vv/vvMainWindow.cxx

   1 /*=========================================================================
   2 Program:   vv                     http://www.creatis.insa-lyon.fr/rio/vv
   3
   4 Authors belong to:
   5 - University of LYON              http://www.universite-lyon.fr/
   6 - Léon Bérard cancer center       http://www.centreleonberard.fr
   7 - CREATIS CNRS laboratory         http://www.creatis.insa-lyon.fr
   8
   9 This software is distributed WITHOUT ANY WARRANTY; without even
  10 the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
  11 PURPOSE.  See the copyright notices for more information.
  12
  13 It is distributed under dual licence
  14
  15 - BSD        See included LICENSE.txt file
  16 - CeCILL-B   http://www.cecill.info/licences/Licence_CeCILL-B_V1-en.html
  17 ===========================================================================**/
  18
  19 #include <algorithm>
  20 #include <QMessageBox>
  21 #include <QInputDialog>
  22 #include <QTimer>
  23 #include "QTreePushButton.h"
  24 #include <QUrl>
  25 #include <QSettings>
  26 #include <QShortcut>
  27
  28 // VV include
  29 #include "vvMainWindow.h"
  30 #include "vvHelpDialog.h"
  31 #include "vvRegisterForm.h"
  32 #include "vvDocumentation.h"
  33 #include "vvProgressDialog.h"
  34 #include "vvQDicomSeriesSelector.h"
  35 #include "vvSlicerManager.h"
  36 #include "clitkImageCommon.h"
  37 #include "vvSlicer.h"
  38 #include "vvInteractorStyleNavigator.h"
  39 #include "vvImageWriter.h"
  40 #include "vvSegmentationDialog.h"
  41 #include "vvSurfaceViewerDialog.h"
  42 #include "vvDeformationDialog.h"
  43 #include "vvImageWarp.h"
  44 #include "vvUtils.h"
  45 #include "vvMidPosition.h"
  46 #include "vvMesh.h"
  47 #include "vvStructSelector.h"
  48 #include "vvMeshReader.h"
  49 #include "vvSaveState.h"
  50 #include "vvReadState.h"
  51 #if CLITK_USE_PACS_CONNECTION
  52 #include "vvQPacsConnection.h"
  53 #endif
  54 #include "clitkConfiguration.h"
  55 #include "clitkMatrix.h"
  56 #ifdef Q_OS_OSX
  57 # include "vvOSXHelper.h"
  58 #endif
  59
  60 // ITK include
  61 #include <itkImage.h>
  62 #include <itkImageFileReader.h>
  63 #include <itkByteSwapper.h>
  64 #include <itkCommand.h>
  65 #include <itkNumericSeriesFileNames.h>
  66
  67 // VTK include
  68 #include <vtkImageMapper3D.h>
  69 #include <vtkInformation.h>
  70 #include <vtkVersion.h>
  71 #include <vtkImageData.h>
  72 #include <vtkImageActor.h>
  73 #include <vtkCornerAnnotation.h>
  74 #include <vtkRenderWindow.h>
  75 #include <vtkRenderWindowInteractor.h>
  76 #include <vtkRenderer.h>
  77 #include <vtkRendererCollection.h>
  78 #include <vtkWindowToImageFilter.h>
  79 #include <vtkBMPWriter.h>
  80 #include <vtkTIFFWriter.h>
  81 #include <vtkPNMWriter.h>
  82 #include <vtkPNGWriter.h>
  83 #include <vtkJPEGWriter.h>
  84 #include <vtkGenericMovieWriter.h>
  85 #include <vvAnimatedGIFWriter.h>
  86 #ifdef VTK_USE_VIDEO_FOR_WINDOWS
  87 #  include <vtkAVIWriter.h>
  88 #endif
  89 #ifdef VTK_USE_FFMPEG_ENCODER
  90 #  include <vtkFFMPEGWriter.h>
  91 #endif
  92 #ifdef VTK_USE_MPEG2_ENCODER
  93 #  include <vtkMPEG2Writer.h>
  94 #endif
  95 #include <vtkMatrix4x4.h>
  96 #include <vtkTransform.h>
  97
  98 // Standard includes
  99 #include <iostream>
 100 #include <fstream>
 101 #include <sstream>
 102 #include <iomanip>
 103
 104 #define COLUMN_TREE 0
 105 #define COLUMN_UL_VIEW 1
 106 #define COLUMN_UR_VIEW 2
 107 #define COLUMN_DL_VIEW 3
 108 #define COLUMN_DR_VIEW 4
 109 #define COLUMN_CLOSE_IMAGE 5
 110 #define COLUMN_RELOAD_IMAGE 6
 111 #define COLUMN_IMAGE_NAME 7
 112
 113 #include <extensions.h>
 114
 115
 116 /*Data Tree values
 117 0,Qt::UserRole full filename
 118 1,Qt::CheckStateRole checkbutton UL View
 119 1,Qt::UserRole overlay, fusion or vector
 120 2,Qt::CheckStateRole checkbutton UR View
 121 3,Qt::CheckStateRole checkbutton DL View
 122 4,Qt::CheckStateRole checkbutton DR View
 123 5,0  short filename
 124 5,Qt::UserRole mSlicerManager id*/
 125
 126 //------------------------------------------------------------------------------
 127 vvMainWindow::vvMainWindow():vvMainWindowBase()
 128 {
 129   setupUi(this); // this sets up the GUI
 130
 131   setDicomClient();
 132
 133   //Qt::WindowFlags flags = windowFlags();
 134   //setWindowFlags(flags | Qt::WindowStaysOnTopHint);
 135
 136   mInputPathName = "";
 137   mMenuTools = menuTools;
 138   //  mMenuSegmentation = menuSegmentation;
 139   mContextMenu = &contextMenu;
 140   mMenuExperimentalTools = menuExperimental;
 141   mMainWidget = this;
 142   mCurrentTime = -1;
 143   mCurrentSelectedImageId = "";
 144   mCurrentPickedImageId = "";
 145   mCurrentPickedImageIndex = 0;
 146
 147   //Init the contextMenu
 148   this->setContextMenuPolicy(Qt::CustomContextMenu);
 149   contextActions.resize(0);
 150   QAction* actionOpen_new_image = contextMenu.addAction(QIcon(QString::fromUtf8(":/common/icons/fileopen.png")),
 151     tr("O&pen new Image"));
 152   connect(actionOpen_new_image,SIGNAL(triggered()),this,SLOT(OpenImages()));
 153   contextActions.push_back(actionOpen_new_image);
 154   contextMenu.addSeparator();
 155
 156   QAction* actionClose_Image = contextMenu.addAction(QIcon(QString::fromUtf8(":/common/icons/exit.png")),
 157     tr("Close Current Image"));
 158   connect(actionClose_Image,SIGNAL(triggered()),this,SLOT(CloseImage()));
 159   contextActions.push_back(actionClose_Image);
 160
 161   QAction* actionReload_image = contextMenu.addAction(QIcon(QString::fromUtf8(":/common/icons/rotateright.png")),
 162     tr("Reload Current Image"));
 163   connect(actionReload_image,SIGNAL(triggered()),this,SLOT(ReloadImage()));
 164   contextActions.push_back(actionReload_image);
 165
 166   QAction* actionSave_image = contextMenu.addAction(QIcon(QString::fromUtf8(":/common/icons/filesave.png")),
 167     tr("Save Current Image"));
 168   connect(actionSave_image,SIGNAL(triggered()),this,SLOT(SaveAs()));
 169   contextActions.push_back(actionSave_image);
 170
 171   QAction* actionSave_state = contextMenu.addAction(QIcon(QString::fromUtf8(":/common/icons/filesave.png")),
 172     tr("Save Current State"));
 173   connect(actionSave_state,SIGNAL(triggered()),this,SLOT(SaveCurrentState()));
 174   contextActions.push_back(actionSave_state);
 175
 176   QAction* actionRead_state = contextMenu.addAction(QIcon(QString::fromUtf8(":/common/icons/filesave.png")),
 177     tr("Read Saved State"));
 178   connect(actionRead_state,SIGNAL(triggered()),this,SLOT(ReadSavedState()));
 179   contextActions.push_back(actionRead_state);
 180
 181   contextMenu.addSeparator();
 182
 183   contextMenu.addAction(actionAdd_VF_to_current_Image);
 184   contextActions.push_back(actionAdd_VF_to_current_Image);
 185
 186   //QAction* actionAdd_Overlay_to_current_Image = menuOverlay->addAction(QIcon(QString::fromUtf8(":/common/icons/GPSup.png")),
 187   //    tr("Add overlay image to current image"));
 188   contextMenu.addAction(actionAdd_overlay_image_to_current_image);
 189   contextActions.push_back(actionAdd_overlay_image_to_current_image);
 190
 191   contextMenu.addAction(actionAdd_fusion_image);
 192   contextActions.push_back(actionAdd_fusion_image);
 193
 194 #ifdef CLITK_EXPERIMENTAL
 195   contextMenu.addAction(actionAdd_USSequence_toCT);
 196   contextActions.push_back(actionAdd_USSequence_toCT);
 197 #endif
 198
 199   contextMenu.addAction(actionAdd_wipe_image);
 200   contextActions.push_back(actionAdd_wipe_image);
 201
 202
 203   contextMenu.addSeparator();
 204   QAction* actionResetMatrix = contextMenu.addAction(QIcon(QString::fromUtf8(":/common/icons/identity.png")),
 205     tr("Reset transformation to identity"));
 206   connect(actionResetMatrix, SIGNAL(triggered()), this,SLOT(ResetTransformationToIdentity()));
 207
 208   //init the DataTree
 209   mSlicerManagers.resize(0);
 210
 211   QStringList header;
 212   header.append("");
 213   header.append("TL");
 214   header.append("TR");
 215   header.append("BL");
 216   header.append("BR");
 217   header.append("");
 218   header.append("");
 219   header.append("Name");
 220
 221   DataTree->setHeaderLabels(header);
 222   DataTree->resizeColumnToContents(COLUMN_TREE);
 223   DataTree->resizeColumnToContents(COLUMN_UL_VIEW);
 224   DataTree->resizeColumnToContents(COLUMN_UR_VIEW);
 225   DataTree->resizeColumnToContents(COLUMN_DL_VIEW);
 226   DataTree->resizeColumnToContents(COLUMN_DR_VIEW);
 227   DataTree->resizeColumnToContents(COLUMN_CLOSE_IMAGE);
 228   DataTree->resizeColumnToContents(COLUMN_RELOAD_IMAGE);
 229   DataTree->resizeColumnToContents(COLUMN_IMAGE_NAME);
 230
 231   viewMode = 1;
 232   documentation = new vvDocumentation();
 233   help_dialog = new vvHelpDialog();
 234   dicomSeriesSelector = new vvDicomSeriesSelector();
 235 #if CLITK_USE_PACS_CONNECTION
 236      PacsConnection = new vvQPacsConnection();
 237 #endif
 238
 239   inverseButton->setEnabled(0);
 240   actionAdd_overlay_image_to_current_image->setEnabled(0);
 241   actionSave_As->setEnabled(0);
 242   actionAdd_VF_to_current_Image->setEnabled(0);
 243   actionAdd_fusion_image->setEnabled(0);
 244   actionAdd_USSequence_toCT->setEnabled(0);
 245   actionAdd_wipe_image->setEnabled(0);
 246
 247   //init the sliders
 248   verticalSliders.push_back(NOVerticalSlider);
 249   verticalSliders.push_back(NEVerticalSlider);
 250   verticalSliders.push_back(SOVerticalSlider);
 251   verticalSliders.push_back(SEVerticalSlider);
 252
 253   for (int i =0; i < 4; i++)
 254     verticalSliders[i]->hide();
 255
 256   horizontalSliders.push_back(NOHorizontalSlider);
 257   horizontalSliders.push_back(NEHorizontalSlider);
 258   horizontalSliders.push_back(SOHorizontalSlider);
 259   horizontalSliders.push_back(SEHorizontalSlider);
 260
 261   for (int i =0; i < 4; i++)
 262     horizontalSliders[i]->hide();
 263
 264
 265   connect(NOVerticalSlider,SIGNAL(valueChanged(int)),this,SLOT(NOVerticalSliderChanged()));
 266   connect(NEVerticalSlider,SIGNAL(valueChanged(int)),this,SLOT(NEVerticalSliderChanged()));
 267   connect(SOVerticalSlider,SIGNAL(valueChanged(int)),this,SLOT(SOVerticalSliderChanged()));
 268   connect(SEVerticalSlider,SIGNAL(valueChanged(int)),this,SLOT(SEVerticalSliderChanged()));
 269
 270   connect(NOHorizontalSlider,SIGNAL(valueChanged(int)),this,SLOT(NOHorizontalSliderMoved()));
 271   connect(NEHorizontalSlider,SIGNAL(valueChanged(int)),this,SLOT(NEHorizontalSliderMoved()));
 272   connect(SOHorizontalSlider,SIGNAL(valueChanged(int)),this,SLOT(SOHorizontalSliderMoved()));
 273   connect(SEHorizontalSlider,SIGNAL(valueChanged(int)),this,SLOT(SEHorizontalSliderMoved()));
 274
 275   //connect everything
 276   connect(actionCompute_mid_position_image,SIGNAL(triggered()),this,SLOT(ComputeMidPosition()));
 277   connect(actionDeformable_Registration,SIGNAL(triggered()),this,SLOT(ComputeDeformableRegistration()));
 278   connect(actionWarp_image_with_vector_field,SIGNAL(triggered()),this,SLOT(WarpImage()));
 279   connect(actionLoad_images,SIGNAL(triggered()),this,SLOT(OpenImages()));
 280   connect(actionOpen_Dicom,SIGNAL(triggered()),this,SLOT(OpenDicom()));
 281 #if CLITK_USE_PACS_CONNECTION
 282   connect(actionConnect_Pacs,SIGNAL(triggered()),this,SLOT(ConnectPacs()));
 283 #endif
 284   //  connect(actionOpen_Dicom_Struct,SIGNAL(triggered()),this,SLOT(OpenDCStructContour()));
 285   connect(actionOpen_VTK_contour,SIGNAL(triggered()),this,SLOT(OpenVTKContour()));
 286   connect(actionOpen_Multiple_Images_As_One,SIGNAL(triggered()),this,SLOT(MergeImages()));
 287   connect(actionSlice_Image_As_Multiple_Images,SIGNAL(triggered()),this,SLOT(SliceImages()));
 288   connect(actionOpen_Image_With_Time,SIGNAL(triggered()),this,SLOT(OpenImageWithTime()));
 289   connect(actionMerge_images_as_n_dim_t, SIGNAL(triggered()), this, SLOT(MergeImagesWithTime()));
 290   connect(actionSave_As,SIGNAL(triggered()),this,SLOT(SaveAs()));
 291   connect(actionSave_current_state,SIGNAL(triggered()),this,SLOT(SaveCurrentState()));
 292   connect(actionRead_saved_state,SIGNAL(triggered()),this,SLOT(ReadSavedState()));
 293   connect(actionExit,SIGNAL(triggered()),this,SLOT(close()));
 294   connect(actionAdd_VF_to_current_Image,SIGNAL(triggered()),this,SLOT(OpenField()));
 295   connect(actionAdd_wipe_image,SIGNAL(triggered()),this,SLOT(SelectWipeImage()));
 296   connect(actionAdd_fusion_image,SIGNAL(triggered()),this,SLOT(SelectFusionImage()));
 297   connect(actionAdd_overlay_image_to_current_image,SIGNAL(triggered()), this,SLOT(SelectOverlayImage()));
 298   connect(actionAdd_USSequence_toCT,SIGNAL(triggered()), this,SLOT(SelectFusionSequence()));
 299   connect(actionNavigation_Help,SIGNAL(triggered()),this,SLOT(ShowHelpDialog()));
 300
 301   QShortcut *shortcutHelp = new QShortcut(QKeySequence(QKeySequence::HelpContents),this);
 302   shortcutHelp->setContext(Qt::ApplicationShortcut);
 303   QObject::connect(shortcutHelp, SIGNAL(activated()), this, SLOT(ShowHelpDialog()));
 304
 305   connect(actionDocumentation,SIGNAL(triggered()),this,SLOT(ShowDocumentation()));
 306   connect(actionRegister_vv,SIGNAL(triggered()),this,SLOT(PopupRegisterForm()));
 307
 308   connect(overlayPanel, SIGNAL(FusionSequenceCorrespondancesButtonPressed()), this, SLOT(SelectFusionSequenceCorrespondances()));
 309
 310
 311   ///////////////////////////////////////////////
 312   connect(actionSegmentation,SIGNAL(triggered()),this,SLOT(SegmentationOnCurrentImage()));
 313   connect(actionSurface_Viewer,SIGNAL(triggered()),this,SLOT(SurfaceViewerLaunch()));
 314   ///////////////////////////////////////////////
 315
 316   actionNorth_East_Window->setEnabled(0);
 317   actionNorth_West_Window->setEnabled(0);
 318   actionSouth_East_Window->setEnabled(0);
 319   actionSouth_West_Window->setEnabled(0);
 320
 321   connect(actionNorth_East_Window,SIGNAL(triggered()),this,SLOT(SaveNEScreenshot()));
 322   connect(actionNorth_West_Window,SIGNAL(triggered()),this,SLOT(SaveNOScreenshot()));
 323   connect(actionSouth_East_Window,SIGNAL(triggered()),this,SLOT(SaveSEScreenshot()));
 324   connect(actionSouth_West_Window,SIGNAL(triggered()),this,SLOT(SaveSOScreenshot()));
 325   connect(actionSave_all_slices,SIGNAL(triggered()),this,SLOT(SaveScreenshotAllSlices()));
 326
 327   connect(DataTree,SIGNAL(itemSelectionChanged()),this,SLOT(ImageInfoChanged()));
 328   connect(DataTree,SIGNAL(itemClicked(QTreeWidgetItem*, int)),this,
 329     SLOT(DisplayChanged(QTreeWidgetItem*, int)));
 330
 331   connect(viewButton,SIGNAL(clicked()),this, SLOT(ChangeViewMode()) );
 332   connect(windowSpinBox,SIGNAL(editingFinished()),this,SLOT(WindowLevelEdited()));
 333   connect(levelSpinBox,SIGNAL(editingFinished()),this,SLOT(WindowLevelEdited()));
 334   connect(colorMapComboBox,SIGNAL(currentIndexChanged(int)),this,SLOT(UpdateColorMap()));
 335   connect(presetComboBox,SIGNAL(currentIndexChanged(int)),this,SLOT(UpdateWindowLevel()));
 336   connect(slicingPresetComboBox, SIGNAL(currentIndexChanged(int)),this,SLOT(UpdateSlicingPreset()));
 337   connect(inverseButton,SIGNAL(clicked()),this,SLOT(SwitchWindowLevel()));
 338   connect(applyWindowLevelToAllButton,SIGNAL(clicked()),this,SLOT(ApplyWindowLevelToAllImages()));
 339
 340   connect(this,SIGNAL(customContextMenuRequested(QPoint)),this,SLOT(ShowContextMenu(QPoint)));
 341
 342   connect(linkPanel,SIGNAL(addLink(QString,QString,bool)),this,SLOT(AddLink(QString,QString,bool)));
 343   connect(linkPanel,SIGNAL(removeLink(QString,QString)),this,SLOT(RemoveLink(QString,QString)));
 344   connect(overlayPanel,SIGNAL(VFPropertyUpdated(int,int,int,int,double,double,double)),this,SLOT(SetVFProperty(int,int,int,int,double,double,double)));
 345   connect(overlayPanel,SIGNAL(OverlayPropertyUpdated(int,int,double,double)),
 346     this,SLOT(SetOverlayProperty(int,int,double,double)));
 347   connect(overlayPanel,SIGNAL(FusionPropertyUpdated(int,int,int,double,double, bool)),
 348     this,SLOT(SetFusionProperty(int,int,int,double,double, bool)));
 349   connect(landmarksPanel,SIGNAL(UpdateRenderWindows()),this,SLOT(UpdateRenderWindows()));
 350   connect(landmarksPanel,SIGNAL(SelectedPointChanged()),this,SLOT(GoToLandmark()));
 351
 352   connect(overlayPanel,SIGNAL(FusionSequencePropertyUpdated(int, bool, unsigned int, bool)),
 353     this,SLOT(SetFusionSequenceProperty(int, bool,unsigned int, bool)));
 354
 355
 356   playMode = 0;//pause
 357   mFrameRate = 10;
 358   playButton->setEnabled(0);
 359   frameRateLabel->setEnabled(0);
 360   frameRateSpinBox->setEnabled(0);
 361   connect(playButton, SIGNAL(clicked()),this,SLOT(PlayPause()));
 362   connect(frameRateSpinBox, SIGNAL(valueChanged(int)),this,SLOT(ChangeFrameRate(int)));
 363
 364   goToCursorPushButton->setEnabled(0);
 365   connect(goToCursorPushButton, SIGNAL(clicked()),this,SLOT(GoToCursor()));
 366
