fr/~dsarrut/vvregister/write.php"), getVVSettingsPath(), getSettingsOptionFormat());
1238   if(!checkCanPush) {
1239     registerForm->show();
1240   } else {
1241     if(registerForm->canPush()) {
1242       registerForm->show();
1243       registerForm->acquitPushed();//too bad if there is not internet connection anymore.
1244     }
1245   }
1246 }
1247 //------------------------------------------------------------------------------
1248
1249 //------------------------------------------------------------------------------
1250 void vvMainWindow::ShowHelpDialog()
1251 {
1252   help_dialog->show();
1253 }
1254 //------------------------------------------------------------------------------
1255
1256 //------------------------------------------------------------------------------
1257 void vvMainWindow::ChangeViewMode()
1258 {
1259   typedef struct _SIZE{
1260     QSplitter* splitter;
1261     QList<int> size1, size2;
1262     int cols[3];
1263   }SplitterSize;
1264   SplitterSize sizes[4];
1265   sizes[0].splitter = OSplitter;
1266   sizes[0].size1.push_back(1);
1267   sizes[0].size1.push_back(0);
1268   sizes[0].size2.push_back(1);
1269   sizes[0].size2.push_back(0);
1270   sizes[0].cols[0] = 2;
1271   sizes[0].cols[1] = 3;
1272   sizes[0].cols[2] = 4;
1273
1274   sizes[1].splitter = ESplitter;
1275   sizes[1].size1.push_back(0);
1276   sizes[1].size1.push_back(1);
1277   sizes[1].size2.push_back(1);
1278   sizes[1].size2.push_back(0);
1279   sizes[1].cols[0] = 1;
1280   sizes[1].cols[1] = 3;
1281   sizes[1].cols[2] = 4;
1282
1283   sizes[2].splitter = OSplitter;
1284   sizes[2].size1.push_back(1);
1285   sizes[2].size1.push_back(0);
1286   sizes[2].size2.push_back(0);
1287   sizes[2].size2.push_back(1);
1288   sizes[2].cols[0] = 1;
1289   sizes[2].cols[1] = 2;
1290   sizes[2].cols[2] = 4;
1291
1292   sizes[3].splitter = ESplitter;
1293   sizes[3].size1.push_back(0);
1294   sizes[3].size1.push_back(1);
1295   sizes[3].size2.push_back(0);
1296   sizes[3].size2.push_back(1);
1297   sizes[3].cols[0] = 1;
1298   sizes[3].cols[1] = 2;
1299   sizes[3].cols[2] = 3;
1300
1301   int slicer = mSlicerManagers[mCurrentPickedImageIndex]->GetSelectedSlicer();
1302   if (viewMode == 1) {
1303     if (slicer >= 0) {
1304       viewMode = 0;
1305       splitter_3->setSizes(sizes[slicer].size1);
1306       sizes[slicer].splitter->setSizes(sizes[slicer].size2);
1307       DataTree->setColumnHidden(sizes[slicer].cols[0],1);
1308       DataTree->setColumnHidden(sizes[slicer].cols[1],1);
1309       DataTree->setColumnHidden(sizes[slicer].cols[2],1);
1310     }
1311   } else {
1312     QList<int> size;
1313     if (slicer >= 0) {
1314       viewMode = 1;
1315       size.push_back(1);
1316       size.push_back(1);
1317       splitter_3->setSizes(size);
1318       sizes[slicer].splitter->setSizes(size);
1319       DataTree->setColumnHidden(sizes[slicer].cols[0],0);
1320       DataTree->setColumnHidden(sizes[slicer].cols[1],0);
1321       DataTree->setColumnHidden(sizes[slicer].cols[2],0);
1322     }
1323   }
1324   UpdateRenderWindows();
1325   /*
1326   ** I don't know why but for both resized QVTKWidget we also need to render
1327   ** the associated Slicer to redraw crosses.
1328   */
1329   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
1330     //     if (DataTree->topLevelItem(i)->data(COLUMN_UL_VIEW,Qt::CheckStateRole).toInt() > 1)
1331     mSlicerManagers[i]->GetSlicer(0)->Render();
1332     mSlicerManagers[i]->GetSlicer(1)->Render();
1333     //     if (DataTree->topLevelItem(i)->data(COLUMN_DL_VIEW,Qt::CheckStateRole).toInt() > 1)
1334     mSlicerManagers[i]->GetSlicer(2)->Render();
1335     mSlicerManagers[i]->GetSlicer(3)->Render();
1336   }
1337 }
1338 //------------------------------------------------------------------------------
1339
1340 //------------------------------------------------------------------------------
1341 QString vvMainWindow::GetSizeInBytes(unsigned long size)
1342 {
1343   QString result = "";// QString::number(size);
1344   //result += " bytes (";
1345   if (size > 1000000000) {
1346     size /= 1000000000;
1347     result += QString::number(size);
1348     result += "Gb";//)";
1349   } else if (size > 1000000) {
1350     size /= 1000000;
1351     result += QString::number(size);
1352     result += "Mb";//)";
1353   } else if (size > 1000) {
1354     size /= 1000;
1355     result += QString::number(size);
1356     result += "kb";//)";
1357   }
1358   return result;
1359 }
1360 //------------------------------------------------------------------------------
1361
1362 //------------------------------------------------------------------------------
1363 QString vvMainWindow::GetVectorDoubleAsString(std::vector<double> vectorDouble)
1364 {
1365   QString result;
1366   for (unsigned int i= 0; i < vectorDouble.size(); i++) {
1367     if (i != 0)
1368       result += " ";
1369     result += QString::number(vectorDouble[i]);
1370   }
1371   return result;
1372 }
1373 //------------------------------------------------------------------------------
1374
1375 //------------------------------------------------------------------------------
1376 QString vvMainWindow::GetVectorIntAsString(std::vector<int> vectorInt)
1377 {
1378   QString result;
1379   for (unsigned int i= 0; i < vectorInt.size(); i++) {
1380     if (i != 0)
1381       result += " ";
1382     result += QString::number(vectorInt[i]);
1383   }
1384   return result;
1385 }
1386 //------------------------------------------------------------------------------
1387
1388 //------------------------------------------------------------------------------
1389 //this actually returns the SlicerManager index!
1390 int vvMainWindow::GetSlicerIndexFromItem(QTreeWidgetItem* item)
1391 {
1392   QString id = item->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString();
1393   for (int i = 0; i < DataTree->topLevelItemCount(); i++) {
1394     if (DataTree->topLevelItem(i)->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString() == id)
1395       return i;
1396   }
1397   return -1;
1398 }
1399 //------------------------------------------------------------------------------
1400
1401 //------------------------------------------------------------------------------
1402 QTreeWidgetItem* vvMainWindow::GetItemFromSlicerManager(vvSlicerManager* sm)
1403 {
1404   QString id = sm->GetId().c_str();
1405   for (int i = 0; i < DataTree->topLevelItemCount(); i++) {
1406     if (DataTree->topLevelItem(i)->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString() == id)
1407       return DataTree->topLevelItem(i);
1408   }
1409   return NULL;
1410 }
1411 //------------------------------------------------------------------------------
1412
1413 //------------------------------------------------------------------------------
1414 void vvMainWindow::DisplayChanged(QTreeWidgetItem *clickedItem, int column)
1415 {
1416   if ( column >= COLUMN_CLOSE_IMAGE || column <= 0)
1417     return;
1418
1419   // Get parent information (might be the same item)
1420   int slicerManagerIndex = GetSlicerIndexFromItem(clickedItem);
1421   QTreeWidgetItem* clickedParentItem = DataTree->topLevelItem(slicerManagerIndex);
1422   vvSlicer* clickedSlicer = mSlicerManagers[slicerManagerIndex]->GetSlicer(column-1);
1423
1424   // Go over the complete item tree (only 2 levels, parents and children)
1425   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
1426     // Trick to avoid redoing twice the job for a key (sr)
1427     mSlicerManagers[i]->GetSlicer(column-1)->GetRenderWindow()->GetInteractor()->SetKeySym("Crap");
1428
1429     QTreeWidgetItem* currentParentItem = DataTree->topLevelItem(i);
1430     if(currentParentItem != clickedParentItem) {
1431       // Not the branch of the clicked item, uncheck all
1432
1433       // Parent
1434       currentParentItem->setData(column,Qt::CheckStateRole, 0);
1435       mSlicerManagers[i]->UpdateSlicer(column-1, false);
1436
1437       // Children
1438       for (int iChild = 0; iChild < currentParentItem->childCount(); iChild++) {
1439         currentParentItem->child(iChild)->setData(column,Qt::CheckStateRole, 0);
1440       }
1441     }
1442     else {
1443       // Branch of the clicked one: get check status from actor visibility in slicer
1444       // and toggle the clicked one
1445
1446       // Parent
1447       bool vis = clickedSlicer->GetActorVisibility("image", 0);
1448       bool draw = clickedSlicer->GetRenderer()->GetDraw();
1449
1450       // Update slicer (after getting visibility)
1451       mSlicerManagers[slicerManagerIndex]->UpdateSlicer(column-1, true);
1452       mSlicerManagers[slicerManagerIndex]->UpdateInfoOnCursorPosition(column-1);
1453       DisplaySliders(slicerManagerIndex, column-1);
1454       if(clickedParentItem == clickedItem) {
1455         // Toggle
1456         vis = !draw || !vis;
1457       }
1458       clickedSlicer->SetActorVisibility("image", 0, vis);
1459       clickedParentItem->setData(column, Qt::CheckStateRole, vis?2:0);
1460
1461       // Children
1462       std::map<std::string, int> actorTypeCounts;
1463       for (int iChild = 0; iChild < clickedParentItem->childCount(); iChild++) {
1464         QTreeWidgetItem* currentChildItem = clickedParentItem->child(iChild);
1465         std::string actorType = currentChildItem->data(1,Qt::UserRole).toString().toStdString();
1466         vis = clickedSlicer->GetActorVisibility(actorType, actorTypeCounts[actorType]);
1467         if(currentChildItem == clickedItem) {
1468           // Toggle or force visibility if it was not on this branch so far
1469           vis = !draw || !vis;
1470           clickedSlicer->SetActorVisibility(actorType, actorTypeCounts[actorType], vis);
1471         }
1472         currentChildItem->setData(column, Qt::CheckStateRole, vis?2:0);
1473         actorTypeCounts[actorType]++;
1474       }
1475     }
1476   }
1477
1478   clickedSlicer->Render();
1479 }
1480 //------------------------------------------------------------------------------
1481
1482 void vvMainWindow::InitSlicers()
1483 {
1484   if (mSlicerManagers.size()) {
1485     mSlicerManagers.back()->GenerateDefaultLookupTable();
1486     mSlicerManagers.back()->SetSlicerWindow(0,NOViewWidget->GetRenderWindow());
1487     mSlicerManagers.back()->SetSlicerWindow(1,NEViewWidget->GetRenderWindow());
1488     mSlicerManagers.back()->SetSlicerWindow(2,SOViewWidget->GetRenderWindow());
1489     mSlicerManagers.back()->SetSlicerWindow(3,SEViewWidget->GetRenderWindow());
1490 #if VTK_MAJOR_VERSION <= 5
1491     mSlicerManagers.back()->Render(); // SR: displayed #slice is wrong without this / TB: With VTK6 and multiple images, all slicers are updated, not only the first
1492 #endif
1493   }
1494 }
1495
1496 //------------------------------------------------------------------------------
1497 void vvMainWindow::InitDisplay()
1498 {
1499   if (mSlicerManagers.size()) {
1500     //BE CAREFUL : this is absolutely necessary to set the interactor style
1501     //in order to have the same style instanciation for all SlicerManagers in
1502     // a same window
1503     for (int j = 0; j < 4; j++) {
1504       vvInteractorStyleNavigator* style = vvInteractorStyleNavigator::New();
1505       style->SetAutoAdjustCameraClippingRange(1);
1506       bool AlreadySelected = false;
1507       for (int i = 0; i < DataTree->topLevelItemCount(); i++) {
1508         mSlicerManagers[i]->SetInteractorStyleNavigator(j,style);
1509         //select the image only if previous are not selected
1510         if (DataTree->topLevelItem(i)->data(j+1,Qt::CheckStateRole).toInt() > 1) {
1511           mSlicerManagers[i]->UpdateSlicer(j,1);
1512           AlreadySelected = true;
1513         } else if (i == DataTree->topLevelItemCount()-1 && !AlreadySelected) {
1514           if (DataTree->selectedItems().size() == 0) {
1515             DataTree->topLevelItem(i)->setSelected(1);
1516           }
1517           DataTree->topLevelItem(i)->setData(j+1,Qt::CheckStateRole,2);
1518           mSlicerManagers[i]->UpdateSlicer(j,1);
1519           DisplaySliders(i,j);
1520         } else {
1521           DataTree->topLevelItem(i)->setData(j+1,Qt::CheckStateRole,0);
1522           mSlicerManagers[i]->UpdateSlicer(j,0);
1523         }
1524       }
1525       style->Delete();
1526     }
1527   }
1528 }
1529 //------------------------------------------------------------------------------
1530
1531 //------------------------------------------------------------------------------
1532 void vvMainWindow::DisplaySliders(int slicer, int window)
1533 {
1534   if(!mSlicerManagers[slicer]->GetSlicer(window)->GetRenderer()->GetDraw())
1535     return;
1536
1537   int range[2];
1538   mSlicerManagers[slicer]->GetSlicer(window)->GetSliceRange(range);
1539   int position = mSlicerManagers[slicer]->GetSlicer(window)->GetSlice();
1540   if (range[1]>0)
1541     verticalSliders[window]->show();
1542   else
1543     verticalSliders[window]->hide();
1544   verticalSliders[window]->setRange(range[0],range[1]);
1545   verticalSliders[window]->setValue(position);
1546
1547   int tRange[2];
1548   tRange[0] = 0;
1549   tRange[1] = mSlicerManagers[slicer]->GetSlicer(window)->GetTMax();
1550   if (tRange[1]>0)
1551     horizontalSliders[window]->show();
1552   else
1553     horizontalSliders[window]->hide();
1554   horizontalSliders[window]->setRange(tRange[0],tRange[1]);
1555   int tPosition = mSlicerManagers[slicer]->GetSlicer(window)->GetMaxCurrentTSlice();
1556   horizontalSliders[window]->setValue(tPosition);
1557 }
1558 //------------------------------------------------------------------------------
1559
1560 //------------------------------------------------------------------------------
1561 void vvMainWindow::CloseImage(QTreeWidgetItem* item, int column)
1562 {
1563   int index = GetSlicerIndexFromItem(item);
1564
1565   if (DataTree->topLevelItem(index) != item) {
1566     QString warning = "Do you really want to close the overlay : ";
1567     warning += item->data(COLUMN_IMAGE_NAME,Qt::DisplayRole).toString();
1568     QMessageBox msgBox(QMessageBox::Warning, tr("Close Overlay"),
1569       warning, 0, this);
1570     msgBox.addButton(tr("Close"), QMessageBox::AcceptRole);
1571     msgBox.addButton(tr("Cancel"), QMessageBox::RejectRole);
1572     if (msgBox.exec() == QMessageBox::AcceptRole) {
1573       std::string overlay_type=item->data(1,Qt::UserRole).toString().toStdString();
1574       int overlay_index=0;
1575       for (int child = 0; child < DataTree->topLevelItem(index)->childCount(); child++) {
1576         if (DataTree->topLevelItem(index)->\
1577           child(child)->data(1,Qt::UserRole).toString().toStdString() == overlay_type)
1578           overlay_index++;
1579         if (DataTree->topLevelItem(index)->child(child) == item) break;
1580       }
1581       if (overlay_type=="fusionSequence") {
1582         //removing the overlay sequence in a fusion sequence visualization mode
1583         //reset the transforms
1584         overlayPanel->getFusionSequenceProperty(-1, false, 0, false);
1585
1586         //unlink and untie the slicer managers
1587         RemoveLink(mSlicerManagers[index]->GetId().c_str(), mSlicerManagers[mSlicerManagers[index]->GetFusionSequenceIndexOfLinkedManager()]->GetId().c_str());
1588         mSlicerManagers[index]->SetFusionSequenceInvolvmentCode(-1);
1589         mSlicerManagers[mSlicerManagers[index]->GetFusionSequenceIndexOfLinkedManager()]->SetFusionSequenceInvolvmentCode(-1);
1590         for (unsigned i=0 ; i<4 ; i++) {
1591             mSlicerManagers[index]->GetSlicer(i)->SetFusionSequenceCode(-1);
1592             mSlicerManagers[mSlicerManagers[index]->GetFusionSequenceIndexOfLinkedManager()]->GetSlicer(i)->SetFusionSequenceCode(-1);
1593         }
1594
1595       }
1596       mSlicerManagers[index]->RemoveActor(overlay_type, overlay_index-1);
1597       mSlicerManagers[index]->SetColorMap(0);
1598       DataTree->topLevelItem(index)->takeChild(DataTree->topLevelItem(index)->indexOfChild(item));
1599       mSlicerManagers[index]->Render();
1600     }
1601   } else if (DataTree->topLevelItemCount() <= 1) {
1602     QString warning = "Do you really want to close the image : ";
1603     warning += item->data(COLUMN_IMAGE_NAME,Qt::DisplayRole).toString();
1604     warning += "\nThis is the last image, you're about to close vv !!!";
1605     QMessageBox msgBox(QMessageBox::Warning, tr("Close Image"),
1606       warning, 0, this);
1607     msgBox.addButton(tr("Close vv"), QMessageBox::AcceptRole);
1608     msgBox.addButton(tr("Cancel"), QMessageBox::RejectRole);
1609     if (msgBox.exec() == QMessageBox::AcceptRole) {
1610       this->close();
1611     }
1612   } else {
1613     QString warning = "Do you really want to close the image : ";
1614     warning += item->data(COLUMN_IMAGE_NAME,Qt::DisplayRole).toString();
1615     QMessageBox msgBox(QMessageBox::Warning, tr("Close Image"),
1616       warning, 0, this);
1617     msgBox.addButton(tr("Close"), QMessageBox::AcceptRole);
1618     msgBox.addButton(tr("Cancel"), QMessageBox::RejectRole);
1619     if (msgBox.exec() == QMessageBox::AcceptRole) {
1620
1621       // Tell tools that we close an image
1622       emit AnImageIsBeingClosed(mSlicerManagers[index]);
1623
1624       std::vector<vvSlicerManager*>::iterator Manageriter = mSlicerManagers.begin();
1625       DataTree->takeTopLevelItem(index);
1626       for (int i = 0; i < index; i++) {
1627         Manageriter++;
1628       }
1629       //if the slicer manager was involved in a fusion sequence visualization...
