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 <QMimeData>
  22 #include <QInputDialog>
  23 #include <QTimer>
  24 #include "QTreePushButton.h"
  25 #include <QUrl>
  26 #include <QSettings>
  27 #include <QShortcut>
  28
  29 // VV include
  30 #include "vvMainWindow.h"
  31 #include "vvHelpDialog.h"
  32 #include "vvRegisterForm.h"
  33 #include "vvDocumentation.h"
  34 #include "vvProgressDialog.h"
  35 #include "vvQDicomSeriesSelector.h"
  36 #include "vvSlicerManager.h"
  37 #include "clitkImageCommon.h"
  38 #include "vvSlicer.h"
  39 #include "vvInteractorStyleNavigator.h"
  40 #include "vvImageWriter.h"
  41 #include "vvSegmentationDialog.h"
  42 #include "vvSurfaceViewerDialog.h"
  43 #include "vvDeformationDialog.h"
  44 #include "vvImageWarp.h"
  45 #include "vvUtils.h"
  46 #include "vvMidPosition.h"
  47 #include "vvMesh.h"
  48 #include "vvStructSelector.h"
  49 #include "vvMeshReader.h"
  50 #include "vvSaveState.h"
  51 #include "vvReadState.h"
  52 #if CLITK_USE_PACS_CONNECTION
  53 #include "vvQPacsConnection.h"
  54 #endif
  55 #include "clitkConfiguration.h"
  56 #include "clitkMatrix.h"
  57 #ifdef Q_OS_OSX
  58 # include "vvOSXHelper.h"
  59 #endif
  60
  61 // ITK include
  62 #include <itkImage.h>
  63 #include <itkImageFileReader.h>
  64 #include <itkByteSwapper.h>
  65 #include <itkCommand.h>
  66 #include <itkNumericSeriesFileNames.h>
  67
  68 // VTK include
  69 #include <vtkImageMapper3D.h>
  70 #include <vtkInformation.h>
  71 #include <vtkVersion.h>
  72 #include <vtkImageData.h>
  73 #include <vtkImageActor.h>
  74 #include <vtkCornerAnnotation.h>
  75 #include <vtkRenderWindow.h>
  76 #include <vtkRenderWindowInteractor.h>
  77 #include <vtkRenderer.h>
  78 #include <vtkRendererCollection.h>
  79 #include <vtkWindowToImageFilter.h>
  80 #include <vtkBMPWriter.h>
  81 #include <vtkTIFFWriter.h>
  82 #include <vtkPNMWriter.h>
  83 #include <vtkPNGWriter.h>
  84 #include <vtkJPEGWriter.h>
  85 #include <vtkGenericMovieWriter.h>
  86 #include <vvAnimatedGIFWriter.h>
  87 #ifdef VTK_USE_VIDEO_FOR_WINDOWS
  88 #  include <vtkAVIWriter.h>
  89 #endif
  90 #ifdef VTK_USE_FFMPEG_ENCODER
  91 #  include <vtkFFMPEGWriter.h>
  92 #endif
  93 #ifdef VTK_USE_MPEG2_ENCODER
  94 #  include <vtkMPEG2Writer.h>
  95 #endif
  96 #include <vtkMatrix4x4.h>
  97 #include <vtkTransform.h>
  98
  99 // Standard includes
 100 #include <iostream>
 101 #include <fstream>
 102 #include <sstream>
 103 #include <iomanip>
 104
 105 #define COLUMN_TREE 0
 106 #define COLUMN_UL_VIEW 1
 107 #define COLUMN_UR_VIEW 2
 108 #define COLUMN_DL_VIEW 3
 109 #define COLUMN_DR_VIEW 4
 110 #define COLUMN_CLOSE_IMAGE 5
 111 #define COLUMN_RELOAD_IMAGE 6
 112 #define COLUMN_IMAGE_NAME 7
 113
 114 #ifdef CLITK_PRIVATE_FEATURES
 115 #define EXTENSIONS "Images ( *.bmp *.dcm *.png *.jpeg *.jpg *.tif *.mhd *.mha *.hdr *.vox *.his *.xdr *.SCAN *.nii *.nrrd *.nhdr *.refscan *.nii.gz *.usf *.svl)"
 116 #else
 117 #define EXTENSIONS "Images ( *.bmp *.dcm *.png *.jpeg *.jpg *.tif *.mhd *.mha *.hdr *.vox *.his *.xdr *.SCAN *.nii *.nrrd *.nhdr *.refscan *.nii.gz)"
 118 #endif
 119
 120
 121 /*Data Tree values
 122 0,Qt::UserRole full filename
 123 1,Qt::CheckStateRole checkbutton UL View
 124 1,Qt::UserRole overlay, fusion or vector
 125 2,Qt::CheckStateRole checkbutton UR View
 126 3,Qt::CheckStateRole checkbutton DL View
 127 4,Qt::CheckStateRole checkbutton DR View
 128 5,0  short filename
 129 5,Qt::UserRole mSlicerManager id*/
 130
 131 //------------------------------------------------------------------------------
 132 vvMainWindow::vvMainWindow():vvMainWindowBase()
 133 {
 134   setupUi(this); // this sets up the GUI
 135
 136   setAcceptDrops(true); // enable to drop into the window
 137
 138   setDicomClient();
 139
 140   //Qt::WindowFlags flags = windowFlags();
 141   //setWindowFlags(flags | Qt::WindowStaysOnTopHint);
 142
 143   mInputPathName = "";
 144   mMenuTools = menuTools;
 145   //  mMenuSegmentation = menuSegmentation;
 146   mContextMenu = &contextMenu;
 147   mMenuExperimentalTools = menuExperimental;
 148   mMainWidget = this;
 149   mCurrentTime = -1;
 150   mCurrentSelectedImageId = "";
 151   mCurrentPickedImageId = "";
 152   mCurrentPickedImageIndex = 0;
 153
 154   //Init the contextMenu
 155   this->setContextMenuPolicy(Qt::CustomContextMenu);
 156   contextActions.resize(0);
 157   QAction* actionOpen_new_image = contextMenu.addAction(QIcon(QString::fromUtf8(":/common/icons/fileopen.png")),
 158     tr("O&pen new Image"));
 159   connect(actionOpen_new_image,SIGNAL(triggered()),this,SLOT(OpenImages()));
 160   contextActions.push_back(actionOpen_new_image);
 161   contextMenu.addSeparator();
 162
 163   QAction* actionClose_Image = contextMenu.addAction(QIcon(QString::fromUtf8(":/common/icons/exit.png")),
 164     tr("Close Current Image"));
 165   connect(actionClose_Image,SIGNAL(triggered()),this,SLOT(CloseImage()));
 166   contextActions.push_back(actionClose_Image);
 167
 168   QAction* actionReload_image = contextMenu.addAction(QIcon(QString::fromUtf8(":/common/icons/rotateright.png")),
 169     tr("Reload Current Image"));
 170   connect(actionReload_image,SIGNAL(triggered()),this,SLOT(ReloadImage()));
 171   contextActions.push_back(actionReload_image);
 172
 173   QAction* actionSave_image = contextMenu.addAction(QIcon(QString::fromUtf8(":/common/icons/filesave.png")),
 174     tr("Save Current Image"));
 175   connect(actionSave_image,SIGNAL(triggered()),this,SLOT(SaveAs()));
 176   contextActions.push_back(actionSave_image);
 177
 178   QAction* actionSave_state = contextMenu.addAction(QIcon(QString::fromUtf8(":/common/icons/filesave.png")),
 179     tr("Save Current State"));
 180   connect(actionSave_state,SIGNAL(triggered()),this,SLOT(SaveCurrentState()));
 181   contextActions.push_back(actionSave_state);
 182
 183   QAction* actionRead_state = contextMenu.addAction(QIcon(QString::fromUtf8(":/common/icons/filesave.png")),
 184     tr("Read Saved State"));
 185   connect(actionRead_state,SIGNAL(triggered()),this,SLOT(ReadSavedState()));
 186   contextActions.push_back(actionRead_state);
 187
 188   contextMenu.addSeparator();
 189
 190   contextMenu.addAction(actionAdd_VF_to_current_Image);
 191   contextActions.push_back(actionAdd_VF_to_current_Image);
 192
 193   //QAction* actionAdd_Overlay_to_current_Image = menuOverlay->addAction(QIcon(QString::fromUtf8(":/common/icons/GPSup.png")),
 194   //    tr("Add overlay image to current image"));
 195   contextMenu.addAction(actionAdd_overlay_image_to_current_image);
 196   contextActions.push_back(actionAdd_overlay_image_to_current_image);
 197
 198   contextMenu.addAction(actionAdd_fusion_image);
 199   contextActions.push_back(actionAdd_fusion_image);
 200
 201 #ifdef CLITK_EXPERIMENTAL
 202   contextMenu.addAction(actionAdd_USSequence_toCT);
 203   contextActions.push_back(actionAdd_USSequence_toCT);
 204 #endif
 205
 206
 207   contextMenu.addSeparator();
 208   QAction* actionResetMatrix = contextMenu.addAction(QIcon(QString::fromUtf8(":/common/icons/identity.png")),
 209     tr("Reset transformation to identity"));
 210   connect(actionResetMatrix, SIGNAL(triggered()), this,SLOT(ResetTransformationToIdentity()));
 211
 212   //init the DataTree
 213   mSlicerManagers.resize(0);
 214
 215   QStringList header;
 216   header.append("");
 217   header.append("TL");
 218   header.append("TR");
 219   header.append("BL");
 220   header.append("BR");
 221   header.append("");
 222   header.append("");
 223   header.append("Name");
 224
 225   DataTree->setHeaderLabels(header);
 226   DataTree->resizeColumnToContents(COLUMN_TREE);
 227   DataTree->resizeColumnToContents(COLUMN_UL_VIEW);
 228   DataTree->resizeColumnToContents(COLUMN_UR_VIEW);
 229   DataTree->resizeColumnToContents(COLUMN_DL_VIEW);
 230   DataTree->resizeColumnToContents(COLUMN_DR_VIEW);
 231   DataTree->resizeColumnToContents(COLUMN_CLOSE_IMAGE);
 232   DataTree->resizeColumnToContents(COLUMN_RELOAD_IMAGE);
 233   DataTree->resizeColumnToContents(COLUMN_IMAGE_NAME);
 234
 235   viewMode = 1;
 236   documentation = new vvDocumentation();
 237   help_dialog = new vvHelpDialog();
 238   dicomSeriesSelector = new vvDicomSeriesSelector();
 239 #if CLITK_USE_PACS_CONNECTION
 240      PacsConnection = new vvQPacsConnection();
 241 #endif
 242
 243   inverseButton->setEnabled(0);
 244   actionAdd_overlay_image_to_current_image->setEnabled(0);
 245   actionSave_As->setEnabled(0);
 246   actionAdd_VF_to_current_Image->setEnabled(0);
 247   actionAdd_fusion_image->setEnabled(0);
 248   actionAdd_USSequence_toCT->setEnabled(0);
 249
 250   //init the sliders
 251   verticalSliders.push_back(NOVerticalSlider);
 252   verticalSliders.push_back(NEVerticalSlider);
 253   verticalSliders.push_back(SOVerticalSlider);
 254   verticalSliders.push_back(SEVerticalSlider);
 255
 256   for (int i =0; i < 4; i++)
 257     verticalSliders[i]->hide();
 258
 259   horizontalSliders.push_back(NOHorizontalSlider);
 260   horizontalSliders.push_back(NEHorizontalSlider);
 261   horizontalSliders.push_back(SOHorizontalSlider);
 262   horizontalSliders.push_back(SEHorizontalSlider);
 263
 264   for (int i =0; i < 4; i++)
 265     horizontalSliders[i]->hide();
 266
 267
 268   connect(NOVerticalSlider,SIGNAL(valueChanged(int)),this,SLOT(NOVerticalSliderChanged()));
 269   connect(NEVerticalSlider,SIGNAL(valueChanged(int)),this,SLOT(NEVerticalSliderChanged()));
 270   connect(SOVerticalSlider,SIGNAL(valueChanged(int)),this,SLOT(SOVerticalSliderChanged()));
 271   connect(SEVerticalSlider,SIGNAL(valueChanged(int)),this,SLOT(SEVerticalSliderChanged()));
 272
 273   connect(NOHorizontalSlider,SIGNAL(valueChanged(int)),this,SLOT(NOHorizontalSliderMoved()));
 274   connect(NEHorizontalSlider,SIGNAL(valueChanged(int)),this,SLOT(NEHorizontalSliderMoved()));
 275   connect(SOHorizontalSlider,SIGNAL(valueChanged(int)),this,SLOT(SOHorizontalSliderMoved()));
 276   connect(SEHorizontalSlider,SIGNAL(valueChanged(int)),this,SLOT(SEHorizontalSliderMoved()));
 277
 278   //connect everything
 279   connect(actionCompute_mid_position_image,SIGNAL(triggered()),this,SLOT(ComputeMidPosition()));
 280   connect(actionDeformable_Registration,SIGNAL(triggered()),this,SLOT(ComputeDeformableRegistration()));
 281   connect(actionWarp_image_with_vector_field,SIGNAL(triggered()),this,SLOT(WarpImage()));
 282   connect(actionLoad_images,SIGNAL(triggered()),this,SLOT(OpenImages()));
 283   connect(actionOpen_Dicom,SIGNAL(triggered()),this,SLOT(OpenDicom()));
 284 #if CLITK_USE_PACS_CONNECTION
 285   connect(actionConnect_Pacs,SIGNAL(triggered()),this,SLOT(ConnectPacs()));
 286 #endif
 287   //  connect(actionOpen_Dicom_Struct,SIGNAL(triggered()),this,SLOT(OpenDCStructContour()));
 288   connect(actionOpen_VTK_contour,SIGNAL(triggered()),this,SLOT(OpenVTKContour()));
 289   connect(actionOpen_Multiple_Images_As_One,SIGNAL(triggered()),this,SLOT(MergeImages()));
 290   connect(actionSlice_Image_As_Multiple_Images,SIGNAL(triggered()),this,SLOT(SliceImages()));
 291   connect(actionOpen_Image_With_Time,SIGNAL(triggered()),this,SLOT(OpenImageWithTime()));
 292   connect(actionMerge_images_as_n_dim_t, SIGNAL(triggered()), this, SLOT(MergeImagesWithTime()));
 293   connect(actionSave_As,SIGNAL(triggered()),this,SLOT(SaveAs()));
 294   connect(actionSave_current_state,SIGNAL(triggered()),this,SLOT(SaveCurrentState()));
 295   connect(actionRead_saved_state,SIGNAL(triggered()),this,SLOT(ReadSavedState()));
 296   connect(actionExit,SIGNAL(triggered()),this,SLOT(close()));
 297   connect(actionAdd_VF_to_current_Image,SIGNAL(triggered()),this,SLOT(OpenField()));
 298   connect(actionAdd_fusion_image,SIGNAL(triggered()),this,SLOT(SelectFusionImage()));
 299   connect(actionAdd_overlay_image_to_current_image,SIGNAL(triggered()), this,SLOT(SelectOverlayImage()));
 300   connect(actionAdd_USSequence_toCT,SIGNAL(triggered()), this,SLOT(SelectFusionSequence()));
 301   connect(actionNavigation_Help,SIGNAL(triggered()),this,SLOT(ShowHelpDialog()));
 302
 303   QShortcut *shortcutHelp = new QShortcut(QKeySequence(QKeySequence::HelpContents),this);
 304   shortcutHelp->setContext(Qt::ApplicationShortcut);
 305   QObject::connect(shortcutHelp, SIGNAL(activated()), this, SLOT(ShowHelpDialog()));
 306
 307   connect(actionDocumentation,SIGNAL(triggered()),this,SLOT(ShowDocumentation()));
 308   connect(actionRegister_vv,SIGNAL(triggered()),this,SLOT(PopupRegisterForm()));
 309
 310   connect(overlayPanel, SIGNAL(FusionSequenceCorrespondancesButtonPressed()), this, SLOT(SelectFusionSequenceCorrespondances()));
 311
 312
 313   ///////////////////////////////////////////////
 314   connect(actionSegmentation,SIGNAL(triggered()),this,SLOT(SegmentationOnCurrentImage()));
 315   connect(actionSurface_Viewer,SIGNAL(triggered()),this,SLOT(SurfaceViewerLaunch()));
 316   ///////////////////////////////////////////////
 317
 318   actionNorth_East_Window->setEnabled(0);
 319   actionNorth_West_Window->setEnabled(0);
 320   actionSouth_East_Window->setEnabled(0);
 321   actionSouth_West_Window->setEnabled(0);
 322
 323   connect(actionNorth_East_Window,SIGNAL(triggered()),this,SLOT(SaveNEScreenshot()));
 324   connect(actionNorth_West_Window,SIGNAL(triggered()),this,SLOT(SaveNOScreenshot()));
 325   connect(actionSouth_East_Window,SIGNAL(triggered()),this,SLOT(SaveSEScreenshot()));
 326   connect(actionSouth_West_Window,SIGNAL(triggered()),this,SLOT(SaveSOScreenshot()));
 327   connect(actionSave_all_slices,SIGNAL(triggered()),this,SLOT(SaveScreenshotAllSlices()));
 328
 329   connect(DataTree,SIGNAL(itemSelectionChanged()),this,SLOT(ImageInfoChanged()));
 330   connect(DataTree,SIGNAL(itemClicked(QTreeWidgetItem*, int)),this,
 331     SLOT(DisplayChanged(QTreeWidgetItem*, int)));
 332
 333   connect(viewButton,SIGNAL(clicked()),this, SLOT(ChangeViewMode()) );
 334   connect(windowSpinBox,SIGNAL(editingFinished()),this,SLOT(WindowLevelEdited()));
 335   connect(levelSpinBox,SIGNAL(editingFinished()),this,SLOT(WindowLevelEdited()));
 336   connect(colorMapComboBox,SIGNAL(currentIndexChanged(int)),this,SLOT(UpdateColorMap()));
 337   connect(presetComboBox,SIGNAL(currentIndexChanged(int)),this,SLOT(UpdateWindowLevel()));
 338   connect(slicingPresetComboBox, SIGNAL(currentIndexChanged(int)),this,SLOT(UpdateSlicingPreset()));
 339   connect(inverseButton,SIGNAL(clicked()),this,SLOT(SwitchWindowLevel()));
 340   connect(applyWindowLevelToAllButton,SIGNAL(clicked()),this,SLOT(ApplyWindowLevelToAllImages()));
 341
 342   connect(this,SIGNAL(customContextMenuRequested(QPoint)),this,SLOT(ShowContextMenu(QPoint)));
 343
 344   connect(linkPanel,SIGNAL(addLink(QString,QString,bool)),this,SLOT(AddLink(QString,QString,bool)));
 345   connect(linkPanel,SIGNAL(removeLink(QString,QString)),this,SLOT(RemoveLink(QString,QString)));
 346   connect(overlayPanel,SIGNAL(VFPropertyUpdated(int,int,int,int,double,double,double)),this,SLOT(SetVFProperty(int,int,int,int,double,double,double)));
 347   connect(overlayPanel,SIGNAL(OverlayPropertyUpdated(int,int,double,double)),
 348     this,SLOT(SetOverlayProperty(int,int,double,double)));
 349   connect(overlayPanel,SIGNAL(FusionPropertyUpdated(int,int,int,double,double, bool)),
 350     this,SLOT(SetFusionProperty(int,int,int,double,double, bool)));
 351   connect(landmarksPanel,SIGNAL(UpdateRenderWindows()),this,SLOT(UpdateRenderWindows()));
 352   connect(landmarksPanel,SIGNAL(SelectedPointChanged()),this,SLOT(GoToLandmark()));
 353
 354   connect(overlayPanel,SIGNAL(FusionSequencePropertyUpdated(int, bool, unsigned int, bool)),
 355     this,SLOT(SetFusionSequenceProperty(int, bool,unsigned int, bool)));
 356
 357
 358   playMode = 0;//pause
 359   mFrameRate = 10;
 360   playButton->setEnabled(0);
 361   frameRateLabel->setEnabled(0);
 362   frameRateSpinBox->setEnabled(0);
 363   connect(playButton, SIGNAL(clicked()),this,SLOT(PlayPause()));
 364   connect(frameRateSpinBox, SIGNAL(valueChanged(int)),this,SLOT(ChangeFrameRate(int)));
 365
 366   goToCursorPushButton->setEnabled(0);
 367   connect(goToCursorPushButton, SIGNAL(clicked()),this,SLOT(GoToCursor()));
 368
 369   NOViewWidget->hide();
 370   NEViewWidget->hide();
 371   SOViewWidget->hide();
 372   SEViewWidget->hide();
 373
 374 #ifdef Q_OS_OSX
 375   disableGLHiDPI(NOViewWidget->winId());
 376   disableGLHiDPI(NEViewWidget->winId());
 377   disableGLHiDPI(SOViewWidget->winId());
 378   disableGLHiDPI(SEViewWidget->winId());
 379 #endif
 380
 381   //Recently opened files
 382   std::list<std::string> recent_files = GetRecentlyOpenedImages();
 383   recentlyOpenedFilesMenu=NULL;
 384   if ( !recent_files.empty() ) {
 385     createRecentlyOpenedFilesMenu();
 386     updateRecentlyOpenedFilesMenu(recent_files);
 387   }
 388
 389   //Update and get vv parameters
 390   setVVSettings();
 391
 392   // Adding all new tools (insertion in the menu)
 393   vvToolManager::GetInstance()->InsertToolsInMenu(this);
 394   vvToolManager::GetInstance()->EnableToolsInMenu(this, false);
 395
 396 //#ifndef CLITK_EXPERIMENTAL
 397 //#define CLITK_EXPERIMENTAL 0
 398 //#endif
 399 #ifdef CLITK_EXPERIMENTAL
 400   if (!CLITK_EXPERIMENTAL)
 401     menuExperimental->menuAction()->setVisible(false);
 402 #endif
 403
 404 #if !CLITK_USE_PACS_CONNECTION
 405     actionConnect_Pacs->setVisible(false);
 406 #endif
 407
 408   QTimer * timerMemory = new QTimer(this);
 409   //timerMemory->setInterval(5);
 410   connect(timerMemory, SIGNAL(timeout()), this, SLOT(UpdateMemoryUsage()));
 411   timerMemory->start(2000);
 412 }
 413
 414 //------------------------------------------------------------------------------
 415 void vvMainWindow::show()
 416 {
 417   vvMainWindowBase::show();
 418   PopupRegisterForm(true);
 419 }
 420 //------------------------------------------------------------------------------
 421 void vvMainWindow::UpdateMemoryUsage()
 422 {
 423   //  clitk::PrintMemory(true);
 424   if (clitk::GetMemoryUsageInMb() == 0) infoPanel->setMemoryInMb("NA");
 425   else infoPanel->setMemoryInMb(QString::number(clitk::GetMemoryUsageInMb())+" MB");
 426 }
 427 //------------------------------------------------------------------------------
 428
 429
 430 //------------------------------------------------------------------------------
 431 void vvMainWindow::createRecentlyOpenedFilesMenu()
 432 {
 433   recentlyOpenedFilesMenu = new QMenu("Recently opened files...");
 434   recentlyOpenedFilesMenu->setIcon(QIcon(QString::fromUtf8(":/common/icons/open.png")));
 435   menuFile->insertMenu(actionOpen_Image_With_Time,recentlyOpenedFilesMenu);
 436   menuFile->insertSeparator(actionOpen_Image_With_Time);
 437 }
 438 //------------------------------------------------------------------------------
 439
 440
 441 //------------------------------------------------------------------------------
 442
 443 void vvMainWindow::updateRecentlyOpenedFilesMenu(const std::list<std::string> &recent_files)
 444 {
 445   if(recentlyOpenedFilesMenu==NULL) {
 446     createRecentlyOpenedFilesMenu();
 447   } else {
 448     recentlyOpenedFilesMenu->clear();
 449   }
 450   for (std::list<std::string>::const_iterator i = recent_files.begin(); i!=recent_files.end(); i++) {
 451     QAction* current=new QAction(QIcon(QString::fromUtf8(":/common/icons/open.png")), i->c_str(),this);
 452     recentlyOpenedFilesMenu->addAction(current);
 453     connect(current,SIGNAL(triggered()),this,SLOT(OpenRecentImage()));
 454   }
 455 }
 456 //------------------------------------------------------------------------------
 457
 458
 459 //------------------------------------------------------------------------------
 460 void vvMainWindow::ComputeMidPosition()
 461 {
 462   bool ok;
 463   int index=GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
 464   int ref = QInputDialog::getInt(this,"Chose reference phase","Reference phase",0,0,\
 465 mSlicerManagers[index]->GetImage()->GetVTKImages().size()-1,1,&ok);
 466   if (ok) {
 467     vvMidPosition midp;
 468     midp.slicer_manager = mSlicerManagers[index];
 469     midp.reference_image_index = ref;
 470     QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
 471     midp.Update();
 472     if (midp.error)
 473       QMessageBox::warning(this, "Error computing midposition image",midp.error_message.c_str());
 474     else {
 475       QFileInfo info(midp.slicer_manager->GetFileName().c_str());
 476       AddImage(midp.output,info.path().toStdString()+"/"+info.completeBaseName().toStdString()+"_midposition.mhd");
 477     }
 478     QApplication::restoreOverrideCursor();
 479   }
 480 }
 481 //------------------------------------------------------------------------------
 482
 483
 484 //------------------------------------------------------------------------------