 367   NOViewWidget->hide();
 368   NEViewWidget->hide();
 369   SOViewWidget->hide();
 370   SEViewWidget->hide();
 371
 372 #ifdef Q_OS_OSX
 373   disableGLHiDPI(NOViewWidget->winId());
 374   disableGLHiDPI(NEViewWidget->winId());
 375   disableGLHiDPI(SOViewWidget->winId());
 376   disableGLHiDPI(SEViewWidget->winId());
 377 #endif
 378
 379   //Recently opened files
 380   std::list<std::string> recent_files = GetRecentlyOpenedImages();
 381   recentlyOpenedFilesMenu=NULL;
 382   if ( !recent_files.empty() ) {
 383     createRecentlyOpenedFilesMenu();
 384     updateRecentlyOpenedFilesMenu(recent_files);
 385   }
 386
 387   // Adding all new tools (insertion in the menu)
 388   vvToolManager::GetInstance()->InsertToolsInMenu(this);
 389   vvToolManager::GetInstance()->EnableToolsInMenu(this, false);
 390
 391 //#ifndef CLITK_EXPERIMENTAL
 392 //#define CLITK_EXPERIMENTAL 0
 393 //#endif
 394 #ifdef CLITK_EXPERIMENTAL
 395   if (!CLITK_EXPERIMENTAL)
 396     menuExperimental->menuAction()->setVisible(false);
 397 #endif
 398
 399 #if !CLITK_USE_PACS_CONNECTION
 400     actionConnect_Pacs->setVisible(false);
 401 #endif
 402
 403   QTimer * timerMemory = new QTimer(this);
 404   //timerMemory->setInterval(5);
 405   connect(timerMemory, SIGNAL(timeout()), this, SLOT(UpdateMemoryUsage()));
 406   timerMemory->start(2000);
 407 }
 408
 409 //------------------------------------------------------------------------------
 410 void vvMainWindow::show()
 411 {
 412   vvMainWindowBase::show();
 413   PopupRegisterForm(true);
 414 }
 415 //------------------------------------------------------------------------------
 416 void vvMainWindow::UpdateMemoryUsage()
 417 {
 418   //  clitk::PrintMemory(true);
 419   if (clitk::GetMemoryUsageInMb() == 0) infoPanel->setMemoryInMb("NA");
 420   else infoPanel->setMemoryInMb(QString::number(clitk::GetMemoryUsageInMb())+" MiB");
 421 }
 422 //------------------------------------------------------------------------------
 423
 424
 425 //------------------------------------------------------------------------------
 426 void vvMainWindow::createRecentlyOpenedFilesMenu()
 427 {
 428   recentlyOpenedFilesMenu = new QMenu("Recently opened files...");
 429   recentlyOpenedFilesMenu->setIcon(QIcon(QString::fromUtf8(":/common/icons/open.png")));
 430   menuFile->insertMenu(actionOpen_Image_With_Time,recentlyOpenedFilesMenu);
 431   menuFile->insertSeparator(actionOpen_Image_With_Time);
 432 }
 433 //------------------------------------------------------------------------------
 434
 435
 436 //------------------------------------------------------------------------------
 437
 438 void vvMainWindow::updateRecentlyOpenedFilesMenu(const std::list<std::string> &recent_files)
 439 {
 440   if(recentlyOpenedFilesMenu==NULL) {
 441     createRecentlyOpenedFilesMenu();
 442   } else {
 443     recentlyOpenedFilesMenu->clear();
 444   }
 445   for (std::list<std::string>::const_iterator i = recent_files.begin(); i!=recent_files.end(); i++) {
 446     QAction* current=new QAction(QIcon(QString::fromUtf8(":/common/icons/open.png")), i->c_str(),this);
 447     recentlyOpenedFilesMenu->addAction(current);
 448     connect(current,SIGNAL(triggered()),this,SLOT(OpenRecentImage()));
 449   }
 450 }
 451 //------------------------------------------------------------------------------
 452
 453
 454 //------------------------------------------------------------------------------
 455 void vvMainWindow::ComputeMidPosition()
 456 {
 457   bool ok;
 458   int index=GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
 459   int ref = QInputDialog::getInt(this,"Chose reference phase","Reference phase",0,0,\
 460 mSlicerManagers[index]->GetImage()->GetVTKImages().size()-1,1,&ok);
 461   if (ok) {
 462     vvMidPosition midp;
 463     midp.slicer_manager = mSlicerManagers[index];
 464     midp.reference_image_index = ref;
 465     QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
 466     midp.Update();
 467     if (midp.error)
 468       QMessageBox::warning(this, "Error computing midposition image",midp.error_message.c_str());
 469     else {
 470       QFileInfo info(midp.slicer_manager->GetFileName().c_str());
 471       AddImage(midp.output,info.path().toStdString()+"/"+info.completeBaseName().toStdString()+"_midposition.mhd");
 472     }
 473     QApplication::restoreOverrideCursor();
 474   }
 475 }
 476 //------------------------------------------------------------------------------
 477
 478
 479 //------------------------------------------------------------------------------
 480 void vvMainWindow::AddContour(int image_index, vvMesh::Pointer contour, bool propagation)
 481 {
 482   QTreeWidgetItem *item = new QTreeWidgetItem();
 483   item->setData(0,Qt::UserRole,"filename.vtk");
 484   item->setData(1,Qt::UserRole,tr("contour"));
 485   QBrush brush;
 486   brush.setColor(QColor(contour->r*255,contour->g*255,contour->b*255));
 487   brush.setStyle(Qt::SolidPattern);
 488   item->setData(COLUMN_IMAGE_NAME,Qt::BackgroundRole,brush);
 489   item->setData(COLUMN_IMAGE_NAME,Qt::DisplayRole,contour->structure_name.c_str());
 490
 491   for (int j = 1; j <= 4; j++)
 492     item->setData(j,Qt::CheckStateRole,DataTree->topLevelItem(image_index)->data(j,Qt::CheckStateRole));
 493
 494   QTreePushButton* cButton = new QTreePushButton;
 495   cButton->setItem(item);
 496   cButton->setColumn(COLUMN_CLOSE_IMAGE);
 497   cButton->setToolTip(tr("close image"));
 498   cButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/exit.png")));
 499   connect(cButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
 500     this,SLOT(CloseImage(QTreeWidgetItem*, int)));
 501
 502   QTreePushButton* rButton = new QTreePushButton;
 503   rButton->setItem(item);
 504   rButton->setColumn(COLUMN_RELOAD_IMAGE);
 505   rButton->setToolTip(tr("reload image"));
 506   rButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/rotateright.png")));
 507   rButton->setEnabled(false);
 508   //Not implemented
 509   //connect(rButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
 510   //this,SLOT(ReloadImage(QTreeWidgetItem*, int)));
 511
 512   DataTree->topLevelItem(image_index)->setExpanded(1);
 513   DataTree->topLevelItem(image_index)->addChild(item);
 514   DataTree->setItemWidget(item, COLUMN_CLOSE_IMAGE, cButton);
 515   DataTree->setItemWidget(item, COLUMN_RELOAD_IMAGE, rButton);
 516   QString id = DataTree->topLevelItem(image_index)->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString();
 517   item->setData(COLUMN_IMAGE_NAME,Qt::UserRole,id.toStdString().c_str());
 518
 519   UpdateTree();
 520   mSlicerManagers[image_index]->AddContour(contour,propagation);
 521   mSlicerManagers[image_index]->Render();
 522 }
 523 //------------------------------------------------------------------------------
 524
 525
 526 //------------------------------------------------------------------------------
 527 void vvMainWindow::OpenVTKContour()
 528 {
 529   if (mSlicerManagers.size() > 0) {
 530     QString Extensions = "Images ( *.vtk *.obj)";
 531     Extensions += ";;All Files (*)";
 532     QString file = QFileDialog::getOpenFileName(this,tr("Open vtkPolyData"),mInputPathName,Extensions);
 533     if (file.isNull())
 534       return;
 535     QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
 536     int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
 537     vvMeshReader reader;
 538     reader.SetImage(mSlicerManagers[index]->GetImage());
 539     reader.SetModeToVTK();
 540     reader.SetFilename(file.toStdString());
 541     reader.Update();
 542     AddContour(index,reader.GetOutput()[0],false);
 543     QApplication::restoreOverrideCursor();
 544   }
 545 }
 546 //------------------------------------------------------------------------------
 547
 548
 549 //------------------------------------------------------------------------------
 550 void vvMainWindow::AddDCStructContour(int index, QString file)
 551 {
 552   vvMeshReader reader;
 553   reader.SetFilename(file.toStdString());
 554   vvStructSelector selector;
 555   selector.SetStructures(reader.GetROINames());
 556   if (!mSlicerManagers[index]->GetVF().IsNull())
 557     selector.EnablePropagationCheckBox();
 558   if (selector.exec()) {
 559     QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
 560     reader.SetSelectedItems(selector.getSelectedItems());
 561     reader.SetImage(mSlicerManagers[index]->GetImage());
 562     if (selector.PropagationEnabled())
 563       reader.SetPropagationVF(mSlicerManagers[index]->GetVF());
 564     reader.Update();
 565     std::vector<vvMesh::Pointer> contours=reader.GetOutput();
 566     for (std::vector<vvMesh::Pointer>::iterator i=contours.begin();
 567       i!=contours.end(); i++)
 568       AddContour(index,*i,selector.PropagationEnabled());
 569     QApplication::restoreOverrideCursor();
 570   }
 571 }
 572
 573 //------------------------------------------------------------------------------
 574 void vvMainWindow::OpenDCStructContour()
 575 {
 576   if (mSlicerManagers.size() > 0) {
 577     QString Extensions = "Dicom Files ( *.dcm RS*)";
 578     Extensions += ";;All Files (*)";
 579     QString file = QFileDialog::getOpenFileName(this,tr("Merge Images"),mInputPathName,Extensions);
 580     if (file.isNull())
 581       return;
 582     int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
 583     AddDCStructContour(index, file);
 584   }
 585 }
 586 //------------------------------------------------------------------------------
 587
 588
 589 //------------------------------------------------------------------------------
 590 void vvMainWindow::ComputeDeformableRegistration()
 591 {
 592   if (mSlicerManagers.size() > 0) {
 593     int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
 594     vvDeformationDialog dialog(index,mSlicerManagers);
 595     if (dialog.exec()) {
 596       std::string base_name=itksys::SystemTools::GetFilenameWithoutExtension(mSlicerManagers[dialog.GetInputFileIndex()]->GetFileName());
 597       AddField(dialog.GetOutput(),dialog.getFieldFile(),dialog.GetInputFileIndex());
 598       WarpImage(dialog.GetSelectedSlicer(),dialog.GetReferenceFrameIndex());
 599     } else
 600       std::cout << "Error or user cancellation while computing deformation field..." << std::endl;
 601   } else QMessageBox::information(this, "Need to open image","You must open an image first.");
 602 }
 603 //------------------------------------------------------------------------------
 604
 605
 606 //------------------------------------------------------------------------------
 607 void vvMainWindow::WarpImage()
 608 {
 609   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
 610   if (!mSlicerManagers[index]->GetVF().IsNull()) {
 611     bool ok;
 612     int ref = QInputDialog::getInt(this,"Chose reference phase","Reference phase",0,0,\
 613       mSlicerManagers[index]->GetImage()->GetVTKImages().size()-1,1,&ok);
 614     if (ok) {
 615       WarpImage(mSlicerManagers[index],ref);
 616     }
 617   } else
 618     QMessageBox::warning(this,tr("No vector field"),tr("Sorry, can't warp without a vector field"));
 619 }
 620 //------------------------------------------------------------------------------
 621
 622
 623 //------------------------------------------------------------------------------
 624 void vvMainWindow::WarpImage(vvSlicerManager* selected_slicer,int reference_phase)
 625 {
 626   if (!selected_slicer->GetVF().IsNull()) {
 627     QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
 628     QFileInfo info(selected_slicer->GetFileName().c_str());
 629     vvImageWarp warp(selected_slicer->GetImage(),selected_slicer->GetVF(),
 630       reference_phase,this);
 631     if (warp.ComputeWarpedImage()) {
 632       AddImage(warp.GetWarpedImage(),info.path().toStdString()+"/"+info.completeBaseName().toStdString()+"_warped.mhd");
 633       AddImage(warp.GetDiffImage()  ,info.path().toStdString()+"/"+info.completeBaseName().toStdString()+"_diff.mhd");
 634       AddImage(warp.GetJacobianImage()  ,info.path().toStdString()+"/"+info.completeBaseName().toStdString()+"_jacobian.mhd");
 635       QApplication::restoreOverrideCursor();
 636     } else {
 637       QApplication::restoreOverrideCursor();
 638       QMessageBox::warning(this,tr("Different spacings"),tr("The vector field and image spacings must be the same in order to warp."));
 639     }
 640   } else
 641     QMessageBox::warning(this,tr("No vector field"),tr("Sorry, can't warp without a vector field."));
 642 }
 643 //------------------------------------------------------------------------------
 644
 645
 646 //------------------------------------------------------------------------------
 647 vvMainWindow::~vvMainWindow()
 648 {
 649   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
 650     if (mSlicerManagers[i] != NULL)
 651       delete mSlicerManagers[i];
 652   }
 653   delete documentation;
 654   delete help_dialog;
 655   delete dicomSeriesSelector;
 656 }
 657 //------------------------------------------------------------------------------
 658
 659 //------------------------------------------------------------------------------
 660 QTabWidget * vvMainWindow::GetTab()
 661 {
 662   return tabWidget;
 663 }
 664 //------------------------------------------------------------------------------
 665
 666
 667 //------------------------------------------------------------------------------
 668 void vvMainWindow::MergeImages()
 669 {
 670   QString Extensions = EXTENSIONS;
 671   Extensions += ";;All Files (*)";
 672   QStringList files = QFileDialog::getOpenFileNames(this,tr("Merge Images"),mInputPathName,Extensions);
 673   if (files.isEmpty())
 674     return;
 675   mInputPathName = itksys::SystemTools::GetFilenamePath(files[0].toStdString()).c_str();
 676   std::vector<std::string> vector;
 677
 678   unsigned int currentDim = 0;
 679   std::vector<double> currentSpacing;
 680   std::vector<int> currentSize;
 681   std::vector<double> currentOrigin;
 682
 683   for (int i = 0; i < files.size(); i++) {
 684     itk::ImageIOBase::Pointer reader = itk::ImageIOFactory::CreateImageIO(
 685       files[i].toStdString().c_str(), itk::ImageIOFactory::ReadMode);
 686     reader->SetFileName(files[i].toStdString().c_str());
 687     reader->ReadImageInformation();
 688     if (reader)        {
 689       //NOViewWidget->hide();
 690       //NEViewWidget->hide();
 691       //SOViewWidget->hide();
 692       //SEViewWidget->hide();
 693       if (i == 0)
 694         currentDim = reader->GetNumberOfDimensions();
 695       bool IsOk = true;
 696       for (unsigned int j = 0; j < currentDim; j++) {
 697         if (i == 0) {
 698           if (j == 0) {
 699             currentSpacing.resize(currentDim);
 700             currentSize.resize(currentDim);
 701             currentOrigin.resize(currentDim);
 702           }
 703           currentOrigin[j] = reader->GetOrigin(j);
 704           currentSpacing[j] = reader->GetSpacing(j);
 705           currentSize[j] = reader->GetDimensions(j);
 706         } else if (currentDim != reader->GetNumberOfDimensions()
 707           || currentSpacing[j] != reader->GetSpacing(j)
 708           || currentSize[j] != (int)reader->GetDimensions(j)
 709           || currentOrigin[j] != reader->GetOrigin(j)) {
 710             QString error = "Cannot read file (too different from others ";
 711             error += files[i].toStdString().c_str();
 712             QMessageBox::information(this,tr("Reading problem"),error);
 713             IsOk = false;
 714             break;
 715         }
 716       }
 717       if (IsOk)
 718         vector.push_back(files[i].toStdString());
 719     }
 720   }
 721   if (vector.size() > 0)
 722     LoadImages(vector, vvImageReader::MERGED);
 723 }
 724 //------------------------------------------------------------------------------
 725
 726 //------------------------------------------------------------------------------
 727 void vvMainWindow::SliceImages()
 728 {
 729   QString Extensions = EXTENSIONS;
 730   Extensions += ";;All Files (*)";
 731
 732   QStringList files = QFileDialog::getOpenFileNames(this,tr("Slice Images"),mInputPathName,Extensions);
 733   if (files.isEmpty())
 734     return;
 735   mInputPathName = itksys::SystemTools::GetFilenamePath(files[0].toStdString()).c_str();
 736   std::vector<std::string> vector;
 737   for (int i = 0; i < files.size(); i++)
 738     vector.push_back(files[i].toStdString());
 739   LoadImages(vector, vvImageReader::SLICED);
 740 }
 741 //------------------------------------------------------------------------------
 742
 743 //------------------------------------------------------------------------------
 744 void vvMainWindow::MergeImagesWithTime()
 745 {
 746   QString Extensions = EXTENSIONS;