1630       if ( mSlicerManagers[index]->IsInvolvedInFusionSequence() ) {
1631         //in both cases, close the overlay: find it... and close it
1632         //ideally, I should duplicate the code, and avoid calling CloseImage, since this pops up another interactive box
1633         QTreeWidgetItem* overlayItem;
1634         if (mSlicerManagers[index]->IsMainSequenceOfFusionSequence()) {
1635           for (unsigned i=0 ; i<item->childCount() ; i++) {
1636             overlayItem = item->child(i);
1637             this->CloseImage( overlayItem, 0 );
1638           }
1639         }
1640         else {
1641           QTreeWidgetItem* linkedItem = this->GetItemFromSlicerManager( mSlicerManagers[mSlicerManagers[index]->GetFusionSequenceIndexOfLinkedManager()] );
1642           for (unsigned i=0 ; i<linkedItem->childCount() ; i++) {
1643             overlayItem = linkedItem->child(i);
1644             this->CloseImage( overlayItem, 0 );
1645           }
1646         }
1647
1648         /* -- this is normally already done when closing the overlay.
1649         //reset the transforms
1650         overlayPanel->getFusionSequenceProperty(-1, false, 0, false);
1651
1652         //unlink and untie the slicer managers
1653         RemoveLink(mSlicerManagers[index]->GetId().c_str(), mSlicerManagers[mSlicerManagers[index]->GetFusionSequenceIndexOfLinkedManager()]->GetId().c_str());
1654         mSlicerManagers[index]->SetFusionSequenceInvolvmentCode(-1);
1655         mSlicerManagers[mSlicerManagers[index]->GetFusionSequenceIndexOfLinkedManager()]->SetFusionSequenceInvolvmentCode(-1);
1656         for (unsigned i=0 ; i<4 ; i++) {
1657             mSlicerManagers[index]->GetSlicer(i)->SetFusionSequenceCode(-1);
1658             mSlicerManagers[mSlicerManagers[index]->GetFusionSequenceIndexOfLinkedManager()]->GetSlicer(i)->SetFusionSequenceCode(-1);
1659         }
1660         */
1661       }
1662
1663       linkPanel->removeImage(index);
1664       mSlicerManagers[index]->RemoveActors();
1665
1666       //remove the slicer manager
1667       delete mSlicerManagers[index];
1668       mSlicerManagers.erase(Manageriter);
1669
1670       //
1671       InitDisplay();
1672     }
1673   }
1674   ImageInfoChanged();
1675 }
1676 //------------------------------------------------------------------------------
1677
1678 //------------------------------------------------------------------------------
1679 void vvMainWindow::ReloadImage(QTreeWidgetItem* item, int column)
1680 {
1681   // int index = GetSlicerIndexFromItem(item);
1682   //   QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
1683   //   if (item->data(1,Qt::UserRole).toString() == "vector")
1684   //     mSlicerManagers[index]->ReloadVF();
1685   //   else
1686   //     mSlicerManagers[index]->Reload();
1687
1688   //   QApplication::restoreOverrideCursor();
1689   int index = GetSlicerIndexFromItem(item);
1690   QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
1691   QString role=item->data(1,Qt::UserRole).toString();
1692   if ( role == "vector") {
1693     mSlicerManagers[index]->ReloadVF();
1694   }
1695   else if (role == "overlay") {
1696     mSlicerManagers[index]->ReloadOverlay();
1697   }
1698   else if (role == "fusion") {
1699     mSlicerManagers[index]->ReloadFusion();
1700   }
1701   else if (role == "fusionSequence") {
1702     //both versions of the secondary sequence must be updated.
1703     mSlicerManagers[index]->ReloadFusionSequence();
1704     mSlicerManagers[mSlicerManagers[index]->GetFusionSequenceIndexOfLinkedManager()]->Reload();
1705   }
1706   else {
1707     mSlicerManagers[index]->Reload();
1708     //if we update the secondary sequence, then the overlay of the main sequence should also be updated
1709     if (mSlicerManagers[index]->IsSecondarySequenceOfFusionSequence()) mSlicerManagers[mSlicerManagers[index]->GetFusionSequenceIndexOfLinkedManager()]->ReloadFusionSequence();
1710   }
1711   // Update view and info
1712   ImageInfoChanged();
1713   mSlicerManagers[index]->Render();
1714   QApplication::restoreOverrideCursor();
1715 }
1716 //------------------------------------------------------------------------------
1717
1718 //------------------------------------------------------------------------------
1719 void vvMainWindow::MousePositionChanged(int visibility,double x, double y, double z, double X, double Y, double Z , double value)
1720 {
1721   infoPanel->setCurrentInfo(visibility,x,y,z,X,Y,Z,value);
1722 }
1723 //------------------------------------------------------------------------------
1724
1725 //------------------------------------------------------------------------------
1726 void vvMainWindow::VectorChanged(int visibility,double x, double y, double z, double value)
1727 {
1728   overlayPanel->getCurrentVectorInfo(visibility,x,y,z,value);
1729 }
1730 //------------------------------------------------------------------------------
1731
1732 //------------------------------------------------------------------------------
1733 void vvMainWindow::OverlayChanged(int visibility, double valueOver, double valueRef)
1734 {
1735   overlayPanel->getCurrentOverlayInfo(visibility,valueOver, valueRef);
1736 }
1737 //------------------------------------------------------------------------------
1738
1739 //------------------------------------------------------------------------------
1740 void vvMainWindow::FusionChanged(int visibility, double value)
1741 {
1742   overlayPanel->getCurrentFusionInfo(visibility,value);
1743 }
1744 //------------------------------------------------------------------------------
1745
1746 //------------------------------------------------------------------------------
1747 //called when AddOverlayImage, AddFusionSequence
1748 //or when UpdateWindowLevel() is called ; when slicerManager emits WindowLevelChanged
1749 //when ImageInfoChanged() is called
1750 void vvMainWindow::WindowLevelChanged()
1751 {
1752   // Base image
1753   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1754   if(index==-1) return;
1755   windowSpinBox->setValue(mSlicerManagers[index]->GetColorWindow());
1756   levelSpinBox->setValue(mSlicerManagers[index]->GetColorLevel());
1757   colorMapComboBox->setCurrentIndex(mSlicerManagers[index]->GetColorMap());
1758   presetComboBox->setCurrentIndex(mSlicerManagers[index]->GetPreset());
1759
1760   // Overlay image
1761   if (mSlicerManagers[index]->GetSlicer(0)->GetOverlay())
1762     overlayPanel->getOverlayProperty(mSlicerManagers[index]->GetOverlayColor(),
1763     mSlicerManagers[index]->GetLinkOverlayWindowLevel(),
1764     mSlicerManagers[index]->GetOverlayColorWindow(),
1765     mSlicerManagers[index]->GetOverlayColorLevel());
1766   else
1767     overlayPanel->getOverlayProperty(-1,0,0.,0.);
1768
1769   // Fusion & SequenceFusion image
1770   if (mSlicerManagers[index]->GetSlicer(0)->GetFusion()) {
1771     overlayPanel->getFusionProperty(mSlicerManagers[index]->GetFusionOpacity(),
1772       mSlicerManagers[index]->GetFusionThresholdOpacity(),
1773       mSlicerManagers[index]->GetFusionColorMap(),
1774       mSlicerManagers[index]->GetFusionWindow(),
1775       mSlicerManagers[index]->GetFusionLevel());
1776     if (mSlicerManagers[index]->IsMainSequenceOfFusionSequence()) {
1777       overlayPanel->getFusionSequenceProperty(mSlicerManagers[index]->GetFusionSequenceFrameIndex(),
1778         mSlicerManagers[index]->GetFusionSequenceSpatialSyncFlag(),
1779         mSlicerManagers[index]->GetFusionSequenceNbFrames(),
1780         mSlicerManagers[index]->GetFusionSequenceTemporalSyncFlag());
1781     }
1782   }
1783   else if ( mSlicerManagers[index]->IsSecondarySequenceOfFusionSequence() ) {
1784     //if the image is involved in a fusion sequence, preserve the overlay panel!