 485 void vvMainWindow::AddContour(int image_index, vvMesh::Pointer contour, bool propagation)
 486 {
 487   QTreeWidgetItem *item = new QTreeWidgetItem();
 488   item->setData(0,Qt::UserRole,"filename.vtk");
 489   item->setData(1,Qt::UserRole,tr("contour"));
 490   QBrush brush;
 491   brush.setColor(QColor(contour->r*255,contour->g*255,contour->b*255));
 492   brush.setStyle(Qt::SolidPattern);
 493   item->setData(COLUMN_IMAGE_NAME,Qt::BackgroundRole,brush);
 494   item->setData(COLUMN_IMAGE_NAME,Qt::DisplayRole,contour->structure_name.c_str());
 495
 496   for (int j = 1; j <= 4; j++)
 497     item->setData(j,Qt::CheckStateRole,DataTree->topLevelItem(image_index)->data(j,Qt::CheckStateRole));
 498
 499   QTreePushButton* cButton = new QTreePushButton;
 500   cButton->setItem(item);
 501   cButton->setColumn(COLUMN_CLOSE_IMAGE);
 502   cButton->setToolTip(tr("close image"));
 503   cButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/exit.png")));
 504   connect(cButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
 505     this,SLOT(CloseImage(QTreeWidgetItem*, int)));
 506
 507   QTreePushButton* rButton = new QTreePushButton;
 508   rButton->setItem(item);
 509   rButton->setColumn(COLUMN_RELOAD_IMAGE);
 510   rButton->setToolTip(tr("reload image"));
 511   rButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/rotateright.png")));
 512   rButton->setEnabled(false);
 513   //Not implemented
 514   //connect(rButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
 515   //this,SLOT(ReloadImage(QTreeWidgetItem*, int)));
 516
 517   DataTree->topLevelItem(image_index)->setExpanded(1);
 518   DataTree->topLevelItem(image_index)->addChild(item);
 519   DataTree->setItemWidget(item, COLUMN_CLOSE_IMAGE, cButton);
 520   DataTree->setItemWidget(item, COLUMN_RELOAD_IMAGE, rButton);
 521   QString id = DataTree->topLevelItem(image_index)->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString();
 522   item->setData(COLUMN_IMAGE_NAME,Qt::UserRole,id.toStdString().c_str());
 523
 524   UpdateTree();
 525   mSlicerManagers[image_index]->AddContour(contour,propagation);
 526   mSlicerManagers[image_index]->Render();
 527 }
 528 //------------------------------------------------------------------------------
 529
 530
 531 //------------------------------------------------------------------------------
 532 void vvMainWindow::OpenVTKContour()
 533 {
 534   if (mSlicerManagers.size() > 0) {
 535     QString Extensions = "Images ( *.vtk *.obj)";
 536     Extensions += ";;All Files (*)";
 537     QString file = QFileDialog::getOpenFileName(this,tr("Open vtkPolyData"),mInputPathName,Extensions);
 538     if (file.isNull())
 539       return;
 540     QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
 541     int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
 542     vvMeshReader reader;
 543     reader.SetImage(mSlicerManagers[index]->GetImage());
 544     reader.SetModeToVTK();
 545     reader.SetFilename(file.toStdString());
 546     reader.Update();
 547     AddContour(index,reader.GetOutput()[0],false);
 548     QApplication::restoreOverrideCursor();
 549   }
 550 }
 551 //------------------------------------------------------------------------------
 552
 553
 554 //------------------------------------------------------------------------------
 555 void vvMainWindow::AddDCStructContour(int index, QString file)
 556 {
 557   vvMeshReader reader;
 558   reader.SetFilename(file.toStdString());
 559   vvStructSelector selector;
 560   selector.SetStructures(reader.GetROINames());
 561   if (!mSlicerManagers[index]->GetVF().IsNull())
 562     selector.EnablePropagationCheckBox();
 563   if (selector.exec()) {
 564     QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
 565     reader.SetSelectedItems(selector.getSelectedItems());
 566     reader.SetImage(mSlicerManagers[index]->GetImage());
 567     if (selector.PropagationEnabled())
 568       reader.SetPropagationVF(mSlicerManagers[index]->GetVF());
 569     reader.Update();
 570     std::vector<vvMesh::Pointer> contours=reader.GetOutput();
 571     for (std::vector<vvMesh::Pointer>::iterator i=contours.begin();
 572       i!=contours.end(); i++)
 573       AddContour(index,*i,selector.PropagationEnabled());
 574     QApplication::restoreOverrideCursor();
 575   }
 576 }
 577
 578 //------------------------------------------------------------------------------
 579 void vvMainWindow::OpenDCStructContour()
 580 {
 581   if (mSlicerManagers.size() > 0) {
 582     QString Extensions = "Dicom Files ( *.dcm RS*)";
 583     Extensions += ";;All Files (*)";
 584     QString file = QFileDialog::getOpenFileName(this,tr("Merge Images"),mInputPathName,Extensions);
 585     if (file.isNull())
 586       return;
 587     int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
 588     AddDCStructContour(index, file);
 589   }
 590 }
 591 //------------------------------------------------------------------------------
 592
 593
 594 //------------------------------------------------------------------------------
 595 void vvMainWindow::ComputeDeformableRegistration()
 596 {
 597   if (mSlicerManagers.size() > 0) {
 598     int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
 599     vvDeformationDialog dialog(index,mSlicerManagers);
 600     if (dialog.exec()) {
 601       std::string base_name=itksys::SystemTools::GetFilenameWithoutExtension(mSlicerManagers[dialog.GetInputFileIndex()]->GetFileName());
 602       AddField(dialog.GetOutput(),dialog.getFieldFile(),dialog.GetInputFileIndex());
 603       WarpImage(dialog.GetSelectedSlicer(),dialog.GetReferenceFrameIndex());
 604     } else
 605       std::cout << "Error or user cancellation while computing deformation field..." << std::endl;
 606   } else QMessageBox::information(this, "Need to open image","You must open an image first.");
 607 }
 608 //------------------------------------------------------------------------------
 609
 610
 611 //------------------------------------------------------------------------------
 612 void vvMainWindow::WarpImage()
 613 {
 614   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
 615   if (!mSlicerManagers[index]->GetVF().IsNull()) {
 616     bool ok;
 617     int ref = QInputDialog::getInt(this,"Chose reference phase","Reference phase",0,0,\
 618       mSlicerManagers[index]->GetImage()->GetVTKImages().size()-1,1,&ok);
 619     if (ok) {
 620       WarpImage(mSlicerManagers[index],ref);
 621     }
 622   } else
 623     QMessageBox::warning(this,tr("No vector field"),tr("Sorry, can't warp without a vector field"));
 624 }
 625 //------------------------------------------------------------------------------
 626
 627
 628 //------------------------------------------------------------------------------
 629 void vvMainWindow::WarpImage(vvSlicerManager* selected_slicer,int reference_phase)
 630 {
 631   if (!selected_slicer->GetVF().IsNull()) {
 632     QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
 633     QFileInfo info(selected_slicer->GetFileName().c_str());
 634     vvImageWarp warp(selected_slicer->GetImage(),selected_slicer->GetVF(),
 635       reference_phase,this);
 636     if (warp.ComputeWarpedImage()) {
 637       AddImage(warp.GetWarpedImage(),info.path().toStdString()+"/"+info.completeBaseName().toStdString()+"_warped.mhd");
 638       AddImage(warp.GetDiffImage()  ,info.path().toStdString()+"/"+info.completeBaseName().toStdString()+"_diff.mhd");
 639       AddImage(warp.GetJacobianImage()  ,info.path().toStdString()+"/"+info.completeBaseName().toStdString()+"_jacobian.mhd");
 640       QApplication::restoreOverrideCursor();
 641     } else {
 642       QApplication::restoreOverrideCursor();
 643       QMessageBox::warning(this,tr("Different spacings"),tr("The vector field and image spacings must be the same in order to warp."));
 644     }
 645   } else
 646     QMessageBox::warning(this,tr("No vector field"),tr("Sorry, can't warp without a vector field."));
 647 }
 648 //------------------------------------------------------------------------------
 649
 650
 651 //------------------------------------------------------------------------------
 652 vvMainWindow::~vvMainWindow()
 653 {
 654   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
 655     if (mSlicerManagers[i] != NULL)
 656       delete mSlicerManagers[i];
 657   }
 658   delete documentation;
 659   delete help_dialog;
 660   delete dicomSeriesSelector;
 661 }
 662 //------------------------------------------------------------------------------
 663
 664 //------------------------------------------------------------------------------
 665 QTabWidget * vvMainWindow::GetTab()
 666 {
 667   return tabWidget;
 668 }
 669 //------------------------------------------------------------------------------
 670
 671
 672 //------------------------------------------------------------------------------
 673 void vvMainWindow::MergeImages()
 674 {
 675   QString Extensions = EXTENSIONS;
 676   Extensions += ";;All Files (*)";
 677   QStringList files = QFileDialog::getOpenFileNames(this,tr("Merge Images"),mInputPathName,Extensions);
 678   if (files.isEmpty())
 679     return;
 680   mInputPathName = itksys::SystemTools::GetFilenamePath(files[0].toStdString()).c_str();
 681   std::vector<std::string> vector;
 682
 683   unsigned int currentDim = 0;
 684   std::vector<double> currentSpacing;
 685   std::vector<int> currentSize;
 686   std::vector<double> currentOrigin;
 687
 688   for (int i = 0; i < files.size(); i++) {
 689     itk::ImageIOBase::Pointer reader = itk::ImageIOFactory::CreateImageIO(
 690       files[i].toStdString().c_str(), itk::ImageIOFactory::ReadMode);
 691     reader->SetFileName(files[i].toStdString().c_str());
 692     reader->ReadImageInformation();
 693     if (reader)        {
 694       //NOViewWidget->hide();
 695       //NEViewWidget->hide();
 696       //SOViewWidget->hide();
 697       //SEViewWidget->hide();
 698       if (i == 0)
 699         currentDim = reader->GetNumberOfDimensions();
 700       bool IsOk = true;
 701       for (unsigned int j = 0; j < currentDim; j++) {
 702         if (i == 0) {
 703           if (j == 0) {
 704             currentSpacing.resize(currentDim);
 705             currentSize.resize(currentDim);
 706             currentOrigin.resize(currentDim);
 707           }
 708           currentOrigin[j] = reader->GetOrigin(j);
 709           currentSpacing[j] = reader->GetSpacing(j);
 710           currentSize[j] = reader->GetDimensions(j);
 711         } else if (currentDim != reader->GetNumberOfDimensions()
 712           || currentSpacing[j] != reader->GetSpacing(j)
 713           || currentSize[j] != (int)reader->GetDimensions(j)
 714           || currentOrigin[j] != reader->GetOrigin(j)) {
 715             QString error = "Cannot read file (too different from others ";
 716             error += files[i].toStdString().c_str();
 717             QMessageBox::information(this,tr("Reading problem"),error);
 718             IsOk = false;
 719             break;
 720         }
 721       }
 722       if (IsOk)
 723         vector.push_back(files[i].toStdString());
 724     }
 725   }
 726   if (vector.size() > 0)
 727     LoadImages(vector, vvImageReader::MERGED);
 728 }
 729 //------------------------------------------------------------------------------
 730
 731 //------------------------------------------------------------------------------
 732 void vvMainWindow::SliceImages()
 733 {
 734   QString Extensions = EXTENSIONS;
 735   Extensions += ";;All Files (*)";
 736
 737   QStringList files = QFileDialog::getOpenFileNames(this,tr("Slice Images"),mInputPathName,Extensions);
 738   if (files.isEmpty())
 739     return;
 740   mInputPathName = itksys::SystemTools::GetFilenamePath(files[0].toStdString()).c_str();
 741   std::vector<std::string> vector;
 742   for (int i = 0; i < files.size(); i++)
 743     vector.push_back(files[i].toStdString());
 744   LoadImages(vector, vvImageReader::SLICED);
 745 }
 746 //------------------------------------------------------------------------------
 747
 748 //------------------------------------------------------------------------------
 749 void vvMainWindow::MergeImagesWithTime()
 750 {
 751   QString Extensions = EXTENSIONS;
 752   Extensions += ";;All Files (*)";
 753   QStringList files = QFileDialog::getOpenFileNames(this,tr("Merge Images With Time"),mInputPathName,Extensions);
 754   if (files.isEmpty())
 755     return;
 756   mInputPathName = itksys::SystemTools::GetFilenamePath(files[0].toStdString()).c_str();
 757   std::vector<std::string> vector;
 758
 759   for (int i = 0; i < files.size(); i++)
 760     vector.push_back(files[i].toStdString());
 761   sort(vector.begin(),vector.end());
 762   if (vector.size() > 1)
 763     LoadImages(vector, vvImageReader::MERGEDWITHTIME);
 764   else
 765     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.");
 766 }
 767 //------------------------------------------------------------------------------
 768
 769
 770 //------------------------------------------------------------------------------
 771 void vvMainWindow::OpenDicom()
 772 {
 773   std::vector<std::string> files;
 774
 775   //std::cout << "dicomSeriesSelector " << std::endl;
 776   if (dicomSeriesSelector->exec() == QDialog::Accepted) {
 777     files = *(dicomSeriesSelector->GetFilenames());
 778     LoadImages(files, vvImageReader::DICOM);
 779   }
 780 }
 781 #if CLITK_USE_PACS_CONNECTION
 782 void vvMainWindow::ConnectPacs()
 783 {
 784   std::vector<std::string> files;
 785
 786   //std::cout << "dicomSeriesSelector " << std::endl;
 787 if (PacsConnection->exec() == QDialog::Accepted) {
 788         for (int i = 0; i < PacsConnection->getSeriesCount(); i++)
 789         {
 790                 files = PacsConnection->getFileNames(i);
 791                 LoadImages(files, vvImageReader::DICOM);
 792         }
 793         PacsConnection->clearMove();
 794   }
 795   }
 796
 797 #endif
 798 //------------------------------------------------------------------------------
 799
 800 //------------------------------------------------------------------------------
 801 void vvMainWindow::OpenImages()
 802 {
 803   QString Extensions = EXTENSIONS;
 804   Extensions += ";;All Files (*)";
 805
 806   QStringList files = QFileDialog::getOpenFileNames(this,tr("Load Images"),mInputPathName,Extensions);
 807   if (files.isEmpty())
 808     return;
 809   mInputPathName = itksys::SystemTools::GetFilenamePath(files[0].toStdString()).c_str();
 810   std::vector<std::string> vector;
 811   for (int i = 0; i < files.size(); i++)
 812     vector.push_back(files[i].toStdString());
 813   LoadImages(vector, vvImageReader::IMAGE);
 814 }
 815 //------------------------------------------------------------------------------
 816 void vvMainWindow::OpenRecentImage()
 817 {
 818   QAction * caller = qobject_cast<QAction*>(sender());
 819   std::vector<std::string> images;
 820   images.push_back(caller->text().toStdString());
 821   mInputPathName = itksys::SystemTools::GetFilenamePath(images[0]).c_str();
 822   LoadImages(images, vvImageReader::IMAGE);
 823 }
 824 //------------------------------------------------------------------------------
 825 void vvMainWindow::dragEnterEvent(QDragEnterEvent *event)
 826 {
 827   if (event->mimeData()->hasUrls()) {
 828     event->acceptProposedAction();
 829   }
 830 }
 831 //------------------------------------------------------------------------------
 832 void vvMainWindow::dropEvent(QDropEvent *event)
 833 {
 834   const QMimeData * mimeData = event->mimeData();
 835   if (!mimeData->hasUrls())
 836     return;
 837   std::vector<std::string> images;
 838   for (int i=0; i<mimeData->urls().size(); ++i) {
 839     images.push_back(mimeData->urls()[i].toLocalFile().toStdString());
 840   }
 841   LoadImages(images, vvImageReader::IMAGE);
 842 }
 843 //------------------------------------------------------------------------------
 844
 845
 846 //------------------------------------------------------------------------------
 847 void vvMainWindow::OpenImageWithTime()
 848 {
 849   QString Extensions = EXTENSIONS;
 850   Extensions += ";;All Files (*)";
 851
 852   QStringList files = QFileDialog::getOpenFileNames(this,tr("Load Images With Time"),mInputPathName,Extensions);
 853   if (files.isEmpty())
 854     return;
 855   mInputPathName = itksys::SystemTools::GetFilenamePath(files[0].toStdString()).c_str();
 856   std::vector<std::string> vector;
 857   for (int i = 0; i < files.size(); i++) {
 858     vector.push_back(files[i].toStdString());
 859   }
 860   LoadImages(vector, vvImageReader::IMAGEWITHTIME);
 861 }
 862 //------------------------------------------------------------------------------
 863
 864
 865 //------------------------------------------------------------------------------
 866 void vvMainWindow::LoadImages(std::vector<std::string> files, vvImageReader::LoadedImageType filetype)
 867 {
 868   //Separate the way to open images and dicoms
 869   int fileSize;
 870   if (filetype == vvImageReader::IMAGE || filetype == vvImageReader::IMAGEWITHTIME)
 871     fileSize = files.size();
 872   else
 873     fileSize = 1;
 874
 875   // For SLICED, we need the number of slices (ndim and #slices)
 876   std::vector<unsigned int> nSlices;
 877   nSlices.resize(files.size());
 878   std::fill(nSlices.begin(), nSlices.end(), 1);
 879   if (filetype == vvImageReader::SLICED) {
 880     for (int i = 0; i < fileSize; i++) {
 881       itk::ImageIOBase::Pointer header = clitk::readImageHeader(files[i]);
 882       QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
 883       if (!header) {
 884         nSlices[i] = 0;
 885         QString error = "Cannot open file \n";
 886         error += files[i].c_str();
 887         QMessageBox::information(this,tr("Reading problem"),error);
 888         return;
 889       }
 890       if (header->GetNumberOfDimensions() < 3) {
 891         nSlices[i] = 0;
 892         QString error = "Dimension problem. Cannot slice \n";
 893         error += files[i].c_str();
 894         QMessageBox::information(this,tr("Reading problem"),error);
 895         return;
 896       }
 897       nSlices[i] = header->GetDimensions( header->GetNumberOfDimensions()-1 );
 898     }
 899   }
 900
 901   //Only add to the list of recently opened files when a single file is opened,
 902   //to avoid polluting the list of recently opened files
 903   if (files.size() == 1) {
 904     QFileInfo finfo=tr(files[0].c_str());
 905     AddToRecentlyOpenedImages(finfo.absoluteFilePath().toStdString());
 906     updateRecentlyOpenedFilesMenu(GetRecentlyOpenedImages());
 907   }
 908   //init the progress events
 909   QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
 910   vvProgressDialog progress("Opening " + files[0],fileSize>1);
 911   qApp->processEvents();
 912
 913   int numberofsuccesulreads=0;
 914   //open images as 1 or multiples
 915   for (int i = 0; i < fileSize; i++) {
 916     progress.SetText("Opening " + files[i]);
 917     progress.SetProgress(i,fileSize);
 918     qApp->processEvents();
 919
 920     for (unsigned int j = 0; j < nSlices[i]; j++) {
 921       //read the image and put it in mSlicerManagers
 922       vvSlicerManager* imageManager = new vvSlicerManager(4);
 923       qApp->processEvents();
 924
 925       bool SetImageSucceed=false;
 926
 927       // Change filename if an image with the same already exist
 928       int number = GetImageDuplicateFilenameNumber(files[i] + std::string("_slice"));
 929
 930       if (filetype == vvImageReader::IMAGE || filetype == vvImageReader::IMAGEWITHTIME || filetype == vvImageReader::SLICED)
 931         SetImageSucceed = imageManager->SetImage(files[i],filetype, number, j);
 932       else if (filetype == vvImageReader::DICOM)
 933         SetImageSucceed = imageManager->SetImages(files,filetype, number, dicomSeriesSelector->IsPatientCoordianteSystemChecked());
 934       else
 935         SetImageSucceed = imageManager->SetImages(files,filetype, number);
 936
 937       if (!SetImageSucceed) {
 938         QApplication::restoreOverrideCursor();
 939         QString error = "Cannot open file \n";
 940         error += imageManager->GetLastError().c_str();
 941         QMessageBox::information(this,tr("Reading problem"),error);
 942         delete imageManager;
 943       } else {
 944
 945         mSlicerManagers.push_back(imageManager);
 946
 947         //create an item in the tree with good settings
 948         QTreeWidgetItem *item = new QTreeWidgetItem();
 949         item->setData(0,Qt::UserRole,files[i].c_str());
 950         QFileInfo fileinfo(imageManager->GetFileName().c_str()); //Do not show the path