 747   Extensions += ";;All Files (*)";
 748   QStringList files = QFileDialog::getOpenFileNames(this,tr("Merge Images With Time"),mInputPathName,Extensions);
 749   if (files.isEmpty())
 750     return;
 751   mInputPathName = itksys::SystemTools::GetFilenamePath(files[0].toStdString()).c_str();
 752   std::vector<std::string> vector;
 753
 754   for (int i = 0; i < files.size(); i++)
 755     vector.push_back(files[i].toStdString());
 756   sort(vector.begin(),vector.end());
 757   if (vector.size() > 1)
 758     LoadImages(vector, vvImageReader::MERGEDWITHTIME);
 759   else
 760     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.");
 761 }
 762 //------------------------------------------------------------------------------
 763
 764
 765 //------------------------------------------------------------------------------
 766 void vvMainWindow::OpenDicom()
 767 {
 768   std::vector<std::string> files;
 769
 770   //std::cout << "dicomSeriesSelector " << std::endl;
 771   if (dicomSeriesSelector->exec() == QDialog::Accepted) {
 772     files = *(dicomSeriesSelector->GetFilenames());
 773     LoadImages(files, vvImageReader::DICOM);
 774   }
 775 }
 776 #if CLITK_USE_PACS_CONNECTION
 777 void vvMainWindow::ConnectPacs()
 778 {
 779   std::vector<std::string> files;
 780
 781   //std::cout << "dicomSeriesSelector " << std::endl;
 782 if (PacsConnection->exec() == QDialog::Accepted) {
 783         for (int i = 0; i < PacsConnection->getSeriesCount(); i++)
 784         {
 785                 files = PacsConnection->getFileNames(i);
 786                 LoadImages(files, vvImageReader::DICOM);
 787         }
 788         PacsConnection->clearMove();
 789   }
 790   }
 791
 792 #endif
 793 //------------------------------------------------------------------------------
 794
 795 //------------------------------------------------------------------------------
 796 void vvMainWindow::OpenImages()
 797 {
 798   QString Extensions = EXTENSIONS;
 799   Extensions += ";;All Files (*)";
 800
 801   QStringList files = QFileDialog::getOpenFileNames(this,tr("Load Images"),mInputPathName,Extensions);
 802   if (files.isEmpty())
 803     return;
 804   mInputPathName = itksys::SystemTools::GetFilenamePath(files[0].toStdString()).c_str();
 805   std::vector<std::string> vector;
 806   for (int i = 0; i < files.size(); i++)
 807     vector.push_back(files[i].toStdString());
 808   LoadImages(vector, vvImageReader::IMAGE);
 809 }
 810 //------------------------------------------------------------------------------
 811 void vvMainWindow::OpenRecentImage()
 812 {
 813   QAction * caller = qobject_cast<QAction*>(sender());
 814   std::vector<std::string> images;
 815   images.push_back(caller->text().toStdString());
 816   mInputPathName = itksys::SystemTools::GetFilenamePath(images[0]).c_str();
 817   LoadImages(images, vvImageReader::IMAGE);
 818 }
 819 //------------------------------------------------------------------------------
 820
 821
 822 //------------------------------------------------------------------------------
 823 void vvMainWindow::OpenImageWithTime()
 824 {
 825   QString Extensions = EXTENSIONS;
 826   Extensions += ";;All Files (*)";
 827
 828   QStringList files = QFileDialog::getOpenFileNames(this,tr("Load Images With Time"),mInputPathName,Extensions);
 829   if (files.isEmpty())
 830     return;
 831   mInputPathName = itksys::SystemTools::GetFilenamePath(files[0].toStdString()).c_str();
 832   std::vector<std::string> vector;
 833   for (int i = 0; i < files.size(); i++) {
 834     vector.push_back(files[i].toStdString());
 835   }
 836   LoadImages(vector, vvImageReader::IMAGEWITHTIME);
 837 }
 838 //------------------------------------------------------------------------------
 839
 840
 841 //------------------------------------------------------------------------------
 842 void vvMainWindow::LoadImages(std::vector<std::string> files, vvImageReader::LoadedImageType filetype)
 843 {
 844   //Separate the way to open images and dicoms
 845   int fileSize;
 846   if (filetype == vvImageReader::IMAGE || filetype == vvImageReader::IMAGEWITHTIME)
 847     fileSize = files.size();
 848   else
 849     fileSize = 1;
 850
 851   // For SLICED, we need the number of slices (ndim and #slices)
 852   std::vector<unsigned int> nSlices;
 853   nSlices.resize(files.size());
 854   std::fill(nSlices.begin(), nSlices.end(), 1);
 855   if (filetype == vvImageReader::SLICED) {
 856     for (int i = 0; i < fileSize; i++) {
 857       itk::ImageIOBase::Pointer header = clitk::readImageHeader(files[i]);
 858       QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
 859       if (!header) {
 860         nSlices[i] = 0;
 861         QString error = "Cannot open file \n";
 862         error += files[i].c_str();
 863         QMessageBox::information(this,tr("Reading problem"),error);
 864         return;
 865       }
 866       if (header->GetNumberOfDimensions() < 3) {
 867         nSlices[i] = 0;
 868         QString error = "Dimension problem. Cannot slice \n";
 869         error += files[i].c_str();
 870         QMessageBox::information(this,tr("Reading problem"),error);
 871         return;
 872       }
 873       nSlices[i] = header->GetDimensions( header->GetNumberOfDimensions()-1 );
 874     }
 875   }
 876
 877   //Only add to the list of recently opened files when a single file is opened,
 878   //to avoid polluting the list of recently opened files
 879   if (files.size() == 1) {
 880     QFileInfo finfo=tr(files[0].c_str());
 881     AddToRecentlyOpenedImages(finfo.absoluteFilePath().toStdString());
 882     updateRecentlyOpenedFilesMenu(GetRecentlyOpenedImages());
 883   }
 884   //init the progress events
 885   QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
 886   vvProgressDialog progress("Opening " + files[0],fileSize>1);
 887   qApp->processEvents();
 888
 889   int numberofsuccesulreads=0;
 890   //open images as 1 or multiples
 891   for (int i = 0; i < fileSize; i++) {
 892     progress.SetText("Opening " + files[i]);
 893     progress.SetProgress(i,fileSize);
 894     qApp->processEvents();
 895
 896     for (unsigned int j = 0; j < nSlices[i]; j++) {
 897       //read the image and put it in mSlicerManagers
 898       vvSlicerManager* imageManager = new vvSlicerManager(4);
 899       qApp->processEvents();
 900
 901       bool SetImageSucceed=false;
 902
 903       // Change filename if an image with the same already exist
 904       int number = GetImageDuplicateFilenameNumber(files[i] + std::string("_slice"));
 905
 906       if (filetype == vvImageReader::IMAGE || filetype == vvImageReader::IMAGEWITHTIME || filetype == vvImageReader::SLICED) {
 907         SetImageSucceed = imageManager->SetImage(files[i],filetype, number, j);
 908       } else {
 909         SetImageSucceed = imageManager->SetImages(files,filetype, number);
 910       }
 911       if (!SetImageSucceed) {
 912         QApplication::restoreOverrideCursor();
 913         QString error = "Cannot open file \n";
 914         error += imageManager->GetLastError().c_str();
 915         QMessageBox::information(this,tr("Reading problem"),error);
 916         delete imageManager;
 917       } else {
 918
 919         mSlicerManagers.push_back(imageManager);
 920
 921         //create an item in the tree with good settings
 922         QTreeWidgetItem *item = new QTreeWidgetItem();
 923         item->setData(0,Qt::UserRole,files[i].c_str());
 924         QFileInfo fileinfo(imageManager->GetFileName().c_str()); //Do not show the path
 925         item->setData(COLUMN_IMAGE_NAME,Qt::DisplayRole,fileinfo.fileName());
 926         item->setData(1,Qt::UserRole,tr("image"));
 927         item->setToolTip(COLUMN_IMAGE_NAME, imageManager->GetListOfAbsoluteFilePathInOneString("image").c_str());
 928         qApp->processEvents();
 929
 930         //Create the buttons for reload and close
 931         qApp->processEvents();
 932         QTreePushButton* cButton = new QTreePushButton;
 933         cButton->setItem(item);
 934         cButton->setColumn(COLUMN_CLOSE_IMAGE);
 935         cButton->setToolTip(tr("close image"));
 936         cButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/exit.png")));
 937         connect(cButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
 938           this,SLOT(CloseImage(QTreeWidgetItem*, int)));
 939
 940         QTreePushButton* rButton = new QTreePushButton;
 941         rButton->setItem(item);
 942         rButton->setColumn(COLUMN_RELOAD_IMAGE);
 943         rButton->setToolTip(tr("reload image"));
 944         rButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/rotateright.png")));
 945         connect(rButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
 946           this,SLOT(ReloadImage(QTreeWidgetItem*, int)));
 947
 948         DataTree->addTopLevelItem(item);
 949         DataTree->setItemWidget(item, COLUMN_CLOSE_IMAGE, cButton);
 950         DataTree->setItemWidget(item, COLUMN_RELOAD_IMAGE, rButton);
 951
 952         //set the id of the image
 953         QString id = QDir::current().absoluteFilePath(files[i].c_str()) + QString::number(mSlicerManagers.size()-1);
 954         item->setData(COLUMN_IMAGE_NAME,Qt::UserRole,id.toStdString().c_str());
 955         mSlicerManagers.back()->SetId(id.toStdString());
 956
 957         linkPanel->addImage(imageManager->GetFileName(), id.toStdString());
 958
 959         connect(mSlicerManagers.back(), SIGNAL(currentImageChanged(std::string)),
 960           this,SLOT(CurrentImageChanged(std::string)));
 961         connect(mSlicerManagers.back(), SIGNAL(currentPickedImageChanged(std::string)),
 962           this, SLOT(CurrentPickedImageChanged(std::string)));
 963         connect(mSlicerManagers.back(), SIGNAL(UpdatePosition(int, double, double, double, double, double, double, double)),
 964           this,SLOT(MousePositionChanged(int,double, double, double, double, double, double, double)));
 965         connect(mSlicerManagers.back(), SIGNAL(UpdateVector(int, double, double, double, double)),
 966           this, SLOT(VectorChanged(int,double,double,double, double)));
 967         connect(mSlicerManagers.back(), SIGNAL(UpdateOverlay(int, double, double)),
 968           this, SLOT(OverlayChanged(int,double,double)));
 969         connect(mSlicerManagers.back(), SIGNAL(UpdateFusion(int, double)),
 970           this, SLOT(FusionChanged(int,double)));
 971         connect(mSlicerManagers.back(), SIGNAL(WindowLevelChanged()),
 972           this,SLOT(WindowLevelChanged()));
 973         connect(mSlicerManagers.back(), SIGNAL(UpdateSlice(int,int)),
 974           this,SLOT(UpdateSlice(int,int)));
 975         connect(mSlicerManagers.back(), SIGNAL(UpdateTSlice(int, int, int)),
 976           this,SLOT(UpdateTSlice(int, int, int)));
 977         connect(mSlicerManagers.back(), SIGNAL(UpdateTSlice(int, int, int)),
 978           this,SLOT(ImageInfoChanged()));
 979         connect(mSlicerManagers.back(), SIGNAL(UpdateSliceRange(int,int,int,int,int)),
 980           this,SLOT(UpdateSliceRange(int,int,int,int,int)));
 981         connect(mSlicerManagers.back(), SIGNAL(UpdateLinkManager(std::string,int,double,double,double,int)),
 982           this,SLOT(UpdateLinkManager(std::string,int,double,double,double,int)));
 983         connect(mSlicerManagers.back(), SIGNAL(UpdateLinkedNavigation(std::string,vvSlicerManager*,vvSlicer*)),
 984           this,SLOT(UpdateLinkedNavigation(std::string,vvSlicerManager*,vvSlicer*)));
 985         connect(mSlicerManagers.back(), SIGNAL(ChangeImageWithIndexOffset(vvSlicerManager*,int,int)),
 986           this,SLOT(ChangeImageWithIndexOffset(vvSlicerManager*,int,int)));
 987         connect(mSlicerManagers.back(),SIGNAL(LandmarkAdded()),landmarksPanel,SLOT(AddPoint()));
 988         connect(landmarksPanel,SIGNAL(UpdateLandmarkTransform()), mSlicerManagers.back(), SLOT(UpdateLandmark()));
 989         InitSlicers();
 990         numberofsuccesulreads++;
 991       }
 992     }
 993   }
 994
 995   if (numberofsuccesulreads) {
 996     NOViewWidget->show();
 997     NEViewWidget->show();
 998     SOViewWidget->show();
 999     SEViewWidget->show();
1000     UpdateTree();
1001     InitDisplay();
1002     ShowLastImage();
1003
1004     // Try to guess default WindowLevel
1005     double range[2];
1006     mSlicerManagers.back()->GetImage()->GetFirstVTKImageData()->GetScalarRange(range);
1007     if ((range[0] == 0) && (range[1] == 1)) {
1008       presetComboBox->setCurrentIndex(WL_BINARY);// binary
1009     } else {
1010       // TODO
1011     }
1012   }
1013   QApplication::restoreOverrideCursor();
1014 }
1015 //------------------------------------------------------------------------------
1016
1017 //------------------------------------------------------------------------------
1018 void vvMainWindow::UpdateTree()
1019 {
1020   DataTree->resizeColumnToContents(COLUMN_TREE);
1021   DataTree->resizeColumnToContents(COLUMN_UL_VIEW);
1022   DataTree->resizeColumnToContents(COLUMN_UR_VIEW);
1023   DataTree->resizeColumnToContents(COLUMN_DL_VIEW);
1024   DataTree->resizeColumnToContents(COLUMN_DR_VIEW);
1025   DataTree->resizeColumnToContents(COLUMN_IMAGE_NAME);
1026   DataTree->resizeColumnToContents(COLUMN_CLOSE_IMAGE);
1027   DataTree->resizeColumnToContents(COLUMN_RELOAD_IMAGE);
1028 }
1029 //------------------------------------------------------------------------------
1030
1031 //------------------------------------------------------------------------------
1032 void vvMainWindow::CurrentImageChanged(std::string id)
1033 {
1034   if (id == mCurrentSelectedImageId) return; // Do nothing
1035   int selected = 0;
1036   for (int i = 0; i < DataTree->topLevelItemCount(); i++) {
1037     if (DataTree->topLevelItem(i)->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString().toStdString() == id) {
1038       selected = i;
1039     } else {
1040       DataTree->topLevelItem(i)->setSelected(0);
1041     }
1042     for (int child = 0; child < DataTree->topLevelItem(i)->childCount(); child++)
1043       DataTree->topLevelItem(i)->child(child)->setSelected(0);
1044
1045   }
1046   DataTree->topLevelItem(selected)->setSelected(1);
1047   mCurrentSelectedImageId = id;
1048
1049   landmarksPanel->SetCurrentLandmarks(mSlicerManagers[selected]->GetLandmarks(),
1050                                       mSlicerManagers[selected]->GetTSlice());
1051   landmarksPanel->SetCurrentPath(mInputPathName.toStdString());
1052   landmarksPanel->SetCurrentImage(mSlicerManagers[selected]->GetFileName().c_str());
1053
1054   emit SelectedImageHasChanged(mSlicerManagers[selected]);
1055 }
1056 //------------------------------------------------------------------------------
1057
1058 //------------------------------------------------------------------------------
1059 void vvMainWindow::CurrentPickedImageChanged(std::string id)
1060 {
1061   if (id == mCurrentPickedImageId) return; // Do nothing
1062   int selected = 0;
1063   for (int i = 0; i < DataTree->topLevelItemCount(); i++) {
1064     if (DataTree->topLevelItem(i)->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString().toStdString() == id) {
1065       selected = i;
1066     } else {
1067       DataTree->topLevelItem(i)->setSelected(0);
1068     }
1069     for (int child = 0; child < DataTree->topLevelItem(i)->childCount(); child++)
1070       DataTree->topLevelItem(i)->child(child)->setSelected(0);
1071
1072   }
1073   DataTree->topLevelItem(selected)->setSelected(1);
1074   mCurrentPickedImageId = id;
1075   mCurrentPickedImageIndex = selected;
1076 }
1077 //------------------------------------------------------------------------------
1078
1079 //------------------------------------------------------------------------------
1080 void vvMainWindow::ImageInfoChanged()
1081 {
1082   contextActions[6]->setEnabled(1);
1083   contextActions[5]->setEnabled(1);
1084   actionSave_As->setEnabled(1);
1085   actionAdd_VF_to_current_Image->setEnabled(1);
1086   actionAdd_fusion_image->setEnabled(1);
1087   actionAdd_wipe_image->setEnabled(1);
1088   actionAdd_overlay_image_to_current_image->setEnabled(1);
1089   actionAdd_USSequence_toCT->setEnabled(1);
1090   actionNorth_East_Window->setEnabled(1);
1091   actionNorth_West_Window->setEnabled(1);
1092   actionSouth_East_Window->setEnabled(1);
1093   actionSouth_West_Window->setEnabled(1);
1094   vvToolManager::GetInstance()->EnableToolsInMenu(this, true);
1095   inverseButton->setEnabled(1);
1096
1097   goToCursorPushButton->setEnabled(1);
1098
1099   if (DataTree->selectedItems().size()) {
1100     int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1101
1102     colorMapComboBox->setEnabled(1);
1103     for (int i = 0; i < DataTree->topLevelItem(index)->childCount(); i++) {
1104       if (DataTree->topLevelItem(index)->child(i)->data(1,Qt::UserRole).toString() == "overlay" ||