1785     int ind = mSlicerManagers[index]->GetFusionSequenceIndexOfLinkedManager();
1786     overlayPanel->getFusionProperty(mSlicerManagers[ind]->GetFusionOpacity(),
1787       mSlicerManagers[ind]->GetFusionThresholdOpacity(),
1788       mSlicerManagers[ind]->GetFusionColorMap(),
1789       mSlicerManagers[ind]->GetFusionWindow(),
1790       mSlicerManagers[ind]->GetFusionLevel());
1791     overlayPanel->getFusionSequenceProperty(mSlicerManagers[ind]->GetFusionSequenceFrameIndex(),
1792       mSlicerManagers[ind]->GetFusionSequenceSpatialSyncFlag(),
1793       mSlicerManagers[ind]->GetFusionSequenceNbFrames(),
1794       mSlicerManagers[ind]->GetFusionSequenceTemporalSyncFlag());
1795   }
1796   else
1797   {
1798     overlayPanel->getFusionProperty(-1, -1, -1, -1, -1);
1799     overlayPanel->getFusionSequenceProperty(-1, false, 0, false);
1800   }
1801 }
1802 //------------------------------------------------------------------------------
1803
1804 //------------------------------------------------------------------------------
1805 void vvMainWindow::WindowLevelEdited()
1806 {
1807   presetComboBox->setCurrentIndex(WL_USER);
1808   UpdateWindowLevel();
1809 }
1810 //------------------------------------------------------------------------------
1811
1812 //------------------------------------------------------------------------------
1813 void vvMainWindow::SetWindowLevel(double w, double l)
1814 {
1815   windowSpinBox->setValue(w);
1816   levelSpinBox->setValue(l);
1817   presetComboBox->setCurrentIndex(WL_USER);
1818   colorMapComboBox->setCurrentIndex(0);
1819   UpdateWindowLevel();
1820 }
1821 //------------------------------------------------------------------------------
1822
1823 //------------------------------------------------------------------------------
1824 void vvMainWindow::UpdateWindowLevel()
1825 {
1826   if (DataTree->selectedItems().size()) {
1827     if (presetComboBox->currentIndex() == WL_VENTILATION) //For ventilation
1828       colorMapComboBox->setCurrentIndex(5);
1829     int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1830     mSlicerManagers[index]->SetColorWindow(windowSpinBox->value());
1831     mSlicerManagers[index]->SetColorLevel(levelSpinBox->value());
1832     mSlicerManagers[index]->SetPreset(presetComboBox->currentIndex());
1833     mSlicerManagers[index]->Render();
1834     WindowLevelChanged();
1835   }
1836 }
1837 //------------------------------------------------------------------------------
1838
1839 //------------------------------------------------------------------------------
1840 void vvMainWindow::UpdateSlicingPreset()
1841 {
1842   if (DataTree->selectedItems().size()) {
1843     int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1844     mSlicerManagers[index]->SetSlicingPreset(vvSlicerManager::SlicingPresetType(slicingPresetComboBox->currentIndex()));
1845   }
1846 }
1847 //------------------------------------------------------------------------------
1848
1849 //------------------------------------------------------------------------------
1850 void vvMainWindow::UpdateColorMap()
1851 {
1852   if (DataTree->selectedItems().size()) {
1853     int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1854     mSlicerManagers[index]->SetColorMap(colorMapComboBox->currentIndex());
1855     mSlicerManagers[index]->Render();
1856   }
1857 }
1858 //------------------------------------------------------------------------------
1859 void vvMainWindow::SwitchWindowLevel()
1860 {
1861   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1862   int window = mSlicerManagers[index]->GetColorWindow();
1863   presetComboBox->setCurrentIndex(WL_USER);
1864   windowSpinBox->setValue(-window);
1865   UpdateWindowLevel();
1866 }
1867 //------------------------------------------------------------------------------
1868
1869 //------------------------------------------------------------------------------
1870 void vvMainWindow::ApplyWindowLevelToAllImages()
1871 {
1872   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1873   if(index==-1) return;
1874   double window = mSlicerManagers[index]->GetColorWindow();
1875   double level = mSlicerManagers[index]->GetColorLevel();
1876
1877   double fusWindow = mSlicerManagers[index]->GetFusionWindow();
1878   double fusLevel = mSlicerManagers[index]->GetFusionLevel();
1879
1880   double overWindow = mSlicerManagers[index]->GetOverlayColorWindow();
1881   double overLevel = mSlicerManagers[index]->GetOverlayColorLevel();
1882
1883   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
1884     if (mSlicerManagers[i] == NULL)
1885       continue;
1886     mSlicerManagers[i]->SetColorWindow(window);
1887     mSlicerManagers[i]->SetColorLevel(level);
1888     mSlicerManagers[i]->SetPreset(WL_USER);
1889     mSlicerManagers[i]->SetFusionWindow(fusWindow);
1890     mSlicerManagers[i]->SetFusionLevel(fusLevel);
1891     mSlicerManagers[i]->SetOverlayColorWindow(overWindow);
1892     mSlicerManagers[i]->SetOverlayColorLevel(overLevel);
1893     mSlicerManagers[i]->Render();
1894   }
1895 }
1896 //------------------------------------------------------------------------------
1897
1898 //------------------------------------------------------------------------------
1899 void vvMainWindow::ApplyWindowToSetOfImages(double window, unsigned int indexMin, unsigned int indexMax)
1900 {
1901   for (unsigned int i = indexMin; i <= indexMax && i < mSlicerManagers.size(); i++) {
1902     if (mSlicerManagers[i] == NULL)
1903       continue;
1904     SetWindowLevel(window, mSlicerManagers[i]->GetColorLevel());
1905     mSlicerManagers[i]->SetColorWindow(window);
1906     mSlicerManagers[i]->SetPreset(WL_USER);
1907     mSlicerManagers[i]->Render();
1908   }
1909 }
1910 //------------------------------------------------------------------------------
1911
1912 //------------------------------------------------------------------------------
1913 void vvMainWindow::ApplyLevelToSetOfImages(double level, unsigned int indexMin, unsigned int indexMax)
1914 {
1915   for (unsigned int i = indexMin; i <= indexMax && i < mSlicerManagers.size(); i++) {
1916     if (mSlicerManagers[i] == NULL)
1917       continue;
1918     SetWindowLevel(mSlicerManagers[i]->GetColorWindow(), level);
1919     mSlicerManagers[i]->SetColorLevel(level);
1920     mSlicerManagers[i]->SetPreset(WL_USER);
1921     mSlicerManagers[i]->Render();
1922   }
1923 }
1924 //------------------------------------------------------------------------------
1925
1926 //------------------------------------------------------------------------------
1927 void vvMainWindow::UpdateLinkManager(std::string id, int slicer, double x, double y, double z, int temps)
1928 {
1929   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
1930     if (mSlicerManagers[i]->GetId() == id) {
1931       mSlicerManagers[i]->GetSlicer(slicer)->SetCurrentPosition(x,y,z,temps);
1932       mSlicerManagers[i]->UpdateViews(0,slicer);
1933       break;
1934     }
1935   }
1936 }
1937 //------------------------------------------------------------------------------
1938
1939 //------------------------------------------------------------------------------
1940 void vvMainWindow::UpdateLinkedNavigation(std::string id, vvSlicerManager * sm, vvSlicer* refSlicer)
1941 {
1942   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
1943     if (id == mSlicerManagers[i]->GetId()) {
1944       mSlicerManagers[i]->UpdateLinkedNavigation(refSlicer);
1945     }
1946   }
1947 }
1948 //------------------------------------------------------------------------------
1949
1950 //------------------------------------------------------------------------------
1951 void vvMainWindow::ShowContextMenu(QPoint point)
1952 {
1953   if (!DataTree->selectedItems().size()) {
1954     contextActions[1]->setEnabled(0);
1955     contextActions[2]->setEnabled(0);
1956     contextActions[3]->setEnabled(0);
1957     contextActions[4]->setEnabled(0);
1958     contextActions[5]->setEnabled(0);
1959     contextActions[6]->setEnabled(0);
1960   } else {
1961     int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1962     contextActions[1]->setEnabled(1);
1963     contextActions[2]->setEnabled(
1964       DataTree->itemWidget(DataTree->selectedItems()[0],
1965       COLUMN_RELOAD_IMAGE)->isEnabled());
1966     contextActions[3]->setEnabled(1);
1967     contextActions[5]->setEnabled(1);
1968     contextActions[6]->setEnabled(1);
1969
1970     if (mSlicerManagers[index]->GetDimension() < 3)
1971       contextActions[4]->setEnabled(0);
1972     else
1973       contextActions[4]->setEnabled(1);
1974   }
1975   contextMenu.exec(QCursor::pos());
1976 }
1977 //------------------------------------------------------------------------------
1978
1979 //------------------------------------------------------------------------------
1980 void vvMainWindow::CloseImage()
1981 {
1982   CloseImage(DataTree->selectedItems()[0],0);
1983 }
1984 //------------------------------------------------------------------------------
1985
1986 //------------------------------------------------------------------------------
1987 void vvMainWindow::ReloadImage()
1988 {
1989   ReloadImage(DataTree->selectedItems()[0],0);
1990 }
1991 //------------------------------------------------------------------------------
1992
1993 //------------------------------------------------------------------------------
1994 void vvMainWindow::SelectOverlayImage()
1995 {
1996   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1997
1998   if (!(CheckAddedImage(index, "overlay")))
1999     return;
2000
2001   QString Extensions = EXTENSIONS;
2002   Extensions += ";;All Files (*)";
2003   QStringList files = QFileDialog::getOpenFileNames(this,tr("Load Overlay image"),mInputPathName,Extensions);
2004   if (files.isEmpty())
2005     return;
2006
2007   std::vector<std::string> vecFileNames;
2008   for (int i = 0; i < files.size(); i++) {
2009     vecFileNames.push_back(files[i].toStdString());
2010   }
2011
2012   AddOverlayImage(index,vecFileNames,vvImageReader::IMAGE);
2013 }
2014 //------------------------------------------------------------------------------
2015
2016 //------------------------------------------------------------------------------
2017 bool vvMainWindow::CheckAddedImage(int index, QString imageType)
2018 {
2019   //check if one overlay image is added
2020   for (int child = 0; child < DataTree->topLevelItem(index)->childCount(); child++)
2021     if (DataTree->topLevelItem(index)->child(child)->data(1,Qt::UserRole).toString().compare(imageType) == 0) {
2022       QString error = "Cannot add more than one compared image\n";
2023       error += "Please remove first ";
2024       error += DataTree->topLevelItem(index)->child(child)->data(COLUMN_IMAGE_NAME,Qt::DisplayRole).toString();
2025       QMessageBox::information(this,tr("Problem adding compared image !"),error);
2026       return false;
2027     }
2028     return true;
2029 }
2030 //------------------------------------------------------------------------------
2031
2032 //------------------------------------------------------------------------------
2033 void vvMainWindow::AddOverlayImage(int index, std::vector<std::string> fileNames, vvImageReader::LoadedImageType type)
2034 {
2035   QString file(fileNames[0].c_str());
2036   if (QFile::exists(file))
2037   {
2038     mInputPathName = itksys::SystemTools::GetFilenamePath(file.toStdString()).c_str();
2039     itk::ImageIOBase::Pointer reader = itk::ImageIOFactory::CreateImageIO(
2040       file.toStdString().c_str(), itk::ImageIOFactory::ReadMode);
2041     reader->SetFileName(fileNames[0].c_str());
2042     reader->ReadImageInformation();
2043     std::string component = reader->GetComponentTypeAsString(reader->GetComponentType());
2044     int dimension = reader->GetNumberOfDimensions();
2045     QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
2046     vvProgressDialog progress("Opening " + file.toStdString());
2047     qApp->processEvents();
2048
2049     std::string filename = itksys::SystemTools::GetFilenameWithoutExtension(file.toStdString()).c_str();
2050     if (mSlicerManagers[index]->SetOverlay(fileNames,dimension, component,type)) {
2051       //create an item in the tree with good settings
2052       QTreeWidgetItem *item = new QTreeWidgetItem();
2053       item->setData(0,Qt::UserRole,file.toStdString().c_str());
2054       item->setData(1,Qt::UserRole,tr("overlay"));
2055       QFileInfo fileinfo(file); //Do not show the path
2056       item->setData(COLUMN_IMAGE_NAME,Qt::DisplayRole,fileinfo.fileName());
2057       item->setToolTip(COLUMN_IMAGE_NAME, mSlicerManagers[index]->GetListOfAbsoluteFilePathInOneString("overlay").c_str());
2058       qApp->processEvents();
2059 #if VTK_MAJOR_VERSION > 5
2060       for ( unsigned int i = 0; i < mSlicerManagers[index]->GetNumberOfSlicers(); i++)
2061         mSlicerManagers[index]->GetSlicer(i)->ForceUpdateDisplayExtent();
2062 #endif
2063
2064       for (int j = 1; j <= 4; j++) {
2065         item->setData(j,Qt::CheckStateRole,DataTree->topLevelItem(index)->data(j,Qt::CheckStateRole));
2066       }
2067
2068       //Create the buttons for reload and close
2069       qApp->processEvents();
2070       QTreePushButton* cButton = new QTreePushButton;
2071       cButton->setItem(item);
2072       cButton->setColumn(COLUMN_CLOSE_IMAGE);
2073       cButton->setToolTip(tr("close image"));
2074       cButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/exit.png")));
2075       connect(cButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
2076         this,SLOT(CloseImage(QTreeWidgetItem*, int)));
2077
2078       QTreePushButton* rButton = new QTreePushButton;
2079       rButton->setItem(item);
2080       rButton->setColumn(COLUMN_RELOAD_IMAGE);
2081       rButton->setToolTip(tr("reload image"));
2082       rButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/rotateright.png")));
2083       connect(rButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
2084         this,SLOT(ReloadImage(QTreeWidgetItem*, int)));
2085
2086       DataTree->topLevelItem(index)->setExpanded(1);
2087       DataTree->topLevelItem(index)->addChild(item);
2088       DataTree->setItemWidget(item, COLUMN_CLOSE_IMAGE, cButton);
2089       DataTree->setItemWidget(item, COLUMN_RELOAD_IMAGE, rButton);
2090
2091       //set the id of the image
2092       QString id = DataTree->topLevelItem(index)->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString();
2093       item->setData(COLUMN_IMAGE_NAME,Qt::UserRole,id.toStdString().c_str());
2094       UpdateTree();
2095       qApp->processEvents();
2096       ImageInfoChanged();
2097       QApplication::restoreOverrideCursor();
2098
2099       // Update the display to update, e.g., the sliders
2100       for(int i=0; i<4; i++)
2101         DisplaySliders(index, i);
2102     } else {
2103       QApplication::restoreOverrideCursor();
2104       QString error = "Cannot import the new image.\n";
2105       error += mSlicerManagers[index]->GetLastError().c_str();
2106       QMessageBox::information(this,tr("Problem reading image !"),error);
2107     }
2108     WindowLevelChanged();
2109   }
2110   else
2111     QMessageBox::information(this,tr("Problem reading Overlay !"),"File doesn't exist!");
2112 }
2113 //------------------------------------------------------------------------------
2114
2115
2116 //------------------------------------------------------------------------------
2117 void vvMainWindow::AddROI(int index, QString file)
2118 {
2119   /*
2120   // Get slice manager
2121
2122   // Load image
2123
2124   vvImageReader * mReader = new vvImageReader;
2125   mReader->SetInputFilename(filename.toStdString());
2126   mReader->Update(IMAGE);
2127   if (mReader->GetLastError().size() != 0) {
2128   std::cerr << "Error while reading " << filename.toStdString() << std::endl;
2129   QString error = "Cannot open file \n";
2130   error += mReader->GetLastError().c_str();
2131   QMessageBox::information(this,tr("Reading problem"),error);
2132   delete mReader;
2133   return;
2134   }
2135   vvImage::Pointer roi = mReader->GetOutput();
2136
2137   // Create roi in new tool
2138   vvToolStructureSetManager::AddImage(mCurrentSlicerManager, roi);
2139   */
2140 }
2141 //------------------------------------------------------------------------------
2142
2143 //------------------------------------------------------------------------------
2144 void vvMainWindow::SelectWipeImage()
2145 {
2146   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2147
2148
2149   if (!(CheckAddedImage(index, "wipe")))
2150     return;
2151
2152   vvWipeImage::Pointer wipeImage = vvWipeImage::New();