 951         item->setData(COLUMN_IMAGE_NAME,Qt::DisplayRole,fileinfo.fileName());
 952         item->setData(1,Qt::UserRole,tr("image"));
 953         item->setToolTip(COLUMN_IMAGE_NAME, imageManager->GetListOfAbsoluteFilePathInOneString("image").c_str());
 954         qApp->processEvents();
 955
 956         //Create the buttons for reload and close
 957         qApp->processEvents();
 958         QTreePushButton* cButton = new QTreePushButton;
 959         cButton->setItem(item);
 960         cButton->setColumn(COLUMN_CLOSE_IMAGE);
 961         cButton->setToolTip(tr("close image"));
 962         cButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/exit.png")));
 963         connect(cButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
 964           this,SLOT(CloseImage(QTreeWidgetItem*, int)));
 965
 966         QTreePushButton* rButton = new QTreePushButton;
 967         rButton->setItem(item);
 968         rButton->setColumn(COLUMN_RELOAD_IMAGE);
 969         rButton->setToolTip(tr("reload image"));
 970         rButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/rotateright.png")));
 971         connect(rButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
 972           this,SLOT(ReloadImage(QTreeWidgetItem*, int)));
 973
 974         DataTree->addTopLevelItem(item);
 975         DataTree->setItemWidget(item, COLUMN_CLOSE_IMAGE, cButton);
 976         DataTree->setItemWidget(item, COLUMN_RELOAD_IMAGE, rButton);
 977
 978         //set the id of the image
 979         QString id = QDir::current().absoluteFilePath(files[i].c_str()) + QString::number(mSlicerManagers.size()-1);
 980         item->setData(COLUMN_IMAGE_NAME,Qt::UserRole,id.toStdString().c_str());
 981         mSlicerManagers.back()->SetId(id.toStdString());
 982
 983         linkPanel->addImage(imageManager->GetFileName(), id.toStdString());
 984
 985         connect(mSlicerManagers.back(), SIGNAL(currentImageChanged(std::string)),
 986           this,SLOT(CurrentImageChanged(std::string)));
 987         connect(mSlicerManagers.back(), SIGNAL(currentPickedImageChanged(std::string)),
 988           this, SLOT(CurrentPickedImageChanged(std::string)));
 989         connect(mSlicerManagers.back(), SIGNAL(UpdatePosition(int, double, double, double, double, double, double, double)),
 990           this,SLOT(MousePositionChanged(int,double, double, double, double, double, double, double)));
 991         connect(mSlicerManagers.back(), SIGNAL(UpdateVector(int, double, double, double, double)),
 992           this, SLOT(VectorChanged(int,double,double,double, double)));
 993         connect(mSlicerManagers.back(), SIGNAL(UpdateOverlay(int, double, double)),
 994           this, SLOT(OverlayChanged(int,double,double)));
 995         connect(mSlicerManagers.back(), SIGNAL(UpdateFusion(int, double)),
 996           this, SLOT(FusionChanged(int,double)));
 997         connect(mSlicerManagers.back(), SIGNAL(WindowLevelChanged()),
 998           this,SLOT(WindowLevelChanged()));
 999         connect(mSlicerManagers.back(), SIGNAL(UpdateSlice(int,int)),
1000           this,SLOT(UpdateSlice(int,int)));
1001         connect(mSlicerManagers.back(), SIGNAL(UpdateTSlice(int, int, int)),
1002           this,SLOT(UpdateTSlice(int, int, int)));
1003         connect(mSlicerManagers.back(), SIGNAL(UpdateTSlice(int, int, int)),
1004           this,SLOT(ImageInfoChanged()));
1005         connect(mSlicerManagers.back(), SIGNAL(UpdateSliceRange(int,int,int,int,int)),
1006           this,SLOT(UpdateSliceRange(int,int,int,int,int)));
1007         connect(mSlicerManagers.back(), SIGNAL(UpdateLinkManager(std::string,int,double,double,double,int)),
1008           this,SLOT(UpdateLinkManager(std::string,int,double,double,double,int)));
1009         connect(mSlicerManagers.back(), SIGNAL(UpdateLinkedNavigation(std::string,vvSlicerManager*,vvSlicer*)),
1010           this,SLOT(UpdateLinkedNavigation(std::string,vvSlicerManager*,vvSlicer*)));
1011         connect(mSlicerManagers.back(), SIGNAL(ChangeImageWithIndexOffset(vvSlicerManager*,int,int)),
1012           this,SLOT(ChangeImageWithIndexOffset(vvSlicerManager*,int,int)));
1013         connect(mSlicerManagers.back(),SIGNAL(LandmarkAdded()),landmarksPanel,SLOT(AddPoint()));
1014         connect(landmarksPanel,SIGNAL(UpdateLandmarkTransform()), mSlicerManagers.back(), SLOT(UpdateLandmark()));
1015         InitSlicers();
1016         numberofsuccesulreads++;
1017       }
1018     }
1019   }
1020
1021   if (numberofsuccesulreads) {
1022     NOViewWidget->show();
1023     NEViewWidget->show();
1024     SOViewWidget->show();
1025     SEViewWidget->show();
1026     UpdateTree();
1027     InitDisplay();
1028     ShowLastImage();
1029
1030     // Try to guess default WindowLevel
1031     double range[2];
1032     mSlicerManagers.back()->GetImage()->GetFirstVTKImageData()->GetScalarRange(range);
1033     if ((range[0] == 0) && (range[1] == 1)) {
1034       presetComboBox->setCurrentIndex(WL_BINARY);// binary
1035     } else {
1036       // TODO
1037     }
1038   }
1039   QApplication::restoreOverrideCursor();
1040 }
1041 //------------------------------------------------------------------------------
1042
1043 //------------------------------------------------------------------------------
1044 void vvMainWindow::UpdateTree()
1045 {
1046   DataTree->resizeColumnToContents(COLUMN_TREE);
1047   DataTree->resizeColumnToContents(COLUMN_UL_VIEW);
1048   DataTree->resizeColumnToContents(COLUMN_UR_VIEW);
1049   DataTree->resizeColumnToContents(COLUMN_DL_VIEW);
1050   DataTree->resizeColumnToContents(COLUMN_DR_VIEW);
1051   DataTree->resizeColumnToContents(COLUMN_IMAGE_NAME);
1052   DataTree->resizeColumnToContents(COLUMN_CLOSE_IMAGE);
1053   DataTree->resizeColumnToContents(COLUMN_RELOAD_IMAGE);
1054 }
1055 //------------------------------------------------------------------------------
1056
1057 //------------------------------------------------------------------------------
1058 void vvMainWindow::CurrentImageChanged(std::string id)
1059 {
1060   if (id == mCurrentSelectedImageId) return; // Do nothing
1061   int selected = 0;
1062   for (int i = 0; i < DataTree->topLevelItemCount(); i++) {
1063     if (DataTree->topLevelItem(i)->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString().toStdString() == id) {
1064       selected = i;
1065     } else {
1066       DataTree->topLevelItem(i)->setSelected(0);
1067     }
1068     for (int child = 0; child < DataTree->topLevelItem(i)->childCount(); child++)
1069       DataTree->topLevelItem(i)->child(child)->setSelected(0);
1070
1071   }
1072   DataTree->topLevelItem(selected)->setSelected(1);
1073   mCurrentSelectedImageId = id;
1074
1075   landmarksPanel->SetCurrentLandmarks(mSlicerManagers[selected]->GetLandmarks(),
1076                                       mSlicerManagers[selected]->GetTSlice());
1077   landmarksPanel->SetCurrentPath(mInputPathName.toStdString());
1078   landmarksPanel->SetCurrentImage(mSlicerManagers[selected]->GetFileName().c_str());
1079
1080   emit SelectedImageHasChanged(mSlicerManagers[selected]);
1081 }
1082 //------------------------------------------------------------------------------
1083
1084 //------------------------------------------------------------------------------
1085 void vvMainWindow::CurrentPickedImageChanged(std::string id)
1086 {
1087   if (id == mCurrentPickedImageId) return; // Do nothing
1088   int selected = 0;
1089   for (int i = 0; i < DataTree->topLevelItemCount(); i++) {
1090     if (DataTree->topLevelItem(i)->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString().toStdString() == id) {
1091       selected = i;
1092     } else {
1093       DataTree->topLevelItem(i)->setSelected(0);
1094     }
1095     for (int child = 0; child < DataTree->topLevelItem(i)->childCount(); child++)
1096       DataTree->topLevelItem(i)->child(child)->setSelected(0);
1097
1098   }
1099   DataTree->topLevelItem(selected)->setSelected(1);
1100   mCurrentPickedImageId = id;
1101   mCurrentPickedImageIndex = selected;
1102 }
1103 //------------------------------------------------------------------------------
1104
1105 //------------------------------------------------------------------------------
1106 void vvMainWindow::ImageInfoChanged()
1107 {
1108   contextActions[6]->setEnabled(1);
1109   contextActions[5]->setEnabled(1);
1110   actionSave_As->setEnabled(1);
1111   actionAdd_VF_to_current_Image->setEnabled(1);
1112   actionAdd_fusion_image->setEnabled(1);
1113   actionAdd_overlay_image_to_current_image->setEnabled(1);
1114   actionAdd_USSequence_toCT->setEnabled(1);
1115   actionNorth_East_Window->setEnabled(1);
1116   actionNorth_West_Window->setEnabled(1);
1117   actionSouth_East_Window->setEnabled(1);
1118   actionSouth_West_Window->setEnabled(1);
1119   vvToolManager::GetInstance()->EnableToolsInMenu(this, true);
1120   inverseButton->setEnabled(1);
1121
1122   goToCursorPushButton->setEnabled(1);
1123
1124   if (DataTree->selectedItems().size()) {
1125     int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1126
1127     colorMapComboBox->setEnabled(1);
1128     for (int i = 0; i < DataTree->topLevelItem(index)->childCount(); i++) {
1129       if (DataTree->topLevelItem(index)->child(i)->data(1,Qt::UserRole).toString() == "overlay" ||
1130         DataTree->topLevelItem(index)->child(i)->data(1,Qt::UserRole).toString() == "fusion" ||
1131         DataTree->topLevelItem(index)->child(i)->data(1,Qt::UserRole).toString() == "fusionSequence") {
1132           colorMapComboBox->setEnabled(0);
1133           break;
1134       }
1135     }
1136
1137     std::vector<double> origin;
1138     std::vector<double> inputSpacing;
1139     std::vector<int> inputSize;
1140     std::vector<double> sizeMM;
1141     vtkSmartPointer<vtkMatrix4x4> transformation;
1142     int dimension=0;
1143     QString pixelType;
1144     QString inputSizeInBytes;
1145     QString image = DataTree->selectedItems()[0]->data(COLUMN_IMAGE_NAME,Qt::DisplayRole).toString();
1146
1147     int nframes = mSlicerManagers[index]->GetSlicer(0)->GetTMax();
1148
1149     if (nframes > 1 || playMode == 1) {
1150       playButton->setEnabled(1);
1151       frameRateLabel->setEnabled(1);
1152       frameRateSpinBox->setEnabled(1);
1153     } else {
1154       playButton->setEnabled(0);
1155       frameRateLabel->setEnabled(0);
1156       frameRateSpinBox->setEnabled(0);
1157     }
1158
1159     //read image header
1160     int NPixel = 1;
1161
1162     int tSlice = 0;
1163     vvImage::Pointer imageSelected;
1164     if (DataTree->topLevelItem(index) == DataTree->selectedItems()[0]) {
1165       imageSelected = mSlicerManagers[index]->GetSlicer(0)->GetImage();
1166       tSlice = mSlicerManagers[index]->GetSlicer(0)->GetTSlice();
1167     } else if (DataTree->selectedItems()[0]->data(1,Qt::UserRole).toString() == "vector") {
1168       imageSelected = mSlicerManagers[index]->GetSlicer(0)->GetVF();
1169       tSlice = mSlicerManagers[index]->GetSlicer(0)->GetOverlayTSlice();
1170     } else if (DataTree->selectedItems()[0]->data(1,Qt::UserRole).toString() == "overlay") {
1171       imageSelected = mSlicerManagers[index]->GetSlicer(0)->GetOverlay();
1172       tSlice = mSlicerManagers[index]->GetSlicer(0)->GetOverlayTSlice();
1173     } else if (DataTree->selectedItems()[0]->data(1,Qt::UserRole).toString() == "fusion") {
1174       imageSelected = mSlicerManagers[index]->GetSlicer(0)->GetFusion();
1175       tSlice = mSlicerManagers[index]->GetSlicer(0)->GetFusionTSlice();
1176     }
1177     else if (DataTree->selectedItems()[0]->data(1,Qt::UserRole).toString() == "fusionSequence") {
1178       imageSelected = mSlicerManagers[index]->GetSlicer(0)->GetFusion();
1179       tSlice = mSlicerManagers[index]->GetSlicer(0)->GetFusionTSlice();
1180     }
1181     else if (DataTree->selectedItems()[0]->data(1,Qt::UserRole).toString() == "contour") {
1182       imageSelected = mSlicerManagers[index]->GetSlicer(0)->GetImage();
1183       tSlice = mSlicerManagers[index]->GetSlicer(0)->GetTSlice();
1184     }
1185     else {
1186       imageSelected = mSlicerManagers[index]->GetSlicer(0)->GetImage();
1187       tSlice = mSlicerManagers[index]->GetSlicer(0)->GetTSlice();
1188     }
1189
1190     dimension = imageSelected->GetNumberOfDimensions();
1191     origin.resize(dimension);
1192     inputSpacing.resize(dimension);
1193     inputSize.resize(dimension);
1194     sizeMM.resize(dimension);
1195     pixelType = mSlicerManagers[index]->GetImage()->GetScalarTypeAsITKString().c_str();
1196     for (int i = 0; i < dimension; i++) {
1197       origin[i] = imageSelected->GetOrigin()[i];
1198       inputSpacing[i] = imageSelected->GetSpacing()[i];
1199       inputSize[i] = imageSelected->GetSize()[i];
1200       sizeMM[i] = inputSize[i]*inputSpacing[i];
1201       NPixel *= inputSize[i];
1202     }
1203     inputSizeInBytes = GetSizeInBytes(imageSelected->GetActualMemorySize());
1204
1205     QString dim = QString::number(dimension) + " (";
1206     dim += pixelType + ")";
1207
1208     infoPanel->setFileName(image);
1209     std::string creationImageTimeValue("No creation time");
1210     itk::ExposeMetaData< std::string > (*imageSelected->GetFirstMetaDataDictionary(), "creationImageTime", creationImageTimeValue);
1211     infoPanel->setImageCreationTime(QString(creationImageTimeValue.c_str()));
1212     infoPanel->setDimension(dim);
1213     infoPanel->setSizePixel(GetVectorIntAsString(inputSize));
1214     infoPanel->setSizeMM(GetVectorDoubleAsString(sizeMM));
1215     infoPanel->setOrigin(GetVectorDoubleAsString(origin));
1216     infoPanel->setSpacing(GetVectorDoubleAsString(inputSpacing));
1217     infoPanel->setNPixel(QString::number(NPixel)+" ("+inputSizeInBytes+")");
1218
1219     transformation = imageSelected->GetTransform()[tSlice]->GetMatrix();
1220     infoPanel->setTransformation(clitk::Get4x4MatrixDoubleAsString(transformation).c_str());
1221
1222     landmarksPanel->SetCurrentLandmarks(mSlicerManagers[index]->GetLandmarks(),
1223                                         mSlicerManagers[index]->GetTSlice());
1224     landmarksPanel->SetCurrentPath(mInputPathName.toStdString());
1225     landmarksPanel->SetCurrentImage(mSlicerManagers[index]->GetFileName().c_str());
1226
1227     overlayPanel->getCurrentImageName(mSlicerManagers[index]->GetFileName().c_str());
1228     for (int i = 0; i < 4; i++) {
1229       if (DataTree->selectedItems()[0]->data(i+1,Qt::CheckStateRole).toInt() > 0 || i == 3) {
1230         mSlicerManagers[index]->UpdateInfoOnCursorPosition(i);
1231         break;
1232       }
1233     }
1234
1235 //     infoPanel->setFileName(image);
1236 //     infoPanel->setDimension(dim);
1237 //     infoPanel->setSizePixel(GetVectorIntAsString(inputSize));
1238 //     infoPanel->setSizeMM(GetVectorDoubleAsString(sizeMM));
1239 //     infoPanel->setOrigin(GetVectorDoubleAsString(origin));
1240 //     infoPanel->setSpacing(GetVectorDoubleAsString(inputSpacing));
1241 //     infoPanel->setNPixel(QString::number(NPixel)+" ("+inputSizeInBytes+")");
1242 //
1243 //     landmarksPanel->SetCurrentLandmarks(mSlicerManagers[index]->GetLandmarks(),
1244 //                                         mSlicerManagers[index]->GetTSlice());
1245 //     landmarksPanel->SetCurrentPath(mInputPathName.toStdString());
1246 //     landmarksPanel->SetCurrentImage(mSlicerManagers[index]->GetFileName().c_str());
1247 //
1248 //     overlayPanel->getCurrentImageName(mSlicerManagers[index]->GetFileName().c_str());
1249 //     for (int i = 0; i < 4; i++) {
1250 //       if (DataTree->selectedItems()[0]->data(i+1,Qt::CheckStateRole).toInt() > 0 || i == 3) {
1251 //         mSlicerManagers[index]->UpdateInfoOnCursorPosition(i);
1252 //         break;
1253 //       }
1254 //     }
1255     WindowLevelChanged();
1256
1257     slicingPresetComboBox->setCurrentIndex(mSlicerManagers[index]->GetSlicingPreset());
1258
1259     if (mSlicerManagers[index]->GetSlicer(0)->GetVF()) {
1260       overlayPanel->getVFName(mSlicerManagers[index]->GetVFName().c_str());
1261       overlayPanel->getVFProperty(mSlicerManagers[index]->GetSlicer(0)->GetVFSubSampling(),
1262         mSlicerManagers[index]->GetSlicer(0)->GetVFScale(),
1263         mSlicerManagers[index]->GetSlicer(0)->GetVFLog());
1264     } else {
1265       overlayPanel->getVFName(mSlicerManagers[index]->GetVFName().c_str());
1266       overlayPanel->getVFProperty(-1,-1,-1);
1267     }
1268     if (mSlicerManagers[index]->GetSlicer(0)->GetOverlay()) {
1269       overlayPanel->getOverlayName(mSlicerManagers[index]->GetOverlayName().c_str());
1270     } else {
1271       overlayPanel->getOverlayName(mSlicerManagers[index]->GetOverlayName().c_str());
1272     }
1273
1274     if (mSlicerManagers[index]->GetSlicer(0)->GetFusion()) {
1275       overlayPanel->getFusionName(mSlicerManagers[index]->GetFusionName().c_str());
1276     } else {
1277       overlayPanel->getFusionName(mSlicerManagers[index]->GetFusionName().c_str());
1278     }
1279   }
1280 }
1281 //------------------------------------------------------------------------------
1282
1283 //------------------------------------------------------------------------------
1284 void vvMainWindow::ShowDocumentation()
1285 {
1286   documentation->show();
1287 }
1288 //------------------------------------------------------------------------------
1289
1290 //------------------------------------------------------------------------------
1291 void vvMainWindow::PopupRegisterForm(bool checkCanPush)
1292 {
1293   vvRegisterForm* registerForm = new vvRegisterForm(QUrl("http://www.creatis.insa-lyon.fr/~dsarrut/vvregister/write.php"), getVVSettingsPath(), getSettingsOptionFormat());
1294   if(!checkCanPush) {
1295     registerForm->show();
1296   } else {
1297     if(registerForm->canPush()) {
1298       registerForm->show();
1299       registerForm->acquitPushed();//too bad if there is not internet connection anymore.
1300     }
1301   }
1302 }
1303 //------------------------------------------------------------------------------
1304
1305 //------------------------------------------------------------------------------
1306 void vvMainWindow::ShowHelpDialog()
1307 {
1308   help_dialog->show();
1309 }
1310 //------------------------------------------------------------------------------
1311
1312 //------------------------------------------------------------------------------
1313 void vvMainWindow::ChangeViewMode()
1314 {
1315   typedef struct _SIZE{
1316     QSplitter* splitter;
1317     QList<int> size1, size2;
1318     int cols[3];
1319   }SplitterSize;
1320   SplitterSize sizes[4];
1321   sizes[0].splitter = OSplitter;
1322   sizes[0].size1.push_back(1);
1323   sizes[0].size1.push_back(0);
1324   sizes[0].size2.push_back(1);
1325   sizes[0].size2.push_back(0);
1326   sizes[0].cols[0] = 2;
1327   sizes[0].cols[1] = 3;
1328   sizes[0].cols[2] = 4;
1329
1330   sizes[1].splitter = ESplitter;
1331   sizes[1].size1.push_back(0);
1332   sizes[1].size1.push_back(1);
1333   sizes[1].size2.push_back(1);
1334   sizes[1].size2.push_back(0);
1335   sizes[1].cols[0] = 1;
1336   sizes[1].cols[1] = 3;
1337   sizes[1].cols[2] = 4;
1338
1339   sizes[2].splitter = OSplitter;
1340   sizes[2].size1.push_back(1);
1341   sizes[2].size1.push_back(0);
1342   sizes[2].size2.push_back(0);
1343   sizes[2].size2.push_back(1);
1344   sizes[2].cols[0] = 1;
1345   sizes[2].cols[1] = 2;
1346   sizes[2].cols[2] = 4;
1347
1348   sizes[3].splitter = ESplitter;
1349   sizes[3].size1.push_back(0);
1350   sizes[3].size1.push_back(1);
1351   sizes[3].size2.push_back(0);
1352   sizes[3].size2.push_back(1);
1353   sizes[3].cols[0] = 1;
1354   sizes[3].cols[1] = 2;
1355   sizes[3].cols[2] = 3;
1356
1357   int slicer = mSlicerManagers[mCurrentPickedImageIndex]->GetSelectedSlicer();
1358   if (viewMode == 1) {
1359     if (slicer >= 0) {
1360       viewMode = 0;
1361       splitter_3->setSizes(sizes[slicer].size1);
1362       sizes[slicer].splitter->setSizes(sizes[slicer].size2);
1363       DataTree->setColumnHidden(sizes[slicer].cols[0],1);
1364       DataTree->setColumnHidden(sizes[slicer].cols[1],1);
1365       DataTree->setColumnHidden(sizes[slicer].cols[2],1);
1366     }
1367   } else {
1368     QList<int> size;
1369     if (slicer >= 0) {
1370       viewMode = 1;
1371       size.push_back(1);
1372       size.push_back(1);
1373       splitter_3->setSizes(size);
1374       sizes[slicer].splitter->setSizes(size);
1375       DataTree->setColumnHidden(sizes[slicer].cols[0],0);
1376       DataTree->setColumnHidden(sizes[slicer].cols[1],0);
1377       DataTree->setColumnHidden(sizes[slicer].cols[2],0);
1378     }
1379   }
1380   UpdateRenderWindows();
1381   /*
1382   ** I don't know why but for both resized QVTKWidget we also need to render
1383   ** the associated Slicer to redraw crosses.