1105         DataTree->topLevelItem(index)->child(i)->data(1,Qt::UserRole).toString() == "fusion" ||
1106         DataTree->topLevelItem(index)->child(i)->data(1,Qt::UserRole).toString() == "fusionSequence") {
1107           colorMapComboBox->setEnabled(0);
1108           break;
1109       }
1110     }
1111
1112     std::vector<double> origin;
1113     std::vector<double> inputSpacing;
1114     std::vector<int> inputSize;
1115     std::vector<double> sizeMM;
1116     vtkSmartPointer<vtkMatrix4x4> transformation;
1117     int dimension=0;
1118     QString pixelType;
1119     QString inputSizeInBytes;
1120     QString image = DataTree->selectedItems()[0]->data(COLUMN_IMAGE_NAME,Qt::DisplayRole).toString();
1121
1122     int nframes = mSlicerManagers[index]->GetSlicer(0)->GetTMax();
1123
1124     if (nframes > 1 || playMode == 1) {
1125       playButton->setEnabled(1);
1126       frameRateLabel->setEnabled(1);
1127       frameRateSpinBox->setEnabled(1);
1128     } else {
1129       playButton->setEnabled(0);
1130       frameRateLabel->setEnabled(0);
1131       frameRateSpinBox->setEnabled(0);
1132     }
1133
1134     //read image header
1135     int NPixel = 1;
1136
1137     int tSlice = 0;
1138     vvImage::Pointer imageSelected;
1139     if (DataTree->topLevelItem(index) == DataTree->selectedItems()[0]) {
1140       imageSelected = mSlicerManagers[index]->GetSlicer(0)->GetImage();
1141       tSlice = mSlicerManagers[index]->GetSlicer(0)->GetTSlice();
1142     } else if (DataTree->selectedItems()[0]->data(1,Qt::UserRole).toString() == "vector") {
1143       imageSelected = mSlicerManagers[index]->GetSlicer(0)->GetVF();
1144       tSlice = mSlicerManagers[index]->GetSlicer(0)->GetOverlayTSlice();
1145     } else if (DataTree->selectedItems()[0]->data(1,Qt::UserRole).toString() == "overlay") {
1146       imageSelected = mSlicerManagers[index]->GetSlicer(0)->GetOverlay();
1147       tSlice = mSlicerManagers[index]->GetSlicer(0)->GetOverlayTSlice();
1148     } else if (DataTree->selectedItems()[0]->data(1,Qt::UserRole).toString() == "fusion") {
1149       imageSelected = mSlicerManagers[index]->GetSlicer(0)->GetFusion();
1150       tSlice = mSlicerManagers[index]->GetSlicer(0)->GetFusionTSlice();
1151     }
1152     else if (DataTree->selectedItems()[0]->data(1,Qt::UserRole).toString() == "fusionSequence") {
1153       imageSelected = mSlicerManagers[index]->GetSlicer(0)->GetFusion();
1154       tSlice = mSlicerManagers[index]->GetSlicer(0)->GetFusionTSlice();
1155     }
1156     else if (DataTree->selectedItems()[0]->data(1,Qt::UserRole).toString() == "contour") {
1157       imageSelected = mSlicerManagers[index]->GetSlicer(0)->GetImage();
1158       tSlice = mSlicerManagers[index]->GetSlicer(0)->GetTSlice();
1159     }
1160     else {
1161       imageSelected = mSlicerManagers[index]->GetSlicer(0)->GetImage();
1162       tSlice = mSlicerManagers[index]->GetSlicer(0)->GetTSlice();
1163     }
1164
1165     dimension = imageSelected->GetNumberOfDimensions();
1166     origin.resize(dimension);
1167     inputSpacing.resize(dimension);
1168     inputSize.resize(dimension);
1169     sizeMM.resize(dimension);
1170     pixelType = mSlicerManagers[index]->GetImage()->GetScalarTypeAsITKString().c_str();
1171     for (int i = 0; i < dimension; i++) {
1172       origin[i] = imageSelected->GetOrigin()[i];
1173       inputSpacing[i] = imageSelected->GetSpacing()[i];
1174       inputSize[i] = imageSelected->GetSize()[i];
1175       sizeMM[i] = inputSize[i]*inputSpacing[i];
1176       NPixel *= inputSize[i];
1177     }
1178     inputSizeInBytes = GetSizeInBytes(imageSelected->GetActualMemorySize()*1000);
1179
1180     QString dim = QString::number(dimension) + " (";
1181     dim += pixelType + ")";
1182
1183     infoPanel->setFileName(image);
1184     std::string creationImageTimeValue("No creation time");
1185     itk::ExposeMetaData< std::string > (*imageSelected->GetFirstMetaDataDictionary(), "creationImageTime", creationImageTimeValue);
1186     infoPanel->setImageCreationTime(QString(creationImageTimeValue.c_str()));
1187     infoPanel->setDimension(dim);
1188     infoPanel->setSizePixel(GetVectorIntAsString(inputSize));
1189     infoPanel->setSizeMM(GetVectorDoubleAsString(sizeMM));
1190     infoPanel->setOrigin(GetVectorDoubleAsString(origin));
1191     infoPanel->setSpacing(GetVectorDoubleAsString(inputSpacing));
1192     infoPanel->setNPixel(QString::number(NPixel)+" ("+inputSizeInBytes+")");
1193
1194     transformation = imageSelected->GetTransform()[tSlice]->GetMatrix();
1195     infoPanel->setTransformation(clitk::Get4x4MatrixDoubleAsString(transformation).c_str());
1196
1197     landmarksPanel->SetCurrentLandmarks(mSlicerManagers[index]->GetLandmarks(),
1198                                         mSlicerManagers[index]->GetTSlice());
1199     landmarksPanel->SetCurrentPath(mInputPathName.toStdString());
1200     landmarksPanel->SetCurrentImage(mSlicerManagers[index]->GetFileName().c_str());
1201
1202     overlayPanel->getCurrentImageName(mSlicerManagers[index]->GetFileName().c_str());
1203     for (int i = 0; i < 4; i++) {
1204       if (DataTree->selectedItems()[0]->data(i+1,Qt::CheckStateRole).toInt() > 0 || i == 3) {
1205         mSlicerManagers[index]->UpdateInfoOnCursorPosition(i);
1206         break;
1207       }
1208     }
1209
1210 //     infoPanel->setFileName(image);
1211 //     infoPanel->setDimension(dim);
1212 //     infoPanel->setSizePixel(GetVectorIntAsString(inputSize));
1213 //     infoPanel->setSizeMM(GetVectorDoubleAsString(sizeMM));
1214 //     infoPanel->setOrigin(GetVectorDoubleAsString(origin));
1215 //     infoPanel->setSpacing(GetVectorDoubleAsString(inputSpacing));
1216 //     infoPanel->setNPixel(QString::number(NPixel)+" ("+inputSizeInBytes+")");
1217 //
1218 //     landmarksPanel->SetCurrentLandmarks(mSlicerManagers[index]->GetLandmarks(),
1219 //                                         mSlicerManagers[index]->GetTSlice());
1220 //     landmarksPanel->SetCurrentPath(mInputPathName.toStdString());
1221 //     landmarksPanel->SetCurrentImage(mSlicerManagers[index]->GetFileName().c_str());
1222 //
1223 //     overlayPanel->getCurrentImageName(mSlicerManagers[index]->GetFileName().c_str());
1224 //     for (int i = 0; i < 4; i++) {
1225 //       if (DataTree->selectedItems()[0]->data(i+1,Qt::CheckStateRole).toInt() > 0 || i == 3) {
1226 //         mSlicerManagers[index]->UpdateInfoOnCursorPosition(i);
1227 //         break;
1228 //       }
1229 //     }
1230     WindowLevelChanged();
1231
1232     slicingPresetComboBox->setCurrentIndex(mSlicerManagers[index]->GetSlicingPreset());
1233
1234     if (mSlicerManagers[index]->GetSlicer(0)->GetVF()) {
1235       overlayPanel->getVFName(mSlicerManagers[index]->GetVFName().c_str());
1236       overlayPanel->getVFProperty(mSlicerManagers[index]->GetSlicer(0)->GetVFSubSampling(),
1237         mSlicerManagers[index]->GetSlicer(0)->GetVFScale(),
1238         mSlicerManagers[index]->GetSlicer(0)->GetVFLog());
1239     } else {
1240       overlayPanel->getVFName(mSlicerManagers[index]->GetVFName().c_str());
1241       overlayPanel->getVFProperty(-1,-1,-1);
1242     }
1243     if (mSlicerManagers[index]->GetSlicer(0)->GetOverlay()) {
1244       overlayPanel->getOverlayName(mSlicerManagers[index]->GetOverlayName().c_str());
1245     } else {
1246       overlayPanel->getOverlayName(mSlicerManagers[index]->GetOverlayName().c_str());
1247     }
1248
1249     if (mSlicerManagers[index]->GetSlicer(0)->GetFusion()) {
1250       overlayPanel->getFusionName(mSlicerManagers[index]->GetFusionName().c_str());
1251     } else {
1252       overlayPanel->getFusionName(mSlicerManagers[index]->GetFusionName().c_str());
1253     }
1254   }
1255 }
1256 //------------------------------------------------------------------------------
1257
1258 //------------------------------------------------------------------------------
1259 void vvMainWindow::ShowDocumentation()
1260 {
1261   documentation->show();
1262 }
1263 //------------------------------------------------------------------------------
1264
1265 //------------------------------------------------------------------------------
1266 void vvMainWindow::PopupRegisterForm(bool checkCanPush)
1267 {
1268   vvRegisterForm* registerForm = new vvRegisterForm(QUrl("http://www.creatis.insa-lyon.fr/~dsarrut/vvregister/write.php"), getVVSettingsPath(), getSettingsOptionFormat());
1269   if(!checkCanPush) {
1270     registerForm->show();
1271   } else {
1272     if(registerForm->canPush()) {
1273       registerForm->show();
1274       registerForm->acquitPushed();//too bad if there is not internet connection anymore.
1275     }
1276   }
1277 }
1278 //------------------------------------------------------------------------------
1279
1280 //------------------------------------------------------------------------------
1281 void vvMainWindow::ShowHelpDialog()
1282 {
1283   help_dialog->show();
1284 }
1285 //------------------------------------------------------------------------------
1286
1287 //------------------------------------------------------------------------------
1288 void vvMainWindow::ChangeViewMode()
1289 {
1290   typedef struct _SIZE{
1291     QSplitter* splitter;
1292     QList<int> size1, size2;
1293     int cols[3];
1294   }SplitterSize;
1295   SplitterSize sizes[4];
1296   sizes[0].splitter = OSplitter;
1297   sizes[0].size1.push_back(1);
1298   sizes[0].size1.push_back(0);
1299   sizes[0].size2.push_back(1);
1300   sizes[0].size2.push_back(0);
1301   sizes[0].cols[0] = 2;
1302   sizes[0].cols[1] = 3;
1303   sizes[0].cols[2] = 4;
1304
1305   sizes[1].splitter = ESplitter;
1306   sizes[1].size1.push_back(0);
1307   sizes[1].size1.push_back(1);
1308   sizes[1].size2.push_back(1);
1309   sizes[1].size2.push_back(0);
1310   sizes[1].cols[0] = 1;
1311   sizes[1].cols[1] = 3;
1312   sizes[1].cols[2] = 4;
1313
1314   sizes[2].splitter = OSplitter;
1315   sizes[2].size1.push_back(1);
1316   sizes[2].size1.push_back(0);
1317   sizes[2].size2.push_back(0);
1318   sizes[2].size2.push_back(1);
1319   sizes[2].cols[0] = 1;
1320   sizes[2].cols[1] = 2;
1321   sizes[2].cols[2] = 4;
1322
1323   sizes[3].splitter = ESplitter;
1324   sizes[3].size1.push_back(0);
1325   sizes[3].size1.push_back(1);
1326   sizes[3].size2.push_back(0);
1327   sizes[3].size2.push_back(1);
1328   sizes[3].cols[0] = 1;
1329   sizes[3].cols[1] = 2;
1330   sizes[3].cols[2] = 3;
1331
1332   int slicer = mSlicerManagers[mCurrentPickedImageIndex]->GetSelectedSlicer();
1333   if (viewMode == 1) {
1334     if (slicer >= 0) {
1335       viewMode = 0;
1336       splitter_3->setSizes(sizes[slicer].size1);
1337       sizes[slicer].splitter->setSizes(sizes[slicer].size2);
1338       DataTree->setColumnHidden(sizes[slicer].cols[0],1);
1339       DataTree->setColumnHidden(sizes[slicer].cols[1],1);
1340       DataTree->setColumnHidden(sizes[slicer].cols[2],1);
1341     }
1342   } else {
1343     QList<int> size;
1344     if (slicer >= 0) {
1345       viewMode = 1;
1346       size.push_back(1);
1347       size.push_back(1);
1348       splitter_3->setSizes(size);
1349       sizes[slicer].splitter->setSizes(size);
1350       DataTree->setColumnHidden(sizes[slicer].cols[0],0);
1351       DataTree->setColumnHidden(sizes[slicer].cols[1],0);
1352       DataTree->setColumnHidden(sizes[slicer].cols[2],0);
1353     }
1354   }
1355   UpdateRenderWindows();
1356   /*
1357   ** I don't know why but for both resized QVTKWidget we also need to render
1358   ** the associated Slicer to redraw crosses.
1359   */
1360   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
1361     //     if (DataTree->topLevelItem(i)->data(COLUMN_UL_VIEW,Qt::CheckStateRole).toInt() > 1)
1362     mSlicerManagers[i]->GetSlicer(0)->Render();
1363     mSlicerManagers[i]->GetSlicer(1)->Render();
1364     //     if (DataTree->topLevelItem(i)->data(COLUMN_DL_VIEW,Qt::CheckStateRole).toInt() > 1)
1365     mSlicerManagers[i]->GetSlicer(2)->Render();
1366     mSlicerManagers[i]->GetSlicer(3)->Render();
1367   }
1368 }
1369 //------------------------------------------------------------------------------
1370
1371 //------------------------------------------------------------------------------
1372 QString vvMainWindow::GetSizeInBytes(unsigned long size)
1373 {
1374   QString result = "";// QString::number(size);
1375   //result += " bytes (";
1376   if (size > 1000000000) {
1377     size /= 1000000000;
1378     result += QString::number(size);
1379     result += "Gb";//)";
1380   } else if (size > 1000000) {
1381     size /= 1000000;
1382     result += QString::number(size);
1383     result += "Mb";//)";
1384   } else if (size > 1000) {
1385     size /= 1000;
1386     result += QString::number(size);
1387     result += "kb";//)";
1388   }
1389   return result;
1390 }
1391 //------------------------------------------------------------------------------
1392
1393 //------------------------------------------------------------------------------
1394 QString vvMainWindow::GetVectorDoubleAsString(std::vector<double> vectorDouble)
1395 {
1396   QString result;
1397   for (unsigned int i= 0; i < vectorDouble.size(); i++) {
1398     if (i != 0)
1399       result += " ";
1400     result += QString::number(vectorDouble[i]);
1401   }
1402   return result;
1403 }
1404 //------------------------------------------------------------------------------
1405
1406 //------------------------------------------------------------------------------
1407 QString vvMainWindow::GetVectorIntAsString(std::vector<int> vectorInt)
1408 {
1409   QString result;
1410   for (unsigned int i= 0; i < vectorInt.size(); i++) {
1411     if (i != 0)
1412       result += " ";
1413     result += QString::number(vectorInt[i]);
1414   }
1415   return result;
1416 }
1417 //------------------------------------------------------------------------------
1418
1419 //------------------------------------------------------------------------------
1420 //this actually returns the SlicerManager index!
1421 int vvMainWindow::GetSlicerIndexFromItem(QTreeWidgetItem* item)
1422 {
1423   QString id = item->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString();
1424   for (int i = 0; i < DataTree->topLevelItemCount(); i++) {
1425     if (DataTree->topLevelItem(i)->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString() == id)
1426       return i;
1427   }
1428   return -1;
1429 }
1430 //------------------------------------------------------------------------------
1431
1432 //------------------------------------------------------------------------------
1433 QTreeWidgetItem* vvMainWindow::GetItemFromSlicerManager(vvSlicerManager* sm)
1434 {
1435   QString id = sm->GetId().c_str();
1436   for (int i = 0; i < DataTree->topLevelItemCount(); i++) {
1437     if (DataTree->topLevelItem(i)->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString() == id)
1438       return DataTree->topLevelItem(i);
1439   }
1440   return NULL;
1441 }
1442 //------------------------------------------------------------------------------
1443
1444 //------------------------------------------------------------------------------
1445 void vvMainWindow::DisplayChanged(QTreeWidgetItem *clickedItem, int column)
1446 {
1447   if ( column >= COLUMN_CLOSE_IMAGE || column <= 0)
1448     return;
1449
1450   // Get parent information (might be the same item)
1451   int slicerManagerIndex = GetSlicerIndexFromItem(clickedItem);
1452   QTreeWidgetItem* clickedParentItem = DataTree->topLevelItem(slicerManagerIndex);
1453   vvSlicer* clickedSlicer = mSlicerManagers[slicerManagerIndex]->GetSlicer(column-1);
1454
1455   // Go over the complete item tree (only 2 levels, parents and children)
1456   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
1457     // Trick to avoid redoing twice the job for a key (sr)
1458     mSlicerManagers[i]->GetSlicer(column-1)->GetRenderWindow()->GetInteractor()->SetKeySym("Crap");
1459
1460     QTreeWidgetItem* currentParentItem = DataTree->topLevelItem(i);
1461     if(currentParentItem != clickedParentItem) {
1462       // Not the branch of the clicked item, uncheck all
1463
1464       // Parent
1465       currentParentItem->setData(column,Qt::CheckStateRole, 0);
1466       mSlicerManagers[i]->UpdateSlicer(column-1, false);
1467
1468       // Children
1469       for (int iChild = 0; iChild < currentParentItem->childCount(); iChild++) {
1470         currentParentItem->child(iChild)->setData(column,Qt::CheckStateRole, 0);
1471       }
1472     }
1473     else {
1474       // Branch of the clicked one: get check status from actor visibility in slicer
1475       // and toggle the clicked one
1476
1477       // Parent
1478       bool vis = clickedSlicer->GetActorVisibility("image", 0);
1479       bool draw = clickedSlicer->GetRenderer()->GetDraw();
1480