2153   wipeImage->Initialize(mInputPathName, mSlicerManagers);
2154   wipeImage->selectWipeImage(index);
2155
2156   /*QString Extensions = EXTENSIONS;
2157   Extensions += ";;All Files (*)";
2158   QStringList files = QFileDialog::getOpenFileNames(this,tr("Load Wipe image"),mInputPathName,Extensions);
2159   if (files.isEmpty())
2160     return;
2161
2162   std::vector<std::string> vecFileNames;
2163   for (int i = 0; i < files.size(); i++) {
2164     vecFileNames.push_back(files[i].toStdString());
2165   }*/
2166
2167   //AddWipeImage(index,vecFileNames,vvImageReader::IMAGE);
2168 }
2169 //------------------------------------------------------------------------------
2170
2171
2172 //------------------------------------------------------------------------------
2173 void vvMainWindow::SelectFusionImage()
2174 {
2175   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2176
2177   if (!(CheckAddedImage(index, "fusion")) || !(CheckAddedImage(index, "fusionSequence")))
2178     return;
2179
2180   QString Extensions = EXTENSIONS;
2181   Extensions += ";;All Files (*)";
2182   QStringList files = QFileDialog::getOpenFileNames(this,tr("Load Fusion image"),mInputPathName,Extensions);
2183   if (files.isEmpty())
2184     return;
2185
2186   std::vector<std::string> vecFileNames;
2187   for (int i = 0; i < files.size(); i++) {
2188     vecFileNames.push_back(files[i].toStdString());
2189   }
2190   AddFusionImage(index,vecFileNames,vvImageReader::IMAGE);
2191 }
2192 //------------------------------------------------------------------------------
2193
2194 //------------------------------------------------------------------------------
2195 void vvMainWindow::ResetTransformationToIdentity()
2196 {
2197   std::string actorType = DataTree->selectedItems()[0]->data(1,Qt::UserRole).toString().toStdString();
2198   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2199   mSlicerManagers[index]->ResetTransformationToIdentity(actorType);
2200   ImageInfoChanged();
2201 }
2202 //------------------------------------------------------------------------------
2203
2204 //------------------------------------------------------------------------------
2205 void vvMainWindow::AddFusionImage(int index, std::vector<std::string> fileNames, vvImageReader::LoadedImageType type)
2206 {
2207   QString file(fileNames[0].c_str());
2208   if (QFile::exists(file))
2209   {
2210     mInputPathName = itksys::SystemTools::GetFilenamePath(file.toStdString()).c_str();
2211     itk::ImageIOBase::Pointer reader = itk::ImageIOFactory::CreateImageIO(
2212       file.toStdString().c_str(), itk::ImageIOFactory::ReadMode);
2213     reader->SetFileName(fileNames[0].c_str());
2214     reader->ReadImageInformation();
2215     std::string component = reader->GetComponentTypeAsString(reader->GetComponentType());
2216     int dimension = reader->GetNumberOfDimensions();
2217     QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
2218     vvProgressDialog progress("Opening fusion");
2219     qApp->processEvents();
2220
2221     std::string filename = itksys::SystemTools::GetFilenameWithoutExtension(file.toStdString()).c_str();
2222     if (mSlicerManagers[index]->SetFusion(fileNames,dimension, component,type)) {
2223       //create an item in the tree with good settings
2224       QTreeWidgetItem *item = new QTreeWidgetItem();
2225       item->setData(0,Qt::UserRole,file.toStdString().c_str());
2226       item->setData(1,Qt::UserRole,tr("fusion"));
2227       QFileInfo fileinfo(file); //Do not show the path
2228           item->setData(COLUMN_IMAGE_NAME,Qt::DisplayRole,fileinfo.fileName());
2229           item->setToolTip(COLUMN_IMAGE_NAME, mSlicerManagers[index]->GetListOfAbsoluteFilePathInOneString("fusion").c_str());
2230           qApp->processEvents();
2231 #if VTK_MAJOR_VERSION > 5
2232       for ( unsigned int i = 0; i < mSlicerManagers[index]->GetNumberOfSlicers(); i++)
2233         mSlicerManagers[index]->GetSlicer(i)->ForceUpdateDisplayExtent();
2234 #endif
2235       for (int j = 1; j <= 4; j++) {
2236         item->setData(j,Qt::CheckStateRole,DataTree->topLevelItem(index)->data(j,Qt::CheckStateRole));
2237       }
2238
2239       //Create the buttons for reload and close
2240       qApp->processEvents();
2241       QTreePushButton* cButton = new QTreePushButton;
2242       cButton->setItem(item);
2243       cButton->setColumn(COLUMN_CLOSE_IMAGE);
2244       cButton->setToolTip(tr("close image"));
2245       cButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/exit.png")));
2246       connect(cButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
2247         this,SLOT(CloseImage(QTreeWidgetItem*, int)));
2248
2249       QTreePushButton* rButton = new QTreePushButton;
2250       rButton->setItem(item);
2251       rButton->setColumn(COLUMN_RELOAD_IMAGE);
2252       rButton->setToolTip(tr("reload image"));
2253       rButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/rotateright.png")));
2254       connect(rButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
2255         this,SLOT(ReloadImage(QTreeWidgetItem*, int)));
2256
2257       DataTree->topLevelItem(index)->setExpanded(1);
2258       DataTree->topLevelItem(index)->addChild(item);
2259       DataTree->setItemWidget(item, COLUMN_CLOSE_IMAGE, cButton);
2260       DataTree->setItemWidget(item, COLUMN_RELOAD_IMAGE, rButton);
2261
2262       //set the id of the image
2263       QString id = DataTree->topLevelItem(index)->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString();
2264       item->setData(COLUMN_IMAGE_NAME,Qt::UserRole,id.toStdString().c_str());
2265       UpdateTree();
2266       qApp->processEvents();
2267       ImageInfoChanged();
2268       QApplication::restoreOverrideCursor();
2269
2270       // Update the display to update, e.g., the sliders
2271       for(int i=0; i<4; i++)
2272         DisplaySliders(index, i);
2273     } else {
2274       QApplication::restoreOverrideCursor();
2275       QString error = "Cannot import the new image.\n";
2276       error += mSlicerManagers[index]->GetLastError().c_str();
2277       QMessageBox::information(this,tr("Problem reading image !"),error);
2278     }
2279     WindowLevelChanged();
2280   }
2281   else
2282     QMessageBox::information(this,tr("Problem reading Fusion !"),"File doesn't exist!");
2283 }
2284 //------------------------------------------------------------------------------
2285 //------------------------------------------------------------------------------
2286 void vvMainWindow::AddLandmarks(int index, std::vector<std::string> files)
2287 {
2288     if (!landmarksPanel->LoadFromFile(files))
2289       QMessageBox::information(this,tr("Problem reading Landmarks !"),"File doesn't exist!");
2290
2291     landmarksPanel->SetCurrentPath(mInputPathName.toStdString());
2292     landmarksPanel->SetCurrentImage(mSlicerManagers[index]->GetFileName().c_str());
2293 }
2294
2295 //------------------------------------------------------------------------------
2296 void vvMainWindow::OpenField()
2297 {
2298   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2299
2300   if (!(CheckAddedImage(index, "vector")))
2301     return;
2302
2303   QString Extensions = "Images ( *.mhd *.mha *.vf *.nii *.nrrd *.nhdr)";
2304   // Extensions += ";;Images ( *.mha)";
2305   // Extensions += ";;VF Images ( *.vf)";
2306   // Extensions += ";;nii Images ( *.nii)";
2307   // Extensions += ";;nrrd Images ( *.nrrd)";
2308   // Extensions += ";;nhdr Images ( *.nhdr)";
2309   Extensions += ";;All Files (*)";
2310   QString file = QFileDialog::getOpenFileName(this,tr("Load deformation field"),mInputPathName,Extensions);
2311   if (!file.isEmpty())
2312     AddField(file,index);
2313 }
2314 //------------------------------------------------------------------------------
2315
2316
2317 //------------------------------------------------------------------------------
2318 void vvMainWindow::AddFieldEntry(QString filename,int index,bool from_disk)
2319 {
2320   //create an item in the tree with good settings
2321   QTreeWidgetItem *item = new QTreeWidgetItem();
2322   item->setData(0,Qt::UserRole,filename.toStdString().c_str());
2323   item->setData(1,Qt::UserRole,tr("vector"));
2324   QFileInfo fileinfo(filename); //Do not show the path
2325   item->setData(COLUMN_IMAGE_NAME,Qt::DisplayRole,fileinfo.fileName());
2326   item->setToolTip(COLUMN_IMAGE_NAME, mSlicerManagers[index]->GetListOfAbsoluteFilePathInOneString("vector").c_str());
2327   qApp->processEvents();
2328
2329   for (int j = 1; j <= 4; j++) {
2330     item->setData(j,Qt::CheckStateRole,DataTree->topLevelItem(index)->data(j,Qt::CheckStateRole));
2331   }
2332
2333   //Create the buttons for reload and close
2334   qApp->processEvents();
2335   QTreePushButton* cButton = new QTreePushButton;
2336   cButton->setItem(item);
2337   cButton->setColumn(COLUMN_CLOSE_IMAGE);
2338   cButton->setToolTip(tr("close vector field"));
2339   cButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/exit.png")));
2340   connect(cButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
2341     this,SLOT(CloseImage(QTreeWidgetItem*, int)));
2342
2343   QTreePushButton* rButton = new QTreePushButton;
2344   rButton->setItem(item);
2345   rButton->setColumn(COLUMN_RELOAD_IMAGE);
2346   rButton->setToolTip(tr("reload vector field"));
2347   rButton->setEnabled(from_disk);
2348   rButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/rotateright.png")));
2349   connect(rButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
2350     this,SLOT(ReloadImage(QTreeWidgetItem*, int)));
2351
2352   DataTree->topLevelItem(index)->setExpanded(1);
2353   DataTree->topLevelItem(index)->addChild(item);
2354   DataTree->setItemWidget(item, COLUMN_RELOAD_IMAGE, rButton);
2355   DataTree->setItemWidget(item, COLUMN_CLOSE_IMAGE, cButton);
2356
2357   //set the id of the image
2358   QString id = DataTree->topLevelItem(index)->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString();
2359   item->setData(COLUMN_IMAGE_NAME,Qt::UserRole,id.toStdString().c_str());
2360   UpdateTree();
2361   qApp->processEvents();
2362   ImageInfoChanged();
2363   QApplication::restoreOverrideCursor();
2364 }
2365 //------------------------------------------------------------------------------
2366
2367
2368 //------------------------------------------------------------------------------
2369 void vvMainWindow::AddField(vvImage::Pointer vf,QString file,int index)
2370 {
2371   QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
2372   vvSlicerManager* imageManager = mSlicerManagers[index];
2373   if (imageManager->SetVF(vf,file.toStdString())) {
2374     AddFieldEntry(file,index,false);
2375 #if VTK_MAJOR_VERSION > 5
2376       for ( unsigned int i = 0; i < mSlicerManagers[index]->GetNumberOfSlicers(); i++)
2377         mSlicerManagers[index]->GetSlicer(i)->ForceUpdateDisplayExtent();
2378 #endif
2379   } else {
2380     QString error = "Cannot import the vector field for this image.\n";
2381     error += imageManager->GetLastError().c_str();
2382     QMessageBox::information(this,tr("Problem reading VF !"),error);
2383   }
2384   QApplication::restoreOverrideCursor();
2385 }
2386 //------------------------------------------------------------------------------
2387
2388
2389 //------------------------------------------------------------------------------
2390 void vvMainWindow::AddField(QString file,int index)
2391 {
2392   if (QFile::exists(file)) {
2393     mInputPathName = itksys::SystemTools::GetFilenamePath(file.toStdString()).c_str();
2394
2395     //init the progress events
2396     QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
2397     vvProgressDialog progress("Opening " + file.toStdString());
2398     qApp->processEvents();
2399
2400     //read the vector and put it in the current mSlicerManager
2401     vvSlicerManager* imageManager = mSlicerManagers[index];
2402     qApp->processEvents();
2403
2404     std::string filename = itksys::SystemTools::GetFilenameWithoutExtension(file.toStdString()).c_str();
2405     if (imageManager->SetVF(file.toStdString())) {
2406       imageManager->Render();
2407       AddFieldEntry(file,index,true);
2408     } else {
2409       QApplication::restoreOverrideCursor();
2410       QString error = "Cannot import the vector field for this image.\n";
2411       error += imageManager->GetLastError().c_str();
2412       QMessageBox::information(this,tr("Problem reading VF !"),error);
2413     }
2414   } else
2415     QMessageBox::information(this,tr("Problem reading VF !"),"File doesn't exist!");
2416
2417 }
2418 //------------------------------------------------------------------------------
2419
2420
2421 //------------------------------------------------------------------------------
2422 void vvMainWindow::SetVFProperty(int subsampling, int scale, int log, int width, double r, double g, double b)
2423 {
2424   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2425   if (mSlicerManagers[index]->GetSlicer(0)->GetVF()) {
2426     for (int i = 0; i < 4; i++) {
2427       mSlicerManagers[index]->GetSlicer(i)->SetVFSubSampling(subsampling);
2428       mSlicerManagers[index]->GetSlicer(i)->SetVFScale(scale);
2429       mSlicerManagers[index]->GetSlicer(i)->SetVFWidth(width);
2430       mSlicerManagers[index]->GetSlicer(i)->SetVFColor(r,g,b);
2431       if (log > 0)
2432         mSlicerManagers[index]->GetSlicer(i)->SetVFLog(1);
2433       else
2434         mSlicerManagers[index]->GetSlicer(i)->SetVFLog(0);
2435     }
2436   }
2437 }
2438 //------------------------------------------------------------------------------
2439
2440
2441 //------------------------------------------------------------------------------
2442 void vvMainWindow::SetOverlayProperty(int color, int linked, double window, double level)
2443 {
2444   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2445   if (mSlicerManagers[index]->GetSlicer(0)->GetOverlay()) {
2446     mSlicerManagers[index]->SetOverlayColor(color);
2447     mSlicerManagers[index]->SetColorMap(0);
2448     mSlicerManagers[index]->SetLinkOverlayWindowLevel(linked);
2449     mSlicerManagers[index]->SetOverlayColorWindow(window);
2450     mSlicerManagers[index]->SetOverlayColorLevel(level);
2451     mSlicerManagers[index]->Render();
2452   }
2453 }
2454 //------------------------------------------------------------------------------
2455
2456 //------------------------------------------------------------------------------
2457 void vvMainWindow::SetFusionProperty(int opacity, int thresOpacity, int colormap,double window, double level, bool showLegend)
2458 {
2459   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2460   if (mSlicerManagers[index]->GetSlicer(0)->GetFusion()) {
2461     mSlicerManagers[index]->SetFusionColorMap(colormap);
2462     mSlicerManagers[index]->SetFusionOpacity(opacity);
2463     mSlicerManagers[index]->SetFusionThresholdOpacity(thresOpacity);
2464     mSlicerManagers[index]->SetFusionWindow(window);
2465     mSlicerManagers[index]->SetFusionLevel(level);
2466     mSlicerManagers[index]->SetFusionShowLegend(showLegend);
2467     mSlicerManagers[index]->SetColorMap(0);
2468     mSlicerManagers[index]->Render();
2469   }
2470 }
2471 //------------------------------------------------------------------------------
2472
2473
2474 //------------------------------------------------------------------------------
2475 void vvMainWindow::SelectFusionSequence()
2476 {
2477   //get the index of the slicer manager of the main sequence (CT)
2478   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2479
2480   if (!(CheckAddedImage(index, "fusion")) || !(CheckAddedImage(index, "fusionSequence")))
2481     return;
2482
2483   QString Extensions = EXTENSIONS;
2484   Extensions += ";;All Files (*)";
2485   QStringList files = QFileDialog::getOpenFileNames(this,tr("Load Overlay image sequence"),mInputPathName,Extensions);
2486   if (files.isEmpty())
2487     return;
2488
2489   std::vector<std::string> vecFileNames;
2490   for (int i = 0; i < files.size(); i++) {
2491     vecFileNames.push_back(files[i].toStdString());
2492   }
2493
2494   //associate the secondary sequence (US) to the main one
2495   AddFusionSequence(index,vecFileNames,vvImageReader::MERGEDWITHTIME);
2496 }
2497 //------------------------------------------------------------------------------
2498
2499
2500 //------------------------------------------------------------------------------
2501 void vvMainWindow::SelectFusionSequenceCorrespondances()
2502 {
2503   //make sure the index is right?
2504   //in the end, I should attach the temporal data to the right sequence!