1384   */
1385   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
1386     //     if (DataTree->topLevelItem(i)->data(COLUMN_UL_VIEW,Qt::CheckStateRole).toInt() > 1)
1387     mSlicerManagers[i]->GetSlicer(0)->Render();
1388     mSlicerManagers[i]->GetSlicer(1)->Render();
1389     //     if (DataTree->topLevelItem(i)->data(COLUMN_DL_VIEW,Qt::CheckStateRole).toInt() > 1)
1390     mSlicerManagers[i]->GetSlicer(2)->Render();
1391     mSlicerManagers[i]->GetSlicer(3)->Render();
1392   }
1393 }
1394 //------------------------------------------------------------------------------
1395
1396 //------------------------------------------------------------------------------
1397 QString vvMainWindow::GetSizeInBytes(unsigned long size)
1398 {
1399   QString result = "";// QString::number(size);
1400   //result += " bytes (";
1401   if (size > 1000000000) {
1402     size /= 1000000000;
1403     result += QString::number(size);
1404     result += "GB";//)";
1405   } else if (size > 1000000) {
1406     size /= 1000000;
1407     result += QString::number(size);
1408     result += "MB";//)";
1409   } else if (size > 1000) {
1410     size /= 1000;
1411     result += QString::number(size);
1412     result += "kB";//)";
1413   }
1414   return result;
1415 }
1416 //------------------------------------------------------------------------------
1417
1418 //------------------------------------------------------------------------------
1419 QString vvMainWindow::GetVectorDoubleAsString(std::vector<double> vectorDouble)
1420 {
1421   QString result;
1422   for (unsigned int i= 0; i < vectorDouble.size(); i++) {
1423     if (i != 0)
1424       result += " ";
1425     result += QString::number(vectorDouble[i]);
1426   }
1427   return result;
1428 }
1429 //------------------------------------------------------------------------------
1430
1431 //------------------------------------------------------------------------------
1432 QString vvMainWindow::GetVectorIntAsString(std::vector<int> vectorInt)
1433 {
1434   QString result;
1435   for (unsigned int i= 0; i < vectorInt.size(); i++) {
1436     if (i != 0)
1437       result += " ";
1438     result += QString::number(vectorInt[i]);
1439   }
1440   return result;
1441 }
1442 //------------------------------------------------------------------------------
1443
1444 //------------------------------------------------------------------------------
1445 //this actually returns the SlicerManager index!
1446 int vvMainWindow::GetSlicerIndexFromItem(QTreeWidgetItem* item)
1447 {
1448   QString id = item->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString();
1449   for (int i = 0; i < DataTree->topLevelItemCount(); i++) {
1450     if (DataTree->topLevelItem(i)->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString() == id)
1451       return i;
1452   }
1453   return -1;
1454 }
1455 //------------------------------------------------------------------------------
1456
1457 //------------------------------------------------------------------------------
1458 QTreeWidgetItem* vvMainWindow::GetItemFromSlicerManager(vvSlicerManager* sm)
1459 {
1460   QString id = sm->GetId().c_str();
1461   for (int i = 0; i < DataTree->topLevelItemCount(); i++) {
1462     if (DataTree->topLevelItem(i)->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString() == id)
1463       return DataTree->topLevelItem(i);
1464   }
1465   return NULL;
1466 }
1467 //------------------------------------------------------------------------------
1468
1469 //------------------------------------------------------------------------------
1470 void vvMainWindow::DisplayChanged(QTreeWidgetItem *clickedItem, int column)
1471 {
1472   if ( column >= COLUMN_CLOSE_IMAGE || column <= 0)
1473     return;
1474
1475   // Get parent information (might be the same item)
1476   int slicerManagerIndex = GetSlicerIndexFromItem(clickedItem);
1477   QTreeWidgetItem* clickedParentItem = DataTree->topLevelItem(slicerManagerIndex);
1478   vvSlicer* clickedSlicer = mSlicerManagers[slicerManagerIndex]->GetSlicer(column-1);
1479
1480   // Go over the complete item tree (only 2 levels, parents and children)
1481   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
1482     // Trick to avoid redoing twice the job for a key (sr)
1483     mSlicerManagers[i]->GetSlicer(column-1)->GetRenderWindow()->GetInteractor()->SetKeySym("Crap");
1484
1485     QTreeWidgetItem* currentParentItem = DataTree->topLevelItem(i);
1486     if(currentParentItem != clickedParentItem) {
1487       // Not the branch of the clicked item, uncheck all
1488
1489       // Parent
1490       currentParentItem->setData(column,Qt::CheckStateRole, 0);
1491       mSlicerManagers[i]->UpdateSlicer(column-1, false);
1492
1493       // Children
1494       for (int iChild = 0; iChild < currentParentItem->childCount(); iChild++) {
1495         currentParentItem->child(iChild)->setData(column,Qt::CheckStateRole, 0);
1496       }
1497     }
1498     else {
1499       // Branch of the clicked one: get check status from actor visibility in slicer
1500       // and toggle the clicked one
1501
1502       // Parent
1503       bool vis = clickedSlicer->GetActorVisibility("image", 0);
1504       bool draw = clickedSlicer->GetRenderer()->GetDraw();
1505
1506       // Update slicer (after getting visibility)
1507       mSlicerManagers[slicerManagerIndex]->UpdateSlicer(column-1, true);
1508       mSlicerManagers[slicerManagerIndex]->UpdateInfoOnCursorPosition(column-1);
1509       DisplaySliders(slicerManagerIndex, column-1);
1510       if(clickedParentItem == clickedItem) {
1511         // Toggle
1512         vis = !draw || !vis;
1513       }
1514       clickedSlicer->SetActorVisibility("image", 0, vis);
1515       clickedParentItem->setData(column, Qt::CheckStateRole, vis?2:0);
1516
1517       // Children
1518       std::map<std::string, int> actorTypeCounts;
1519       for (int iChild = 0; iChild < clickedParentItem->childCount(); iChild++) {
1520         QTreeWidgetItem* currentChildItem = clickedParentItem->child(iChild);
1521         std::string actorType = currentChildItem->data(1,Qt::UserRole).toString().toStdString();
1522         vis = clickedSlicer->GetActorVisibility(actorType, actorTypeCounts[actorType]);
1523         if(currentChildItem == clickedItem) {
1524           // Toggle or force visibility if it was not on this branch so far
1525           vis = !draw || !vis;
1526           clickedSlicer->SetActorVisibility(actorType, actorTypeCounts[actorType], vis);
1527         }
1528         currentChildItem->setData(column, Qt::CheckStateRole, vis?2:0);
1529         actorTypeCounts[actorType]++;
1530       }
1531     }
1532   }
1533
1534   clickedSlicer->Render();
1535 }
1536 //------------------------------------------------------------------------------
1537
1538 void vvMainWindow::InitSlicers()
1539 {
1540   if (mSlicerManagers.size()) {
1541     mSlicerManagers.back()->GenerateDefaultLookupTable();
1542     mSlicerManagers.back()->SetSlicerWindow(0,NOViewWidget->GetRenderWindow());
1543     mSlicerManagers.back()->SetSlicerWindow(1,NEViewWidget->GetRenderWindow());
1544     mSlicerManagers.back()->SetSlicerWindow(2,SOViewWidget->GetRenderWindow());
1545     mSlicerManagers.back()->SetSlicerWindow(3,SEViewWidget->GetRenderWindow());
1546 #if VTK_MAJOR_VERSION <= 5
1547     mSlicerManagers.back()->Render(); // SR: displayed #slice is wrong without this / TB: With VTK6 and multiple images, all slicers are updated, not only the first
1548 #endif
1549   }
1550 }
1551
1552 //------------------------------------------------------------------------------
1553 void vvMainWindow::InitDisplay()
1554 {
1555   if (mSlicerManagers.size()) {
1556     //BE CAREFUL : this is absolutely necessary to set the interactor style
1557     //in order to have the same style instanciation for all SlicerManagers in
1558     // a same window
1559     for (int j = 0; j < 4; j++) {
1560       vvInteractorStyleNavigator* style = vvInteractorStyleNavigator::New();
1561       style->SetAutoAdjustCameraClippingRange(1);
1562       bool AlreadySelected = false;
1563       for (int i = 0; i < DataTree->topLevelItemCount(); i++) {
1564         mSlicerManagers[i]->SetInteractorStyleNavigator(j,style);
1565         //select the image only if previous are not selected
1566         if (DataTree->topLevelItem(i)->data(j+1,Qt::CheckStateRole).toInt() > 1) {
1567           mSlicerManagers[i]->UpdateSlicer(j,1);
1568           AlreadySelected = true;
1569         } else if (i == DataTree->topLevelItemCount()-1 && !AlreadySelected) {
1570           if (DataTree->selectedItems().size() == 0) {
1571             DataTree->topLevelItem(i)->setSelected(1);
1572           }
1573           DataTree->topLevelItem(i)->setData(j+1,Qt::CheckStateRole,2);
1574           mSlicerManagers[i]->UpdateSlicer(j,1);
1575           DisplaySliders(i,j);
1576         } else {
1577           DataTree->topLevelItem(i)->setData(j+1,Qt::CheckStateRole,0);
1578           mSlicerManagers[i]->UpdateSlicer(j,0);
1579         }
1580       }
1581       style->Delete();
1582     }
1583   }
1584 }
1585 //------------------------------------------------------------------------------
1586
1587 //------------------------------------------------------------------------------
1588 void vvMainWindow::DisplaySliders(int slicer, int window)
1589 {
1590   if(!mSlicerManagers[slicer]->GetSlicer(window)->GetRenderer()->GetDraw())
1591     return;
1592
1593   int range[2];
1594   mSlicerManagers[slicer]->GetSlicer(window)->GetSliceRange(range);
1595   int position = mSlicerManagers[slicer]->GetSlicer(window)->GetSlice();
1596   if (range[1]>0)
1597     verticalSliders[window]->show();
1598   else
1599     verticalSliders[window]->hide();
1600   verticalSliders[window]->setRange(range[0],range[1]);
1601   verticalSliders[window]->setValue(position);
1602
1603   int tRange[2];
1604   tRange[0] = 0;
1605   tRange[1] = mSlicerManagers[slicer]->GetSlicer(window)->GetTMax();
1606   if (tRange[1]>0)
1607     horizontalSliders[window]->show();
1608   else
1609     horizontalSliders[window]->hide();
1610   horizontalSliders[window]->setRange(tRange[0],tRange[1]);
1611   int tPosition = mSlicerManagers[slicer]->GetSlicer(window)->GetMaxCurrentTSlice();
1612   horizontalSliders[window]->setValue(tPosition);
1613 }
1614 //------------------------------------------------------------------------------
1615
1616 //------------------------------------------------------------------------------
1617 void vvMainWindow::CloseImage(QTreeWidgetItem* item, int column)
1618 {
1619   int index = GetSlicerIndexFromItem(item);
1620
1621   if (DataTree->topLevelItem(index) != item) {
1622     QString warning = "Do you really want to close the overlay : ";
1623     warning += item->data(COLUMN_IMAGE_NAME,Qt::DisplayRole).toString();
1624     QMessageBox msgBox(QMessageBox::Warning, tr("Close Overlay"),
1625       warning, 0, this);
1626     msgBox.addButton(tr("Close"), QMessageBox::AcceptRole);
1627     msgBox.addButton(tr("Cancel"), QMessageBox::RejectRole);
1628     if (msgBox.exec() == QMessageBox::AcceptRole) {
1629       std::string overlay_type=item->data(1,Qt::UserRole).toString().toStdString();
1630       int overlay_index=0;
1631       for (int child = 0; child < DataTree->topLevelItem(index)->childCount(); child++) {
1632         if (DataTree->topLevelItem(index)->\
1633           child(child)->data(1,Qt::UserRole).toString().toStdString() == overlay_type)
1634           overlay_index++;
1635         if (DataTree->topLevelItem(index)->child(child) == item) break;
1636       }
1637       if (overlay_type=="fusionSequence") {
1638         //removing the overlay sequence in a fusion sequence visualization mode
1639         //reset the transforms
1640         overlayPanel->getFusionSequenceProperty(-1, false, 0, false);
1641
1642         //unlink and untie the slicer managers
1643         RemoveLink(mSlicerManagers[index]->GetId().c_str(), mSlicerManagers[mSlicerManagers[index]->GetFusionSequenceIndexOfLinkedManager()]->GetId().c_str());
1644         mSlicerManagers[index]->SetFusionSequenceInvolvmentCode(-1);
1645         mSlicerManagers[mSlicerManagers[index]->GetFusionSequenceIndexOfLinkedManager()]->SetFusionSequenceInvolvmentCode(-1);
1646         for (unsigned i=0 ; i<4 ; i++) {
1647             mSlicerManagers[index]->GetSlicer(i)->SetFusionSequenceCode(-1);
1648             mSlicerManagers[mSlicerManagers[index]->GetFusionSequenceIndexOfLinkedManager()]->GetSlicer(i)->SetFusionSequenceCode(-1);
1649         }
1650
1651       }
1652       mSlicerManagers[index]->RemoveActor(overlay_type, overlay_index-1);
1653       mSlicerManagers[index]->SetColorMap(0);
1654       DataTree->topLevelItem(index)->takeChild(DataTree->topLevelItem(index)->indexOfChild(item));
1655       mSlicerManagers[index]->Render();
1656     }
1657   } else if (DataTree->topLevelItemCount() <= 1) {
1658     QString warning = "Do you really want to close the image : ";
1659     warning += item->data(COLUMN_IMAGE_NAME,Qt::DisplayRole).toString();
1660     warning += "\nThis is the last image, you're about to close vv !!!";
1661     QMessageBox msgBox(QMessageBox::Warning, tr("Close Image"),
1662       warning, 0, this);
1663     msgBox.addButton(tr("Close vv"), QMessageBox::AcceptRole);
1664     msgBox.addButton(tr("Cancel"), QMessageBox::RejectRole);
1665     if (msgBox.exec() == QMessageBox::AcceptRole) {
1666       this->close();
1667     }
1668   } else {
1669     QString warning = "Do you really want to close the image : ";
1670     warning += item->data(COLUMN_IMAGE_NAME,Qt::DisplayRole).toString();
1671     QMessageBox msgBox(QMessageBox::Warning, tr("Close Image"),
1672       warning, 0, this);
1673     msgBox.addButton(tr("Close"), QMessageBox::AcceptRole);
1674     msgBox.addButton(tr("Cancel"), QMessageBox::RejectRole);
1675     if (msgBox.exec() == QMessageBox::AcceptRole) {
1676
1677       // Tell tools that we close an image
1678       emit AnImageIsBeingClosed(mSlicerManagers[index]);
1679
1680       std::vector<vvSlicerManager*>::iterator Manageriter = mSlicerManagers.begin();
1681       DataTree->takeTopLevelItem(index);
1682       for (int i = 0; i < index; i++) {
1683         Manageriter++;
1684       }
1685       //if the slicer manager was involved in a fusion sequence visualization...
1686       if ( mSlicerManagers[index]->IsInvolvedInFusionSequence() ) {
1687         //in both cases, close the overlay: find it... and close it
1688         //ideally, I should duplicate the code, and avoid calling CloseImage, since this pops up another interactive box
1689         QTreeWidgetItem* overlayItem;
1690         if (mSlicerManagers[index]->IsMainSequenceOfFusionSequence()) {
1691           for (unsigned i=0 ; i<item->childCount() ; i++) {
1692             overlayItem = item->child(i);
1693             this->CloseImage( overlayItem, 0 );
1694           }
1695         }
1696         else {
1697           QTreeWidgetItem* linkedItem = this->GetItemFromSlicerManager( mSlicerManagers[mSlicerManagers[index]->GetFusionSequenceIndexOfLinkedManager()] );
1698           for (unsigned i=0 ; i<linkedItem->childCount() ; i++) {
1699             overlayItem = linkedItem->child(i);
1700             this->CloseImage( overlayItem, 0 );
1701           }
1702         }
1703
1704         /* -- this is normally already done when closing the overlay.
1705         //reset the transforms
1706         overlayPanel->getFusionSequenceProperty(-1, false, 0, false);
1707
1708         //unlink and untie the slicer managers
1709         RemoveLink(mSlicerManagers[index]->GetId().c_str(), mSlicerManagers[mSlicerManagers[index]->GetFusionSequenceIndexOfLinkedManager()]->GetId().c_str());
1710         mSlicerManagers[index]->SetFusionSequenceInvolvmentCode(-1);
1711         mSlicerManagers[mSlicerManagers[index]->GetFusionSequenceIndexOfLinkedManager()]->SetFusionSequenceInvolvmentCode(-1);
1712         for (unsigned i=0 ; i<4 ; i++) {
1713             mSlicerManagers[index]->GetSlicer(i)->SetFusionSequenceCode(-1);
1714             mSlicerManagers[mSlicerManagers[index]->GetFusionSequenceIndexOfLinkedManager()]->GetSlicer(i)->SetFusionSequenceCode(-1);
1715         }
1716         */
1717       }
1718
1719       linkPanel->removeImage(index);
1720       mSlicerManagers[index]->RemoveActors();
1721
1722       //remove the slicer manager
1723       delete mSlicerManagers[index];
1724       mSlicerManagers.erase(Manageriter);
1725
1726       //
1727       InitDisplay();
1728     }
1729   }
1730   ImageInfoChanged();
1731 }
1732 //------------------------------------------------------------------------------
1733
1734 //------------------------------------------------------------------------------
1735 void vvMainWindow::ReloadImage(QTreeWidgetItem* item, int column)
1736 {
1737   // int index = GetSlicerIndexFromItem(item);
1738   //   QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
1739   //   if (item->data(1,Qt::UserRole).toString() == "vector")
1740   //     mSlicerManagers[index]->ReloadVF();
1741   //   else
1742   //     mSlicerManagers[index]->Reload();
1743
1744   //   QApplication::restoreOverrideCursor();
1745   int index = GetSlicerIndexFromItem(item);
1746   QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
1747   QString role=item->data(1,Qt::UserRole).toString();
1748   if ( role == "vector") {
1749     mSlicerManagers[index]->ReloadVF();
1750   }
1751   else if (role == "overlay") {
1752     mSlicerManagers[index]->ReloadOverlay();
1753   }
1754   else if (role == "fusion") {
1755     mSlicerManagers[index]->ReloadFusion();
1756   }
1757   else if (role == "fusionSequence") {
1758     //both versions of the secondary sequence must be updated.
1759     mSlicerManagers[index]->ReloadFusionSequence();
1760     mSlicerManagers[mSlicerManagers[index]->GetFusionSequenceIndexOfLinkedManager()]->Reload();
1761   }
1762   else {
1763     mSlicerManagers[index]->Reload();
1764     //if we update the secondary sequence, then the overlay of the main sequence should also be updated
1765     if (mSlicerManagers[index]->IsSecondarySequenceOfFusionSequence()) mSlicerManagers[mSlicerManagers[index]->GetFusionSequenceIndexOfLinkedManager()]->ReloadFusionSequence();
1766   }
1767   // Update view and info
1768   ImageInfoChanged();
1769   mSlicerManagers[index]->Render();
1770   QApplication::restoreOverrideCursor();
1771 }
1772 //------------------------------------------------------------------------------
1773
1774 //------------------------------------------------------------------------------
1775 void vvMainWindow::MousePositionChanged(int visibility,double x, double y, double z, double X, double Y, double Z , double value)
1776 {
1777   infoPanel->setCurrentInfo(visibility,x,y,z,X,Y,Z,value);
1778 }
1779 //------------------------------------------------------------------------------
1780
1781 //------------------------------------------------------------------------------
1782 void vvMainWindow::VectorChanged(int visibility,double x, double y, double z, double value)
1783 {
1784   overlayPanel->getCurrentVectorInfo(visibility,x,y,z,value);
1785 }
1786 //------------------------------------------------------------------------------
1787
1788 //------------------------------------------------------------------------------
1789 void vvMainWindow::OverlayChanged(int visibility, double valueOver, double valueRef)
1790 {
1791   overlayPanel->getCurrentOverlayInfo(visibility,valueOver, valueRef);
1792 }
1793 //------------------------------------------------------------------------------
1794
1795 //------------------------------------------------------------------------------
1796 void vvMainWindow::FusionChanged(int visibility, double value)
1797 {
1798   overlayPanel->getCurrentFusionInfo(visibility,value);
1799 }
1800 //------------------------------------------------------------------------------
1801
1802 //------------------------------------------------------------------------------
1803 //called when AddOverlayImage, AddFusionSequence
1804 //or when UpdateWindowLevel() is called ; when slicerManager emits WindowLevelChanged
1805 //when ImageInfoChanged() is called
1806 void vvMainWindow::WindowLevelChanged()
1807 {
1808   // Base image
1809   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1810   if(index==-1) return;
1811   windowSpinBox->setValue(mSlicerManagers[index]->GetColorWindow());
1812   levelSpinBox->setValue(mSlicerManagers[index]->GetColorLevel());
1813   colorMapComboBox->setCurrentIndex(mSlicerManagers[index]->GetColorMap());
1814   presetComboBox->setCurrentIndex(mSlicerManagers[index]->GetPreset());
1815
1816   // Overlay image
1817   if (mSlicerManagers[index]->GetSlicer(0)->GetOverlay())
1818     overlayPanel->getOverlayProperty(mSlicerManagers[index]->GetOverlayColor(),
1819     mSlicerManagers[index]->GetLinkOverlayWindowLevel(),
1820     mSlicerManagers[index]->GetOverlayColorWindow(),
1821     mSlicerManagers[index]->GetOverlayColorLevel());
1822   else
1823     overlayPanel->getOverlayProperty(-1,0,0.,0.);
1824
1825   // Fusion & SequenceFusion image
1826   if (mSlicerManagers[index]->GetSlicer(0)->GetFusion()) {
1827     overlayPanel->getFusionProperty(mSlicerManagers[index]->GetFusionOpacity(),
1828       mSlicerManagers[index]->GetFusionThresholdOpacity(),
1829       mSlicerManagers[index]->GetFusionColorMap(),
1830       mSlicerManagers[index]->GetFusionWindow(),
1831       mSlicerManagers[index]->GetFusionLevel());
1832     if (mSlicerManagers[index]->IsMainSequenceOfFusionSequence()) {
1833       overlayPanel->getFusionSequenceProperty(mSlicerManagers[index]->GetFusionSequenceFrameIndex(),
1834         mSlicerManagers[index]->GetFusionSequenceSpatialSyncFlag(),
1835         mSlicerManagers[index]->GetFusionSequenceNbFrames(),
1836         mSlicerManagers[index]->GetFusionSequenceTemporalSyncFlag());
1837     }
1838   }
1839   else if ( mSlicerManagers[index]->IsSecondarySequenceOfFusionSequence() ) {
1840     //if the image is involved in a fusion sequence, preserve the overlay panel!