1481       // Update slicer (after getting visibility)
1482       mSlicerManagers[slicerManagerIndex]->UpdateSlicer(column-1, true);
1483       mSlicerManagers[slicerManagerIndex]->UpdateInfoOnCursorPosition(column-1);
1484       DisplaySliders(slicerManagerIndex, column-1);
1485       if(clickedParentItem == clickedItem) {
1486         // Toggle
1487         vis = !draw || !vis;
1488       }
1489       clickedSlicer->SetActorVisibility("image", 0, vis);
1490       clickedParentItem->setData(column, Qt::CheckStateRole, vis?2:0);
1491
1492       // Children
1493       std::map<std::string, int> actorTypeCounts;
1494       for (int iChild = 0; iChild < clickedParentItem->childCount(); iChild++) {
1495         QTreeWidgetItem* currentChildItem = clickedParentItem->child(iChild);
1496         std::string actorType = currentChildItem->data(1,Qt::UserRole).toString().toStdString();
1497         vis = clickedSlicer->GetActorVisibility(actorType, actorTypeCounts[actorType]);
1498         if(currentChildItem == clickedItem) {
1499           // Toggle or force visibility if it was not on this branch so far
1500           vis = !draw || !vis;
1501           clickedSlicer->SetActorVisibility(actorType, actorTypeCounts[actorType], vis);
1502         }
1503         currentChildItem->setData(column, Qt::CheckStateRole, vis?2:0);
1504         actorTypeCounts[actorType]++;
1505       }
1506     }
1507   }
1508
1509   clickedSlicer->Render();
1510 }
1511 //------------------------------------------------------------------------------
1512
1513 void vvMainWindow::InitSlicers()
1514 {
1515   if (mSlicerManagers.size()) {
1516     mSlicerManagers.back()->GenerateDefaultLookupTable();
1517     mSlicerManagers.back()->SetSlicerWindow(0,NOViewWidget->GetRenderWindow());
1518     mSlicerManagers.back()->SetSlicerWindow(1,NEViewWidget->GetRenderWindow());
1519     mSlicerManagers.back()->SetSlicerWindow(2,SOViewWidget->GetRenderWindow());
1520     mSlicerManagers.back()->SetSlicerWindow(3,SEViewWidget->GetRenderWindow());
1521 #if VTK_MAJOR_VERSION <= 5
1522     mSlicerManagers.back()->Render(); // SR: displayed #slice is wrong without this / TB: With VTK6 and multiple images, all slicers are updated, not only the first
1523 #endif
1524   }
1525 }
1526
1527 //------------------------------------------------------------------------------
1528 void vvMainWindow::InitDisplay()
1529 {
1530   if (mSlicerManagers.size()) {
1531     //BE CAREFUL : this is absolutely necessary to set the interactor style
1532     //in order to have the same style instanciation for all SlicerManagers in
1533     // a same window
1534     for (int j = 0; j < 4; j++) {
1535       vvInteractorStyleNavigator* style = vvInteractorStyleNavigator::New();
1536       style->SetAutoAdjustCameraClippingRange(1);
1537       bool AlreadySelected = false;
1538       for (int i = 0; i < DataTree->topLevelItemCount(); i++) {
1539         mSlicerManagers[i]->SetInteractorStyleNavigator(j,style);
1540         //select the image only if previous are not selected
1541         if (DataTree->topLevelItem(i)->data(j+1,Qt::CheckStateRole).toInt() > 1) {
1542           mSlicerManagers[i]->UpdateSlicer(j,1);
1543           AlreadySelected = true;
1544         } else if (i == DataTree->topLevelItemCount()-1 && !AlreadySelected) {
1545           if (DataTree->selectedItems().size() == 0) {
1546             DataTree->topLevelItem(i)->setSelected(1);
1547           }
1548           DataTree->topLevelItem(i)->setData(j+1,Qt::CheckStateRole,2);
1549           mSlicerManagers[i]->UpdateSlicer(j,1);
1550           DisplaySliders(i,j);
1551         } else {
1552           DataTree->topLevelItem(i)->setData(j+1,Qt::CheckStateRole,0);
1553           mSlicerManagers[i]->UpdateSlicer(j,0);
1554         }
1555       }
1556       style->Delete();
1557     }
1558   }
1559 }
1560 //------------------------------------------------------------------------------
1561
1562 //------------------------------------------------------------------------------
1563 void vvMainWindow::DisplaySliders(int slicer, int window)
1564 {
1565   if(!mSlicerManagers[slicer]->GetSlicer(window)->GetRenderer()->GetDraw())
1566     return;
1567
1568   int range[2];
1569   mSlicerManagers[slicer]->GetSlicer(window)->GetSliceRange(range);
1570   int position = mSlicerManagers[slicer]->GetSlicer(window)->GetSlice();
1571   if (range[1]>0)
1572     verticalSliders[window]->show();
1573   else
1574     verticalSliders[window]->hide();
1575   verticalSliders[window]->setRange(range[0],range[1]);
1576   verticalSliders[window]->setValue(position);
1577
1578   int tRange[2];
1579   tRange[0] = 0;
1580   tRange[1] = mSlicerManagers[slicer]->GetSlicer(window)->GetTMax();
1581   if (tRange[1]>0)
1582     horizontalSliders[window]->show();
1583   else
1584     horizontalSliders[window]->hide();
1585   horizontalSliders[window]->setRange(tRange[0],tRange[1]);
1586   int tPosition = mSlicerManagers[slicer]->GetSlicer(window)->GetMaxCurrentTSlice();
1587   horizontalSliders[window]->setValue(tPosition);
1588 }
1589 //------------------------------------------------------------------------------
1590
1591 //------------------------------------------------------------------------------
1592 void vvMainWindow::CloseImage(QTreeWidgetItem* item, int column)
1593 {
1594   int index = GetSlicerIndexFromItem(item);
1595
1596   if (DataTree->topLevelItem(index) != item) {
1597     QString warning = "Do you really want to close the overlay : ";
1598     warning += item->data(COLUMN_IMAGE_NAME,Qt::DisplayRole).toString();
1599     QMessageBox msgBox(QMessageBox::Warning, tr("Close Overlay"),
1600       warning, 0, this);
1601     msgBox.addButton(tr("Close"), QMessageBox::AcceptRole);
1602     msgBox.addButton(tr("Cancel"), QMessageBox::RejectRole);
1603     if (msgBox.exec() == QMessageBox::AcceptRole) {
1604       std::string overlay_type=item->data(1,Qt::UserRole).toString().toStdString();
1605       int overlay_index=0;
1606       for (int child = 0; child < DataTree->topLevelItem(index)->childCount(); child++) {
1607         if (DataTree->topLevelItem(index)->\
1608           child(child)->data(1,Qt::UserRole).toString().toStdString() == overlay_type)
1609           overlay_index++;
1610         if (DataTree->topLevelItem(index)->child(child) == item) break;
1611       }
1612       if (overlay_type=="fusionSequence") {
1613         //removing the overlay sequence in a fusion sequence visualization mode
1614         //reset the transforms
1615         overlayPanel->getFusionSequenceProperty(-1, false, 0, false);
1616
1617         //unlink and untie the slicer managers
1618         RemoveLink(mSlicerManagers[index]->GetId().c_str(), mSlicerManagers[mSlicerManagers[index]->GetFusionSequenceIndexOfLinkedManager()]->GetId().c_str());
1619         mSlicerManagers[index]->SetFusionSequenceInvolvmentCode(-1);
1620         mSlicerManagers[mSlicerManagers[index]->GetFusionSequenceIndexOfLinkedManager()]->SetFusionSequenceInvolvmentCode(-1);
1621         for (unsigned i=0 ; i<4 ; i++) {
1622             mSlicerManagers[index]->GetSlicer(i)->SetFusionSequenceCode(-1);
1623             mSlicerManagers[mSlicerManagers[index]->GetFusionSequenceIndexOfLinkedManager()]->GetSlicer(i)->SetFusionSequenceCode(-1);
1624         }
1625
1626       }
1627       mSlicerManagers[index]->RemoveActor(overlay_type, overlay_index-1);
1628       mSlicerManagers[index]->SetColorMap(0);
1629       DataTree->topLevelItem(index)->takeChild(DataTree->topLevelItem(index)->indexOfChild(item));
1630       mSlicerManagers[index]->Render();
1631     }
1632   } else if (DataTree->topLevelItemCount() <= 1) {
1633     QString warning = "Do you really want to close the image : ";
1634     warning += item->data(COLUMN_IMAGE_NAME,Qt::DisplayRole).toString();
1635     warning += "\nThis is the last image, you're about to close vv !!!";
1636     QMessageBox msgBox(QMessageBox::Warning, tr("Close Image"),
1637       warning, 0, this);
1638     msgBox.addButton(tr("Close vv"), QMessageBox::AcceptRole);
1639     msgBox.addButton(tr("Cancel"), QMessageBox::RejectRole);
1640     if (msgBox.exec() == QMessageBox::AcceptRole) {
1641       this->close();
1642     }
1643   } else {
1644     QString warning = "Do you really want to close the image : ";
1645     warning += item->data(COLUMN_IMAGE_NAME,Qt::DisplayRole).toString();
1646     QMessageBox msgBox(QMessageBox::Warning, tr("Close Image"),
1647       warning, 0, this);
1648     msgBox.addButton(tr("Close"), QMessageBox::AcceptRole);
1649     msgBox.addButton(tr("Cancel"), QMessageBox::RejectRole);
1650     if (msgBox.exec() == QMessageBox::AcceptRole) {
1651
1652       // Tell tools that we close an image
1653       emit AnImageIsBeingClosed(mSlicerManagers[index]);
1654
1655       std::vector<vvSlicerManager*>::iterator Manageriter = mSlicerManagers.begin();
1656       DataTree->takeTopLevelItem(index);
1657       for (int i = 0; i < index; i++) {
1658         Manageriter++;
1659       }
1660       //if the slicer manager was involved in a fusion sequence visualization...
1661       if ( mSlicerManagers[index]->IsInvolvedInFusionSequence() ) {
1662         //in both cases, close the overlay: find it... and close it
1663         //ideally, I should duplicate the code, and avoid calling CloseImage, since this pops up another interactive box
1664         QTreeWidgetItem* overlayItem;
1665         if (mSlicerManagers[index]->IsMainSequenceOfFusionSequence()) {
1666           for (unsigned i=0 ; i<item->childCount() ; i++) {
1667             overlayItem = item->child(i);
1668             this->CloseImage( overlayItem, 0 );
1669           }
1670         }
1671         else {
1672           QTreeWidgetItem* linkedItem = this->GetItemFromSlicerManager( mSlicerManagers[mSlicerManagers[index]->GetFusionSequenceIndexOfLinkedManager()] );
1673           for (unsigned i=0 ; i<linkedItem->childCount() ; i++) {
1674             overlayItem = linkedItem->child(i);
1675             this->CloseImage( overlayItem, 0 );
1676           }
1677         }
1678
1679         /* -- this is normally already done when closing the overlay.
1680         //reset the transforms
1681         overlayPanel->getFusionSequenceProperty(-1, false, 0, false);
1682
1683         //unlink and untie the slicer managers
1684         RemoveLink(mSlicerManagers[index]->GetId().c_str(), mSlicerManagers[mSlicerManagers[index]->GetFusionSequenceIndexOfLinkedManager()]->GetId().c_str());
1685         mSlicerManagers[index]->SetFusionSequenceInvolvmentCode(-1);
1686         mSlicerManagers[mSlicerManagers[index]->GetFusionSequenceIndexOfLinkedManager()]->SetFusionSequenceInvolvmentCode(-1);
1687         for (unsigned i=0 ; i<4 ; i++) {
1688             mSlicerManagers[index]->GetSlicer(i)->SetFusionSequenceCode(-1);
1689             mSlicerManagers[mSlicerManagers[index]->GetFusionSequenceIndexOfLinkedManager()]->GetSlicer(i)->SetFusionSequenceCode(-1);
1690         }
1691         */
1692       }
1693
1694       linkPanel->removeImage(index);
1695       mSlicerManagers[index]->RemoveActors();
1696
1697       //remove the slicer manager
1698       delete mSlicerManagers[index];
1699       mSlicerManagers.erase(Manageriter);
1700
1701       //
1702       InitDisplay();
1703     }
1704   }
1705   ImageInfoChanged();
1706 }
1707 //------------------------------------------------------------------------------
1708
1709 //------------------------------------------------------------------------------
1710 void vvMainWindow::ReloadImage(QTreeWidgetItem* item, int column)
1711 {
1712   // int index = GetSlicerIndexFromItem(item);
1713   //   QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
1714   //   if (item->data(1,Qt::UserRole).toString() == "vector")
1715   //     mSlicerManagers[index]->ReloadVF();
1716   //   else
1717   //     mSlicerManagers[index]->Reload();
1718
1719   //   QApplication::restoreOverrideCursor();
1720   int index = GetSlicerIndexFromItem(item);
1721   QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
1722   QString role=item->data(1,Qt::UserRole).toString();
1723   if ( role == "vector") {
1724     mSlicerManagers[index]->ReloadVF();
1725   }
1726   else if (role == "overlay") {
1727     mSlicerManagers[index]->ReloadOverlay();
1728   }
1729   else if (role == "fusion") {
1730     mSlicerManagers[index]->ReloadFusion();
1731   }
1732   else if (role == "fusionSequence") {
1733     //both versions of the secondary sequence must be updated.
1734     mSlicerManagers[index]->ReloadFusionSequence();
1735     mSlicerManagers[mSlicerManagers[index]->GetFusionSequenceIndexOfLinkedManager()]->Reload();
1736   }
1737   else {
1738     mSlicerManagers[index]->Reload();
1739     //if we update the secondary sequence, then the overlay of the main sequence should also be updated
1740     if (mSlicerManagers[index]->IsSecondarySequenceOfFusionSequence()) mSlicerManagers[mSlicerManagers[index]->GetFusionSequenceIndexOfLinkedManager()]->ReloadFusionSequence();
1741   }
1742   // Update view and info
1743   ImageInfoChanged();
1744   mSlicerManagers[index]->Render();
1745   QApplication::restoreOverrideCursor();
1746 }
1747 //------------------------------------------------------------------------------
1748
1749 //------------------------------------------------------------------------------
1750 void vvMainWindow::MousePositionChanged(int visibility,double x, double y, double z, double X, double Y, double Z , double value)
1751 {
1752   infoPanel->setCurrentInfo(visibility,x,y,z,X,Y,Z,value);
1753 }
1754 //------------------------------------------------------------------------------
1755
1756 //------------------------------------------------------------------------------
1757 void vvMainWindow::VectorChanged(int visibility,double x, double y, double z, double value)
1758 {
1759   overlayPanel->getCurrentVectorInfo(visibility,x,y,z,value);
1760 }
1761 //------------------------------------------------------------------------------
1762
1763 //------------------------------------------------------------------------------
1764 void vvMainWindow::OverlayChanged(int visibility, double valueOver, double valueRef)
1765 {
1766   overlayPanel->getCurrentOverlayInfo(visibility,valueOver, valueRef);
1767 }
1768 //------------------------------------------------------------------------------
1769
1770 //------------------------------------------------------------------------------
1771 void vvMainWindow::FusionChanged(int visibility, double value)
1772 {
1773   overlayPanel->getCurrentFusionInfo(visibility,value);
1774 }
1775 //------------------------------------------------------------------------------
1776
1777 //------------------------------------------------------------------------------
1778 //called when AddOverlayImage, AddFusionSequence
1779 //or when UpdateWindowLevel() is called ; when slicerManager emits WindowLevelChanged
1780 //when ImageInfoChanged() is called
1781 void vvMainWindow::WindowLevelChanged()
1782 {
1783   // Base image
1784   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1785   if(index==-1) return;
1786   windowSpinBox->setValue(mSlicerManagers[index]->GetColorWindow());
1787   levelSpinBox->setValue(mSlicerManagers[index]->GetColorLevel());
1788   colorMapComboBox->setCurrentIndex(mSlicerManagers[index]->GetColorMap());
1789   presetComboBox->setCurrentIndex(mSlicerManagers[index]->GetPreset());
1790
1791   // Overlay image
1792   if (mSlicerManagers[index]->GetSlicer(0)->GetOverlay())
1793     overlayPanel->getOverlayProperty(mSlicerManagers[index]->GetOverlayColor(),
1794     mSlicerManagers[index]->GetLinkOverlayWindowLevel(),
1795     mSlicerManagers[index]->GetOverlayColorWindow(),
1796     mSlicerManagers[index]->GetOverlayColorLevel());
1797   else
1798     overlayPanel->getOverlayProperty(-1,0,0.,0.);
1799
1800   // Fusion & SequenceFusion image
1801   if (mSlicerManagers[index]->GetSlicer(0)->GetFusion()) {
1802     overlayPanel->getFusionProperty(mSlicerManagers[index]->GetFusionOpacity(),
1803       mSlicerManagers[index]->GetFusionThresholdOpacity(),
1804       mSlicerManagers[index]->GetFusionColorMap(),
1805       mSlicerManagers[index]->GetFusionWindow(),
1806       mSlicerManagers[index]->GetFusionLevel());
1807     if (mSlicerManagers[index]->IsMainSequenceOfFusionSequence()) {
1808       overlayPanel->getFusionSequenceProperty(mSlicerManagers[index]->GetFusionSequenceFrameIndex(),
1809         mSlicerManagers[index]->GetFusionSequenceSpatialSyncFlag(),
1810         mSlicerManagers[index]->GetFusionSequenceNbFrames(),
1811         mSlicerManagers[index]->GetFusionSequenceTemporalSyncFlag());
1812     }
1813   }
1814   else if ( mSlicerManagers[index]->IsSecondarySequenceOfFusionSequence() ) {
1815     //if the image is involved in a fusion sequence, preserve the overlay panel!