2505   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2506   //in case the other sequence got selected, make sure we select the primary sequence
2507   if ( (!mSlicerManagers[index]->GetSlicer(0)->GetFusion()) && mSlicerManagers[index]->GetFusionSequenceIndexOfLinkedManager()>=0 ) {
2508     index = mSlicerManagers[index]->GetFusionSequenceIndexOfLinkedManager();
2509   }
2510
2511   //open a dialog box to find a file
2512   //QString Extensions = EXTENSIONS;
2513   QString Extensions = ";;All Files (*)";
2514   QString fileName = QFileDialog::getOpenFileName(this,tr("Load respiratory signal for fused sequence"),mInputPathName,Extensions);
2515   if (fileName.isNull())
2516     return;
2517
2518   //read it as a vector of values
2519   vnl_vector<double> tmpVect;
2520
2521   std::ifstream file;
2522   file.open(fileName.toStdString().c_str());
2523   tmpVect.read_ascii(file);
2524   file.close();
2525
2526   //if compatible with the fused image sequence (number of entries = nb of entries in main sequence + nb of entries in joint sequence), enable the temporalSync
2527   bool signalOK = true;
2528   unsigned nbFrameMain = mSlicerManagers[index]->GetImage()->GetTransform().size();
2529   unsigned nbFrameSecondary = mSlicerManagers[index]->GetFusionSequenceNbFrames();
2530   std::cout<<"nbFrameMain = "<<nbFrameMain<<", nbFrameSecondary= "<<nbFrameSecondary<<", signal size: "<<tmpVect.size()<<std::endl;
2531   std::vector<unsigned> temporalCorrespondances;
2532   if ( tmpVect.size() == nbFrameMain + nbFrameSecondary ) {
2533     for (unsigned i=0 ; i<tmpVect.size() ; i++) {
2534       if (i<nbFrameMain) { //first part of the file: i -> index in secondary seq.
2535         if ( tmpVect(i)<nbFrameSecondary ) temporalCorrespondances.push_back(tmpVect(i));
2536         else { signalOK=false; break; } //pointing outside the secondary sequence...
2537       }
2538       else { //first part of the file -> index in secondary seq.
2539         if ( tmpVect(i)<nbFrameMain ) temporalCorrespondances.push_back(tmpVect(i));
2540         else { signalOK=false; break; } //pointing outside the secondary sequence...
2541       }
2542     }
2543   }
2544   else {signalOK=false;}
2545   if (!signalOK) {//else, send a message to signal the failure...
2546     QString error = "The provided temporal correspondances is invalid - check tooltip.\n";
2547     error += "Ignoring file: " + fileName;
2548     QMessageBox::information(this,tr("Problem adding temporal correspondances!"),error);
2549     return;
2550   }
2551   else {
2552     //for convenience, associate this sequence to both the current slicer manager, and to the linked one
2553     mSlicerManagers[index]->SetFusionSequenceCorrespondances(temporalCorrespondances);
2554     mSlicerManagers[ mSlicerManagers[index]->GetFusionSequenceIndexOfLinkedManager() ]->SetFusionSequenceCorrespondances(temporalCorrespondances);
2555     overlayPanel->enableFusionSequenceTemporalSync();
2556   }
2557
2558 }
2559 //------------------------------------------------------------------------------
2560
2561
2562 //------------------------------------------------------------------------------
2563 //when this function is called index is the slicer manager index corresponding to the main sequence (CT)
2564 //the files behind fileNames points to the data for the secondary sequence
2565 void vvMainWindow::AddFusionSequence(int index, std::vector<std::string> fileNames, vvImageReader::LoadedImageType type)
2566 {
2567   QString file(fileNames[0].c_str());
2568   if (QFile::exists(file))
2569   {
2570     mInputPathName = itksys::SystemTools::GetFilenamePath(file.toStdString()).c_str();
2571     itk::ImageIOBase::Pointer reader = itk::ImageIOFactory::CreateImageIO(
2572       file.toStdString().c_str(), itk::ImageIOFactory::ReadMode);
2573     std::sort (fileNames.begin(), fileNames.end());//make sure the files are sorted.
2574     reader->SetFileName(fileNames[0].c_str());
2575     reader->ReadImageInformation();
2576     std::string component = reader->GetComponentTypeAsString(reader->GetComponentType());
2577     int dimension = reader->GetNumberOfDimensions();
2578     QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
2579     vvProgressDialog progress("Opening " + file.toStdString());
2580     qApp->processEvents();
2581
2582     std::string filename = itksys::SystemTools::GetFilenameWithoutExtension(file.toStdString()).c_str();
2583
2584     if (mSlicerManagers[index]->SetFusionSequence(fileNames,dimension, component,type)) {
2585       //create an item in the tree with good settings
2586       QTreeWidgetItem *item = new QTreeWidgetItem();
2587       item->setData(0,Qt::UserRole,file.toStdString().c_str());
2588       item->setData(1,Qt::UserRole,tr("fusionSequence"));
2589
2590       QFileInfo fileinfo(file); //Do not show the path
2591       item->setData(COLUMN_IMAGE_NAME,Qt::DisplayRole,fileinfo.fileName());
2592       item->setToolTip(COLUMN_IMAGE_NAME, mSlicerManagers[index]->GetListOfAbsoluteFilePathInOneString("fusionSequence").c_str());
2593       qApp->processEvents();
2594 #if VTK_MAJOR_VERSION > 5
2595       for ( unsigned int i = 0; i < mSlicerManagers[index]->GetNumberOfSlicers(); i++)
2596         mSlicerManagers[index]->GetSlicer(i)->ForceUpdateDisplayExtent();
2597 #endif
2598       for (int j = 1; j <= 4; j++) {
2599         item->setData(j,Qt::CheckStateRole,DataTree->topLevelItem(index)->data(j,Qt::CheckStateRole));
2600       }
2601
2602       //Create the buttons for reload and close
2603       qApp->processEvents();
2604       QTreePushButton* cButton = new QTreePushButton;
2605       cButton->setItem(item);
2606       cButton->setColumn(COLUMN_CLOSE_IMAGE);
2607       cButton->setToolTip(tr("close image"));
2608       cButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/exit.png")));
2609       connect(cButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
2610         this,SLOT(CloseImage(QTreeWidgetItem*, int)));
2611
2612       QTreePushButton* rButton = new QTreePushButton;
2613       rButton->setItem(item);
2614       rButton->setColumn(COLUMN_RELOAD_IMAGE);
2615       rButton->setToolTip(tr("reload image"));
2616       rButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/rotateright.png")));
2617       connect(rButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
2618         this,SLOT(ReloadImage(QTreeWidgetItem*, int)));
2619
2620       DataTree->topLevelItem(index)->setExpanded(1);
2621       DataTree->topLevelItem(index)->addChild(item);
2622       DataTree->setItemWidget(item, COLUMN_CLOSE_IMAGE, cButton);
2623       DataTree->setItemWidget(item, COLUMN_RELOAD_IMAGE, rButton);
2624
2625       //store the original transform matrix
2626       int indexParent = GetSlicerIndexFromItem( DataTree->topLevelItem(index) );
2627       mSlicerManagers[indexParent]->SetFusionSequenceMainTransformMatrix( mSlicerManagers[indexParent]->GetSlicer(0)->GetImage()->GetTransform()[0]->GetMatrix() );
2628
2629       //set the id of the image
2630       QString id = DataTree->topLevelItem(index)->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString();
2631       item->setData(COLUMN_IMAGE_NAME,Qt::UserRole,id.toStdString().c_str());
2632       UpdateTree();
2633       qApp->processEvents();
2634
2635       //ImageInfoChanged();
2636
2637       QApplication::restoreOverrideCursor();
2638       // Update the display to update, e.g., the sliders
2639       for(int i=0; i<4; i++)
2640         DisplaySliders(index, i);
2641
2642
2643       //This loads the secondary sequence (US) as an independent sequence
2644       LoadImages(fileNames, type);
2645       //reset the transforms to identity
2646       //FIX -- and set the thickness of the US slices to a large value (necessary for visualization purposes...)
2647       double sp_x, sp_y, sp_z;
2648       mSlicerManagers[indexParent]->GetImage()->GetVTKImages()[0]->GetSpacing(sp_x, sp_y, sp_z);
2649       sp_z = std::max(sp_x, std::max(sp_y, sp_z)) + 0.5; //
2650       for (unsigned i=0 ; i<mSlicerManagers.back()->GetImage()->GetTransform().size() ; i++) {
2651         sp_x = mSlicerManagers.back()->GetImage()->GetVTKImages()[i]->GetSpacing()[0];
2652         sp_y = mSlicerManagers.back()->GetImage()->GetVTKImages()[i]->GetSpacing()[1];
2653         mSlicerManagers.back()->GetImage()->GetVTKImages()[i]->SetSpacing( sp_x, sp_y, sp_z);
2654         mSlicerManagers.back()->GetImage()->GetTransform()[i]->Identity();
2655         mSlicerManagers.back()->GetImage()->GetTransform()[i]->Update();
2656       }
2657
2658       //automatically link both images...
2659       AddLink(mSlicerManagers[indexParent]->GetId().c_str(), mSlicerManagers.back()->GetId().c_str(), false);
2660
2661       //tie the main and secondary sequences by raising flags and informing each another of their respective SlicerManager indices
2662       mSlicerManagers[indexParent]->SetFusionSequenceIndexOfLinkedManager(mSlicerManagers.size()-1);
2663       mSlicerManagers[indexParent]->SetFusionSequenceInvolvmentCode(0); //main sequence
2664       mSlicerManagers.back()->SetFusionSequenceIndexOfLinkedManager(indexParent);
2665       mSlicerManagers.back()->SetFusionSequenceInvolvmentCode(1); //secondary sequence
2666       for (unsigned i=0 ; i<4 ; i++) {
2667         mSlicerManagers.back()->GetSlicer(i)->SetFusionSequenceCode(1); //flag the slicers of the secondary sequence
2668       }
2669
2670     } else {
2671       QApplication::restoreOverrideCursor();
2672       QString error = "Cannot import the new image.\n";
2673       error += mSlicerManagers[index]->GetLastError().c_str();
2674       QMessageBox::information(this,tr("Problem reading image !"),error);
2675     }
2676     WindowLevelChanged();
2677     ImageInfoChanged(); //this internally calls WindowLevelChanged...
2678   }
2679   else {
2680     QMessageBox::information(this,tr("Problem reading fusion sequence !"),"File doesn't exist!");
2681     return;
2682   }
2683
2684 }
2685 //------------------------------------------------------------------------------
2686
2687
2688 //------------------------------------------------------------------------------
2689 //fusionSequenceFrameIndex and fusionSequenceNbFrames are relative to the secondary sequence (US)
2690 void vvMainWindow::SetFusionSequenceProperty(int fusionSequenceFrameIndex, bool spatialSyncFlag, unsigned int fusionSequenceNbFrames, bool temporalSyncFlag)
2691 {
2692   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2693
2694   if (!mSlicerManagers[index]->IsInvolvedInFusionSequence()) return;
2695
2696   //check if the focus moved to the linked sequence, and in this case, select the master sequence instead
2697   if (!mSlicerManagers[index]->IsMainSequenceOfFusionSequence()) {
2698     index = mSlicerManagers[index]->GetFusionSequenceIndexOfLinkedManager();
2699   }
2700   int secondaryIndex = mSlicerManagers[index]->GetFusionSequenceIndexOfLinkedManager();
2701   if (secondaryIndex==-1) return; //this should never happen
2702   if ( (!mSlicerManagers[index]->IsMainSequenceOfFusionSequence()) ||
2703     (!mSlicerManagers[secondaryIndex]->IsSecondarySequenceOfFusionSequence()) )
2704   {return;} //this should never happen, raise an exception?
2705
2706   if (mSlicerManagers[index]->GetSlicer(0)->GetFusion()) {
2707
2708     //First, if the spatialSync button is unchecked, then reposition the parent sequence (CT) in its original coordinate frame
2709     if ( (!spatialSyncFlag) && (mSlicerManagers[index]->GetFusionSequenceSpatialSyncFlag()) ) {
2710       for ( unsigned i=0 ; i<mSlicerManagers[index]->GetSlicer(0)->GetImage()->GetTransform().size() ; i++ ) {
2711         mSlicerManagers[index]->GetSlicer(0)->GetImage()->GetTransform()[i]->SetMatrix( mSlicerManagers[index]->GetFusionSequenceMainTransformMatrix() );
2712         mSlicerManagers[index]->GetSlicer(0)->GetImage()->GetTransform()[i]->Update();
2713       }
2714
2715       for (int i=0; i<mSlicerManagers[index]->GetNumberOfSlicers(); i++) {
2716         mSlicerManagers[index]->GetSlicer(i)->ForceUpdateDisplayExtent();
2717         mSlicerManagers[index]->GetSlicer(i)->Render();
2718       }
2719     }
2720
2721     //then, update the property values in the slicer manager
2722     mSlicerManagers[index]->SetFusionSequenceLength(fusionSequenceNbFrames);
2723     mSlicerManagers[index]->SetFusionSequenceSpatialSyncFlag(spatialSyncFlag);
2724     mSlicerManagers[index]->SetFusionSequenceTemporalSyncFlag(temporalSyncFlag);
2725     mSlicerManagers[index]->SetFusionSequenceFrameIndex(fusionSequenceFrameIndex);
2726
2727     //select the right frame of the US sequence
2728     mSlicerManagers[index]->SetFusionSequenceTSlice(fusionSequenceFrameIndex); //here, I should only update the overlayed sequence
2729     mSlicerManagers[secondaryIndex]->SetTSlice(fusionSequenceFrameIndex, false); //this should update the secondary sequence (individual version)
2730
2731     //update the horizontal sliders of the main window
2732     overlayPanel->updateFusionSequenceSliderValueFromWindow(fusionSequenceFrameIndex, false);
2733
2734     if (spatialSyncFlag) { //reslice the CT
2735
2736       if (temporalSyncFlag) { //do the temporal synchronisation
2737         int mainSequenceFrameIndex=0;
2738         //estimate the TSlice to set to the CT
2739         unsigned nbFramesMain = mSlicerManagers[index]->GetImage()->GetTransform().size();
2740         mainSequenceFrameIndex = mSlicerManagers[index]->GetFusionSequenceCorrespondances()[ nbFramesMain + fusionSequenceFrameIndex];
2741         //and set it!
2742         mSlicerManagers[index]->SetTSlice(mainSequenceFrameIndex, false);
2743         //warning, there is a loopback, and modification of the TSlice in main sequence forces an update of the TSlice in secondary, etc...