1841     int ind = mSlicerManagers[index]->GetFusionSequenceIndexOfLinkedManager();
1842     overlayPanel->getFusionProperty(mSlicerManagers[ind]->GetFusionOpacity(),
1843       mSlicerManagers[ind]->GetFusionThresholdOpacity(),
1844       mSlicerManagers[ind]->GetFusionColorMap(),
1845       mSlicerManagers[ind]->GetFusionWindow(),
1846       mSlicerManagers[ind]->GetFusionLevel());
1847     overlayPanel->getFusionSequenceProperty(mSlicerManagers[ind]->GetFusionSequenceFrameIndex(),
1848       mSlicerManagers[ind]->GetFusionSequenceSpatialSyncFlag(),
1849       mSlicerManagers[ind]->GetFusionSequenceNbFrames(),
1850       mSlicerManagers[ind]->GetFusionSequenceTemporalSyncFlag());
1851   }
1852   else
1853   {
1854     overlayPanel->getFusionProperty(-1, -1, -1, -1, -1);
1855     overlayPanel->getFusionSequenceProperty(-1, false, 0, false);
1856   }
1857 }
1858 //------------------------------------------------------------------------------
1859
1860 //------------------------------------------------------------------------------
1861 void vvMainWindow::WindowLevelEdited()
1862 {
1863   presetComboBox->setCurrentIndex(WL_USER);
1864   UpdateWindowLevel();
1865 }
1866 //------------------------------------------------------------------------------
1867
1868 //------------------------------------------------------------------------------
1869 void vvMainWindow::SetWindowLevel(double w, double l)
1870 {
1871   windowSpinBox->setValue(w);
1872   levelSpinBox->setValue(l);
1873   presetComboBox->setCurrentIndex(WL_USER);
1874   colorMapComboBox->setCurrentIndex(0);
1875   UpdateWindowLevel();
1876 }
1877 //------------------------------------------------------------------------------
1878
1879 //------------------------------------------------------------------------------
1880 void vvMainWindow::UpdateWindowLevel()
1881 {
1882   if (DataTree->selectedItems().size()) {
1883     if (presetComboBox->currentIndex() == WL_VENTILATION) //For ventilation
1884       colorMapComboBox->setCurrentIndex(5);
1885     int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1886     mSlicerManagers[index]->SetColorWindow(windowSpinBox->value());
1887     mSlicerManagers[index]->SetColorLevel(levelSpinBox->value());
1888     mSlicerManagers[index]->SetPreset(presetComboBox->currentIndex());
1889     mSlicerManagers[index]->Render();
1890     WindowLevelChanged();
1891   }
1892 }
1893 //------------------------------------------------------------------------------
1894
1895 //------------------------------------------------------------------------------
1896 void vvMainWindow::UpdateSlicingPreset()
1897 {
1898   if (DataTree->selectedItems().size()) {
1899     int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1900     mSlicerManagers[index]->SetSlicingPreset(vvSlicerManager::SlicingPresetType(slicingPresetComboBox->currentIndex()));
1901   }
1902 }
1903 //------------------------------------------------------------------------------
1904
1905 //------------------------------------------------------------------------------
1906 void vvMainWindow::UpdateColorMap()
1907 {
1908   if (DataTree->selectedItems().size()) {
1909     int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1910     mSlicerManagers[index]->SetColorMap(colorMapComboBox->currentIndex());
1911     mSlicerManagers[index]->Render();
1912   }
1913 }
1914 //------------------------------------------------------------------------------
1915 void vvMainWindow::SwitchWindowLevel()
1916 {
1917   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1918   int window = mSlicerManagers[index]->GetColorWindow();
1919   presetComboBox->setCurrentIndex(WL_USER);
1920   windowSpinBox->setValue(-window);
1921   UpdateWindowLevel();
1922 }
1923 //------------------------------------------------------------------------------
1924
1925 //------------------------------------------------------------------------------
1926 void vvMainWindow::ApplyWindowLevelToAllImages()
1927 {
1928   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1929   if(index==-1) return;
1930   double window = mSlicerManagers[index]->GetColorWindow();
1931   double level = mSlicerManagers[index]->GetColorLevel();
1932
1933   double fusWindow = mSlicerManagers[index]->GetFusionWindow();
1934   double fusLevel = mSlicerManagers[index]->GetFusionLevel();
1935
1936   double overWindow = mSlicerManagers[index]->GetOverlayColorWindow();
1937   double overLevel = mSlicerManagers[index]->GetOverlayColorLevel();
1938
1939   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
1940     if (mSlicerManagers[i] == NULL)
1941       continue;
1942     mSlicerManagers[i]->SetColorWindow(window);
1943     mSlicerManagers[i]->SetColorLevel(level);
1944     mSlicerManagers[i]->SetPreset(WL_USER);
1945     mSlicerManagers[i]->SetFusionWindow(fusWindow);
1946     mSlicerManagers[i]->SetFusionLevel(fusLevel);
1947     mSlicerManagers[i]->SetOverlayColorWindow(overWindow);
1948     mSlicerManagers[i]->SetOverlayColorLevel(overLevel);
1949     mSlicerManagers[i]->Render();
1950   }
1951 }
1952 //------------------------------------------------------------------------------
1953
1954 //------------------------------------------------------------------------------
1955 void vvMainWindow::ApplyWindowToSetOfImages(double window, unsigned int indexMin, unsigned int indexMax)
1956 {
1957   for (unsigned int i = indexMin; i <= indexMax && i < mSlicerManagers.size(); i++) {
1958     if (mSlicerManagers[i] == NULL)
1959       continue;
1960     SetWindowLevel(window, mSlicerManagers[i]->GetColorLevel());
1961     mSlicerManagers[i]->SetColorWindow(window);
1962     mSlicerManagers[i]->SetPreset(WL_USER);
1963     mSlicerManagers[i]->Render();
1964   }
1965 }
1966 //------------------------------------------------------------------------------
1967
1968 //------------------------------------------------------------------------------
1969 void vvMainWindow::ApplyLevelToSetOfImages(double level, unsigned int indexMin, unsigned int indexMax)
1970 {
1971   for (unsigned int i = indexMin; i <= indexMax && i < mSlicerManagers.size(); i++) {
1972     if (mSlicerManagers[i] == NULL)
1973       continue;
1974     SetWindowLevel(mSlicerManagers[i]->GetColorWindow(), level);
1975     mSlicerManagers[i]->SetColorLevel(level);
1976     mSlicerManagers[i]->SetPreset(WL_USER);
1977     mSlicerManagers[i]->Render();
1978   }
1979 }
1980 //------------------------------------------------------------------------------
1981
1982 //------------------------------------------------------------------------------
1983 void vvMainWindow::UpdateLinkManager(std::string id, int slicer, double x, double y, double z, int temps)
1984 {
1985   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
1986     if (mSlicerManagers[i]->GetId() == id) {
1987       mSlicerManagers[i]->GetSlicer(slicer)->SetCurrentPosition(x,y,z,temps);
1988       mSlicerManagers[i]->UpdateViews(0,slicer);
1989       break;
1990     }
1991   }
1992 }
1993 //------------------------------------------------------------------------------
1994
1995 //------------------------------------------------------------------------------
1996 void vvMainWindow::UpdateLinkedNavigation(std::string id, vvSlicerManager * sm, vvSlicer* refSlicer)
1997 {
1998   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
1999     if (id == mSlicerManagers[i]->GetId()) {
2000       mSlicerManagers[i]->UpdateLinkedNavigation(refSlicer);
2001     }
2002   }
2003 }
2004 //------------------------------------------------------------------------------
2005
2006 //------------------------------------------------------------------------------
2007 void vvMainWindow::ShowContextMenu(QPoint point)
2008 {
2009   if (!DataTree->selectedItems().size()) {
2010     contextActions[1]->setEnabled(0);
2011     contextActions[2]->setEnabled(0);
2012     contextActions[3]->setEnabled(0);
2013     contextActions[4]->setEnabled(0);
2014     contextActions[5]->setEnabled(0);
2015     contextActions[6]->setEnabled(0);
2016   } else {
2017     int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2018     contextActions[1]->setEnabled(1);
2019     contextActions[2]->setEnabled(
2020       DataTree->itemWidget(DataTree->selectedItems()[0],
2021       COLUMN_RELOAD_IMAGE)->isEnabled());
2022     contextActions[3]->setEnabled(1);
2023     contextActions[5]->setEnabled(1);
2024     contextActions[6]->setEnabled(1);
2025
2026     if (mSlicerManagers[index]->GetDimension() < 3)
2027       contextActions[4]->setEnabled(0);
2028     else
2029       contextActions[4]->setEnabled(1);
2030   }
2031   contextMenu.exec(QCursor::pos());
2032 }
2033 //------------------------------------------------------------------------------
2034
2035 //------------------------------------------------------------------------------
2036 void vvMainWindow::CloseImage()
2037 {
2038   CloseImage(DataTree->selectedItems()[0],0);
2039 }
2040 //------------------------------------------------------------------------------
2041
2042 //------------------------------------------------------------------------------
2043 void vvMainWindow::ReloadImage()
2044 {
2045   ReloadImage(DataTree->selectedItems()[0],0);
2046 }
2047 //------------------------------------------------------------------------------
2048
2049 //------------------------------------------------------------------------------
2050 void vvMainWindow::SelectOverlayImage()
2051 {
2052   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2053
2054   if (!(CheckAddedImage(index, "overlay")))
2055     return;
2056
2057   QString Extensions = EXTENSIONS;
2058   Extensions += ";;All Files (*)";
2059   QStringList files = QFileDialog::getOpenFileNames(this,tr("Load Overlay image"),mInputPathName,Extensions);
2060   if (files.isEmpty())
2061     return;
2062
2063   std::vector<std::string> vecFileNames;
2064   for (int i = 0; i < files.size(); i++) {
2065     vecFileNames.push_back(files[i].toStdString());
2066   }
2067
2068   AddOverlayImage(index,vecFileNames,vvImageReader::IMAGE);
2069 }
2070 //------------------------------------------------------------------------------
2071
2072 //------------------------------------------------------------------------------
2073 bool vvMainWindow::CheckAddedImage(int index, QString imageType)
2074 {
2075   //check if one overlay image is added
2076   for (int child = 0; child < DataTree->topLevelItem(index)->childCount(); child++)
2077     if (DataTree->topLevelItem(index)->child(child)->data(1,Qt::UserRole).toString().compare(imageType) == 0) {
2078       QString error = "Cannot add more than one compared image\n";
2079       error += "Please remove first ";
2080       error += DataTree->topLevelItem(index)->child(child)->data(COLUMN_IMAGE_NAME,Qt::DisplayRole).toString();
2081       QMessageBox::information(this,tr("Problem adding compared image !"),error);
2082       return false;
2083     }
2084     return true;
2085 }
2086 //------------------------------------------------------------------------------
2087
2088 //------------------------------------------------------------------------------
2089 void vvMainWindow::AddOverlayImage(int index, std::vector<std::string> fileNames, vvImageReader::LoadedImageType type)
2090 {
2091   QString file(fileNames[0].c_str());
2092   if (QFile::exists(file))
2093   {
2094     mInputPathName = itksys::SystemTools::GetFilenamePath(file.toStdString()).c_str();
2095     itk::ImageIOBase::Pointer reader = itk::ImageIOFactory::CreateImageIO(
2096       file.toStdString().c_str(), itk::ImageIOFactory::ReadMode);
2097     reader->SetFileName(fileNames[0].c_str());
2098     reader->ReadImageInformation();
2099     std::string component = reader->GetComponentTypeAsString(reader->GetComponentType());
2100     int dimension = reader->GetNumberOfDimensions();
2101     QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
2102     vvProgressDialog progress("Opening " + file.toStdString());
2103     qApp->processEvents();
2104
2105     std::string filename = itksys::SystemTools::GetFilenameWithoutExtension(file.toStdString()).c_str();
2106     if (mSlicerManagers[index]->SetOverlay(fileNames,dimension, component,type)) {
2107       //create an item in the tree with good settings
2108       QTreeWidgetItem *item = new QTreeWidgetItem();
2109       item->setData(0,Qt::UserRole,file.toStdString().c_str());
2110       item->setData(1,Qt::UserRole,tr("overlay"));
2111       QFileInfo fileinfo(file); //Do not show the path
2112       item->setData(COLUMN_IMAGE_NAME,Qt::DisplayRole,fileinfo.fileName());
2113       item->setToolTip(COLUMN_IMAGE_NAME, mSlicerManagers[index]->GetListOfAbsoluteFilePathInOneString("overlay").c_str());
2114       qApp->processEvents();
2115 #if VTK_MAJOR_VERSION > 5
2116       for ( unsigned int i = 0; i < mSlicerManagers[index]->GetNumberOfSlicers(); i++)
2117         mSlicerManagers[index]->GetSlicer(i)->ForceUpdateDisplayExtent();
2118 #endif
2119
2120       for (int j = 1; j <= 4; j++) {
2121         item->setData(j,Qt::CheckStateRole,DataTree->topLevelItem(index)->data(j,Qt::CheckStateRole));
2122       }
2123
2124       //Create the buttons for reload and close
2125       qApp->processEvents();
2126       QTreePushButton* cButton = new QTreePushButton;
2127       cButton->setItem(item);
2128       cButton->setColumn(COLUMN_CLOSE_IMAGE);
2129       cButton->setToolTip(tr("close image"));
2130       cButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/exit.png")));
2131       connect(cButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
2132         this,SLOT(CloseImage(QTreeWidgetItem*, int)));
2133
2134       QTreePushButton* rButton = new QTreePushButton;
2135       rButton->setItem(item);
2136       rButton->setColumn(COLUMN_RELOAD_IMAGE);
2137       rButton->setToolTip(tr("reload image"));
2138       rButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/rotateright.png")));
2139       connect(rButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
2140         this,SLOT(ReloadImage(QTreeWidgetItem*, int)));
2141
2142       DataTree->topLevelItem(index)->setExpanded(1);
2143       DataTree->topLevelItem(index)->addChild(item);
2144       DataTree->setItemWidget(item, COLUMN_CLOSE_IMAGE, cButton);
2145       DataTree->setItemWidget(item, COLUMN_RELOAD_IMAGE, rButton);
2146
2147       //set the id of the image
2148       QString id = DataTree->topLevelItem(index)->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString();
2149       item->setData(COLUMN_IMAGE_NAME,Qt::UserRole,id.toStdString().c_str());
2150       UpdateTree();
2151       qApp->processEvents();
2152       ImageInfoChanged();
2153       QApplication::restoreOverrideCursor();
2154
2155       // Update the display to update, e.g., the sliders
2156       for(int i=0; i<4; i++)
2157         DisplaySliders(index, i);
2158     } else {
2159       QApplication::restoreOverrideCursor();
2160       QString error = "Cannot import the new image.\n";
2161       error += mSlicerManagers[index]->GetLastError().c_str();
2162       QMessageBox::information(this,tr("Problem reading image !"),error);
2163     }
2164     WindowLevelChanged();
2165   }
2166   else
2167     QMessageBox::information(this,tr("Problem reading Overlay !"),"File doesn't exist!");
2168 }
2169 //------------------------------------------------------------------------------
2170
2171
2172 //------------------------------------------------------------------------------
2173 void vvMainWindow::AddROI(int index, QString file)
2174 {
2175   /*
2176   // Get slice manager
2177
2178   // Load image
2179
2180   vvImageReader * mReader = new vvImageReader;
2181   mReader->SetInputFilename(filename.toStdString());
2182   mReader->Update(IMAGE);
2183   if (mReader->GetLastError().size() != 0) {
2184   std::cerr << "Error while reading " << filename.toStdString() << std::endl;
2185   QString error = "Cannot open file \n";
2186   error += mReader->GetLastError().c_str();
2187   QMessageBox::information(this,tr("Reading problem"),error);
2188   delete mReader;
2189   return;
2190   }
2191   vvImage::Pointer roi = mReader->GetOutput();
2192
2193   // Create roi in new tool
2194   vvToolStructureSetManager::AddImage(mCurrentSlicerManager, roi);
2195   */
2196 }
2197 //------------------------------------------------------------------------------
2198
2199 //------------------------------------------------------------------------------
2200 void vvMainWindow::SelectFusionImage()
2201 {
2202   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2203
2204   if (!(CheckAddedImage(index, "fusion")) || !(CheckAddedImage(index, "fusionSequence")))
2205     return;
2206
2207   QString Extensions = EXTENSIONS;
2208   Extensions += ";;All Files (*)";
2209   QStringList files = QFileDialog::getOpenFileNames(this,tr("Load Fusion image"),mInputPathName,Extensions);
2210   if (files.isEmpty())
2211     return;
2212
2213   std::vector<std::string> vecFileNames;
2214   for (int i = 0; i < files.size(); i++) {
2215     vecFileNames.push_back(files[i].toStdString());
2216   }
2217   AddFusionImage(index,vecFileNames,vvImageReader::IMAGE);
2218 }
2219 //------------------------------------------------------------------------------
2220
2221 //------------------------------------------------------------------------------
2222 void vvMainWindow::ResetTransformationToIdentity()
2223 {
2224   std::string actorType = DataTree->selectedItems()[0]->data(1,Qt::UserRole).toString().toStdString();
2225   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2226   mSlicerManagers[index]->ResetTransformationToIdentity(actorType);
2227   ImageInfoChanged();
2228 }
2229 //------------------------------------------------------------------------------
2230
2231 //------------------------------------------------------------------------------
2232 void vvMainWindow::AddFusionImage(int index, std::vector<std::string> fileNames, vvImageReader::LoadedImageType type)
2233 {
2234   QString file(fileNames[0].c_str());
2235   if (QFile::exists(file))
2236   {
2237     mInputPathName = itksys::SystemTools::GetFilenamePath(file.toStdString()).c_str();
2238     itk::ImageIOBase::Pointer reader = itk::ImageIOFactory::CreateImageIO(
2239       file.toStdString().c_str(), itk::ImageIOFactory::ReadMode);
2240     reader->SetFileName(fileNames[0].c_str());
2241     reader->ReadImageInformation();
2242     std::string component = reader->GetComponentTypeAsString(reader->GetComponentType());
2243     int dimension = reader->GetNumberOfDimensions();
2244     QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
2245     vvProgressDialog progress("Opening fusion");
2246     qApp->processEvents();
2247
2248     std::string filename = itksys::SystemTools::GetFilenameWithoutExtension(file.toStdString()).c_str();
2249     if (mSlicerManagers[index]->SetFusion(fileNames,dimension, component,type)) {
2250       //create an item in the tree with good settings
2251       QTreeWidgetItem *item = new QTreeWidgetItem();
2252       item->setData(0,Qt::UserRole,file.toStdString().c_str());
2253       item->setData(1,Qt::UserRole,tr("fusion"));
2254       QFileInfo fileinfo(file); //Do not show the path
2255           item->setData(COLUMN_IMAGE_NAME,Qt::DisplayRole,fileinfo.fileName());
2256           item->setToolTip(COLUMN_IMAGE_NAME, mSlicerManagers[index]->GetListOfAbsoluteFilePathInOneString("fusion").c_str());
2257           qApp->processEvents();
2258 #if VTK_MAJOR_VERSION > 5
2259       for ( unsigned int i = 0; i < mSlicerManagers[index]->GetNumberOfSlicers(); i++)
2260         mSlicerManagers[index]->GetSlicer(i)->ForceUpdateDisplayExtent();
2261 #endif
2262       for (int j = 1; j <= 4; j++) {
2263         item->setData(j,Qt::CheckStateRole,DataTree->topLevelItem(index)->data(j,Qt::CheckStateRole));
2264       }
2265
2266       //Create the buttons for reload and close
2267       qApp->processEvents();
2268       QTreePushButton* cButton = new QTreePushButton;
2269       cButton->setItem(item);
2270       cButton->setColumn(COLUMN_CLOSE_IMAGE);
2271       cButton->setToolTip(tr("close image"));
2272       cButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/exit.png")));
2273       connect(cButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
2274         this,SLOT(CloseImage(QTreeWidgetItem*, int)));
2275
2276       QTreePushButton* rButton = new QTreePushButton;
2277       rButton->setItem(item);
2278       rButton->setColumn(COLUMN_RELOAD_IMAGE);
2279       rButton->setToolTip(tr("reload image"));
2280       rButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/rotateright.png")));
2281       connect(rButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
2282         this,SLOT(ReloadImage(QTreeWidgetItem*, int)));
2283
2284       DataTree->topLevelItem(index)->setExpanded(1);
2285       DataTree->topLevelItem(index)->addChild(item);
2286       DataTree->setItemWidget(item, COLUMN_CLOSE_IMAGE, cButton);
2287       DataTree->setItemWidget(item, COLUMN_RELOAD_IMAGE, rButton);
2288
2289       //set the id of the image
2290       QString id = DataTree->topLevelItem(index)->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString();
2291       item->setData(COLUMN_IMAGE_NAME,Qt::UserRole,id.toStdString().c_str());
2292       UpdateTree();
2293       qApp->processEvents();
2294       ImageInfoChanged();
2295       QApplication::restoreOverrideCursor();
2296
2297       // Update the display to update, e.g., the sliders
2298       for(int i=0; i<4; i++)
2299         DisplaySliders(index, i);
2300     } else {
2301       QApplication::restoreOverrideCursor();
2302       QString error = "Cannot import the new image.\n";
2303       error += mSlicerManagers[index]->GetLastError().c_str();
2304       QMessageBox::information(this,tr("Problem reading image !"),error);
2305     }
2306     WindowLevelChanged();
2307   }
2308   else
2309     QMessageBox::information(this,tr("Problem reading Fusion !"),"File doesn't exist!");
2310 }
2311 //------------------------------------------------------------------------------
2312 //------------------------------------------------------------------------------
2313 void vvMainWindow::AddLandmarks(int index, std::vector<std::string> files)
2314 {
2315     if (!landmarksPanel->LoadFromFile(files))
2316       QMessageBox::information(this,tr("Problem reading Landmarks !"),"File doesn't exist!");
2317
2318     landmarksPanel->SetCurrentPath(mInputPathName.toStdString());
2319     landmarksPanel->SetCurrentImage(mSlicerManagers[index]->GetFileName().c_str());
2320 }
2321
2322 //------------------------------------------------------------------------------
2323 void vvMainWindow::OpenField()
2324 {
2325   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2326
2327   if (!(CheckAddedImage(index, "vector")))
2328     return;
2329
2330   QString Extensions = "Images ( *.mhd *.mha *.vf *.nii *.nrrd *.nhdr)";
2331   // Extensions += ";;Images ( *.mha)";
2332   // Extensions += ";;VF Images ( *.vf)";