1816     int ind = mSlicerManagers[index]->GetFusionSequenceIndexOfLinkedManager();
1817     overlayPanel->getFusionProperty(mSlicerManagers[ind]->GetFusionOpacity(),
1818       mSlicerManagers[ind]->GetFusionThresholdOpacity(),
1819       mSlicerManagers[ind]->GetFusionColorMap(),
1820       mSlicerManagers[ind]->GetFusionWindow(),
1821       mSlicerManagers[ind]->GetFusionLevel());
1822     overlayPanel->getFusionSequenceProperty(mSlicerManagers[ind]->GetFusionSequenceFrameIndex(),
1823       mSlicerManagers[ind]->GetFusionSequenceSpatialSyncFlag(),
1824       mSlicerManagers[ind]->GetFusionSequenceNbFrames(),
1825       mSlicerManagers[ind]->GetFusionSequenceTemporalSyncFlag());
1826   }
1827   else
1828   {
1829     overlayPanel->getFusionProperty(-1, -1, -1, -1, -1);
1830     overlayPanel->getFusionSequenceProperty(-1, false, 0, false);
1831   }
1832 }
1833 //------------------------------------------------------------------------------
1834
1835 //------------------------------------------------------------------------------
1836 void vvMainWindow::WindowLevelEdited()
1837 {
1838   presetComboBox->setCurrentIndex(WL_USER);
1839   UpdateWindowLevel();
1840 }
1841 //------------------------------------------------------------------------------
1842
1843 //------------------------------------------------------------------------------
1844 void vvMainWindow::SetWindowLevel(double w, double l)
1845 {
1846   windowSpinBox->setValue(w);
1847   levelSpinBox->setValue(l);
1848   presetComboBox->setCurrentIndex(WL_USER);
1849   colorMapComboBox->setCurrentIndex(0);
1850   UpdateWindowLevel();
1851 }
1852 //------------------------------------------------------------------------------
1853
1854 //------------------------------------------------------------------------------
1855 void vvMainWindow::UpdateWindowLevel()
1856 {
1857   if (DataTree->selectedItems().size()) {
1858     if (presetComboBox->currentIndex() == WL_VENTILATION) //For ventilation
1859       colorMapComboBox->setCurrentIndex(5);
1860     int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1861     mSlicerManagers[index]->SetColorWindow(windowSpinBox->value());
1862     mSlicerManagers[index]->SetColorLevel(levelSpinBox->value());
1863     mSlicerManagers[index]->SetPreset(presetComboBox->currentIndex());
1864     mSlicerManagers[index]->Render();
1865     WindowLevelChanged();
1866   }
1867 }
1868 //------------------------------------------------------------------------------
1869
1870 //------------------------------------------------------------------------------
1871 void vvMainWindow::UpdateSlicingPreset()
1872 {
1873   if (DataTree->selectedItems().size()) {
1874     int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1875     mSlicerManagers[index]->SetSlicingPreset(vvSlicerManager::SlicingPresetType(slicingPresetComboBox->currentIndex()));
1876   }
1877 }
1878 //------------------------------------------------------------------------------
1879
1880 //------------------------------------------------------------------------------
1881 void vvMainWindow::UpdateColorMap()
1882 {
1883   if (DataTree->selectedItems().size()) {
1884     int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1885     mSlicerManagers[index]->SetColorMap(colorMapComboBox->currentIndex());
1886     mSlicerManagers[index]->Render();
1887   }
1888 }
1889 //------------------------------------------------------------------------------
1890 void vvMainWindow::SwitchWindowLevel()
1891 {
1892   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1893   int window = mSlicerManagers[index]->GetColorWindow();
1894   presetComboBox->setCurrentIndex(WL_USER);
1895   windowSpinBox->setValue(-window);
1896   UpdateWindowLevel();
1897 }
1898 //------------------------------------------------------------------------------
1899
1900 //------------------------------------------------------------------------------
1901 void vvMainWindow::ApplyWindowLevelToAllImages()
1902 {
1903   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1904   if(index==-1) return;
1905   double window = mSlicerManagers[index]->GetColorWindow();
1906   double level = mSlicerManagers[index]->GetColorLevel();
1907
1908   double fusWindow = mSlicerManagers[index]->GetFusionWindow();
1909   double fusLevel = mSlicerManagers[index]->GetFusionLevel();
1910
1911   double overWindow = mSlicerManagers[index]->GetOverlayColorWindow();
1912   double overLevel = mSlicerManagers[index]->GetOverlayColorLevel();
1913
1914   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
1915     if (mSlicerManagers[i] == NULL)
1916       continue;
1917     mSlicerManagers[i]->SetColorWindow(window);
1918     mSlicerManagers[i]->SetColorLevel(level);
1919     mSlicerManagers[i]->SetPreset(WL_USER);
1920     mSlicerManagers[i]->SetFusionWindow(fusWindow);
1921     mSlicerManagers[i]->SetFusionLevel(fusLevel);
1922     mSlicerManagers[i]->SetOverlayColorWindow(overWindow);
1923     mSlicerManagers[i]->SetOverlayColorLevel(overLevel);
1924     mSlicerManagers[i]->Render();
1925   }
1926 }
1927 //------------------------------------------------------------------------------
1928
1929 //------------------------------------------------------------------------------
1930 void vvMainWindow::ApplyWindowToSetOfImages(double window, unsigned int indexMin, unsigned int indexMax)
1931 {
1932   for (unsigned int i = indexMin; i <= indexMax && i < mSlicerManagers.size(); i++) {
1933     if (mSlicerManagers[i] == NULL)
1934       continue;
1935     SetWindowLevel(window, mSlicerManagers[i]->GetColorLevel());
1936     mSlicerManagers[i]->SetColorWindow(window);
1937     mSlicerManagers[i]->SetPreset(WL_USER);
1938     mSlicerManagers[i]->Render();
1939   }
1940 }
1941 //------------------------------------------------------------------------------
1942
1943 //------------------------------------------------------------------------------
1944 void vvMainWindow::ApplyLevelToSetOfImages(double level, unsigned int indexMin, unsigned int indexMax)
1945 {
1946   for (unsigned int i = indexMin; i <= indexMax && i < mSlicerManagers.size(); i++) {
1947     if (mSlicerManagers[i] == NULL)
1948       continue;
1949     SetWindowLevel(mSlicerManagers[i]->GetColorWindow(), level);
1950     mSlicerManagers[i]->SetColorLevel(level);
1951     mSlicerManagers[i]->SetPreset(WL_USER);
1952     mSlicerManagers[i]->Render();
1953   }
1954 }
1955 //------------------------------------------------------------------------------
1956
1957 //------------------------------------------------------------------------------
1958 void vvMainWindow::UpdateLinkManager(std::string id, int slicer, double x, double y, double z, int temps)
1959 {
1960   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
1961     if (mSlicerManagers[i]->GetId() == id) {
1962       mSlicerManagers[i]->GetSlicer(slicer)->SetCurrentPosition(x,y,z,temps);
1963       mSlicerManagers[i]->UpdateViews(0,slicer);
1964       break;
1965     }
1966   }
1967 }
1968 //------------------------------------------------------------------------------
1969
1970 //------------------------------------------------------------------------------
1971 void vvMainWindow::UpdateLinkedNavigation(std::string id, vvSlicerManager * sm, vvSlicer* refSlicer)
1972 {
1973   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
1974     if (id == mSlicerManagers[i]->GetId()) {
1975       mSlicerManagers[i]->UpdateLinkedNavigation(refSlicer);
1976     }
1977   }
1978 }
1979 //------------------------------------------------------------------------------
1980
1981 //------------------------------------------------------------------------------
1982 void vvMainWindow::ShowContextMenu(QPoint point)
1983 {
1984   if (!DataTree->selectedItems().size()) {
1985     contextActions[1]->setEnabled(0);
1986     contextActions[2]->setEnabled(0);
1987     contextActions[3]->setEnabled(0);
1988     contextActions[4]->setEnabled(0);
1989     contextActions[5]->setEnabled(0);
1990     contextActions[6]->setEnabled(0);
1991   } else {
1992     int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1993     contextActions[1]->setEnabled(1);
1994     contextActions[2]->setEnabled(
1995       DataTree->itemWidget(DataTree->selectedItems()[0],
1996       COLUMN_RELOAD_IMAGE)->isEnabled());
1997     contextActions[3]->setEnabled(1);
1998     contextActions[5]->setEnabled(1);
1999     contextActions[6]->setEnabled(1);
2000
2001     if (mSlicerManagers[index]->GetDimension() < 3)
2002       contextActions[4]->setEnabled(0);
2003     else
2004       contextActions[4]->setEnabled(1);
2005   }
2006   contextMenu.exec(QCursor::pos());
2007 }
2008 //------------------------------------------------------------------------------
2009
2010 //------------------------------------------------------------------------------
2011 void vvMainWindow::CloseImage()
2012 {
2013   CloseImage(DataTree->selectedItems()[0],0);
2014 }
2015 //------------------------------------------------------------------------------
2016
2017 //------------------------------------------------------------------------------
2018 void vvMainWindow::ReloadImage()
2019 {
2020   ReloadImage(DataTree->selectedItems()[0],0);
2021 }
2022 //------------------------------------------------------------------------------
2023
2024 //------------------------------------------------------------------------------
2025 void vvMainWindow::SelectOverlayImage()
2026 {
2027   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2028
2029   if (!(CheckAddedImage(index, "overlay")))
2030     return;
2031
2032   QString Extensions = EXTENSIONS;
2033   Extensions += ";;All Files (*)";
2034   QStringList files = QFileDialog::getOpenFileNames(this,tr("Load Overlay image"),mInputPathName,Extensions);
2035   if (files.isEmpty())
2036     return;
2037
2038   std::vector<std::string> vecFileNames;
2039   for (int i = 0; i < files.size(); i++) {
2040     vecFileNames.push_back(files[i].toStdString());
2041   }
2042
2043   AddOverlayImage(index,vecFileNames,vvImageReader::IMAGE);
2044 }
2045 //------------------------------------------------------------------------------
2046
2047 //------------------------------------------------------------------------------
2048 bool vvMainWindow::CheckAddedImage(int index, QString imageType)
2049 {
2050   //check if one overlay image is added
2051   for (int child = 0; child < DataTree->topLevelItem(index)->childCount(); child++)
2052     if (DataTree->topLevelItem(index)->child(child)->data(1,Qt::UserRole).toString().compare(imageType) == 0) {
2053       QString error = "Cannot add more than one compared image\n";
2054       error += "Please remove first ";
2055       error += DataTree->topLevelItem(index)->child(child)->data(COLUMN_IMAGE_NAME,Qt::DisplayRole).toString();
2056       QMessageBox::information(this,tr("Problem adding compared image !"),error);
2057       return false;
2058     }
2059     return true;
2060 }
2061 //------------------------------------------------------------------------------
2062
2063 //------------------------------------------------------------------------------
2064 void vvMainWindow::AddOverlayImage(int index, std::vector<std::string> fileNames, vvImageReader::LoadedImageType type)
2065 {
2066   QString file(fileNames[0].c_str());
2067   if (QFile::exists(file))
2068   {
2069     mInputPathName = itksys::SystemTools::GetFilenamePath(file.toStdString()).c_str();
2070     itk::ImageIOBase::Pointer reader = itk::ImageIOFactory::CreateImageIO(
2071       file.toStdString().c_str(), itk::ImageIOFactory::ReadMode);
2072     reader->SetFileName(fileNames[0].c_str());
2073     reader->ReadImageInformation();
2074     std::string component = reader->GetComponentTypeAsString(reader->GetComponentType());
2075     int dimension = reader->GetNumberOfDimensions();
2076     QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
2077     vvProgressDialog progress("Opening " + file.toStdString());
2078     qApp->processEvents();
2079
2080     std::string filename = itksys::SystemTools::GetFilenameWithoutExtension(file.toStdString()).c_str();
2081     if (mSlicerManagers[index]->SetOverlay(fileNames,dimension, component,type)) {
2082       //create an item in the tree with good settings
2083       QTreeWidgetItem *item = new QTreeWidgetItem();
2084       item->setData(0,Qt::UserRole,file.toStdString().c_str());
2085       item->setData(1,Qt::UserRole,tr("overlay"));
2086       QFileInfo fileinfo(file); //Do not show the path
2087       item->setData(COLUMN_IMAGE_NAME,Qt::DisplayRole,fileinfo.fileName());
2088       item->setToolTip(COLUMN_IMAGE_NAME, mSlicerManagers[index]->GetListOfAbsoluteFilePathInOneString("overlay").c_str());
2089       qApp->processEvents();
2090 #if VTK_MAJOR_VERSION > 5
2091       for ( unsigned int i = 0; i < mSlicerManagers[index]->GetNumberOfSlicers(); i++)
2092         mSlicerManagers[index]->GetSlicer(i)->ForceUpdateDisplayExtent();
2093 #endif
2094
2095       for (int j = 1; j <= 4; j++) {
2096         item->setData(j,Qt::CheckStateRole,DataTree->topLevelItem(index)->data(j,Qt::CheckStateRole));
2097       }
2098
2099       //Create the buttons for reload and close
2100       qApp->processEvents();
2101       QTreePushButton* cButton = new QTreePushButton;
2102       cButton->setItem(item);
2103       cButton->setColumn(COLUMN_CLOSE_IMAGE);
2104       cButton->setToolTip(tr("close image"));
2105       cButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/exit.png")));
2106       connect(cButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
2107         this,SLOT(CloseImage(QTreeWidgetItem*, int)));
2108
2109       QTreePushButton* rButton = new QTreePushButton;
2110       rButton->setItem(item);
2111       rButton->setColumn(COLUMN_RELOAD_IMAGE);
2112       rButton->setToolTip(tr("reload image"));
2113       rButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/rotateright.png")));
2114       connect(rButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
2115         this,SLOT(ReloadImage(QTreeWidgetItem*, int)));
2116
2117       DataTree->topLevelItem(index)->setExpanded(1);
2118       DataTree->topLevelItem(index)->addChild(item);
2119       DataTree->setItemWidget(item, COLUMN_CLOSE_IMAGE, cButton);
2120       DataTree->setItemWidget(item, COLUMN_RELOAD_IMAGE, rButton);
2121
2122       //set the id of the image
2123       QString id = DataTree->topLevelItem(index)->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString();
2124       item->setData(COLUMN_IMAGE_NAME,Qt::UserRole,id.toStdString().c_str());
2125       UpdateTree();
2126       qApp->processEvents();
2127       ImageInfoChanged();
2128       QApplication::restoreOverrideCursor();
2129
2130       // Update the display to update, e.g., the sliders
2131       for(int i=0; i<4; i++)
2132         DisplaySliders(index, i);
2133     } else {
2134       QApplication::restoreOverrideCursor();
2135       QString error = "Cannot import the new image.\n";
2136       error += mSlicerManagers[index]->GetLastError().c_str();
2137       QMessageBox::information(this,tr("Problem reading image !"),error);
2138     }
2139     WindowLevelChanged();
2140   }
2141   else
2142     QMessageBox::information(this,tr("Problem reading Overlay !"),"File doesn't exist!");
2143 }
2144 //------------------------------------------------------------------------------
2145
2146
2147 //------------------------------------------------------------------------------
2148 void vvMainWindow::AddROI(int index, QString file)
2149 {
2150   /*
2151   // Get slice manager
2152
2153   // Load image
2154
2155   vvImageReader * mReader = new vvImageReader;
2156   mReader->SetInputFilename(filename.toStdString());
2157   mReader->Update(IMAGE);
2158   if (mReader->GetLastError().size() != 0) {
2159   std::cerr << "Error while reading " << filename.toStdString() << std::endl;
2160   QString error = "Cannot open file \n";
2161   error += mReader->GetLastError().c_str();
2162   QMessageBox::information(this,tr("Reading problem"),error);
2163   delete mReader;
2164   return;
2165   }
2166   vvImage::Pointer roi = mReader->GetOutput();
2167
2168   // Create roi in new tool
2169   vvToolStructureSetManager::AddImage(mCurrentSlicerManager, roi);
2170   */
2171 }
2172 //------------------------------------------------------------------------------
2173
2174 //------------------------------------------------------------------------------
2175 void vvMainWindow::SelectWipeImage()
2176 {
2177   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2178
2179
2180   if (!(CheckAddedImage(index, "wipe")))
2181     return;
2182
2183   vvWipeImage::Pointer wipeImage = vvWipeImage::New();
2184   wipeImage->Initialize(mInputPathName, mSlicerManagers);
2185   wipeImage->selectWipeImage(index, GetTree());
2186   QTreeWidgetItem *item = DataTree->itemAt(index, COLUMN_CLOSE_IMAGE);
2187   //connect(item,SIGNAL(clickedInto(QTreeWidgetItem*, int)), this,SLOT(CloseImage(QTreeWidgetItem*, int)));
2188   UpdateTree();
2189   ImageInfoChanged();
2190   for(int i=0; i<4; i++)
2191         DisplaySliders(index, i);
2192   WindowLevelChanged();
2193
2194   /*QString Extensions = EXTENSIONS;
2195   Extensions += ";;All Files (*)";
2196   QStringList files = QFileDialog::getOpenFileNames(this,tr("Load Wipe image"),mInputPathName,Extensions);
2197   if (files.isEmpty())
2198     return;
2199
2200   std::vector<std::string> vecFileNames;
2201   for (int i = 0; i < files.size(); i++) {
2202     vecFileNames.push_back(files[i].toStdString());
2203   }*/
2204
2205   //AddWipeImage(index,vecFileNames,vvImageReader::IMAGE);
2206 }
2207 //------------------------------------------------------------------------------
2208
2209
2210 //------------------------------------------------------------------------------
2211 void vvMainWindow::SelectFusionImage()
2212 {
2213   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2214
2215   if (!(CheckAddedImage(index, "fusion")) || !(CheckAddedImage(index, "fusionSequence")))
2216     return;
2217
2218   QString Extensions = EXTENSIONS;
2219   Extensions += ";;All Files (*)";
2220   QStringList files = QFileDialog::getOpenFileNames(this,tr("Load Fusion image"),mInputPathName,Extensions);
2221   if (files.isEmpty())
2222     return;
2223
2224   std::vector<std::string> vecFileNames;
2225   for (int i = 0; i < files.size(); i++) {
2226     vecFileNames.push_back(files[i].toStdString());
2227   }
2228   AddFusionImage(index,vecFileNames,vvImageReader::IMAGE);
2229 }
2230 //------------------------------------------------------------------------------
2231
2232 //------------------------------------------------------------------------------
2233 void vvMainWindow::ResetTransformationToIdentity()
2234 {
2235   std::string actorType = DataTree->selectedItems()[0]->data(1,Qt::UserRole).toString().toStdString();
2236   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2237   mSlicerManagers[index]->ResetTransformationToIdentity(actorType);
2238   ImageInfoChanged();
2239 }
2240 //------------------------------------------------------------------------------
2241
2242 //------------------------------------------------------------------------------
2243 void vvMainWindow::AddFusionImage(int index, std::vector<std::string> fileNames, vvImageReader::LoadedImageType type)
2244 {
2245   QString file(fileNames[0].c_str());
2246   if (QFile::exists(file))
2247   {
2248     mInputPathName = itksys::SystemTools::GetFilenamePath(file.toStdString()).c_str();
2249     itk::ImageIOBase::Pointer reader = itk::ImageIOFactory::CreateImageIO(
2250       file.toStdString().c_str(), itk::ImageIOFactory::ReadMode);
2251     reader->SetFileName(fileNames[0].c_str());
2252     reader->ReadImageInformation();
2253     std::string component = reader->GetComponentTypeAsString(reader->GetComponentType());
2254     int dimension = reader->GetNumberOfDimensions();
2255     QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
2256     vvProgressDialog progress("Opening fusion");
2257     qApp->processEvents();
2258
2259     std::string filename = itksys::SystemTools::GetFilenameWithoutExtension(file.toStdString()).c_str();
2260     if (mSlicerManagers[index]->SetFusion(fileNames,dimension, component,type)) {
2261       //create an item in the tree with good settings
2262       QTreeWidgetItem *item = new QTreeWidgetItem();
2263       item->setData(0,Qt::UserRole,file.toStdString().c_str());
2264       item->setData(1,Qt::UserRole,tr("fusion"));
2265       QFileInfo fileinfo(file); //Do not show the path
2266           item->setData(COLUMN_IMAGE_NAME,Qt::DisplayRole,fileinfo.fileName());
2267           item->setToolTip(COLUMN_IMAGE_NAME, mSlicerManagers[index]->GetListOfAbsoluteFilePathInOneString("fusion").c_str());
2268           qApp->processEvents();
2269 #if VTK_MAJOR_VERSION > 5
2270       for ( unsigned int i = 0; i < mSlicerManagers[index]->GetNumberOfSlicers(); i++)
2271         mSlicerManagers[index]->GetSlicer(i)->ForceUpdateDisplayExtent();
2272 #endif
2273       for (int j = 1; j <= 4; j++) {
2274         item->setData(j,Qt::CheckStateRole,DataTree->topLevelItem(index)->data(j,Qt::CheckStateRole));
2275       }
2276
2277       //Create the buttons for reload and close
2278       qApp->processEvents();
2279       QTreePushButton* cButton = new QTreePushButton;
2280       cButton->setItem(item);
2281       cButton->setColumn(COLUMN_CLOSE_IMAGE);
2282       cButton->setToolTip(tr("close image"));
2283       cButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/exit.png")));
2284       connect(cButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
2285         this,SLOT(CloseImage(QTreeWidgetItem*, int)));
2286
2287       QTreePushButton* rButton = new QTreePushButton;
2288       rButton->setItem(item);
2289       rButton->setColumn(COLUMN_RELOAD_IMAGE);
2290       rButton->setToolTip(tr("reload image"));
2291       rButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/rotateright.png")));
2292       connect(rButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
2293         this,SLOT(ReloadImage(QTreeWidgetItem*, int)));
2294
2295       DataTree->topLevelItem(index)->setExpanded(1);
2296       DataTree->topLevelItem(index)->addChild(item);
2297       DataTree->setItemWidget(item, COLUMN_CLOSE_IMAGE, cButton);
2298       DataTree->setItemWidget(item, COLUMN_RELOAD_IMAGE, rButton);
2299