2744       }
2745
2746
2747       //Set the transform matrix of the parent sequence (typically CT / 4DCT)
2748       vtkSmartPointer<vtkMatrix4x4> tmpMat = vtkSmartPointer<vtkMatrix4x4>::New();
2749       vtkMatrix4x4::Invert( mSlicerManagers[index]->GetFusionSequenceInitialTransformMatrixAtFrame(fusionSequenceFrameIndex), tmpMat );
2750       for ( unsigned i=0 ; i<mSlicerManagers[index]->GetSlicer(0)->GetImage()->GetTransform().size() ; i++ ) {
2751         mSlicerManagers[index]->GetSlicer(0)->GetImage()->GetTransform()[i]->SetMatrix( mSlicerManagers[index]->GetFusionSequenceMainTransformMatrix() );
2752         mSlicerManagers[index]->GetSlicer(0)->GetImage()->GetTransform()[i]->PreMultiply();
2753         mSlicerManagers[index]->GetSlicer(0)->GetImage()->GetTransform()[i]->Concatenate( tmpMat );
2754         mSlicerManagers[index]->GetSlicer(0)->GetImage()->GetTransform()[i]->Update();
2755       }
2756
2757       for (int i=0; i<mSlicerManagers[index]->GetNumberOfSlicers(); i++) {
2758         mSlicerManagers[index]->GetSlicer(i)->ForceUpdateDisplayExtent();
2759         mSlicerManagers[index]->GetSlicer(i)->Render();
2760       }
2761
2762     }
2763
2764   }
2765 }
2766 //------------------------------------------------------------------------------
2767
2768
2769 //------------------------------------------------------------------------------
2770 void vvMainWindow::SaveAs()
2771 {
2772   if (DataTree->selectedItems()[0]->data(1,Qt::UserRole).toString() == "vector") {
2773     QMessageBox::warning(this,tr("Unsupported type"),tr("Sorry, saving a vector field is unsupported for the moment"));
2774     return;
2775   }
2776
2777   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2778   int dimension = mSlicerManagers[index]->GetDimension();
2779   QStringList OutputListeFormat;
2780   OutputListeFormat.clear();
2781   if (dimension == 1) {
2782     OutputListeFormat.push_back(".mhd");
2783     OutputListeFormat.push_back(".mha");
2784   }
2785   if (dimension == 2) {
2786     OutputListeFormat.push_back(".bmp");
2787     OutputListeFormat.push_back(".png");
2788     OutputListeFormat.push_back(".jpeg");
2789     OutputListeFormat.push_back(".tif");
2790     OutputListeFormat.push_back(".mhd");
2791     OutputListeFormat.push_back(".mha");
2792     OutputListeFormat.push_back(".hdr");
2793     OutputListeFormat.push_back(".vox");
2794   } else if (dimension == 3) {
2795     OutputListeFormat.push_back(".mhd");
2796     OutputListeFormat.push_back(".mha");
2797     OutputListeFormat.push_back(".nii");
2798     OutputListeFormat.push_back(".nrrd");
2799     OutputListeFormat.push_back(".nhdr");
2800     OutputListeFormat.push_back(".hdr");
2801     OutputListeFormat.push_back(".vox");
2802   } else if (dimension == 4) {
2803     OutputListeFormat.push_back(".mhd");
2804     OutputListeFormat.push_back(".mha");
2805     OutputListeFormat.push_back(".nii");
2806     OutputListeFormat.push_back(".nrrd");
2807     OutputListeFormat.push_back(".nhdr");
2808   }
2809   QString Extensions = "AllFiles(*.*)";
2810   for (int i = 0; i < OutputListeFormat.count(); i++) {
2811     Extensions += ";;Images ( *";
2812     Extensions += OutputListeFormat[i];
2813     Extensions += ")";
2814   }
2815   QString fileName = QFileDialog::getSaveFileName(this,
2816     tr("Save As"),
2817     mSlicerManagers[index]->GetFileName().c_str(),
2818     Extensions);
2819   if (!fileName.isEmpty()) {
2820     std::string fileformat = itksys::SystemTools::GetFilenameLastExtension(fileName.toStdString());
2821     if (OutputListeFormat.contains(
2822       fileformat.c_str())) {
2823         QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
2824         std::string action = "Saving";
2825         vvProgressDialog progress("Saving "+fileName.toStdString());
2826         qApp->processEvents();
2827         vvImageWriter::Pointer writer = vvImageWriter::New();
2828         writer->SetOutputFileName(fileName.toStdString());
2829         writer->SetInput(mSlicerManagers[index]->GetImage());
2830
2831         // Check on transform and prompt user
2832         writer->SetSaveTransform(false);
2833         bool bId = true;
2834         for(int i=0; i<4; i++)
2835           for(int j=0; j<4; j++) {
2836             // TODO SR and BP: check on the list of transforms and not the first only
2837             double elt = mSlicerManagers[index]->GetImage()->GetTransform()[0]->GetMatrix()->GetElement(i,j);
2838             if(i==j && elt!=1.)
2839               bId = false;
2840             if(i!=j && elt!=0.)
2841               bId = false;
2842           }
2843           if( !bId ) {
2844             QString warning = "The image has an associated linear transform. Do you want to save it along?";
2845             QMessageBox msgBox(QMessageBox::Warning, tr("Save transform"), warning, 0, this);
2846             msgBox.addButton(tr("Yes"), QMessageBox::AcceptRole);
2847             msgBox.addButton(tr("No"), QMessageBox::RejectRole);
2848             if (msgBox.exec() == QMessageBox::AcceptRole)
2849               writer->SetSaveTransform(true);
2850           }
2851
2852           writer->Update();
2853           QApplication::restoreOverrideCursor();
2854           if (writer->GetLastError().size()) {
2855             QString error = "Saving did not succeed\n";
2856             error += writer->GetLastError().c_str();
2857             QMessageBox::information(this,tr("Saving Problem"),error);
2858             SaveAs();
2859           }
2860     } else {
2861       QString error = fileformat.c_str();
2862       if (error.isEmpty())
2863         error += "no file format specified !";
2864       else
2865         error += " format unknown !!!\n";
2866       QMessageBox::information(this,tr("Saving Problem"),error);
2867       SaveAs();
2868     }
2869   }
2870 }
2871 //------------------------------------------------------------------------------
2872
2873 //------------------------------------------------------------------------------
2874 void vvMainWindow::SaveCurrentState()
2875 {
2876   QString Extensions = "XML Files(*.xml)";
2877   QString fileName = QFileDialog::getSaveFileName(this,
2878     tr("Save Current Window State"),
2879     "",
2880     Extensions);
2881
2882   SaveCurrentStateAs(fileName.toStdString());
2883 }
2884 //------------------------------------------------------------------------------
2885
2886 //------------------------------------------------------------------------------
2887 void vvMainWindow::SaveCurrentStateAs(const std::string& stateFile)
2888 {
2889   vvSaveState save_state;
2890   save_state.Run(this, stateFile);
2891 }
2892
2893 //------------------------------------------------------------------------------
2894 void vvMainWindow::ReadSavedState()
2895 {
2896   QString Extensions = "XML Files(*.xml)";
2897   QString fileName = QFileDialog::getOpenFileName(this,
2898     tr("Load Window State"),
2899     "",
2900     Extensions);
2901
2902   ReadSavedStateFile(fileName.toStdString());
2903 }
2904 //------------------------------------------------------------------------------
2905
2906 //------------------------------------------------------------------------------
2907 void vvMainWindow::ReadSavedStateFile(const std::string& stateFile)
2908 {
2909   vvReadState read_state;
2910   read_state.Run(this, stateFile);
2911 }
2912 //------------------------------------------------------------------------------
2913
2914 //------------------------------------------------------------------------------
2915 void vvMainWindow::LinkAllImages()
2916 {
2917   linkPanel->linkAll();
2918 }
2919
2920 //------------------------------------------------------------------------------
2921 void vvMainWindow::AddLink(QString image1,QString image2,bool fromPanel)
2922 {
2923   if (!fromPanel) {
2924     // delegate to linkPanel if call came from elsewhere...
2925     linkPanel->addLinkFromIds(image1, image2);
2926     return;
2927   }
2928
2929   unsigned int sm1 = 0;
2930   unsigned int sm2 = 0;
2931
2932   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
2933     if (image1.toStdString() == mSlicerManagers[i]->GetId()) {
2934       mSlicerManagers[i]->AddLink(image2.toStdString());
2935       sm1 = i;
2936     }
2937     if (image2.toStdString() == mSlicerManagers[i]->GetId()) {
2938       mSlicerManagers[i]->AddLink(image1.toStdString());
2939       sm2 = i;
2940     }
2941   }
2942
2943   if (linkPanel->isLinkAll())   {
2944     emit UpdateLinkedNavigation(mSlicerManagers[sm1]->GetId(), mSlicerManagers[mCurrentPickedImageIndex], mSlicerManagers[mCurrentPickedImageIndex]->GetSlicer(0));
2945     emit UpdateLinkedNavigation(mSlicerManagers[sm2]->GetId(), mSlicerManagers[mCurrentPickedImageIndex], mSlicerManagers[mCurrentPickedImageIndex]->GetSlicer(0));
2946   } else {
2947     emit UpdateLinkedNavigation(mSlicerManagers[sm2]->GetId(), mSlicerManagers[sm1], mSlicerManagers[sm1]->GetSlicer(0));
2948   }
2949 }
2950
2951 //------------------------------------------------------------------------------
2952
2953
2954 //------------------------------------------------------------------------------
2955 void vvMainWindow::RemoveLink(QString image1,QString image2)
2956 {
2957   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
2958     if (image1.toStdString() == mSlicerManagers[i]->GetId()) {
2959       mSlicerManagers[i]->RemoveLink(image2.toStdString());
2960     }
2961     if (image2.toStdString() == mSlicerManagers[i]->GetId()) {
2962       mSlicerManagers[i]->RemoveLink(image1.toStdString());
2963     }
2964   }
2965 }
2966 //------------------------------------------------------------------------------
2967
2968 //------------------------------------------------------------------------------
2969 void vvMainWindow::ChangeImageWithIndexOffset(vvSlicerManager *sm, int slicer, int offset)
2970 {
2971   if(mSlicerManagers.size()==1)
2972     return;
2973
2974   int index = 0;
2975   while(sm != mSlicerManagers[index])
2976     index++;
2977   index = (index+offset+mSlicerManagers.size()) % mSlicerManagers.size();
2978
2979   QTreeWidgetItem* item = GetItemFromSlicerManager(mSlicerManagers[index]);
2980   item->setData(slicer+1,Qt::CheckStateRole,2);         //change checkbox
2981   CurrentImageChanged(mSlicerManagers[index]->GetId()); //select new image
2982   DisplayChanged(item,slicer+1);
2983 }
2984 //------------------------------------------------------------------------------
2985 void vvMainWindow::HorizontalSliderMoved(int value,int column, int slicer_index)
2986 {
2987   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
2988     if (DataTree->topLevelItem(i)->data(column,Qt::CheckStateRole).toInt() > 1) {
2989       //i is the SlicerManager that is in charge of this slicer.
2990       if (mSlicerManagers[i]->IsInvolvedInFusionSequence()) {
2991         //if the slicerManager is involved in a fusionSequence as the secondary sequence, then update the slider position in the overlay panel and everything accordingly
2992         if (mSlicerManagers[i]->IsSecondarySequenceOfFusionSequence()) {
2993           overlayPanel->updateFusionSequenceSliderValueFromWindow(value, true);
2994         }
2995         else { //if this is the primary sequence that has been modified
2996           if (mSlicerManagers[i]->GetFusionSequenceTemporalSyncFlag()) {
2997             //WARNING: for some obscure reason, there are problems when accessing mSlicerManagers[mSlicerManagers[i]->GetFusionSequenceIndexOfLinkedManager()]->GetFusionSequenceFrameIndex();
2998
2999             int estimatedValue=0;
3000             //estimate a corresponding time index for the secondary (US) sequence, and update it accordingly.
3001             estimatedValue = mSlicerManagers[i]->GetFusionSequenceCorrespondances()[ value ];
3002             //TODO: at the moment, there is a loop in TSlice modifications
3003             //modifying sequence 1 causes seq 2 to update, which in turns update seq1...
3004             //I disable control on seq1 at the moment.
3005             //overlayPanel->updateFusionSequenceSliderValueFromWindow(estimatedValue, true);
3006           }
3007         }
3008       }
3009
3010       for (int j = 0; j < 4; j++) {
3011         mSlicerManagers[i]->SetTSliceInSlicer(value,j);
3012       }
3013       mSlicerManagers[i]->GetSlicer(slicer_index)->Render();
3014       break;
3015     }
3016   }
3017 }
3018 //------------------------------------------------------------------------------
3019
3020
3021 //------------------------------------------------------------------------------
3022 void vvMainWindow::NOHorizontalSliderMoved()
3023 {
3024   // if (mCurrentTime == NOHorizontalSlider->value()) return;
3025   HorizontalSliderMoved(NOHorizontalSlider->value(),COLUMN_UL_VIEW,0);
3026   //  mCurrentTime = NOHorizontalSlider->value();
3027 }
3028 //------------------------------------------------------------------------------
3029
3030
3031 //------------------------------------------------------------------------------
3032 void vvMainWindow::NEHorizontalSliderMoved()
3033 {
3034   // if (mCurrentTime == NEHorizontalSlider->value()) return;
3035   HorizontalSliderMoved(NEHorizontalSlider->value(),COLUMN_UR_VIEW,1);
3036   //  mCurrentTime = NEHorizontalSlider->value();
3037 }
3038 //------------------------------------------------------------------------------
3039
3040
3041 //------------------------------------------------------------------------------
3042 void vvMainWindow::SOHorizontalSliderMoved()
3043 {
3044   // if (mCurrentTime == SOHorizontalSlider->value()) return;
3045   HorizontalSliderMoved(SOHorizontalSlider->value(),COLUMN_DL_VIEW,2);
3046   // mCurrentTime = SOHorizontalSlider->value();
3047 }
3048 //------------------------------------------------------------------------------
3049
3050
3051 //------------------------------------------------------------------------------
3052 void vvMainWindow::SEHorizontalSliderMoved()
3053 {
3054   // if (mCurrentTime == SEHorizontalSlider->value()) return;
3055   HorizontalSliderMoved(SEHorizontalSlider->value(),COLUMN_DR_VIEW,3);
3056   // mCurrentTime = SEHorizontalSlider->value();
3057 }
3058 //------------------------------------------------------------------------------
3059
3060 //------------------------------------------------------------------------------
3061 void vvMainWindow::NOVerticalSliderChanged()
3062 {
3063   static int value=-1;
3064   if (value == NOVerticalSlider->value()) return;
3065   else value = NOVerticalSlider->value();
3066   //  int value = NOVerticalSlider->value();
3067   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
3068     if (DataTree->topLevelItem(i)->data(COLUMN_UL_VIEW,Qt::CheckStateRole).toInt() > 1) {
3069       if (mSlicerManagers[i]->GetSlicer(0)->GetSlice() != value) {
3070         mSlicerManagers[i]->GetSlicer(0)->SetSlice(value);
3071         mSlicerManagers[i]->VerticalSliderHasChanged(0, value);
3072
3073         // If nor Update/Render -> slider not work
3074         // only render = ok navigation, but for contour Update needed but slower ?