2333   // Extensions += ";;nii Images ( *.nii)";
2334   // Extensions += ";;nrrd Images ( *.nrrd)";
2335   // Extensions += ";;nhdr Images ( *.nhdr)";
2336   Extensions += ";;All Files (*)";
2337   QString file = QFileDialog::getOpenFileName(this,tr("Load deformation field"),mInputPathName,Extensions);
2338   if (!file.isEmpty())
2339     AddField(file,index);
2340 }
2341 //------------------------------------------------------------------------------
2342
2343
2344 //------------------------------------------------------------------------------
2345 void vvMainWindow::AddFieldEntry(QString filename,int index,bool from_disk)
2346 {
2347   //create an item in the tree with good settings
2348   QTreeWidgetItem *item = new QTreeWidgetItem();
2349   item->setData(0,Qt::UserRole,filename.toStdString().c_str());
2350   item->setData(1,Qt::UserRole,tr("vector"));
2351   QFileInfo fileinfo(filename); //Do not show the path
2352   item->setData(COLUMN_IMAGE_NAME,Qt::DisplayRole,fileinfo.fileName());
2353   item->setToolTip(COLUMN_IMAGE_NAME, mSlicerManagers[index]->GetListOfAbsoluteFilePathInOneString("vector").c_str());
2354   qApp->processEvents();
2355
2356   for (int j = 1; j <= 4; j++) {
2357     item->setData(j,Qt::CheckStateRole,DataTree->topLevelItem(index)->data(j,Qt::CheckStateRole));
2358   }
2359
2360   //Create the buttons for reload and close
2361   qApp->processEvents();
2362   QTreePushButton* cButton = new QTreePushButton;
2363   cButton->setItem(item);
2364   cButton->setColumn(COLUMN_CLOSE_IMAGE);
2365   cButton->setToolTip(tr("close vector field"));
2366   cButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/exit.png")));
2367   connect(cButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
2368     this,SLOT(CloseImage(QTreeWidgetItem*, int)));
2369
2370   QTreePushButton* rButton = new QTreePushButton;
2371   rButton->setItem(item);
2372   rButton->setColumn(COLUMN_RELOAD_IMAGE);
2373   rButton->setToolTip(tr("reload vector field"));
2374   rButton->setEnabled(from_disk);
2375   rButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/rotateright.png")));
2376   connect(rButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
2377     this,SLOT(ReloadImage(QTreeWidgetItem*, int)));
2378
2379   DataTree->topLevelItem(index)->setExpanded(1);
2380   DataTree->topLevelItem(index)->addChild(item);
2381   DataTree->setItemWidget(item, COLUMN_RELOAD_IMAGE, rButton);
2382   DataTree->setItemWidget(item, COLUMN_CLOSE_IMAGE, cButton);
2383
2384   //set the id of the image
2385   QString id = DataTree->topLevelItem(index)->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString();
2386   item->setData(COLUMN_IMAGE_NAME,Qt::UserRole,id.toStdString().c_str());
2387   UpdateTree();
2388   qApp->processEvents();
2389   ImageInfoChanged();
2390   QApplication::restoreOverrideCursor();
2391 }
2392 //------------------------------------------------------------------------------
2393
2394
2395 //------------------------------------------------------------------------------
2396 void vvMainWindow::AddField(vvImage::Pointer vf,QString file,int index)
2397 {
2398   QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
2399   vvSlicerManager* imageManager = mSlicerManagers[index];
2400   if (imageManager->SetVF(vf,file.toStdString())) {
2401     AddFieldEntry(file,index,false);
2402 #if VTK_MAJOR_VERSION > 5
2403       for ( unsigned int i = 0; i < mSlicerManagers[index]->GetNumberOfSlicers(); i++)
2404         mSlicerManagers[index]->GetSlicer(i)->ForceUpdateDisplayExtent();
2405 #endif
2406   } else {
2407     QString error = "Cannot import the vector field for this image.\n";
2408     error += imageManager->GetLastError().c_str();
2409     QMessageBox::information(this,tr("Problem reading VF !"),error);
2410   }
2411   QApplication::restoreOverrideCursor();
2412 }
2413 //------------------------------------------------------------------------------
2414
2415
2416 //------------------------------------------------------------------------------
2417 void vvMainWindow::AddField(QString file,int index)
2418 {
2419   if (QFile::exists(file)) {
2420     mInputPathName = itksys::SystemTools::GetFilenamePath(file.toStdString()).c_str();
2421
2422     //init the progress events
2423     QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
2424     vvProgressDialog progress("Opening " + file.toStdString());
2425     qApp->processEvents();
2426
2427     //read the vector and put it in the current mSlicerManager
2428     vvSlicerManager* imageManager = mSlicerManagers[index];
2429     qApp->processEvents();
2430
2431     std::string filename = itksys::SystemTools::GetFilenameWithoutExtension(file.toStdString()).c_str();
2432     if (imageManager->SetVF(file.toStdString())) {
2433       imageManager->Render();
2434       AddFieldEntry(file,index,true);
2435     } else {
2436       QApplication::restoreOverrideCursor();
2437       QString error = "Cannot import the vector field for this image.\n";
2438       error += imageManager->GetLastError().c_str();
2439       QMessageBox::information(this,tr("Problem reading VF !"),error);
2440     }
2441   } else
2442     QMessageBox::information(this,tr("Problem reading VF !"),"File doesn't exist!");
2443
2444 }
2445 //------------------------------------------------------------------------------
2446
2447
2448 //------------------------------------------------------------------------------
2449 void vvMainWindow::SetVFProperty(int subsampling, int scale, int log, int width, double r, double g, double b)
2450 {
2451   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2452   if (mSlicerManagers[index]->GetSlicer(0)->GetVF()) {
2453     for (int i = 0; i < 4; i++) {
2454       mSlicerManagers[index]->GetSlicer(i)->SetVFSubSampling(subsampling);
2455       mSlicerManagers[index]->GetSlicer(i)->SetVFScale(scale);
2456       mSlicerManagers[index]->GetSlicer(i)->SetVFWidth(width);
2457       mSlicerManagers[index]->GetSlicer(i)->SetVFColor(r,g,b);
2458       if (log > 0)
2459         mSlicerManagers[index]->GetSlicer(i)->SetVFLog(1);
2460       else
2461         mSlicerManagers[index]->GetSlicer(i)->SetVFLog(0);
2462     }
2463   }
2464 }
2465 //------------------------------------------------------------------------------
2466
2467
2468 //------------------------------------------------------------------------------
2469 void vvMainWindow::SetOverlayProperty(int color, int linked, double window, double level)
2470 {
2471   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2472   if (mSlicerManagers[index]->GetSlicer(0)->GetOverlay()) {
2473     mSlicerManagers[index]->SetOverlayColor(color);
2474     mSlicerManagers[index]->SetColorMap(0);
2475     mSlicerManagers[index]->SetLinkOverlayWindowLevel(linked);
2476     mSlicerManagers[index]->SetOverlayColorWindow(window);
2477     mSlicerManagers[index]->SetOverlayColorLevel(level);
2478     mSlicerManagers[index]->Render();
2479   }
2480 }
2481 //------------------------------------------------------------------------------
2482
2483 //------------------------------------------------------------------------------
2484 void vvMainWindow::SetFusionProperty(int opacity, int thresOpacity, int colormap,double window, double level, bool showLegend)
2485 {
2486   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2487   if (mSlicerManagers[index]->GetSlicer(0)->GetFusion()) {
2488     mSlicerManagers[index]->SetFusionColorMap(colormap);
2489     mSlicerManagers[index]->SetFusionOpacity(opacity);
2490     mSlicerManagers[index]->SetFusionThresholdOpacity(thresOpacity);
2491     mSlicerManagers[index]->SetFusionWindow(window);
2492     mSlicerManagers[index]->SetFusionLevel(level);
2493     mSlicerManagers[index]->SetFusionShowLegend(showLegend);
2494     mSlicerManagers[index]->SetColorMap(0);
2495     mSlicerManagers[index]->Render();
2496   }
2497 }
2498 //------------------------------------------------------------------------------
2499
2500
2501 //------------------------------------------------------------------------------
2502 void vvMainWindow::SelectFusionSequence()
2503 {
2504   //get the index of the slicer manager of the main sequence (CT)
2505   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2506
2507   if (!(CheckAddedImage(index, "fusion")) || !(CheckAddedImage(index, "fusionSequence")))
2508     return;
2509
2510   QString Extensions = EXTENSIONS;
2511   Extensions += ";;All Files (*)";
2512   QStringList files = QFileDialog::getOpenFileNames(this,tr("Load Overlay image sequence"),mInputPathName,Extensions);
2513   if (files.isEmpty())
2514     return;
2515
2516   std::vector<std::string> vecFileNames;
2517   for (int i = 0; i < files.size(); i++) {
2518     vecFileNames.push_back(files[i].toStdString());
2519   }
2520
2521   //associate the secondary sequence (US) to the main one
2522   AddFusionSequence(index,vecFileNames,vvImageReader::MERGEDWITHTIME);
2523 }
2524 //------------------------------------------------------------------------------
2525
2526
2527 //------------------------------------------------------------------------------
2528 void vvMainWindow::SelectFusionSequenceCorrespondances()
2529 {
2530   //make sure the index is right?
2531   //in the end, I should attach the temporal data to the right sequence!
2532   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2533   //in case the other sequence got selected, make sure we select the primary sequence
2534   if ( (!mSlicerManagers[index]->GetSlicer(0)->GetFusion()) && mSlicerManagers[index]->GetFusionSequenceIndexOfLinkedManager()>=0 ) {
2535     index = mSlicerManagers[index]->GetFusionSequenceIndexOfLinkedManager();
2536   }
2537
2538   //open a dialog box to find a file
2539   //QString Extensions = EXTENSIONS;
2540   QString Extensions = ";;All Files (*)";
2541   QString fileName = QFileDialog::getOpenFileName(this,tr("Load respiratory signal for fused sequence"),mInputPathName,Extensions);
2542   if (fileName.isNull())
2543     return;
2544
2545   //read it as a vector of values
2546   vnl_vector<double> tmpVect;
2547
2548   std::ifstream file;
2549   file.open(fileName.toStdString().c_str());
2550   tmpVect.read_ascii(file);
2551   file.close();
2552
2553   //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
2554   bool signalOK = true;
2555   unsigned nbFrameMain = mSlicerManagers[index]->GetImage()->GetTransform().size();
2556   unsigned nbFrameSecondary = mSlicerManagers[index]->GetFusionSequenceNbFrames();
2557   std::cout<<"nbFrameMain = "<<nbFrameMain<<", nbFrameSecondary= "<<nbFrameSecondary<<", signal size: "<<tmpVect.size()<<std::endl;
2558   std::vector<unsigned> temporalCorrespondances;
2559   if ( tmpVect.size() == nbFrameMain + nbFrameSecondary ) {
2560     for (unsigned i=0 ; i<tmpVect.size() ; i++) {
2561       if (i<nbFrameMain) { //first part of the file: i -> index in secondary seq.
2562         if ( tmpVect(i)<nbFrameSecondary ) temporalCorrespondances.push_back(tmpVect(i));
2563         else { signalOK=false; break; } //pointing outside the secondary sequence...
2564       }
2565       else { //first part of the file -> index in secondary seq.
2566         if ( tmpVect(i)<nbFrameMain ) temporalCorrespondances.push_back(tmpVect(i));
2567         else { signalOK=false; break; } //pointing outside the secondary sequence...
2568       }
2569     }
2570   }
2571   else {signalOK=false;}
2572   if (!signalOK) {//else, send a message to signal the failure...
2573     QString error = "The provided temporal correspondances is invalid - check tooltip.\n";
2574     error += "Ignoring file: " + fileName;
2575     QMessageBox::information(this,tr("Problem adding temporal correspondances!"),error);
2576     return;
2577   }
2578   else {
2579     //for convenience, associate this sequence to both the current slicer manager, and to the linked one
2580     mSlicerManagers[index]->SetFusionSequenceCorrespondances(temporalCorrespondances);
2581     mSlicerManagers[ mSlicerManagers[index]->GetFusionSequenceIndexOfLinkedManager() ]->SetFusionSequenceCorrespondances(temporalCorrespondances);
2582     overlayPanel->enableFusionSequenceTemporalSync();
2583   }
2584
2585 }
2586 //------------------------------------------------------------------------------
2587
2588
2589 //------------------------------------------------------------------------------
2590 //when this function is called index is the slicer manager index corresponding to the main sequence (CT)
2591 //the files behind fileNames points to the data for the secondary sequence
2592 void vvMainWindow::AddFusionSequence(int index, std::vector<std::string> fileNames, vvImageReader::LoadedImageType type)
2593 {
2594   QString file(fileNames[0].c_str());
2595   if (QFile::exists(file))
2596   {
2597     mInputPathName = itksys::SystemTools::GetFilenamePath(file.toStdString()).c_str();
2598     itk::ImageIOBase::Pointer reader = itk::ImageIOFactory::CreateImageIO(
2599       file.toStdString().c_str(), itk::ImageIOFactory::ReadMode);
2600     std::sort (fileNames.begin(), fileNames.end());//make sure the files are sorted.
2601     reader->SetFileName(fileNames[0].c_str());
2602     reader->ReadImageInformation();
2603     std::string component = reader->GetComponentTypeAsString(reader->GetComponentType());
2604     int dimension = reader->GetNumberOfDimensions();
2605     QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
2606     vvProgressDialog progress("Opening " + file.toStdString());
2607     qApp->processEvents();
2608
2609     std::string filename = itksys::SystemTools::GetFilenameWithoutExtension(file.toStdString()).c_str();
2610
2611     if (mSlicerManagers[index]->SetFusionSequence(fileNames,dimension, component,type)) {
2612       //create an item in the tree with good settings
2613       QTreeWidgetItem *item = new QTreeWidgetItem();
2614       item->setData(0,Qt::UserRole,file.toStdString().c_str());
2615       item->setData(1,Qt::UserRole,tr("fusionSequence"));
2616
2617       QFileInfo fileinfo(file); //Do not show the path
2618       item->setData(COLUMN_IMAGE_NAME,Qt::DisplayRole,fileinfo.fileName());
2619       item->setToolTip(COLUMN_IMAGE_NAME, mSlicerManagers[index]->GetListOfAbsoluteFilePathInOneString("fusionSequence").c_str());
2620       qApp->processEvents();
2621 #if VTK_MAJOR_VERSION > 5
2622       for ( unsigned int i = 0; i < mSlicerManagers[index]->GetNumberOfSlicers(); i++)
2623         mSlicerManagers[index]->GetSlicer(i)->ForceUpdateDisplayExtent();
2624 #endif
2625       for (int j = 1; j <= 4; j++) {
2626         item->setData(j,Qt::CheckStateRole,DataTree->topLevelItem(index)->data(j,Qt::CheckStateRole));
2627       }
2628
2629       //Create the buttons for reload and close
2630       qApp->processEvents();
2631       QTreePushButton* cButton = new QTreePushButton;
2632       cButton->setItem(item);
2633       cButton->setColumn(COLUMN_CLOSE_IMAGE);
2634       cButton->setToolTip(tr("close image"));
2635       cButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/exit.png")));
2636       connect(cButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
2637         this,SLOT(CloseImage(QTreeWidgetItem*, int)));
2638
2639       QTreePushButton* rButton = new QTreePushButton;
2640       rButton->setItem(item);
2641       rButton->setColumn(COLUMN_RELOAD_IMAGE);
2642       rButton->setToolTip(tr("reload image"));
2643       rButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/rotateright.png")));
2644       connect(rButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
2645         this,SLOT(ReloadImage(QTreeWidgetItem*, int)));
2646
2647       DataTree->topLevelItem(index)->setExpanded(1);
2648       DataTree->topLevelItem(index)->addChild(item);
2649       DataTree->setItemWidget(item, COLUMN_CLOSE_IMAGE, cButton);
2650       DataTree->setItemWidget(item, COLUMN_RELOAD_IMAGE, rButton);
2651
2652       //store the original transform matrix
2653       int indexParent = GetSlicerIndexFromItem( DataTree->topLevelItem(index) );
2654       mSlicerManagers[indexParent]->SetFusionSequenceMainTransformMatrix( mSlicerManagers[indexParent]->GetSlicer(0)->GetImage()->GetTransform()[0]->GetMatrix() );
2655
2656       //set the id of the image
2657       QString id = DataTree->topLevelItem(index)->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString();
2658       item->setData(COLUMN_IMAGE_NAME,Qt::UserRole,id.toStdString().c_str());
2659       UpdateTree();
2660       qApp->processEvents();
2661
2662       //ImageInfoChanged();
2663
2664       QApplication::restoreOverrideCursor();
2665       // Update the display to update, e.g., the sliders
2666       for(int i=0; i<4; i++)
2667         DisplaySliders(index, i);
2668
2669
2670       //This loads the secondary sequence (US) as an independent sequence
2671       LoadImages(fileNames, type);
2672       //reset the transforms to identity
2673       //FIX -- and set the thickness of the US slices to a large value (necessary for visualization purposes...)
2674       double sp_x, sp_y, sp_z;
2675       mSlicerManagers[indexParent]->GetImage()->GetVTKImages()[0]->GetSpacing(sp_x, sp_y, sp_z);
2676       sp_z = std::max(sp_x, std::max(sp_y, sp_z)) + 0.5; //
2677       for (unsigned i=0 ; i<mSlicerManagers.back()->GetImage()->GetTransform().size() ; i++) {
2678         sp_x = mSlicerManagers.back()->GetImage()->GetVTKImages()[i]->GetSpacing()[0];
2679         sp_y = mSlicerManagers.back()->GetImage()->GetVTKImages()[i]->GetSpacing()[1];
2680         mSlicerManagers.back()->GetImage()->GetVTKImages()[i]->SetSpacing( sp_x, sp_y, sp_z);
2681         mSlicerManagers.back()->GetImage()->GetTransform()[i]->Identity();
2682         mSlicerManagers.back()->GetImage()->GetTransform()[i]->Update();
2683       }
2684
2685       //automatically link both images...
2686       AddLink(mSlicerManagers[indexParent]->GetId().c_str(), mSlicerManagers.back()->GetId().c_str(), false);
2687
2688       //tie the main and secondary sequences by raising flags and informing each another of their respective SlicerManager indices
2689       mSlicerManagers[indexParent]->SetFusionSequenceIndexOfLinkedManager(mSlicerManagers.size()-1);
2690       mSlicerManagers[indexParent]->SetFusionSequenceInvolvmentCode(0); //main sequence
2691       mSlicerManagers.back()->SetFusionSequenceIndexOfLinkedManager(indexParent);
2692       mSlicerManagers.back()->SetFusionSequenceInvolvmentCode(1); //secondary sequence
2693       for (unsigned i=0 ; i<4 ; i++) {
2694         mSlicerManagers.back()->GetSlicer(i)->SetFusionSequenceCode(1); //flag the slicers of the secondary sequence
2695       }
2696
2697     } else {
2698       QApplication::restoreOverrideCursor();
2699       QString error = "Cannot import the new image.\n";
2700       error += mSlicerManagers[index]->GetLastError().c_str();
2701       QMessageBox::information(this,tr("Problem reading image !"),error);
2702     }
2703     WindowLevelChanged();
2704     ImageInfoChanged(); //this internally calls WindowLevelChanged...
2705   }
2706   else {
2707     QMessageBox::information(this,tr("Problem reading fusion sequence !"),"File doesn't exist!");
2708     return;
2709   }
2710
2711 }
2712 //------------------------------------------------------------------------------
2713
2714
2715 //------------------------------------------------------------------------------
2716 //fusionSequenceFrameIndex and fusionSequenceNbFrames are relative to the secondary sequence (US)
2717 void vvMainWindow::SetFusionSequenceProperty(int fusionSequenceFrameIndex, bool spatialSyncFlag, unsigned int fusionSequenceNbFrames, bool temporalSyncFlag)
2718 {
2719   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2720
2721   if (!mSlicerManagers[index]->IsInvolvedInFusionSequence()) return;
2722
2723   //check if the focus moved to the linked sequence, and in this case, select the master sequence instead
2724   if (!mSlicerManagers[index]->IsMainSequenceOfFusionSequence()) {
2725     index = mSlicerManagers[index]->GetFusionSequenceIndexOfLinkedManager();
2726   }
2727   int secondaryIndex = mSlicerManagers[index]->GetFusionSequenceIndexOfLinkedManager();
2728   if (secondaryIndex==-1) return; //this should never happen
2729   if ( (!mSlicerManagers[index]->IsMainSequenceOfFusionSequence()) ||
2730     (!mSlicerManagers[secondaryIndex]->IsSecondarySequenceOfFusionSequence()) )
2731   {return;} //this should never happen, raise an exception?
2732
2733   if (mSlicerManagers[index]->GetSlicer(0)->GetFusion()) {
2734
2735     //First, if the spatialSync button is unchecked, then reposition the parent sequence (CT) in its original coordinate frame
2736     if ( (!spatialSyncFlag) && (mSlicerManagers[index]->GetFusionSequenceSpatialSyncFlag()) ) {
2737       for ( unsigned i=0 ; i<mSlicerManagers[index]->GetSlicer(0)->GetImage()->GetTransform().size() ; i++ ) {
2738         mSlicerManagers[index]->GetSlicer(0)->GetImage()->GetTransform()[i]->SetMatrix( mSlicerManagers[index]->GetFusionSequenceMainTransformMatrix() );
2739         mSlicerManagers[index]->GetSlicer(0)->GetImage()->GetTransform()[i]->Update();
2740       }
2741
2742       for (int i=0; i<mSlicerManagers[index]->GetNumberOfSlicers(); i++) {
2743         mSlicerManagers[index]->GetSlicer(i)->ForceUpdateDisplayExtent();
2744         mSlicerManagers[index]->GetSlicer(i)->Render();
2745       }
2746     }
2747
2748     //then, update the property values in the slicer manager
2749     mSlicerManagers[index]->SetFusionSequenceLength(fusionSequenceNbFrames);
2750     mSlicerManagers[index]->SetFusionSequenceSpatialSyncFlag(spatialSyncFlag);
2751     mSlicerManagers[index]->SetFusionSequenceTemporalSyncFlag(temporalSyncFlag);
2752     mSlicerManagers[index]->SetFusionSequenceFrameIndex(fusionSequenceFrameIndex);
2753
2754     //select the right frame of the US sequence
2755     mSlicerManagers[index]->SetFusionSequenceTSlice(fusionSequenceFrameIndex); //here, I should only update the overlayed sequence
2756     mSlicerManagers[secondaryIndex]->SetTSlice(fusionSequenceFrameIndex, false); //this should update the secondary sequence (individual version)
2757
2758     //update the horizontal sliders of the main window
2759     overlayPanel->updateFusionSequenceSliderValueFromWindow(fusionSequenceFrameIndex, false);
2760
2761     if (spatialSyncFlag) { //reslice the CT
2762
2763       if (temporalSyncFlag) { //do the temporal synchronisation
2764         int mainSequenceFrameIndex=0;
2765         //estimate the TSlice to set to the CT
2766         unsigned nbFramesMain = mSlicerManagers[index]->GetImage()->GetTransform().size();
2767         mainSequenceFrameIndex = mSlicerManagers[index]->GetFusionSequenceCorrespondances()[ nbFramesMain + fusionSequenceFrameIndex];
2768         //and set it!
2769         mSlicerManagers[index]->SetTSlice(mainSequenceFrameIndex, false);
2770         //warning, there is a loopback, and modification of the TSlice in main sequence forces an update of the TSlice in secondary, etc...