2300       //set the id of the image
2301       QString id = DataTree->topLevelItem(index)->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString();
2302       item->setData(COLUMN_IMAGE_NAME,Qt::UserRole,id.toStdString().c_str());
2303       UpdateTree();
2304       qApp->processEvents();
2305       ImageInfoChanged();
2306       QApplication::restoreOverrideCursor();
2307
2308       // Update the display to update, e.g., the sliders
2309       for(int i=0; i<4; i++)
2310         DisplaySliders(index, i);
2311     } else {
2312       QApplication::restoreOverrideCursor();
2313       QString error = "Cannot import the new image.\n";
2314       error += mSlicerManagers[index]->GetLastError().c_str();
2315       QMessageBox::information(this,tr("Problem reading image !"),error);
2316     }
2317     WindowLevelChanged();
2318   }
2319   else
2320     QMessageBox::information(this,tr("Problem reading Fusion !"),"File doesn't exist!");
2321 }
2322 //------------------------------------------------------------------------------
2323 //------------------------------------------------------------------------------
2324 void vvMainWindow::AddLandmarks(int index, std::vector<std::string> files)
2325 {
2326     if (!landmarksPanel->LoadFromFile(files))
2327       QMessageBox::information(this,tr("Problem reading Landmarks !"),"File doesn't exist!");
2328
2329     landmarksPanel->SetCurrentPath(mInputPathName.toStdString());
2330     landmarksPanel->SetCurrentImage(mSlicerManagers[index]->GetFileName().c_str());
2331 }
2332
2333 //------------------------------------------------------------------------------
2334 void vvMainWindow::OpenField()
2335 {
2336   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2337
2338   if (!(CheckAddedImage(index, "vector")))
2339     return;
2340
2341   QString Extensions = "Images ( *.mhd *.mha *.vf *.nii *.nrrd *.nhdr)";
2342   // Extensions += ";;Images ( *.mha)";
2343   // Extensions += ";;VF Images ( *.vf)";
2344   // Extensions += ";;nii Images ( *.nii)";
2345   // Extensions += ";;nrrd Images ( *.nrrd)";
2346   // Extensions += ";;nhdr Images ( *.nhdr)";
2347   Extensions += ";;All Files (*)";
2348   QString file = QFileDialog::getOpenFileName(this,tr("Load deformation field"),mInputPathName,Extensions);
2349   if (!file.isEmpty())
2350     AddField(file,index);
2351 }
2352 //------------------------------------------------------------------------------
2353
2354
2355 //------------------------------------------------------------------------------
2356 void vvMainWindow::AddFieldEntry(QString filename,int index,bool from_disk)
2357 {
2358   //create an item in the tree with good settings
2359   QTreeWidgetItem *item = new QTreeWidgetItem();
2360   item->setData(0,Qt::UserRole,filename.toStdString().c_str());
2361   item->setData(1,Qt::UserRole,tr("vector"));
2362   QFileInfo fileinfo(filename); //Do not show the path
2363   item->setData(COLUMN_IMAGE_NAME,Qt::DisplayRole,fileinfo.fileName());
2364   item->setToolTip(COLUMN_IMAGE_NAME, mSlicerManagers[index]->GetListOfAbsoluteFilePathInOneString("vector").c_str());
2365   qApp->processEvents();
2366
2367   for (int j = 1; j <= 4; j++) {
2368     item->setData(j,Qt::CheckStateRole,DataTree->topLevelItem(index)->data(j,Qt::CheckStateRole));
2369   }
2370
2371   //Create the buttons for reload and close
2372   qApp->processEvents();
2373   QTreePushButton* cButton = new QTreePushButton;
2374   cButton->setItem(item);
2375   cButton->setColumn(COLUMN_CLOSE_IMAGE);
2376   cButton->setToolTip(tr("close vector field"));
2377   cButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/exit.png")));
2378   connect(cButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
2379     this,SLOT(CloseImage(QTreeWidgetItem*, int)));
2380
2381   QTreePushButton* rButton = new QTreePushButton;
2382   rButton->setItem(item);
2383   rButton->setColumn(COLUMN_RELOAD_IMAGE);
2384   rButton->setToolTip(tr("reload vector field"));
2385   rButton->setEnabled(from_disk);
2386   rButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/rotateright.png")));
2387   connect(rButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
2388     this,SLOT(ReloadImage(QTreeWidgetItem*, int)));
2389
2390   DataTree->topLevelItem(index)->setExpanded(1);
2391   DataTree->topLevelItem(index)->addChild(item);
2392   DataTree->setItemWidget(item, COLUMN_RELOAD_IMAGE, rButton);
2393   DataTree->setItemWidget(item, COLUMN_CLOSE_IMAGE, cButton);
2394
2395   //set the id of the image
2396   QString id = DataTree->topLevelItem(index)->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString();
2397   item->setData(COLUMN_IMAGE_NAME,Qt::UserRole,id.toStdString().c_str());
2398   UpdateTree();
2399   qApp->processEvents();
2400   ImageInfoChanged();
2401   QApplication::restoreOverrideCursor();
2402 }
2403 //------------------------------------------------------------------------------
2404
2405
2406 //------------------------------------------------------------------------------
2407 void vvMainWindow::AddField(vvImage::Pointer vf,QString file,int index)
2408 {
2409   QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
2410   vvSlicerManager* imageManager = mSlicerManagers[index];
2411   if (imageManager->SetVF(vf,file.toStdString())) {
2412     AddFieldEntry(file,index,false);
2413 #if VTK_MAJOR_VERSION > 5
2414       for ( unsigned int i = 0; i < mSlicerManagers[index]->GetNumberOfSlicers(); i++)
2415         mSlicerManagers[index]->GetSlicer(i)->ForceUpdateDisplayExtent();
2416 #endif
2417   } else {
2418     QString error = "Cannot import the vector field for this image.\n";
2419     error += imageManager->GetLastError().c_str();
2420     QMessageBox::information(this,tr("Problem reading VF !"),error);
2421   }
2422   QApplication::restoreOverrideCursor();
2423 }
2424 //------------------------------------------------------------------------------
2425
2426
2427 //------------------------------------------------------------------------------
2428 void vvMainWindow::AddField(QString file,int index)
2429 {
2430   if (QFile::exists(file)) {
2431     mInputPathName = itksys::SystemTools::GetFilenamePath(file.toStdString()).c_str();
2432
2433     //init the progress events
2434     QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
2435     vvProgressDialog progress("Opening " + file.toStdString());
2436     qApp->processEvents();
2437
2438     //read the vector and put it in the current mSlicerManager
2439     vvSlicerManager* imageManager = mSlicerManagers[index];
2440     qApp->processEvents();
2441
2442     std::string filename = itksys::SystemTools::GetFilenameWithoutExtension(file.toStdString()).c_str();
2443     if (imageManager->SetVF(file.toStdString())) {
2444       imageManager->Render();
2445       AddFieldEntry(file,index,true);
2446     } else {
2447       QApplication::restoreOverrideCursor();
2448       QString error = "Cannot import the vector field for this image.\n";
2449       error += imageManager->GetLastError().c_str();
2450       QMessageBox::information(this,tr("Problem reading VF !"),error);
2451     }
2452   } else
2453     QMessageBox::information(this,tr("Problem reading VF !"),"File doesn't exist!");
2454
2455 }
2456 //------------------------------------------------------------------------------
2457
2458
2459 //------------------------------------------------------------------------------
2460 void vvMainWindow::SetVFProperty(int subsampling, int scale, int log, int width, double r, double g, double b)
2461 {
2462   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2463   if (mSlicerManagers[index]->GetSlicer(0)->GetVF()) {
2464     for (int i = 0; i < 4; i++) {
2465       mSlicerManagers[index]->GetSlicer(i)->SetVFSubSampling(subsampling);
2466       mSlicerManagers[index]->GetSlicer(i)->SetVFScale(scale);
2467       mSlicerManagers[index]->GetSlicer(i)->SetVFWidth(width);
2468       mSlicerManagers[index]->GetSlicer(i)->SetVFColor(r,g,b);
2469       if (log > 0)
2470         mSlicerManagers[index]->GetSlicer(i)->SetVFLog(1);
2471       else
2472         mSlicerManagers[index]->GetSlicer(i)->SetVFLog(0);
2473     }
2474   }
2475 }
2476 //------------------------------------------------------------------------------
2477
2478
2479 //------------------------------------------------------------------------------
2480 void vvMainWindow::SetOverlayProperty(int color, int linked, double window, double level)
2481 {
2482   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2483   if (mSlicerManagers[index]->GetSlicer(0)->GetOverlay()) {
2484     mSlicerManagers[index]->SetOverlayColor(color);
2485     mSlicerManagers[index]->SetColorMap(0);
2486     mSlicerManagers[index]->SetLinkOverlayWindowLevel(linked);
2487     mSlicerManagers[index]->SetOverlayColorWindow(window);
2488     mSlicerManagers[index]->SetOverlayColorLevel(level);
2489     mSlicerManagers[index]->Render();
2490   }
2491 }
2492 //------------------------------------------------------------------------------
2493
2494 //------------------------------------------------------------------------------
2495 void vvMainWindow::SetFusionProperty(int opacity, int thresOpacity, int colormap,double window, double level, bool showLegend)
2496 {
2497   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2498   if (mSlicerManagers[index]->GetSlicer(0)->GetFusion()) {
2499     mSlicerManagers[index]->SetFusionColorMap(colormap);
2500     mSlicerManagers[index]->SetFusionOpacity(opacity);
2501     mSlicerManagers[index]->SetFusionThresholdOpacity(thresOpacity);
2502     mSlicerManagers[index]->SetFusionWindow(window);
2503     mSlicerManagers[index]->SetFusionLevel(level);
2504     mSlicerManagers[index]->SetFusionShowLegend(showLegend);
2505     mSlicerManagers[index]->SetColorMap(0);
2506     mSlicerManagers[index]->Render();
2507   }
2508 }
2509 //------------------------------------------------------------------------------
2510
2511
2512 //------------------------------------------------------------------------------
2513 void vvMainWindow::SelectFusionSequence()
2514 {
2515   //get the index of the slicer manager of the main sequence (CT)
2516   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2517
2518   if (!(CheckAddedImage(index, "fusion")) || !(CheckAddedImage(index, "fusionSequence")))
2519     return;
2520
2521   QString Extensions = EXTENSIONS;
2522   Extensions += ";;All Files (*)";
2523   QStringList files = QFileDialog::getOpenFileNames(this,tr("Load Overlay image sequence"),mInputPathName,Extensions);
2524   if (files.isEmpty())
2525     return;
2526
2527   std::vector<std::string> vecFileNames;
2528   for (int i = 0; i < files.size(); i++) {
2529     vecFileNames.push_back(files[i].toStdString());
2530   }
2531
2532   //associate the secondary sequence (US) to the main one
2533   AddFusionSequence(index,vecFileNames,vvImageReader::MERGEDWITHTIME);
2534 }
2535 //------------------------------------------------------------------------------
2536
2537
2538 //------------------------------------------------------------------------------
2539 void vvMainWindow::SelectFusionSequenceCorrespondances()
2540 {
2541   //make sure the index is right?
2542   //in the end, I should attach the temporal data to the right sequence!
2543   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2544   //in case the other sequence got selected, make sure we select the primary sequence
2545   if ( (!mSlicerManagers[index]->GetSlicer(0)->GetFusion()) && mSlicerManagers[index]->GetFusionSequenceIndexOfLinkedManager()>=0 ) {
2546     index = mSlicerManagers[index]->GetFusionSequenceIndexOfLinkedManager();
2547   }
2548
2549   //open a dialog box to find a file
2550   //QString Extensions = EXTENSIONS;
2551   QString Extensions = ";;All Files (*)";
2552   QString fileName = QFileDialog::getOpenFileName(this,tr("Load respiratory signal for fused sequence"),mInputPathName,Extensions);
2553   if (fileName.isNull())
2554     return;
2555
2556   //read it as a vector of values
2557   vnl_vector<double> tmpVect;
2558
2559   std::ifstream file;
2560   file.open(fileName.toStdString().c_str());
2561   tmpVect.read_ascii(file);
2562   file.close();
2563
2564   //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
2565   bool signalOK = true;
2566   unsigned nbFrameMain = mSlicerManagers[index]->GetImage()->GetTransform().size();
2567   unsigned nbFrameSecondary = mSlicerManagers[index]->GetFusionSequenceNbFrames();
2568   std::cout<<"nbFrameMain = "<<nbFrameMain<<", nbFrameSecondary= "<<nbFrameSecondary<<", signal size: "<<tmpVect.size()<<std::endl;
2569   std::vector<unsigned> temporalCorrespondances;
2570   if ( tmpVect.size() == nbFrameMain + nbFrameSecondary ) {
2571     for (unsigned i=0 ; i<tmpVect.size() ; i++) {
2572       if (i<nbFrameMain) { //first part of the file: i -> index in secondary seq.
2573         if ( tmpVect(i)<nbFrameSecondary ) temporalCorrespondances.push_back(tmpVect(i));
2574         else { signalOK=false; break; } //pointing outside the secondary sequence...
2575       }
2576       else { //first part of the file -> index in secondary seq.
2577         if ( tmpVect(i)<nbFrameMain ) temporalCorrespondances.push_back(tmpVect(i));
2578         else { signalOK=false; break; } //pointing outside the secondary sequence...
2579       }
2580     }
2581   }
2582   else {signalOK=false;}
2583   if (!signalOK) {//else, send a message to signal the failure...
2584     QString error = "The provided temporal correspondances is invalid - check tooltip.\n";
2585     error += "Ignoring file: " + fileName;
2586     QMessageBox::information(this,tr("Problem adding temporal correspondances!"),error);
2587     return;
2588   }
2589   else {
2590     //for convenience, associate this sequence to both the current slicer manager, and to the linked one
2591     mSlicerManagers[index]->SetFusionSequenceCorrespondances(temporalCorrespondances);
2592     mSlicerManagers[ mSlicerManagers[index]->GetFusionSequenceIndexOfLinkedManager() ]->SetFusionSequenceCorrespondances(temporalCorrespondances);
2593     overlayPanel->enableFusionSequenceTemporalSync();
2594   }
2595
2596 }
2597 //------------------------------------------------------------------------------
2598
2599
2600 //------------------------------------------------------------------------------
2601 //when this function is called index is the slicer manager index corresponding to the main sequence (CT)
2602 //the files behind fileNames points to the data for the secondary sequence
2603 void vvMainWindow::AddFusionSequence(int index, std::vector<std::string> fileNames, vvImageReader::LoadedImageType type)
2604 {
2605   QString file(fileNames[0].c_str());
2606   if (QFile::exists(file))
2607   {
2608     mInputPathName = itksys::SystemTools::GetFilenamePath(file.toStdString()).c_str();
2609     itk::ImageIOBase::Pointer reader = itk::ImageIOFactory::CreateImageIO(
2610       file.toStdString().c_str(), itk::ImageIOFactory::ReadMode);
2611     std::sort (fileNames.begin(), fileNames.end());//make sure the files are sorted.
2612     reader->SetFileName(fileNames[0].c_str());
2613     reader->ReadImageInformation();
2614     std::string component = reader->GetComponentTypeAsString(reader->GetComponentType());
2615     int dimension = reader->GetNumberOfDimensions();
2616     QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
2617     vvProgressDialog progress("Opening " + file.toStdString());
2618     qApp->processEvents();
2619
2620     std::string filename = itksys::SystemTools::GetFilenameWithoutExtension(file.toStdString()).c_str();
2621
2622     if (mSlicerManagers[index]->SetFusionSequence(fileNames,dimension, component,type)) {
2623       //create an item in the tree with good settings
2624       QTreeWidgetItem *item = new QTreeWidgetItem();
2625       item->setData(0,Qt::UserRole,file.toStdString().c_str());
2626       item->setData(1,Qt::UserRole,tr("fusionSequence"));
2627
2628       QFileInfo fileinfo(file); //Do not show the path
2629       item->setData(COLUMN_IMAGE_NAME,Qt::DisplayRole,fileinfo.fileName());
2630       item->setToolTip(COLUMN_IMAGE_NAME, mSlicerManagers[index]->GetListOfAbsoluteFilePathInOneString("fusionSequence").c_str());
2631       qApp->processEvents();
2632 #if VTK_MAJOR_VERSION > 5
2633       for ( unsigned int i = 0; i < mSlicerManagers[index]->GetNumberOfSlicers(); i++)
2634         mSlicerManagers[index]->GetSlicer(i)->ForceUpdateDisplayExtent();
2635 #endif
2636       for (int j = 1; j <= 4; j++) {
2637         item->setData(j,Qt::CheckStateRole,DataTree->topLevelItem(index)->data(j,Qt::CheckStateRole));
2638       }
2639
2640       //Create the buttons for reload and close
2641       qApp->processEvents();
2642       QTreePushButton* cButton = new QTreePushButton;
2643       cButton->setItem(item);
2644       cButton->setColumn(COLUMN_CLOSE_IMAGE);
2645       cButton->setToolTip(tr("close image"));
2646       cButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/exit.png")));
2647       connect(cButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
2648         this,SLOT(CloseImage(QTreeWidgetItem*, int)));
2649
2650       QTreePushButton* rButton = new QTreePushButton;
2651       rButton->setItem(item);
2652       rButton->setColumn(COLUMN_RELOAD_IMAGE);
2653       rButton->setToolTip(tr("reload image"));
2654       rButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/rotateright.png")));
2655       connect(rButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
2656         this,SLOT(ReloadImage(QTreeWidgetItem*, int)));
2657
2658       DataTree->topLevelItem(index)->setExpanded(1);
2659       DataTree->topLevelItem(index)->addChild(item);
2660       DataTree->setItemWidget(item, COLUMN_CLOSE_IMAGE, cButton);
2661       DataTree->setItemWidget(item, COLUMN_RELOAD_IMAGE, rButton);
2662
2663       //store the original transform matrix
2664       int indexParent = GetSlicerIndexFromItem( DataTree->topLevelItem(index) );
2665       mSlicerManagers[indexParent]->SetFusionSequenceMainTransformMatrix( mSlicerManagers[indexParent]->GetSlicer(0)->GetImage()->GetTransform()[0]->GetMatrix() );
2666
2667       //set the id of the image
2668       QString id = DataTree->topLevelItem(index)->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString();
2669       item->setData(COLUMN_IMAGE_NAME,Qt::UserRole,id.toStdString().c_str());
2670       UpdateTree();
2671       qApp->processEvents();
2672
2673       //ImageInfoChanged();
2674
2675       QApplication::restoreOverrideCursor();
2676       // Update the display to update, e.g., the sliders
2677       for(int i=0; i<4; i++)
2678         DisplaySliders(index, i);
2679
2680
2681       //This loads the secondary sequence (US) as an independent sequence
2682       LoadImages(fileNames, type);
2683       //reset the transforms to identity
2684       //FIX -- and set the thickness of the US slices to a large value (necessary for visualization purposes...)
2685       double sp_x, sp_y, sp_z;
2686       mSlicerManagers[indexParent]->GetImage()->GetVTKImages()[0]->GetSpacing(sp_x, sp_y, sp_z);
2687       sp_z = std::max(sp_x, std::max(sp_y, sp_z)) + 0.5; //
2688       for (unsigned i=0 ; i<mSlicerManagers.back()->GetImage()->GetTransform().size() ; i++) {
2689         sp_x = mSlicerManagers.back()->GetImage()->GetVTKImages()[i]->GetSpacing()[0];
2690         sp_y = mSlicerManagers.back()->GetImage()->GetVTKImages()[i]->GetSpacing()[1];
2691         mSlicerManagers.back()->GetImage()->GetVTKImages()[i]->SetSpacing( sp_x, sp_y, sp_z);
2692         mSlicerManagers.back()->GetImage()->GetTransform()[i]->Identity();
2693         mSlicerManagers.back()->GetImage()->GetTransform()[i]->Update();
2694       }
2695
2696       //automatically link both images...
2697       AddLink(mSlicerManagers[indexParent]->GetId().c_str(), mSlicerManagers.back()->GetId().c_str(), false);
2698
2699       //tie the main and secondary sequences by raising flags and informing each another of their respective SlicerManager indices
2700       mSlicerManagers[indexParent]->SetFusionSequenceIndexOfLinkedManager(mSlicerManagers.size()-1);
2701       mSlicerManagers[indexParent]->SetFusionSequenceInvolvmentCode(0); //main sequence
2702       mSlicerManagers.back()->SetFusionSequenceIndexOfLinkedManager(indexParent);
2703       mSlicerManagers.back()->SetFusionSequenceInvolvmentCode(1); //secondary sequence
2704       for (unsigned i=0 ; i<4 ; i++) {
2705         mSlicerManagers.back()->GetSlicer(i)->SetFusionSequenceCode(1); //flag the slicers of the secondary sequence
2706       }
2707
2708     } else {
2709       QApplication::restoreOverrideCursor();
2710       QString error = "Cannot import the new image.\n";
2711       error += mSlicerManagers[index]->GetLastError().c_str();
2712       QMessageBox::information(this,tr("Problem reading image !"),error);
2713     }
2714     WindowLevelChanged();
2715     ImageInfoChanged(); //this internally calls WindowLevelChanged...
2716   }
2717   else {
2718     QMessageBox::information(this,tr("Problem reading fusion sequence !"),"File doesn't exist!");
2719     return;
2720   }
2721
2722 }
2723 //------------------------------------------------------------------------------
2724
2725
2726 //------------------------------------------------------------------------------
2727 //fusionSequenceFrameIndex and fusionSequenceNbFrames are relative to the secondary sequence (US)
2728 void vvMainWindow::SetFusionSequenceProperty(int fusionSequenceFrameIndex, bool spatialSyncFlag, unsigned int fusionSequenceNbFrames, bool temporalSyncFlag)
2729 {
2730   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2731
2732   if (!mSlicerManagers[index]->IsInvolvedInFusionSequence()) return;
2733
2734   //check if the focus moved to the linked sequence, and in this case, select the master sequence instead
2735   if (!mSlicerManagers[index]->IsMainSequenceOfFusionSequence()) {
2736     index = mSlicerManagers[index]->GetFusionSequenceIndexOfLinkedManager();
2737   }
2738   int secondaryIndex = mSlicerManagers[index]->GetFusionSequenceIndexOfLinkedManager();
2739   if (secondaryIndex==-1) return; //this should never happen
2740   if ( (!mSlicerManagers[index]->IsMainSequenceOfFusionSequence()) ||
2741     (!mSlicerManagers[secondaryIndex]->IsSecondarySequenceOfFusionSequence()) )
2742   {return;} //this should never happen, raise an exception?