3075
3076         mSlicerManagers[i]->UpdateSlice(0);  // <-- DS add this. Not too much update ? YES. but needed for ImageContour ...
3077         //mSlicerManagers[i]->GetSlicer(0)->Render(); // <-- DS add this, needed for contour, seems ok ? not too slow ?
3078       }
3079       break;
3080     }
3081   }
3082 }
3083 //------------------------------------------------------------------------------
3084
3085
3086 //------------------------------------------------------------------------------
3087 void vvMainWindow::NEVerticalSliderChanged()
3088 {
3089   static int value=-1;
3090   if (value == NEVerticalSlider->value()) return;
3091   else value = NEVerticalSlider->value();
3092   //  int value = NEVerticalSlider->value();
3093   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
3094     if (DataTree->topLevelItem(i)->data(COLUMN_UR_VIEW,Qt::CheckStateRole).toInt() > 1) {
3095       if (mSlicerManagers[i]->GetSlicer(1)->GetSlice() != value) {
3096         mSlicerManagers[i]->GetSlicer(1)->SetSlice(value);
3097         mSlicerManagers[i]->VerticalSliderHasChanged(1, value);
3098         mSlicerManagers[i]->UpdateSlice(1);
3099         //mSlicerManagers[i]->GetSlicer(1)->Render(); // <-- DS add this, needed for contour, seems ok ? not too slow ?
3100       }
3101       break;
3102     }
3103   }
3104 }
3105 //------------------------------------------------------------------------------
3106
3107
3108 //------------------------------------------------------------------------------
3109 void vvMainWindow::SOVerticalSliderChanged()
3110 {
3111   static int value=-1;
3112   if (value == SOVerticalSlider->value()) return;
3113   else value = SOVerticalSlider->value();
3114   //int value = SOVerticalSlider->value();
3115   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
3116     if (DataTree->topLevelItem(i)->data(COLUMN_DL_VIEW,Qt::CheckStateRole).toInt() > 1) {
3117       if (mSlicerManagers[i]->GetSlicer(2)->GetSlice() != value) {
3118         mSlicerManagers[i]->GetSlicer(2)->SetSlice(value);
3119         mSlicerManagers[i]->VerticalSliderHasChanged(2, value);
3120         mSlicerManagers[i]->UpdateSlice(2);
3121         //mSlicerManagers[i]->GetSlicer(2)->Render(); // <-- DS add this, needed for contour, seems ok ? not too slow ?
3122       }
3123       // else { DD("avoid SOVerticalSlider slicer update"); }
3124       break;
3125     }
3126   }
3127 }
3128 //------------------------------------------------------------------------------
3129
3130
3131 //------------------------------------------------------------------------------
3132 void vvMainWindow::SEVerticalSliderChanged()
3133 {
3134   static int value=-1;
3135   if (value == SEVerticalSlider->value()) return;
3136   else value = SEVerticalSlider->value();
3137   // int value = SEVerticalSlider->value();
3138   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
3139     if (DataTree->topLevelItem(i)->data(COLUMN_DR_VIEW,Qt::CheckStateRole).toInt() > 1) {
3140       if (mSlicerManagers[i]->GetSlicer(3)->GetSlice() != value) {
3141         mSlicerManagers[i]->GetSlicer(3)->SetSlice(value);
3142         mSlicerManagers[i]->VerticalSliderHasChanged(3, value);
3143         mSlicerManagers[i]->UpdateSlice(3);
3144         //mSlicerManagers[i]->GetSlicer(3)->Render(); // <-- DS add this, needed for contour, seems ok ? not too slow ?
3145       }
3146       break;
3147     }
3148   }
3149 }
3150 //------------------------------------------------------------------------------
3151
3152
3153 //------------------------------------------------------------------------------
3154 void vvMainWindow::UpdateSlice(int slicer, int slice)
3155 {
3156   // DD("vvMainWindow::UpdateSlice");
3157   //   DD(slicer);
3158   //   DD(slice);
3159   if (slicer == 0) {
3160     //    if (slice != NOVerticalSlider->value())
3161     NOVerticalSlider->setValue(slice);
3162   } else {
3163     if (slicer == 1)
3164       NEVerticalSlider->setValue(slice);
3165     else {
3166       if (slicer == 2)
3167         SOVerticalSlider->setValue(slice);
3168       else {
3169         if (slicer == 3)
3170           SEVerticalSlider->setValue(slice);
3171       }
3172     }
3173   }
3174   // DD("vvMainWindow:UpdateSlice END");
3175 }
3176 //------------------------------------------------------------------------------
3177
3178
3179 //------------------------------------------------------------------------------
3180 void vvMainWindow::UpdateTSlice(int slicer, int slice, int code)
3181 {
3182   //FusionSequence: the slider value should be updated for slicers which show the same sequence as requested
3183   bool doUpdate=false;
3184   if (code==-1) doUpdate=true;
3185   else {
3186     for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
3187       if (DataTree->topLevelItem(i)->data(slicer+1,Qt::CheckStateRole).toInt() > 1) {
3188         //i is the active SlicerManager
3189         if (mSlicerManagers[i]->GetFusionSequenceInvolvmentCode()==code) doUpdate=true;
3190         break;
3191       }
3192     }
3193   }
3194   if (!doUpdate) return;
3195
3196   switch (slicer) {
3197   case 0:
3198     if (NOHorizontalSlider->value()==slice) return;
3199     NOHorizontalSlider->setValue(slice);
3200     break;
3201   case 1:
3202     if (NEHorizontalSlider->value()==slice) return;
3203     NEHorizontalSlider->setValue(slice);
3204     break;
3205   case 2:
3206     if (SOHorizontalSlider->value()==slice) return;
3207     SOHorizontalSlider->setValue(slice);
3208     break;
3209   case 3:
3210     if (SEHorizontalSlider->value()==slice) return;
3211     SEHorizontalSlider->setValue(slice);
3212     break;
3213   }
3214 }
3215 //------------------------------------------------------------------------------
3216
3217
3218 //------------------------------------------------------------------------------
3219 void vvMainWindow::UpdateSliceRange(int slicer, int min, int max, int tmin, int tmax)
3220 {
3221   //int position = int((min+max)/2);
3222   int position = mSlicerManagers[mCurrentPickedImageIndex]->GetSlicer(slicer)->GetSlice();
3223   if (slicer == 0) {
3224     NOVerticalSlider->setRange(min,max);
3225     NOHorizontalSlider->setRange(tmin,tmax);
3226     NOVerticalSlider->setValue(position);
3227   } else if (slicer == 1) {
3228     NEVerticalSlider->setRange(min,max);
3229     NEHorizontalSlider->setRange(tmin,tmax);
3230     NEVerticalSlider->setValue(position);
3231   } else if (slicer == 2) {
3232     SOVerticalSlider->setRange(min,max);
3233     SOHorizontalSlider->setRange(tmin,tmax);
3234     SOVerticalSlider->setValue(position);
3235   } else if (slicer == 3) {
3236     SEVerticalSlider->setRange(min,max);
3237     SEHorizontalSlider->setRange(tmin,tmax);
3238     SEVerticalSlider->setValue(position);
3239   }
3240 }
3241 //------------------------------------------------------------------------------
3242
3243
3244 //------------------------------------------------------------------------------
3245 void vvMainWindow::SaveNOScreenshot()
3246 {
3247   SaveScreenshot(NOViewWidget);
3248 }
3249 //------------------------------------------------------------------------------
3250
3251
3252 //------------------------------------------------------------------------------
3253 void vvMainWindow::SaveNEScreenshot()
3254 {
3255   SaveScreenshot(NEViewWidget);
3256 }
3257 //------------------------------------------------------------------------------
3258
3259
3260 //------------------------------------------------------------------------------
3261 void vvMainWindow::SaveSOScreenshot()
3262 {
3263   SaveScreenshot(SOViewWidget);
3264 }
3265 //------------------------------------------------------------------------------
3266
3267
3268 //------------------------------------------------------------------------------
3269 void vvMainWindow::SaveSEScreenshot()
3270 {
3271   SaveScreenshot(SEViewWidget);
3272 }
3273 //------------------------------------------------------------------------------
3274
3275
3276 //------------------------------------------------------------------------------
3277 void vvMainWindow::SaveScreenshotAllSlices()
3278 {
3279   QVTKWidget *widget = NOViewWidget;
3280
3281   int index = 0;// GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
3282   vvSlicerManager * SM = mSlicerManagers[index];
3283   vvImage * image = SM->GetImage();
3284   vvSlicer * slicer = SM->GetSlicer(0);
3285   int orientation = slicer->GetOrientation();
3286   int nbSlices = image->GetSize()[orientation];
3287   vtkSmartPointer<vtkRenderWindow>  renderWindow = widget->GetRenderWindow();
3288
3289   // Select filename base
3290   QString filename = QFileDialog::getSaveFileName(this,
3291     tr("Save As (filename will be completed by slice number)"),
3292     itksys::SystemTools::GetFilenamePath(mSlicerManagers[index]->GetFileName()).c_str(),
3293     "Images( *.png);;Images( *.jpg)");
3294
3295   // Loop on slices
3296   for(int i=0; i<nbSlices; i++) {
3297     // Change the slice
3298     slicer->SetSlice(i); // -> change the slice of the current slicer
3299     SM->UpdateSlice(0); // --> this one emit UpdateSlice
3300     QCoreApplication::flush(); // -> needed to force display of contours
3301
3302     // Screenshot
3303     vtkSmartPointer<vtkWindowToImageFilter> windowToImageFilter = vtkSmartPointer<vtkWindowToImageFilter>::New();
3304     windowToImageFilter->SetInput(renderWindow);
3305     windowToImageFilter->SetMagnification(1);
3306     windowToImageFilter->SetInputBufferTypeToRGBA(); //also record the alpha (transparency) channel
3307     windowToImageFilter->Update();
3308
3309     vtkSmartPointer<vtkPNGWriter> writer = vtkSmartPointer<vtkPNGWriter>::New();
3310     std::string fn = itksys::SystemTools::GetFilenameWithoutLastExtension(filename.toStdString());
3311     std::string num = clitk::toString(i);
3312     if (i<10) num = "0"+num;
3313     if (i<100) num = "0"+num;
3314     if (i<1000) num = "0"+num;
3315
3316     fn = itksys::SystemTools::GetFilenamePath(filename.toStdString()) + "/"+ fn
3317       + "_" + num + itksys::SystemTools::GetFilenameLastExtension(filename.toStdString());
3318     writer->SetFileName(fn.c_str());
3319 #if VTK_MAJOR_VERSION <= 5
3320     writer->SetInput(windowToImageFilter->GetOutput());
3321 #else
3322     writer->SetInputConnection(windowToImageFilter->GetOutputPort());
3323 #endif
3324     writer->Write();
3325   }
3326 }
3327 //------------------------------------------------------------------------------
3328
3329
3330 //------------------------------------------------------------------------------
3331 void vvMainWindow::SaveScreenshot(QVTKWidget *widget)
3332 {
3333   QString Extensions = "Images( *.png);;";
3334   Extensions += "Images( *.jpg);;";
3335   Extensions += "Images( *.bmp);;";
3336   Extensions += "Images( *.tif);;";
3337   Extensions += "Images( *.ppm)";
3338 #if defined(VTK_USE_FFMPEG_ENCODER) || defined(VTK_USE_VIDEO_FOR_WINDOWS)
3339   Extensions += ";;Video( *.avi)";
3340 #endif
3341 #ifdef VTK_USE_MPEG2_ENCODER
3342   Extensions += ";;Video( *.mpg)";
3343 #endif
3344 #ifdef CLITK_EXPERIMENTAL
3345   Extensions += ";;Video( *.gif)";
3346 #endif
3347
3348   int smIndex=GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
3349   QString fileName = QFileDialog::getSaveFileName(this,
3350     tr("Save As"),
3351     itksys::SystemTools::GetFilenamePath(mSlicerManagers[smIndex]->GetFileName()).c_str(),
3352     Extensions);
3353
3354   if (!fileName.isEmpty()) {
3355     vtkSmartPointer<vtkWindowToImageFilter> w2i = vtkSmartPointer<vtkWindowToImageFilter>::New();
3356     w2i->SetInput(widget->GetRenderWindow());
3357     w2i->Update();
3358     vtkImageData *image = w2i->GetOutput();
3359
3360     std::string ext(itksys::SystemTools::GetFilenameLastExtension(fileName.toStdString()));
3361
3362     // Image
3363     vtkImageWriter *imgwriter = NULL;
3364     if (ext==".bmp")
3365       imgwriter = vtkBMPWriter::New();
3366     else if (ext==".tif")
3367       imgwriter = vtkTIFFWriter::New();
3368     else if (ext==".ppm")
3369       imgwriter = vtkPNMWriter::New();
3370     else if (ext==".png")
3371       imgwriter = vtkPNGWriter::New();
3372     else if (ext==".jpg")
3373       imgwriter = vtkJPEGWriter::New();
3374
3375     // Snapshot image if not null
3376     if(imgwriter!=NULL) {
3377 #if VTK_MAJOR_VERSION <= 5
3378       imgwriter->SetInput(image);
3379 #else
3380       imgwriter->SetInputConnection(w2i->GetOutputPort());
3381 #endif
3382       imgwriter->SetFileName(fileName.toStdString().c_str());
3383       imgwriter->Write();
3384       return;
3385     }
3386
3387     // Video
3388     vtkGenericMovieWriter *vidwriter = NULL;
3389 #if CLITK_EXPERIMENTAL == 1
3390     if (ext==".gif") {
3391       vvAnimatedGIFWriter *gif = vvAnimatedGIFWriter::New();
3392       vidwriter = gif;
3393
3394       // FPS
3395       bool ok;
3396       int fps = QInputDialog::getInt(this, tr("Number of frames per second"),
3397         tr("FPS:"), 5, 0, 1000, 1, &ok);
3398       if(ok)
3399         gif->SetRate(fps);
3400
3401       // Loops
3402       int loops = QInputDialog::getInt(this, tr("Loops"),
3403         tr("Number of loops (0 means infinite):"), 0, 0, 1000000000, 1, &ok);
3404       if(ok)
3405         gif->SetLoops(loops);
3406
3407       // Dithering
3408       QString msg = "Would you like to activate dithering?";
3409       QMessageBox msgBox(QMessageBox::Question, tr("Dithering"),msg, 0, this);
3410       msgBox.addButton(tr("Yes"), QMessageBox::AcceptRole);
3411       msgBox.addButton(tr("No"), QMessageBox::RejectRole);
3412       gif->SetDither(msgBox.exec() == QMessageBox::AcceptRole);
3413     }
3414 #endif
3415 #ifdef VTK_USE_VIDEO_FOR_WINDOWS
3416     if (ext==".avi") {
3417       vtkAVIWriter *mpg = vtkAVIWriter::New();
3418       vidwriter = mpg;
3419       mpg->SetQuality(2);
3420       bool ok;