2771       }
2772
2773
2774       //Set the transform matrix of the parent sequence (typically CT / 4DCT)
2775       vtkSmartPointer<vtkMatrix4x4> tmpMat = vtkSmartPointer<vtkMatrix4x4>::New();
2776       vtkMatrix4x4::Invert( mSlicerManagers[index]->GetFusionSequenceInitialTransformMatrixAtFrame(fusionSequenceFrameIndex), tmpMat );
2777       for ( unsigned i=0 ; i<mSlicerManagers[index]->GetSlicer(0)->GetImage()->GetTransform().size() ; i++ ) {
2778         mSlicerManagers[index]->GetSlicer(0)->GetImage()->GetTransform()[i]->SetMatrix( mSlicerManagers[index]->GetFusionSequenceMainTransformMatrix() );
2779         mSlicerManagers[index]->GetSlicer(0)->GetImage()->GetTransform()[i]->PreMultiply();
2780         mSlicerManagers[index]->GetSlicer(0)->GetImage()->GetTransform()[i]->Concatenate( tmpMat );
2781         mSlicerManagers[index]->GetSlicer(0)->GetImage()->GetTransform()[i]->Update();
2782       }
2783
2784       for (int i=0; i<mSlicerManagers[index]->GetNumberOfSlicers(); i++) {
2785         mSlicerManagers[index]->GetSlicer(i)->ForceUpdateDisplayExtent();
2786         mSlicerManagers[index]->GetSlicer(i)->Render();
2787       }
2788
2789     }
2790
2791   }
2792 }
2793 //------------------------------------------------------------------------------
2794
2795
2796 //------------------------------------------------------------------------------
2797 void vvMainWindow::SaveAs()
2798 {
2799   if (DataTree->selectedItems()[0]->data(1,Qt::UserRole).toString() == "vector") {
2800     QMessageBox::warning(this,tr("Unsupported type"),tr("Sorry, saving a vector field is unsupported for the moment"));
2801     return;
2802   }
2803
2804   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2805   int dimension = mSlicerManagers[index]->GetDimension();
2806   QStringList OutputListeFormat;
2807   OutputListeFormat.clear();
2808   if (dimension == 1) {
2809     OutputListeFormat.push_back(".mhd");
2810     OutputListeFormat.push_back(".mha");
2811   }
2812   if (dimension == 2) {
2813     OutputListeFormat.push_back(".bmp");
2814     OutputListeFormat.push_back(".png");
2815     OutputListeFormat.push_back(".jpeg");
2816     OutputListeFormat.push_back(".tif");
2817     OutputListeFormat.push_back(".mhd");
2818     OutputListeFormat.push_back(".mha");
2819     OutputListeFormat.push_back(".hdr");
2820     OutputListeFormat.push_back(".vox");
2821   } else if (dimension == 3) {
2822     OutputListeFormat.push_back(".mhd");
2823     OutputListeFormat.push_back(".mha");
2824     OutputListeFormat.push_back(".nii");
2825     OutputListeFormat.push_back(".nrrd");
2826     OutputListeFormat.push_back(".nhdr");
2827     OutputListeFormat.push_back(".hdr");
2828     OutputListeFormat.push_back(".vox");
2829   } else if (dimension == 4) {
2830     OutputListeFormat.push_back(".mhd");
2831     OutputListeFormat.push_back(".mha");
2832     OutputListeFormat.push_back(".nii");
2833     OutputListeFormat.push_back(".nrrd");
2834     OutputListeFormat.push_back(".nhdr");
2835   }
2836   QString Extensions = "AllFiles(*.*)";
2837   for (int i = 0; i < OutputListeFormat.count(); i++) {
2838     Extensions += ";;Images ( *";
2839     Extensions += OutputListeFormat[i];
2840     Extensions += ")";
2841   }
2842   QString fileName = QFileDialog::getSaveFileName(this,
2843     tr("Save As"),
2844     mSlicerManagers[index]->GetFileName().c_str(),
2845     Extensions);
2846   if (!fileName.isEmpty()) {
2847     std::string fileformat = itksys::SystemTools::GetFilenameLastExtension(fileName.toStdString());
2848     if (OutputListeFormat.contains(
2849       fileformat.c_str())) {
2850         QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
2851         std::string action = "Saving";
2852         vvProgressDialog progress("Saving "+fileName.toStdString());
2853         qApp->processEvents();
2854         vvImageWriter::Pointer writer = vvImageWriter::New();
2855         writer->SetOutputFileName(fileName.toStdString());
2856         writer->SetInput(mSlicerManagers[index]->GetImage());
2857
2858         // Check on transform and prompt user
2859         writer->SetSaveTransform(false);
2860         bool bId = true;
2861         for(int i=0; i<4; i++)
2862           for(int j=0; j<4; j++) {
2863             // TODO SR and BP: check on the list of transforms and not the first only
2864             double elt = mSlicerManagers[index]->GetImage()->GetTransform()[0]->GetMatrix()->GetElement(i,j);
2865             if(i==j && elt!=1.)
2866               bId = false;
2867             if(i!=j && elt!=0.)
2868               bId = false;
2869           }
2870           if( !bId ) {
2871             QString warning = "The image has an associated linear transform. Do you want to save it along?";
2872             QMessageBox msgBox(QMessageBox::Warning, tr("Save transform"), warning, 0, this);
2873             msgBox.addButton(tr("Yes"), QMessageBox::AcceptRole);
2874             msgBox.addButton(tr("No"), QMessageBox::RejectRole);
2875             if (msgBox.exec() == QMessageBox::AcceptRole)
2876               writer->SetSaveTransform(true);
2877           }
2878
2879           writer->Update();
2880           QApplication::restoreOverrideCursor();
2881           if (writer->GetLastError().size()) {
2882             QString error = "Saving did not succeed\n";
2883             error += writer->GetLastError().c_str();
2884             QMessageBox::information(this,tr("Saving Problem"),error);
2885             SaveAs();
2886           }
2887     } else {
2888       QString error = fileformat.c_str();
2889       if (error.isEmpty())
2890         error += "no file format specified !";
2891       else
2892         error += " format unknown !!!\n";
2893       QMessageBox::information(this,tr("Saving Problem"),error);
2894       SaveAs();
2895     }
2896   }
2897 }
2898 //------------------------------------------------------------------------------
2899
2900 //------------------------------------------------------------------------------
2901 void vvMainWindow::SaveCurrentState()
2902 {
2903   QString Extensions = "XML Files(*.xml)";
2904   QString fileName = QFileDialog::getSaveFileName(this,
2905     tr("Save Current Window State"),
2906     "",
2907     Extensions);
2908
2909   SaveCurrentStateAs(fileName.toStdString());
2910 }
2911 //------------------------------------------------------------------------------
2912
2913 //------------------------------------------------------------------------------
2914 void vvMainWindow::SaveCurrentStateAs(const std::string& stateFile)
2915 {
2916   vvSaveState save_state;
2917   save_state.Run(this, stateFile);
2918 }
2919
2920 //------------------------------------------------------------------------------
2921 void vvMainWindow::ReadSavedState()
2922 {
2923   QString Extensions = "XML Files(*.xml)";
2924   QString fileName = QFileDialog::getOpenFileName(this,
2925     tr("Load Window State"),
2926     "",
2927     Extensions);
2928
2929   ReadSavedStateFile(fileName.toStdString());
2930 }
2931 //------------------------------------------------------------------------------
2932
2933 //------------------------------------------------------------------------------
2934 void vvMainWindow::ReadSavedStateFile(const std::string& stateFile)
2935 {
2936   vvReadState read_state;
2937   read_state.Run(this, stateFile);
2938 }
2939 //------------------------------------------------------------------------------
2940
2941 //------------------------------------------------------------------------------
2942 void vvMainWindow::LinkAllImages()
2943 {
2944   linkPanel->linkAll();
2945 }
2946
2947 //------------------------------------------------------------------------------
2948 void vvMainWindow::AddLink(QString image1,QString image2,bool fromPanel)
2949 {
2950   if (!fromPanel) {
2951     // delegate to linkPanel if call came from elsewhere...
2952     linkPanel->addLinkFromIds(image1, image2);
2953     return;
2954   }
2955
2956   unsigned int sm1 = 0;
2957   unsigned int sm2 = 0;
2958
2959   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
2960     if (image1.toStdString() == mSlicerManagers[i]->GetId()) {
2961       mSlicerManagers[i]->AddLink(image2.toStdString());
2962       sm1 = i;
2963     }
2964     if (image2.toStdString() == mSlicerManagers[i]->GetId()) {
2965       mSlicerManagers[i]->AddLink(image1.toStdString());
2966       sm2 = i;
2967     }
2968   }
2969
2970   if (linkPanel->isLinkAll())   {
2971     emit UpdateLinkedNavigation(mSlicerManagers[sm1]->GetId(), mSlicerManagers[mCurrentPickedImageIndex], mSlicerManagers[mCurrentPickedImageIndex]->GetSlicer(0));
2972     emit UpdateLinkedNavigation(mSlicerManagers[sm2]->GetId(), mSlicerManagers[mCurrentPickedImageIndex], mSlicerManagers[mCurrentPickedImageIndex]->GetSlicer(0));
2973   } else {
2974     emit UpdateLinkedNavigation(mSlicerManagers[sm2]->GetId(), mSlicerManagers[sm1], mSlicerManagers[sm1]->GetSlicer(0));
2975   }
2976 }
2977
2978 //------------------------------------------------------------------------------
2979
2980
2981 //------------------------------------------------------------------------------
2982 void vvMainWindow::RemoveLink(QString image1,QString image2)
2983 {
2984   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
2985     if (image1.toStdString() == mSlicerManagers[i]->GetId()) {
2986       mSlicerManagers[i]->RemoveLink(image2.toStdString());
2987     }
2988     if (image2.toStdString() == mSlicerManagers[i]->GetId()) {
2989       mSlicerManagers[i]->RemoveLink(image1.toStdString());
2990     }
2991   }
2992 }
2993 //------------------------------------------------------------------------------
2994
2995 //------------------------------------------------------------------------------
2996 void vvMainWindow::ChangeImageWithIndexOffset(vvSlicerManager *sm, int slicer, int offset)
2997 {
2998   if(mSlicerManagers.size()==1)
2999     return;
3000
3001   int index = 0;
3002   while(sm != mSlicerManagers[index])
3003     index++;
3004   index = (index+offset+mSlicerManagers.size()) % mSlicerManagers.size();
3005
3006   QTreeWidgetItem* item = GetItemFromSlicerManager(mSlicerManagers[index]);
3007   item->setData(slicer+1,Qt::CheckStateRole,2);         //change checkbox
3008   CurrentImageChanged(mSlicerManagers[index]->GetId()); //select new image
3009   DisplayChanged(item,slicer+1);
3010 }
3011 //------------------------------------------------------------------------------
3012 void vvMainWindow::HorizontalSliderMoved(int value,int column, int slicer_index)
3013 {
3014   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
3015     if (DataTree->topLevelItem(i)->data(column,Qt::CheckStateRole).toInt() > 1) {
3016       //i is the SlicerManager that is in charge of this slicer.
3017       if (mSlicerManagers[i]->IsInvolvedInFusionSequence()) {
3018         //if the slicerManager is involved in a fusionSequence as the secondary sequence, then update the slider position in the overlay panel and everything accordingly
3019         if (mSlicerManagers[i]->IsSecondarySequenceOfFusionSequence()) {
3020           overlayPanel->updateFusionSequenceSliderValueFromWindow(value, true);
3021         }
3022         else { //if this is the primary sequence that has been modified
3023           if (mSlicerManagers[i]->GetFusionSequenceTemporalSyncFlag()) {
3024             //WARNING: for some obscure reason, there are problems when accessing mSlicerManagers[mSlicerManagers[i]->GetFusionSequenceIndexOfLinkedManager()]->GetFusionSequenceFrameIndex();
3025
3026             int estimatedValue=0;
3027             //estimate a corresponding time index for the secondary (US) sequence, and update it accordingly.
3028             estimatedValue = mSlicerManagers[i]->GetFusionSequenceCorrespondances()[ value ];
3029             //TODO: at the moment, there is a loop in TSlice modifications
3030             //modifying sequence 1 causes seq 2 to update, which in turns update seq1...
3031             //I disable control on seq1 at the moment.
3032             //overlayPanel->updateFusionSequenceSliderValueFromWindow(estimatedValue, true);
3033           }
3034         }
3035       }
3036
3037       for (int j = 0; j < 4; j++) {
3038         mSlicerManagers[i]->SetTSliceInSlicer(value,j);
3039       }
3040       mSlicerManagers[i]->GetSlicer(slicer_index)->Render();
3041       break;
3042     }
3043   }
3044 }
3045 //------------------------------------------------------------------------------
3046
3047
3048 //------------------------------------------------------------------------------
3049 void vvMainWindow::NOHorizontalSliderMoved()
3050 {
3051   // if (mCurrentTime == NOHorizontalSlider->value()) return;
3052   HorizontalSliderMoved(NOHorizontalSlider->value(),COLUMN_UL_VIEW,0);
3053   //  mCurrentTime = NOHorizontalSlider->value();
3054 }
3055 //------------------------------------------------------------------------------
3056
3057
3058 //------------------------------------------------------------------------------
3059 void vvMainWindow::NEHorizontalSliderMoved()
3060 {
3061   // if (mCurrentTime == NEHorizontalSlider->value()) return;
3062   HorizontalSliderMoved(NEHorizontalSlider->value(),COLUMN_UR_VIEW,1);
3063   //  mCurrentTime = NEHorizontalSlider->value();
3064 }
3065 //------------------------------------------------------------------------------
3066
3067
3068 //------------------------------------------------------------------------------
3069 void vvMainWindow::SOHorizontalSliderMoved()
3070 {
3071   // if (mCurrentTime == SOHorizontalSlider->value()) return;
3072   HorizontalSliderMoved(SOHorizontalSlider->value(),COLUMN_DL_VIEW,2);
3073   // mCurrentTime = SOHorizontalSlider->value();
3074 }
3075 //------------------------------------------------------------------------------
3076
3077
3078 //------------------------------------------------------------------------------
3079 void vvMainWindow::SEHorizontalSliderMoved()
3080 {
3081   // if (mCurrentTime == SEHorizontalSlider->value()) return;
3082   HorizontalSliderMoved(SEHorizontalSlider->value(),COLUMN_DR_VIEW,3);
3083   // mCurrentTime = SEHorizontalSlider->value();
3084 }
3085 //------------------------------------------------------------------------------
3086
3087 //------------------------------------------------------------------------------
3088 void vvMainWindow::NOVerticalSliderChanged()
3089 {
3090   static int value=-1;
3091   if (value == NOVerticalSlider->value()) return;
3092   else value = NOVerticalSlider->value();
3093   //  int value = NOVerticalSlider->value();
3094   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
3095     if (DataTree->topLevelItem(i)->data(COLUMN_UL_VIEW,Qt::CheckStateRole).toInt() > 1) {
3096       if (mSlicerManagers[i]->GetSlicer(0)->GetSlice() != value) {
3097         mSlicerManagers[i]->GetSlicer(0)->SetSlice(value);
3098         mSlicerManagers[i]->VerticalSliderHasChanged(0, value);
3099
3100         // If nor Update/Render -> slider not work
3101         // only render = ok navigation, but for contour Update needed but slower ?
3102
3103         mSlicerManagers[i]->UpdateSlice(0);  // <-- DS add this. Not too much update ? YES. but needed for ImageContour ...
3104         //mSlicerManagers[i]->GetSlicer(0)->Render(); // <-- DS add this, needed for contour, seems ok ? not too slow ?
3105       }
3106       break;
3107     }
3108   }
3109 }
3110 //------------------------------------------------------------------------------
3111
3112
3113 //------------------------------------------------------------------------------
3114 void vvMainWindow::NEVerticalSliderChanged()
3115 {
3116   static int value=-1;
3117   if (value == NEVerticalSlider->value()) return;
3118   else value = NEVerticalSlider->value();
3119   //  int value = NEVerticalSlider->value();
3120   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
3121     if (DataTree->topLevelItem(i)->data(COLUMN_UR_VIEW,Qt::CheckStateRole).toInt() > 1) {
3122       if (mSlicerManagers[i]->GetSlicer(1)->GetSlice() != value) {
3123         mSlicerManagers[i]->GetSlicer(1)->SetSlice(value);
3124         mSlicerManagers[i]->VerticalSliderHasChanged(1, value);
3125         mSlicerManagers[i]->UpdateSlice(1);
3126         //mSlicerManagers[i]->GetSlicer(1)->Render(); // <-- DS add this, needed for contour, seems ok ? not too slow ?
3127       }
3128       break;
3129     }
3130   }
3131 }
3132 //------------------------------------------------------------------------------
3133
3134
3135 //------------------------------------------------------------------------------
3136 void vvMainWindow::SOVerticalSliderChanged()
3137 {
3138   static int value=-1;
3139   if (value == SOVerticalSlider->value()) return;
3140   else value = SOVerticalSlider->value();
3141   //int value = SOVerticalSlider->value();
3142   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
3143     if (DataTree->topLevelItem(i)->data(COLUMN_DL_VIEW,Qt::CheckStateRole).toInt() > 1) {
3144       if (mSlicerManagers[i]->GetSlicer(2)->GetSlice() != value) {
3145         mSlicerManagers[i]->GetSlicer(2)->SetSlice(value);
3146         mSlicerManagers[i]->VerticalSliderHasChanged(2, value);
3147         mSlicerManagers[i]->UpdateSlice(2);
3148         //mSlicerManagers[i]->GetSlicer(2)->Render(); // <-- DS add this, needed for contour, seems ok ? not too slow ?
3149       }
3150       // else { DD("avoid SOVerticalSlider slicer update"); }
3151       break;
3152     }
3153   }
3154 }
3155 //------------------------------------------------------------------------------
3156
3157
3158 //------------------------------------------------------------------------------
3159 void vvMainWindow::SEVerticalSliderChanged()
3160 {
3161   static int value=-1;
3162   if (value == SEVerticalSlider->value()) return;
3163   else value = SEVerticalSlider->value();
3164   // int value = SEVerticalSlider->value();
3165   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
3166     if (DataTree->topLevelItem(i)->data(COLUMN_DR_VIEW,Qt::CheckStateRole).toInt() > 1) {
3167       if (mSlicerManagers[i]->GetSlicer(3)->GetSlice() != value) {
3168         mSlicerManagers[i]->GetSlicer(3)->SetSlice(value);
3169         mSlicerManagers[i]->VerticalSliderHasChanged(3, value);
3170         mSlicerManagers[i]->UpdateSlice(3);
3171         //mSlicerManagers[i]->GetSlicer(3)->Render(); // <-- DS add this, needed for contour, seems ok ? not too slow ?