3421       int fps = QInputDialog::getInt(this, tr("Number of frames per second"),
3422         tr("FPS:"), 5, 0, 1024, 1, &ok);
3423       if(!ok)
3424         fps = 5;
3425       mpg->SetRate(fps);
3426     }
3427 #endif
3428 #ifdef VTK_USE_FFMPEG_ENCODER
3429     if (ext==".avi") {
3430       vtkFFMPEGWriter *mpg = vtkFFMPEGWriter::New();
3431       vidwriter = mpg;
3432       mpg->SetQuality(2);
3433       bool ok;
3434       int fps = QInputDialog::getInt(this, tr("Number of frames per second"),
3435         tr("FPS:"), 5, 0, 1024, 1, &ok);
3436       if(!ok)
3437         fps = 5;
3438       mpg->SetRate(fps);
3439       mpg->SetBitRateTolerance(int(ceil(12.0*1024*1024/fps)));
3440     }
3441 #endif
3442 #ifdef VTK_USE_MPEG2_ENCODER
3443     if (ext==".mpg") {
3444       vtkMPEG2Writer *mpg = vtkMPEG2Writer::New();
3445       vidwriter = mpg;
3446     }
3447 #endif
3448
3449     // Take video if not null
3450     if(vidwriter!=NULL){
3451 #if VTK_MAJOR_VERSION <= 5
3452       vidwriter->SetInput(image);
3453 #else
3454       vidwriter->SetInputConnection(w2i->GetOutputPort());
3455 #endif
3456       vidwriter->SetFileName(fileName.toStdString().c_str());
3457       vidwriter->Start();
3458       int nSlice = mSlicerManagers[smIndex]->GetSlicer(0)->GetTMax();
3459       for(int i=0; i<=nSlice; i++) {
3460         mSlicerManagers[smIndex]->SetNextTSlice(0);
3461         vtkSmartPointer<vtkWindowToImageFilter> w2i = vtkSmartPointer<vtkWindowToImageFilter>::New();
3462         w2i->SetInput(widget->GetRenderWindow());
3463         w2i->Update();
3464 #if VTK_MAJOR_VERSION <= 5
3465         vidwriter->SetInput(w2i->GetOutput());
3466 #else
3467         vidwriter->SetInputConnection(w2i->GetOutputPort());
3468 #endif
3469         vidwriter->Write();
3470       }
3471       vidwriter->End();
3472       vidwriter->Delete();
3473       return;
3474     }
3475
3476     QMessageBox::information(this,tr("Problem saving screenshot !"),tr("Cannot save image.\nPlease set a file extension !!!"));
3477   }
3478 }
3479 //------------------------------------------------------------------------------
3480
3481
3482 //------------------------------------------------------------------------------
3483 void vvMainWindow::GoToCursor()
3484 {
3485   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
3486   for (int column = 1; column < 5; column++) {
3487     if (DataTree->selectedItems()[0]->data(column,Qt::CheckStateRole).toInt() > 1) {
3488       double* cursorPos = mSlicerManagers[index]->GetSlicer(column-1)->GetCursorPosition();
3489       mSlicerManagers[index]->GetSlicer(column-1)->SetCurrentPosition(
3490         cursorPos[0],cursorPos[1],cursorPos[2],cursorPos[3]);
3491       mSlicerManagers[index]->UpdateViews(1,column-1);
3492       mSlicerManagers[index]->UpdateLinked(column-1);
3493       break;
3494     }
3495   }
3496 }
3497 //------------------------------------------------------------------------------
3498
3499 //------------------------------------------------------------------------------
3500 void vvMainWindow::GoToLandmark()
3501 {
3502   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
3503   for (int column = 1; column < 5; column++) {
3504     if (DataTree->selectedItems()[0]->data(column,Qt::CheckStateRole).toInt() > 1) {
3505       double* cursorPos = landmarksPanel->GetSelectedPoint();
3506       mSlicerManagers[index]->GetSlicer(column-1)->SetCurrentPosition(
3507         cursorPos[0],cursorPos[1],cursorPos[2],cursorPos[3]);
3508       mSlicerManagers[index]->UpdateViews(1,column-1);
3509       mSlicerManagers[index]->UpdateLinked(column-1);
3510       break;
3511     }
3512   }
3513 }
3514 //------------------------------------------------------------------------------
3515
3516 //------------------------------------------------------------------------------
3517 void vvMainWindow::PlayPause()
3518 {
3519   if (playMode) {
3520     playMode = 0;
3521     playButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/player_play.png")));
3522     ImageInfoChanged();
3523     return;
3524   } else {
3525     int image_number=DataTree->topLevelItemCount();
3526     bool has_temporal;
3527     for (int i=0; i<image_number; i++)
3528       if (mSlicerManagers[i]->GetSlicer(0)->GetTMax() > 0) {
3529         has_temporal=true;
3530         break;
3531       }
3532       if (has_temporal) {
3533         playMode = 1;
3534         playButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/player_pause.png")));
3535         QTimer::singleShot(1000/mFrameRate, this, SLOT(PlayNext()));
3536       }
3537   }
3538 }
3539 //------------------------------------------------------------------------------
3540
3541 //------------------------------------------------------------------------------
3542 void vvMainWindow::PlayNext()
3543 {
3544   if (playMode && !this->isHidden()) {
3545     int image_number=DataTree->topLevelItemCount();
3546     ///Only play one slicer per SM, and only if the SM is being displayed
3547     for (int i=0; i<image_number; i++)
3548       for (int j=0; j<4; j++)
3549         if (mSlicerManagers[i]->GetSlicer(0)->GetTMax() > 0 &&
3550           DataTree->topLevelItem(i)->data(j+1,Qt::CheckStateRole).toInt() > 0) {
3551             mSlicerManagers[i]->SetNextTSlice(j);
3552             break;
3553         }
3554         QTimer::singleShot(1000/mFrameRate, this, SLOT(PlayNext()));
3555   }
3556 }
3557 //------------------------------------------------------------------------------
3558
3559 void vvMainWindow::ShowLastImage()
3560 {
3561   if (mSlicerManagers.size() > 1) {
3562     QTreeWidgetItem * item=DataTree->topLevelItem(DataTree->topLevelItemCount()-1);
3563     CurrentImageChanged(mSlicerManagers.back()->GetId()); //select new image
3564     item->setData(1,Qt::CheckStateRole,2); //show the new image in the first panel
3565     //mSlicerManagers[GetSlicerIndexFromItem(item)]->GetSlicer(0)->SetActorVisibility("image", 0, 1); //Set the Last Image visibles
3566     DisplayChanged(item,1);
3567   }
3568 }
3569
3570 //------------------------------------------------------------------------------
3571 void vvMainWindow::UpdateRenderWindows()
3572 {
3573   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
3574       for (unsigned int j = 0; j < 4; ++j) {
3575         mSlicerManagers[i]->GetSlicer(j)->RemoveLandmarks();
3576         mSlicerManagers[i]->GetSlicer(j)->DisplayLandmarks();
3577       }
3578   }
3579   if (NOViewWidget->GetRenderWindow()) NOViewWidget->GetRenderWindow()->Render();
3580   if (NEViewWidget->GetRenderWindow()) NEViewWidget->GetRenderWindow()->Render();
3581   if (SOViewWidget->GetRenderWindow()) SOViewWidget->GetRenderWindow()->Render();
3582   if (SEViewWidget->GetRenderWindow()) SEViewWidget->GetRenderWindow()->Render();
3583 }
3584 //------------------------------------------------------------------------------
3585
3586 //------------------------------------------------------------------------------
3587 void vvMainWindow::SegmentationOnCurrentImage()
3588 {
3589   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
3590
3591   vvSegmentationDialog segmentation;
3592   segmentation.SetImage(mSlicerManagers[index]->GetSlicer(0)->GetImage());
3593   segmentation.exec();
3594 }
3595 //------------------------------------------------------------------------------
3596
3597 void vvMainWindow::SurfaceViewerLaunch()
3598 {
3599   vvSurfaceViewerDialog surfaceViewer;
3600   surfaceViewer.exec();
3601 }
3602 //------------------------------------------------------------------------------
3603
3604
3605 //------------------------------------------------------------------------------
3606 int vvMainWindow::GetImageDuplicateFilenameNumber(std::string filename)
3607 {
3608   int number=0;
3609   for(unsigned int l=0; l<mSlicerManagers.size(); l++) {
3610     vvSlicerManager * v = mSlicerManagers[l];
3611     if (v->GetBaseFileName() ==
3612       vtksys::SystemTools::GetFilenameName(vtksys::SystemTools::GetFilenameWithoutLastExtension(filename))) {
3613         number = std::max(number, v->GetBaseFileNameNumber()+1);
3614     }
3615   }
3616   return number;
3617 }
3618 //------------------------------------------------------------------------------
3619
3620
3621 //------------------------------------------------------------------------------
3622 vvSlicerManager* vvMainWindow::AddImage(vvImage::Pointer image,std::string filename)
3623 {
3624   // Change filename if another image exist with the same name
3625   int number = GetImageDuplicateFilenameNumber(filename);
3626
3627   // Create new SliceManager
3628   vvSlicerManager* slicer_manager = new vvSlicerManager(4);
3629   slicer_manager->SetImage(image);//, IMAGE, number);
3630   //  filename = filename+"_"+clitk::toString(number);
3631   slicer_manager->SetFilename(filename, number);
3632   mSlicerManagers.push_back(slicer_manager);
3633
3634   //create an item in the tree with good settings
3635   QTreeWidgetItem *item = new QTreeWidgetItem();
3636   item->setData(0,Qt::UserRole,slicer_manager->GetFileName().c_str());//files[i].c_str());
3637   item->setData(1,Qt::UserRole,tr("image"));
3638   item->setData(COLUMN_IMAGE_NAME,Qt::DisplayRole,slicer_manager->GetFileName().c_str());//filename.c_str());
3639   qApp->processEvents();
3640
3641   for (int j = 1; j <= 4; j++) item->setData(j,Qt::CheckStateRole,1);
3642
3643   //Create the buttons for reload and close
3644   qApp->processEvents();
3645   QTreePushButton* cButton = new QTreePushButton;
3646   cButton->setItem(item);
3647   cButton->setColumn(COLUMN_CLOSE_IMAGE);
3648   cButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/exit.png")));
3649   connect(cButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
3650     this,SLOT(CloseImage(QTreeWidgetItem*, int)));
3651
3652   QTreePushButton* rButton = new QTreePushButton;
3653   rButton->setItem(item);
3654   rButton->setColumn(COLUMN_RELOAD_IMAGE);
3655   rButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/rotateright.png")));
3656   rButton->setEnabled(0);
3657   connect(rButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
3658     this,SLOT(ReloadImage(QTreeWidgetItem*, int)));
3659
3660   DataTree->addTopLevelItem(item);
3661   DataTree->setItemWidget(item, COLUMN_CLOSE_IMAGE, cButton);
3662   DataTree->setItemWidget(item, COLUMN_RELOAD_IMAGE, rButton);
3663
3664   //set the id of the image
3665   QString id = QDir::current().absoluteFilePath(slicer_manager->GetFileName().c_str()) + QString::number(mSlicerManagers.size()-1);
3666   item->setData(COLUMN_IMAGE_NAME,Qt::UserRole,id.toStdString().c_str());
3667   mSlicerManagers.back()->SetId(id.toStdString());
3668
3669   linkPanel->addImage(slicer_manager->GetFileName().c_str()// filename
3670     , id.toStdString());
3671
3672   connect(mSlicerManagers.back(), SIGNAL(currentImageChanged(std::string)),
3673     this, SLOT(CurrentImageChanged(std::string)));
3674   connect(mSlicerManagers.back(), SIGNAL(currentPickedImageChanged(std::string)),
3675     this, SLOT(CurrentPickedImageChanged(std::string)));
3676   connect(mSlicerManagers.back(), SIGNAL(UpdatePosition(int, double, double, double, double, double, double, double)),
3677     this, SLOT(MousePositionChanged(int,double, double, double, double, double, double, double)));
3678   connect(mSlicerManagers.back(), SIGNAL(UpdateVector(int, double, double, double, double)),
3679     this, SLOT(VectorChanged(int,double,double,double, double)));
3680   connect(mSlicerManagers.back(), SIGNAL(UpdateOverlay(int, double, double)),
3681     this, SLOT(OverlayChanged(int,double,double)));
3682   connect(mSlicerManagers.back(), SIGNAL(UpdateFusion(int, double)),
3683     this, SLOT(FusionChanged(int,double)));
3684   //connect(mSlicerManagers.back(), SIGNAL(UpdateFusionSequence(int, bool, unsigned int)),
3685   //  this, SLOT(FusionSequenceChanged(int, bool, unsigned int)));
3686   connect(mSlicerManagers.back(), SIGNAL(WindowLevelChanged()),
3687     this,SLOT(WindowLevelChanged()));
3688   connect(mSlicerManagers.back(), SIGNAL(UpdateSlice(int,int)),
3689     this,SLOT(UpdateSlice(int,int)));
3690   connect(mSlicerManagers.back(), SIGNAL(UpdateTSlice(int, int, int)),
3691     this,SLOT(UpdateTSlice(int, int, int)));
3692   connect(mSlicerManagers.back(), SIGNAL(UpdateTSlice(int, int, int)),
3693     this,SLOT(ImageInfoChanged()));
3694   connect(mSlicerManagers.back(), SIGNAL(UpdateSliceRange(int,int,int,int,int)),
3695     this,SLOT(UpdateSliceRange(int,int,int,int,int)));
3696   connect(mSlicerManagers.back(), SIGNAL(UpdateLinkManager(std::string,int,double,double,double,int)),
3697     this,SLOT(UpdateLinkManager(std::string,int,double,double,double,int)));
3698   connect(mSlicerManagers.back(), SIGNAL(UpdateLinkedNavigation(std::string,vvSlicerManager*,vvSlicer*)),
3699     this,SLOT(UpdateLinkedNavigation(std::string,vvSlicerManager*,vvSlicer*)));
3700   connect(mSlicerManagers.back(), SIGNAL(ChangeImageWithIndexOffset(vvSlicerManager*,int,int)),
3701     this,SLOT(ChangeImageWithIndexOffset(vvSlicerManager*,int,int)));
3702   connect(mSlicerManagers.back(), SIGNAL(LandmarkAdded()),landmarksPanel,SLOT(AddPoint()));
3703
3704
3705
3706   InitSlicers();
3707   UpdateTree();
3708   qApp->processEvents();
3709   InitDisplay();
3710   ShowLastImage();
3711   qApp->processEvents();
3712   // End
3713   ImageInfoChanged();
3714   return slicer_manager;
3715 }
3716 //------------------------------------------------------------------------------
3717
3718
3719 //------------------------------------------------------------------------------
3720 void vvMainWindow::UpdateCurrentSlicer()
3721 {
3722   int index = -1;
3723   if (DataTree->selectedItems().size() > 0) {
3724     index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
3725   }
3726   mSlicerManagerCurrentIndex = index;
3727 }
3728 //------------------------------------------------------------------------------