3172       }
3173       break;
3174     }
3175   }
3176 }
3177 //------------------------------------------------------------------------------
3178
3179
3180 //------------------------------------------------------------------------------
3181 void vvMainWindow::UpdateSlice(int slicer, int slice)
3182 {
3183   // DD("vvMainWindow::UpdateSlice");
3184   //   DD(slicer);
3185   //   DD(slice);
3186   if (slicer == 0) {
3187     //    if (slice != NOVerticalSlider->value())
3188     NOVerticalSlider->setValue(slice);
3189   } else {
3190     if (slicer == 1)
3191       NEVerticalSlider->setValue(slice);
3192     else {
3193       if (slicer == 2)
3194         SOVerticalSlider->setValue(slice);
3195       else {
3196         if (slicer == 3)
3197           SEVerticalSlider->setValue(slice);
3198       }
3199     }
3200   }
3201   // DD("vvMainWindow:UpdateSlice END");
3202 }
3203 //------------------------------------------------------------------------------
3204
3205
3206 //------------------------------------------------------------------------------
3207 void vvMainWindow::UpdateTSlice(int slicer, int slice, int code)
3208 {
3209   //FusionSequence: the slider value should be updated for slicers which show the same sequence as requested
3210   bool doUpdate=false;
3211   if (code==-1) doUpdate=true;
3212   else {
3213     for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
3214       if (DataTree->topLevelItem(i)->data(slicer+1,Qt::CheckStateRole).toInt() > 1) {
3215         //i is the active SlicerManager
3216         if (mSlicerManagers[i]->GetFusionSequenceInvolvmentCode()==code) doUpdate=true;
3217         break;
3218       }
3219     }
3220   }
3221   if (!doUpdate) return;
3222
3223   switch (slicer) {
3224   case 0:
3225     if (NOHorizontalSlider->value()==slice) return;
3226     NOHorizontalSlider->setValue(slice);
3227     break;
3228   case 1:
3229     if (NEHorizontalSlider->value()==slice) return;
3230     NEHorizontalSlider->setValue(slice);
3231     break;
3232   case 2:
3233     if (SOHorizontalSlider->value()==slice) return;
3234     SOHorizontalSlider->setValue(slice);
3235     break;
3236   case 3:
3237     if (SEHorizontalSlider->value()==slice) return;
3238     SEHorizontalSlider->setValue(slice);
3239     break;
3240   }
3241 }
3242 //------------------------------------------------------------------------------
3243
3244
3245 //------------------------------------------------------------------------------
3246 void vvMainWindow::UpdateSliceRange(int slicer, int min, int max, int tmin, int tmax)
3247 {
3248   //int position = int((min+max)/2);
3249   int position = mSlicerManagers[mCurrentPickedImageIndex]->GetSlicer(slicer)->GetSlice();
3250   if (slicer == 0) {
3251     NOVerticalSlider->setRange(min,max);
3252     NOHorizontalSlider->setRange(tmin,tmax);
3253     NOVerticalSlider->setValue(position);
3254   } else if (slicer == 1) {
3255     NEVerticalSlider->setRange(min,max);
3256     NEHorizontalSlider->setRange(tmin,tmax);
3257     NEVerticalSlider->setValue(position);
3258   } else if (slicer == 2) {
3259     SOVerticalSlider->setRange(min,max);
3260     SOHorizontalSlider->setRange(tmin,tmax);
3261     SOVerticalSlider->setValue(position);
3262   } else if (slicer == 3) {
3263     SEVerticalSlider->setRange(min,max);
3264     SEHorizontalSlider->setRange(tmin,tmax);
3265     SEVerticalSlider->setValue(position);
3266   }
3267 }
3268 //------------------------------------------------------------------------------
3269
3270
3271 //------------------------------------------------------------------------------
3272 void vvMainWindow::SaveNOScreenshot()
3273 {
3274   SaveScreenshot(NOViewWidget);
3275 }
3276 //------------------------------------------------------------------------------
3277
3278
3279 //------------------------------------------------------------------------------
3280 void vvMainWindow::SaveNEScreenshot()
3281 {
3282   SaveScreenshot(NEViewWidget);
3283 }
3284 //------------------------------------------------------------------------------
3285
3286
3287 //------------------------------------------------------------------------------
3288 void vvMainWindow::SaveSOScreenshot()
3289 {
3290   SaveScreenshot(SOViewWidget);
3291 }
3292 //------------------------------------------------------------------------------
3293
3294
3295 //------------------------------------------------------------------------------
3296 void vvMainWindow::SaveSEScreenshot()
3297 {
3298   SaveScreenshot(SEViewWidget);
3299 }
3300 //------------------------------------------------------------------------------
3301
3302
3303 //------------------------------------------------------------------------------
3304 void vvMainWindow::SaveScreenshotAllSlices()
3305 {
3306 #if (VTK_MAJOR_VERSION == 8 && VTK_MINOR_VERSION >= 1) || VTK_MAJOR_VERSION >= 9
3307   QVTKOpenGLNativeWidget *widget = NOViewWidget;
3308 #else
3309   QVTKWidget *widget = NOViewWidget;
3310 #endif
3311
3312   int index = 0;// GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
3313   vvSlicerManager * SM = mSlicerManagers[index];
3314   vvImage * image = SM->GetImage();
3315   vvSlicer * slicer = SM->GetSlicer(0);
3316   int orientation = slicer->GetOrientation();
3317   int nbSlices = image->GetSize()[orientation];
3318   vtkSmartPointer<vtkRenderWindow>  renderWindow = widget->GetRenderWindow();
3319
3320   // Select filename base
3321   QString filename = QFileDialog::getSaveFileName(this,
3322     tr("Save As (filename will be completed by slice number)"),
3323     itksys::SystemTools::GetFilenamePath(mSlicerManagers[index]->GetFileName()).c_str(),
3324     "Images( *.png);;Images( *.jpg)");
3325
3326   // Loop on slices
3327   for(int i=0; i<nbSlices; i++) {
3328     // Change the slice
3329     slicer->SetSlice(i); // -> change the slice of the current slicer
3330     SM->UpdateSlice(0); // --> this one emit UpdateSlice
3331     QCoreApplication::flush(); // -> needed to force display of contours
3332
3333     // Screenshot
3334     vtkSmartPointer<vtkWindowToImageFilter> windowToImageFilter = vtkSmartPointer<vtkWindowToImageFilter>::New();
3335     windowToImageFilter->SetInput(renderWindow);
3336 #if (VTK_MAJOR_VERSION >= 8 && VTK_MINOR_VERSION >= 1) || VTK_MAJOR_VERSION >= 9
3337     windowToImageFilter->SetScale(1);
3338 #else
3339     windowToImageFilter->SetMagnification(1);
3340 #endif
3341     windowToImageFilter->SetInputBufferTypeToRGBA(); //also record the alpha (transparency) channel
3342     windowToImageFilter->Update();
3343
3344     vtkSmartPointer<vtkPNGWriter> writer = vtkSmartPointer<vtkPNGWriter>::New();
3345     std::string fn = itksys::SystemTools::GetFilenameWithoutLastExtension(filename.toStdString());
3346     std::string num = clitk::toString(i);
3347     if (i<10) num = "0"+num;
3348     if (i<100) num = "0"+num;
3349     if (i<1000) num = "0"+num;
3350
3351     fn = itksys::SystemTools::GetFilenamePath(filename.toStdString()) + "/"+ fn
3352       + "_" + num + itksys::SystemTools::GetFilenameLastExtension(filename.toStdString());
3353     writer->SetFileName(fn.c_str());
3354 #if VTK_MAJOR_VERSION <= 5
3355     writer->SetInput(windowToImageFilter->GetOutput());
3356 #else
3357     writer->SetInputConnection(windowToImageFilter->GetOutputPort());
3358 #endif
3359     writer->Write();
3360   }
3361 }
3362 //------------------------------------------------------------------------------
3363
3364
3365 //------------------------------------------------------------------------------
3366 #if (VTK_MAJOR_VERSION == 8 && VTK_MINOR_VERSION >= 1) || VTK_MAJOR_VERSION >= 9
3367 void vvMainWindow::SaveScreenshot(QVTKOpenGLNativeWidget *widget)
3368 #else
3369 void vvMainWindow::SaveScreenshot(QVTKWidget *widget)
3370 #endif
3371 {
3372   QString Extensions = "Images( *.png);;";
3373   Extensions += "Images( *.jpg);;";
3374   Extensions += "Images( *.bmp);;";
3375   Extensions += "Images( *.tif);;";
3376   Extensions += "Images( *.ppm)";
3377 #if defined(VTK_USE_FFMPEG_ENCODER) || defined(VTK_USE_VIDEO_FOR_WINDOWS)
3378   Extensions += ";;Video( *.avi)";
3379 #endif
3380 #ifdef VTK_USE_MPEG2_ENCODER
3381   Extensions += ";;Video( *.mpg)";
3382 #endif
3383   Extensions += ";;Video( *.gif)";
3384
3385   int smIndex=GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
3386   QString fileName = QFileDialog::getSaveFileName(this,
3387     tr("Save As"),
3388     itksys::SystemTools::GetFilenamePath(mSlicerManagers[smIndex]->GetFileName()).c_str(),
3389     Extensions);
3390
3391   if (!fileName.isEmpty()) {
3392     vtkSmartPointer<vtkWindowToImageFilter> w2i = vtkSmartPointer<vtkWindowToImageFilter>::New();
3393     w2i->SetInput(widget->GetRenderWindow());
3394 #if (VTK_MAJOR_VERSION >= 8 && VTK_MINOR_VERSION >= 1) || VTK_MAJOR_VERSION >= 9
3395     w2i->SetScale(1);
3396 #else
3397     w2i->SetMagnification(1);
3398 #endif
3399     w2i->SetInputBufferTypeToRGBA(); //also record the alpha (transparency) channel
3400     w2i->Update();
3401     vtkImageData *image = w2i->GetOutput();
3402
3403     std::string ext(itksys::SystemTools::GetFilenameLastExtension(fileName.toStdString()));
3404
3405     // Image
3406     vtkImageWriter *imgwriter = NULL;
3407     if (ext==".bmp")
3408       imgwriter = vtkBMPWriter::New();
3409     else if (ext==".tif")
3410       imgwriter = vtkTIFFWriter::New();
3411     else if (ext==".ppm")
3412       imgwriter = vtkPNMWriter::New();
3413     else if (ext==".png")
3414       imgwriter = vtkPNGWriter::New();
3415     else if (ext==".jpg")
3416       imgwriter = vtkJPEGWriter::New();
3417
3418     // Snapshot image if not null
3419     if(imgwriter!=NULL) {
3420 #if VTK_MAJOR_VERSION <= 5
3421       imgwriter->SetInput(image);
3422 #else
3423       imgwriter->SetInputConnection(w2i->GetOutputPort());
3424 #endif
3425       imgwriter->SetFileName(fileName.toStdString().c_str());
3426       imgwriter->Write();
3427       return;
3428     }
3429
3430     // Video
3431     vtkGenericMovieWriter *vidwriter = NULL;
3432     if (ext==".gif") {
3433       vvAnimatedGIFWriter *gif = vvAnimatedGIFWriter::New();
3434       vidwriter = gif;
3435
3436       // FPS
3437       bool ok;
3438       int fps = QInputDialog::getInt(this, tr("Number of frames per second"),
3439         tr("FPS:"), 5, 0, 1000, 1, &ok);
3440       if(ok)
3441         gif->SetRate(fps);
3442
3443       // Loops
3444       int loops = QInputDialog::getInt(this, tr("Loops"),
3445         tr("Number of loops (0 means infinite):"), 0, 0, 1000000000, 1, &ok);
3446       if(ok)
3447         gif->SetLoops(loops);
3448
3449       // Dithering
3450       QString msg = "Would you like to activate dithering?";
3451       QMessageBox msgBox(QMessageBox::Question, tr("Dithering"),msg, 0, this);
3452       msgBox.addButton(tr("Yes"), QMessageBox::AcceptRole);
3453       msgBox.addButton(tr("No"), QMessageBox::RejectRole);
3454       gif->SetDither(msgBox.exec() == QMessageBox::AcceptRole);
3455     }
3456 #ifdef VTK_USE_VIDEO_FOR_WINDOWS
3457     if (ext==".avi") {
3458       vtkAVIWriter *mpg = vtkAVIWriter::New();
3459       vidwriter = mpg;
3460       mpg->SetQuality(2);
3461       bool ok;
3462       int fps = QInputDialog::getInt(this, tr("Number of frames per second"),
3463         tr("FPS:"), 5, 0, 1024, 1, &ok);
3464       if(!ok)
3465         fps = 5;
3466       mpg->SetRate(fps);
3467     }
3468 #endif
3469 #ifdef VTK_USE_FFMPEG_ENCODER
3470     if (ext==".avi") {
3471       vtkFFMPEGWriter *mpg = vtkFFMPEGWriter::New();
3472       vidwriter = mpg;
3473       mpg->SetQuality(2);
3474       bool ok;
3475       int fps = QInputDialog::getInt(this, tr("Number of frames per second"),
3476         tr("FPS:"), 5, 0, 1024, 1, &ok);
3477       if(!ok)
3478         fps = 5;
3479       mpg->SetRate(fps);
3480       mpg->SetBitRateTolerance(int(ceil(12.0*1024*1024/fps)));
3481     }
3482 #endif
3483 #ifdef VTK_USE_MPEG2_ENCODER
3484     if (ext==".mpg") {
3485       vtkMPEG2Writer *mpg = vtkMPEG2Writer::New();
3486       vidwriter = mpg;
3487     }
3488 #endif
3489
3490     // Take video if not null
3491     if(vidwriter!=NULL){
3492 #if VTK_MAJOR_VERSION <= 5
3493       vidwriter->SetInput(image);
3494 #else
3495       vidwriter->SetInputConnection(w2i->GetOutputPort());
3496 #endif
3497       vidwriter->SetFileName(fileName.toStdString().c_str());
3498       vidwriter->Start();
3499       int nSlice = mSlicerManagers[smIndex]->GetSlicer(0)->GetTMax();
3500       for(int i=0; i<=nSlice; i++) {
3501         mSlicerManagers[smIndex]->SetNextTSlice(0);
3502         vtkSmartPointer<vtkWindowToImageFilter> w2i = vtkSmartPointer<vtkWindowToImageFilter>::New();
3503         w2i->SetInput(widget->GetRenderWindow());
3504         w2i->Update();
3505 #if VTK_MAJOR_VERSION <= 5
3506         vidwriter->SetInput(w2i->GetOutput());
3507 #else
3508         vidwriter->SetInputConnection(w2i->GetOutputPort());
3509 #endif
3510         vidwriter->Write();
3511       }
3512       vidwriter->End();
3513       vidwriter->Delete();
3514       return;
3515     }
3516
3517     QMessageBox::information(this,tr("Problem saving screenshot !"),tr("Cannot save image.\nPlease set a file extension !!!"));
3518   }
3519 }
3520 //------------------------------------------------------------------------------
3521
3522
3523 //------------------------------------------------------------------------------
3524 void vvMainWindow::GoToCursor()
3525 {
3526   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
3527   for (int column = 1; column < 5; column++) {
3528     if (DataTree->selectedItems()[0]->data(column,Qt::CheckStateRole).toInt() > 1) {
3529       double* cursorPos = mSlicerManagers[index]->GetSlicer(column-1)->GetCursorPosition();
3530       mSlicerManagers[index]->GetSlicer(column-1)->SetCurrentPosition(
3531         cursorPos[0],cursorPos[1],cursorPos[2],cursorPos[3]);
3532       mSlicerManagers[index]->UpdateViews(1,column-1);
3533       mSlicerManagers[index]->UpdateLinked(column-1);
3534       break;
3535     }
3536   }
3537 }
3538 //------------------------------------------------------------------------------
3539
3540 //------------------------------------------------------------------------------
3541 void vvMainWindow::GoToLandmark()
3542 {
3543   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
3544   for (int column = 1; column < 5; column++) {
3545     if (DataTree->selectedItems()[0]->data(column,Qt::CheckStateRole).toInt() > 1) {
3546       double* cursorPos = landmarksPanel->GetSelectedPoint();
3547       mSlicerManagers[index]->GetSlicer(column-1)->SetCurrentPosition(
3548         cursorPos[0],cursorPos[1],cursorPos[2],cursorPos[3]);
3549       mSlicerManagers[index]->UpdateViews(1,column-1);
3550       mSlicerManagers[index]->UpdateLinked(column-1);
3551       break;
3552     }
3553   }
3554 }
3555 //------------------------------------------------------------------------------
3556
3557 //------------------------------------------------------------------------------
3558 void vvMainWindow::PlayPause()
3559 {
3560   if (playMode) {
3561     playMode = 0;
3562     playButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/player_play.png")));
3563     ImageInfoChanged();
3564     return;
3565   } else {
3566     int image_number=DataTree->topLevelItemCount();
3567     bool has_temporal;
3568     for (int i=0; i<image_number; i++)
3569       if (mSlicerManagers[i]->GetSlicer(0)->GetTMax() > 0) {
3570         has_temporal=true;
3571         break;
3572       }
3573       if (has_temporal) {
3574         playMode = 1;
3575         playButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/player_pause.png")));
3576         QTimer::singleShot(1000/mFrameRate, this, SLOT(PlayNext()));
3577       }
3578   }
3579 }
3580 //------------------------------------------------------------------------------
3581
3582 //------------------------------------------------------------------------------
3583 void vvMainWindow::PlayNext()
3584 {
3585   if (playMode && !this->isHidden()) {
3586     int image_number=DataTree->topLevelItemCount();
3587     ///Only play one slicer per SM, and only if the SM is being displayed
3588     for (int i=0; i<image_number; i++)
3589       for (int j=0; j<4; j++)
3590         if (mSlicerManagers[i]->GetSlicer(0)->GetTMax() > 0 &&
3591           DataTree->topLevelItem(i)->data(j+1,Qt::CheckStateRole).toInt() > 0) {
3592             mSlicerManagers[i]->SetNextTSlice(j);
3593             break;
3594         }
3595         QTimer::singleShot(1000/mFrameRate, this, SLOT(PlayNext()));
3596   }
3597 }
3598 //------------------------------------------------------------------------------
3599
3600 void vvMainWindow::ShowLastImage()
3601 {
3602   if (mSlicerManagers.size() > 1) {
3603     QTreeWidgetItem * item=DataTree->topLevelItem(DataTree->topLevelItemCount()-1);
3604     CurrentImageChanged(mSlicerManagers.back()->GetId()); //select new image
3605     item->setData(1,Qt::CheckStateRole,2); //show the new image in the first panel
3606     //mSlicerManagers[GetSlicerIndexFromItem(item)]->GetSlicer(0)->SetActorVisibility("image", 0, 1); //Set the Last Image visibles
3607     DisplayChanged(item,1);
3608   }
3609 }
3610
3611 //------------------------------------------------------------------------------
3612 void vvMainWindow::UpdateRenderWindows()
3613 {
3614   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
3615       for (unsigned int j = 0; j < 4; ++j) {
3616         mSlicerManagers[i]->GetSlicer(j)->RemoveLandmarks();
3617         mSlicerManagers[i]->GetSlicer(j)->DisplayLandmarks();
3618       }
3619   }
3620   if (NOViewWidget->GetRenderWindow()) NOViewWidget->GetRenderWindow()->Render();
3621   if (NEViewWidget->GetRenderWindow()) NEViewWidget->GetRenderWindow()->Render();
3622   if (SOViewWidget->GetRenderWindow()) SOViewWidget->GetRenderWindow()->Render();
3623   if (SEViewWidget->GetRenderWindow()) SEViewWidget->GetRenderWindow()->Render();
3624 }
3625 //------------------------------------------------------------------------------
3626
3627 //------------------------------------------------------------------------------
3628 void vvMainWindow::SegmentationOnCurrentImage()
3629 {
3630   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
3631
3632   vvSegmentationDialog segmentation;
3633   segmentation.SetImage(mSlicerManagers[index]->GetSlicer(0)->GetImage());
3634   segmentation.exec();
3635 }
3636 //------------------------------------------------------------------------------
3637
3638 void vvMainWindow::SurfaceViewerLaunch()
3639 {
3640   vvSurfaceViewerDialog surfaceViewer;
3641   surfaceViewer.exec();
3642 }
3643 //------------------------------------------------------------------------------
3644
3645
3646 //------------------------------------------------------------------------------
3647 int vvMainWindow::GetImageDuplicateFilenameNumber(std::string filename)
3648 {
3649   int number=0;
3650   for(unsigned int l=0; l<mSlicerManagers.size(); l++) {
3651     vvSlicerManager * v = mSlicerManagers[l];
3652     if (v->GetBaseFileName() ==
3653       vtksys::SystemTools::GetFilenameName(vtksys::SystemTools::GetFilenameWithoutLastExtension(filename))) {
3654         number = std::max(number, v->GetBaseFileNameNumber()+1);
3655     }
3656   }
3657   return number;
3658 }
3659 //------------------------------------------------------------------------------
3660
3661
3662 //------------------------------------------------------------------------------
3663 vvSlicerManager* vvMainWindow::AddImage(vvImage::Pointer image,std::string filename)
3664 {
3665   // Change filename if another image exist with the same name
3666   int number = GetImageDuplicateFilenameNumber(filename);
3667
3668   // Create new SliceManager
3669   vvSlicerManager* slicer_manager = new vvSlicerManager(4);
3670   slicer_manager->SetImage(image);//, IMAGE, number);
3671   //  filename = filename+"_"+clitk::toString(number);
3672   slicer_manager->SetFilename(filename, number);
3673   mSlicerManagers.push_back(slicer_manager);
3674
3675   //create an item in the tree with good settings
3676   QTreeWidgetItem *item = new QTreeWidgetItem();
3677   item->setData(0,Qt::UserRole,slicer_manager->GetFileName().c_str());//files[i].c_str());
3678   item->setData(1,Qt::UserRole,tr("image"));
3679   item->setData(COLUMN_IMAGE_NAME,Qt::DisplayRole,slicer_manager->GetFileName().c_str());//filename.c_str());
3680   qApp->processEvents();
3681
3682   for (int j = 1; j <= 4; j++) item->setData(j,Qt::CheckStateRole,1);
3683
3684   //Create the buttons for reload and close
3685   qApp->processEvents();
3686   QTreePushButton* cButton = new QTreePushButton;
3687   cButton->setItem(item);
3688   cButton->setColumn(COLUMN_CLOSE_IMAGE);
3689   cButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/exit.png")));
3690   connect(cButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
3691     this,SLOT(CloseImage(QTreeWidgetItem*, int)));
3692
3693   QTreePushButton* rButton = new QTreePushButton;
3694   rButton->setItem(item);
3695   rButton->setColumn(COLUMN_RELOAD_IMAGE);
3696   rButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/rotateright.png")));
3697   rButton->setEnabled(0);
3698   connect(rButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
3699     this,SLOT(ReloadImage(QTreeWidgetItem*, int)));
3700
3701   DataTree->addTopLevelItem(item);
3702   DataTree->setItemWidget(item, COLUMN_CLOSE_IMAGE, cButton);
3703   DataTree->setItemWidget(item, COLUMN_RELOAD_IMAGE, rButton);
3704
3705   //set the id of the image
3706   QString id = QDir::current().absoluteFilePath(slicer_manager->GetFileName().c_str()) + QString::number(mSlicerManagers.size()-1);
3707   item->setData(COLUMN_IMAGE_NAME,Qt::UserRole,id.toStdString().c_str());
3708   mSlicerManagers.back()->SetId(id.toStdString());
3709
3710   linkPanel->addImage(slicer_manager->GetFileName().c_str()// filename
3711     , id.toStdString());
3712
3713   connect(mSlicerManagers.back(), SIGNAL(currentImageChanged(std::string)),
3714     this, SLOT(CurrentImageChanged(std::string)));
3715   connect(mSlicerManagers.back(), SIGNAL(currentPickedImageChanged(std::string)),
3716     this, SLOT(CurrentPickedImageChanged(std::string)));
3717   connect(mSlicerManagers.back(), SIGNAL(UpdatePosition(int, double, double, double, double, double, double, double)),
3718     this, SLOT(MousePositionChanged(int,double, double, double, double, double, double, double)));
3719   connect(mSlicerManagers.back(), SIGNAL(UpdateVector(int, double, double, double, double)),
3720     this, SLOT(VectorChanged(int,double,double,double, double)));
3721   connect(mSlicerManagers.back(), SIGNAL(UpdateOverlay(int, double, double)),
3722     this, SLOT(OverlayChanged(int,double,double)));
3723   connect(mSlicerManagers.back(), SIGNAL(UpdateFusion(int, double)),
3724     this, SLOT(FusionChanged(int,double)));
3725   //connect(mSlicerManagers.back(), SIGNAL(UpdateFusionSequence(int, bool, unsigned int)),
3726   //  this, SLOT(FusionSequenceChanged(int, bool, unsigned int)));
3727   connect(mSlicerManagers.back(), SIGNAL(WindowLevelChanged()),
3728     this,SLOT(WindowLevelChanged()));
3729   connect(mSlicerManagers.back(), SIGNAL(UpdateSlice(int,int)),
3730     this,SLOT(UpdateSlice(int,int)));
3731   connect(mSlicerManagers.back(), SIGNAL(UpdateTSlice(int, int, int)),
3732     this,SLOT(UpdateTSlice(int, int, int)));
3733   connect(mSlicerManagers.back(), SIGNAL(UpdateTSlice(int, int, int)),
3734     this,SLOT(ImageInfoChanged()));
3735   connect(mSlicerManagers.back(), SIGNAL(UpdateSliceRange(int,int,int,int,int)),
3736     this,SLOT(UpdateSliceRange(int,int,int,int,int)));
3737   connect(mSlicerManagers.back(), SIGNAL(UpdateLinkManager(std::string,int,double,double,double,int)),
3738     this,SLOT(UpdateLinkManager(std::string,int,double,double,double,int)));
3739   connect(mSlicerManagers.back(), SIGNAL(UpdateLinkedNavigation(std::string,vvSlicerManager*,vvSlicer*)),
3740     this,SLOT(UpdateLinkedNavigation(std::string,vvSlicerManager*,vvSlicer*)));
3741   connect(mSlicerManagers.back(), SIGNAL(ChangeImageWithIndexOffset(vvSlicerManager*,int,int)),
3742     this,SLOT(ChangeImageWithIndexOffset(vvSlicerManager*,int,int)));
3743   connect(mSlicerManagers.back(), SIGNAL(LandmarkAdded()),landmarksPanel,SLOT(AddPoint()));
3744   connect(landmarksPanel,SIGNAL(UpdateLandmarkTransform()), mSlicerManagers.back(), SLOT(UpdateLandmark()));
3745
3746
3747
3748   InitSlicers();
3749   UpdateTree();
3750   qApp->processEvents();
3751   InitDisplay();
3752   ShowLastImage();
3753   qApp->processEvents();
3754   // End
3755   ImageInfoChanged();
3756   return slicer_manager;
3757 }
3758 //------------------------------------------------------------------------------
3759
3760
3761 //------------------------------------------------------------------------------
3762 void vvMainWindow::UpdateCurrentSlicer()
3763 {
3764   int index = -1;
3765   if (DataTree->selectedItems().size() > 0) {
3766     index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
3767   }
3768   mSlicerManagerCurrentIndex = index;
3769 }
3770 //------------------------------------------------------------------------------