2743
2744   if (mSlicerManagers[index]->GetSlicer(0)->GetFusion()) {
2745
2746     //First, if the spatialSync button is unchecked, then reposition the parent sequence (CT) in its original coordinate frame
2747     if ( (!spatialSyncFlag) && (mSlicerManagers[index]->GetFusionSequenceSpatialSyncFlag()) ) {
2748       for ( unsigned i=0 ; i<mSlicerManagers[index]->GetSlicer(0)->GetImage()->GetTransform().size() ; i++ ) {
2749         mSlicerManagers[index]->GetSlicer(0)->GetImage()->GetTransform()[i]->SetMatrix( mSlicerManagers[index]->GetFusionSequenceMainTransformMatrix() );
2750         mSlicerManagers[index]->GetSlicer(0)->GetImage()->GetTransform()[i]->Update();
2751       }
2752
2753       for (int i=0; i<mSlicerManagers[index]->GetNumberOfSlicers(); i++) {
2754         mSlicerManagers[index]->GetSlicer(i)->ForceUpdateDisplayExtent();
2755         mSlicerManagers[index]->GetSlicer(i)->Render();
2756       }
2757     }
2758
2759     //then, update the property values in the slicer manager
2760     mSlicerManagers[index]->SetFusionSequenceLength(fusionSequenceNbFrames);
2761     mSlicerManagers[index]->SetFusionSequenceSpatialSyncFlag(spatialSyncFlag);
2762     mSlicerManagers[index]->SetFusionSequenceTemporalSyncFlag(temporalSyncFlag);
2763     mSlicerManagers[index]->SetFusionSequenceFrameIndex(fusionSequenceFrameIndex);
2764
2765     //select the right frame of the US sequence
2766     mSlicerManagers[index]->SetFusionSequenceTSlice(fusionSequenceFrameIndex); //here, I should only update the overlayed sequence
2767     mSlicerManagers[secondaryIndex]->SetTSlice(fusionSequenceFrameIndex, false); //this should update the secondary sequence (individual version)
2768
2769     //update the horizontal sliders of the main window
2770     overlayPanel->updateFusionSequenceSliderValueFromWindow(fusionSequenceFrameIndex, false);
2771
2772     if (spatialSyncFlag) { //reslice the CT
2773
2774       if (temporalSyncFlag) { //do the temporal synchronisation
2775         int mainSequenceFrameIndex=0;
2776         //estimate the TSlice to set to the CT
2777         unsigned nbFramesMain = mSlicerManagers[index]->GetImage()->GetTransform().size();
2778         mainSequenceFrameIndex = mSlicerManagers[index]->GetFusionSequenceCorrespondances()[ nbFramesMain + fusionSequenceFrameIndex];
2779         //and set it!
2780         mSlicerManagers[index]->SetTSlice(mainSequenceFrameIndex, false);
2781         //warning, there is a loopback, and modification of the TSlice in main sequence forces an update of the TSlice in secondary, etc...
2782       }
2783
2784
2785       //Set the transform matrix of the parent sequence (typically CT / 4DCT)
2786       vtkSmartPointer<vtkMatrix4x4> tmpMat = vtkSmartPointer<vtkMatrix4x4>::New();
2787       vtkMatrix4x4::Invert( mSlicerManagers[index]->GetFusionSequenceInitialTransformMatrixAtFrame(fusionSequenceFrameIndex), tmpMat );
2788       for ( unsigned i=0 ; i<mSlicerManagers[index]->GetSlicer(0)->GetImage()->GetTransform().size() ; i++ ) {
2789         mSlicerManagers[index]->GetSlicer(0)->GetImage()->GetTransform()[i]->SetMatrix( mSlicerManagers[index]->GetFusionSequenceMainTransformMatrix() );
2790         mSlicerManagers[index]->GetSlicer(0)->GetImage()->GetTransform()[i]->PreMultiply();
2791         mSlicerManagers[index]->GetSlicer(0)->GetImage()->GetTransform()[i]->Concatenate( tmpMat );
2792         mSlicerManagers[index]->GetSlicer(0)->GetImage()->GetTransform()[i]->Update();
2793       }
2794
2795       for (int i=0; i<mSlicerManagers[index]->GetNumberOfSlicers(); i++) {
2796         mSlicerManagers[index]->GetSlicer(i)->ForceUpdateDisplayExtent();
2797         mSlicerManagers[index]->GetSlicer(i)->Render();
2798       }
2799
2800     }
2801
2802   }
2803 }
2804 //------------------------------------------------------------------------------
2805
2806
2807 //------------------------------------------------------------------------------
2808 void vvMainWindow::SaveAs()
2809 {
2810   if (DataTree->selectedItems()[0]->data(1,Qt::UserRole).toString() == "vector") {
2811     QMessageBox::warning(this,tr("Unsupported type"),tr("Sorry, saving a vector field is unsupported for the moment"));
2812     return;
2813   }
2814
2815   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2816   int dimension = mSlicerManagers[index]->GetDimension();
2817   QStringList OutputListeFormat;
2818   OutputListeFormat.clear();
2819   if (dimension == 1) {
2820     OutputListeFormat.push_back(".mhd");
2821     OutputListeFormat.push_back(".mha");
2822   }
2823   if (dimension == 2) {
2824     OutputListeFormat.push_back(".bmp");
2825     OutputListeFormat.push_back(".png");
2826     OutputListeFormat.push_back(".jpeg");
2827     OutputListeFormat.push_back(".tif");
2828     OutputListeFormat.push_back(".mhd");
2829     OutputListeFormat.push_back(".mha");
2830     OutputListeFormat.push_back(".hdr");
2831     OutputListeFormat.push_back(".vox");
2832   } else if (dimension == 3) {
2833     OutputListeFormat.push_back(".mhd");
2834     OutputListeFormat.push_back(".mha");
2835     OutputListeFormat.push_back(".nii");
2836     OutputListeFormat.push_back(".nrrd");
2837     OutputListeFormat.push_back(".nhdr");
2838     OutputListeFormat.push_back(".hdr");
2839     OutputListeFormat.push_back(".vox");
2840   } else if (dimension == 4) {
2841     OutputListeFormat.push_back(".mhd");
2842     OutputListeFormat.push_back(".mha");
2843     OutputListeFormat.push_back(".nii");
2844     OutputListeFormat.push_back(".nrrd");
2845     OutputListeFormat.push_back(".nhdr");
2846   }
2847   QString Extensions = "AllFiles(*.*)";
2848   for (int i = 0; i < OutputListeFormat.count(); i++) {
2849     Extensions += ";;Images ( *";
2850     Extensions += OutputListeFormat[i];
2851     Extensions += ")";
2852   }
2853   QString fileName = QFileDialog::getSaveFileName(this,
2854     tr("Save As"),
2855     mSlicerManagers[index]->GetFileName().c_str(),
2856     Extensions);
2857   if (!fileName.isEmpty()) {
2858     std::string fileformat = itksys::SystemTools::GetFilenameLastExtension(fileName.toStdString());
2859     if (OutputListeFormat.contains(
2860       fileformat.c_str())) {
2861         QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
2862         std::string action = "Saving";
2863         vvProgressDialog progress("Saving "+fileName.toStdString());
2864         qApp->processEvents();
2865         vvImageWriter::Pointer writer = vvImageWriter::New();
2866         writer->SetOutputFileName(fileName.toStdString());
2867         writer->SetInput(mSlicerManagers[index]->GetImage());
2868
2869         // Check on transform and prompt user
2870         writer->SetSaveTransform(false);
2871         bool bId = true;
2872         for(int i=0; i<4; i++)
2873           for(int j=0; j<4; j++) {
2874             // TODO SR and BP: check on the list of transforms and not the first only
2875             double elt = mSlicerManagers[index]->GetImage()->GetTransform()[0]->GetMatrix()->GetElement(i,j);
2876             if(i==j && elt!=1.)
2877               bId = false;
2878             if(i!=j && elt!=0.)
2879               bId = false;
2880           }
2881           if( !bId ) {
2882             QString warning = "The image has an associated linear transform. Do you want to save it along?";
2883             QMessageBox msgBox(QMessageBox::Warning, tr("Save transform"), warning, 0, this);
2884             msgBox.addButton(tr("Yes"), QMessageBox::AcceptRole);
2885             msgBox.addButton(tr("No"), QMessageBox::RejectRole);
2886             if (msgBox.exec() == QMessageBox::AcceptRole)
2887               writer->SetSaveTransform(true);
2888           }
2889
2890           writer->Update();
2891           QApplication::restoreOverrideCursor();
2892           if (writer->GetLastError().size()) {
2893             QString error = "Saving did not succeed\n";
2894             error += writer->GetLastError().c_str();
2895             QMessageBox::information(this,tr("Saving Problem"),error);
2896             SaveAs();
2897           }
2898     } else {
2899       QString error = fileformat.c_str();
2900       if (error.isEmpty())
2901         error += "no file format specified !";
2902       else
2903         error += " format unknown !!!\n";
2904       QMessageBox::information(this,tr("Saving Problem"),error);
2905       SaveAs();
2906     }
2907   }
2908 }
2909 //------------------------------------------------------------------------------
2910
2911 //------------------------------------------------------------------------------
2912 void vvMainWindow::SaveCurrentState()
2913 {
2914   QString Extensions = "XML Files(*.xml)";
2915   QString fileName = QFileDialog::getSaveFileName(this,
2916     tr("Save Current Window State"),
2917     "",
2918     Extensions);
2919
2920   SaveCurrentStateAs(fileName.toStdString());
2921 }
2922 //------------------------------------------------------------------------------
2923
2924 //------------------------------------------------------------------------------
2925 void vvMainWindow::SaveCurrentStateAs(const std::string& stateFile)
2926 {
2927   vvSaveState save_state;
2928   save_state.Run(this, stateFile);
2929 }
2930
2931 //------------------------------------------------------------------------------
2932 void vvMainWindow::ReadSavedState()
2933 {
2934   QString Extensions = "XML Files(*.xml)";
2935   QString fileName = QFileDialog::getOpenFileName(this,
2936     tr("Load Window State"),
2937     "",
2938     Extensions);
2939
2940   ReadSavedStateFile(fileName.toStdString());
2941 }
2942 //------------------------------------------------------------------------------
2943
2944 //------------------------------------------------------------------------------
2945 void vvMainWindow::ReadSavedStateFile(const std::string& stateFile)
2946 {
2947   vvReadState read_state;
2948   read_state.Run(this, stateFile);
2949 }
2950 //------------------------------------------------------------------------------
2951
2952 //------------------------------------------------------------------------------
2953 void vvMainWindow::LinkAllImages()
2954 {
2955   linkPanel->linkAll();
2956 }
2957
2958 //------------------------------------------------------------------------------
2959 void vvMainWindow::AddLink(QString image1,QString image2,bool fromPanel)
2960 {
2961   if (!fromPanel) {
2962     // delegate to linkPanel if call came from elsewhere...
2963     linkPanel->addLinkFromIds(image1, image2);
2964     return;
2965   }
2966
2967   unsigned int sm1 = 0;
2968   unsigned int sm2 = 0;
2969
2970   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
2971     if (image1.toStdString() == mSlicerManagers[i]->GetId()) {
2972       mSlicerManagers[i]->AddLink(image2.toStdString());
2973       sm1 = i;
2974     }
2975     if (image2.toStdString() == mSlicerManagers[i]->GetId()) {
2976       mSlicerManagers[i]->AddLink(image1.toStdString());
2977       sm2 = i;
2978     }
2979   }
2980
2981   if (linkPanel->isLinkAll())   {
2982     emit UpdateLinkedNavigation(mSlicerManagers[sm1]->GetId(), mSlicerManagers[mCurrentPickedImageIndex], mSlicerManagers[mCurrentPickedImageIndex]->GetSlicer(0));
2983     emit UpdateLinkedNavigation(mSlicerManagers[sm2]->GetId(), mSlicerManagers[mCurrentPickedImageIndex], mSlicerManagers[mCurrentPickedImageIndex]->GetSlicer(0));
2984   } else {
2985     emit UpdateLinkedNavigation(mSlicerManagers[sm2]->GetId(), mSlicerManagers[sm1], mSlicerManagers[sm1]->GetSlicer(0));
2986   }
2987 }
2988
2989 //------------------------------------------------------------------------------
2990
2991
2992 //------------------------------------------------------------------------------
2993 void vvMainWindow::RemoveLink(QString image1,QString image2)
2994 {
2995   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
2996     if (image1.toStdString() == mSlicerManagers[i]->GetId()) {
2997       mSlicerManagers[i]->RemoveLink(image2.toStdString());
2998     }
2999     if (image2.toStdString() == mSlicerManagers[i]->GetId()) {
3000       mSlicerManagers[i]->RemoveLink(image1.toStdString());
3001     }
3002   }
3003 }
3004 //------------------------------------------------------------------------------
3005
3006 //------------------------------------------------------------------------------
3007 void vvMainWindow::ChangeImageWithIndexOffset(vvSlicerManager *sm, int slicer, int offset)
3008 {
3009   if(mSlicerManagers.size()==1)
3010     return;
3011
3012   int index = 0;
3013   while(sm != mSlicerManagers[index])
3014     index++;
3015   index = (index+offset+mSlicerManagers.size()) % mSlicerManagers.size();
3016
3017   QTreeWidgetItem* item = GetItemFromSlicerManager(mSlicerManagers[index]);
3018   item->setData(slicer+1,Qt::CheckStateRole,2);         //change checkbox
3019   CurrentImageChanged(mSlicerManagers[index]->GetId()); //select new image
3020   DisplayChanged(item,slicer+1);
3021 }
3022 //------------------------------------------------------------------------------
3023 void vvMainWindow::HorizontalSliderMoved(int value,int column, int slicer_index)
3024 {
3025   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
3026     if (DataTree->topLevelItem(i)->data(column,Qt::CheckStateRole).toInt() > 1) {
3027       //i is the SlicerManager that is in charge of this slicer.
3028       if (mSlicerManagers[i]->IsInvolvedInFusionSequence()) {
3029         //if the slicerManager is involved in a fusionSequence as the secondary sequence, then update the slider position in the overlay panel and everything accordingly
3030         if (mSlicerManagers[i]->IsSecondarySequenceOfFusionSequence()) {
3031           overlayPanel->updateFusionSequenceSliderValueFromWindow(value, true);
3032         }
3033         else { //if this is the primary sequence that has been modified
3034           if (mSlicerManagers[i]->GetFusionSequenceTemporalSyncFlag()) {
3035             //WARNING: for some obscure reason, there are problems when accessing mSlicerManagers[mSlicerManagers[i]->GetFusionSequenceIndexOfLinkedManager()]->GetFusionSequenceFrameIndex();
3036
3037             int estimatedValue=0;
3038             //estimate a corresponding time index for the secondary (US) sequence, and update it accordingly.
3039             estimatedValue = mSlicerManagers[i]->GetFusionSequenceCorrespondances()[ value ];
3040             //TODO: at the moment, there is a loop in TSlice modifications
3041             //modifying sequence 1 causes seq 2 to update, which in turns update seq1...
3042             //I disable control on seq1 at the moment.
3043             //overlayPanel->updateFusionSequenceSliderValueFromWindow(estimatedValue, true);
3044           }
3045         }
3046       }
3047
3048       for (int j = 0; j < 4; j++) {
3049         mSlicerManagers[i]->SetTSliceInSlicer(value,j);
3050       }
3051       mSlicerManagers[i]->GetSlicer(slicer_index)->Render();
3052       break;
3053     }
3054   }
3055 }
3056 //------------------------------------------------------------------------------
3057
3058
3059 //------------------------------------------------------------------------------
3060 void vvMainWindow::NOHorizontalSliderMoved()
3061 {
3062   // if (mCurrentTime == NOHorizontalSlider->value()) return;
3063   HorizontalSliderMoved(NOHorizontalSlider->value(),COLUMN_UL_VIEW,0);
3064   //  mCurrentTime = NOHorizontalSlider->value();
3065 }
3066 //------------------------------------------------------------------------------
3067
3068
3069 //------------------------------------------------------------------------------
3070 void vvMainWindow::NEHorizontalSliderMoved()
3071 {
3072   // if (mCurrentTime == NEHorizontalSlider->value()) return;
3073   HorizontalSliderMoved(NEHorizontalSlider->value(),COLUMN_UR_VIEW,1);
3074   //  mCurrentTime = NEHorizontalSlider->value();
3075 }
3076 //------------------------------------------------------------------------------
3077
3078
3079 //------------------------------------------------------------------------------
3080 void vvMainWindow::SOHorizontalSliderMoved()
3081 {
3082   // if (mCurrentTime == SOHorizontalSlider->value()) return;
3083   HorizontalSliderMoved(SOHorizontalSlider->value(),COLUMN_DL_VIEW,2);
3084   // mCurrentTime = SOHorizontalSlider->value();
3085 }
3086 //------------------------------------------------------------------------------
3087
3088
3089 //------------------------------------------------------------------------------
3090 void vvMainWindow::SEHorizontalSliderMoved()
3091 {
3092   // if (mCurrentTime == SEHorizontalSlider->value()) return;
3093   HorizontalSliderMoved(SEHorizontalSlider->value(),COLUMN_DR_VIEW,3);
3094   // mCurrentTime = SEHorizontalSlider->value();
3095 }
3096 //------------------------------------------------------------------------------
3097
3098 //------------------------------------------------------------------------------
3099 void vvMainWindow::NOVerticalSliderChanged()
3100 {
3101   static int value=-1;
3102   if (value == NOVerticalSlider->value()) return;
3103   else value = NOVerticalSlider->value();
3104   //  int value = NOVerticalSlider->value();
3105   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
3106     if (DataTree->topLevelItem(i)->data(COLUMN_UL_VIEW,Qt::CheckStateRole).toInt() > 1) {
3107       if (mSlicerManagers[i]->GetSlicer(0)->GetSlice() != value) {
3108         mSlicerManagers[i]->GetSlicer(0)->SetSlice(value);
3109         mSlicerManagers[i]->VerticalSliderHasChanged(0, value);
3110
3111         // If nor Update/Render -> slider not work
3112         // only render = ok navigation, but for contour Update needed but slower ?
3113
3114         mSlicerManagers[i]->UpdateSlice(0);  // <-- DS add this. Not too much update ? YES. but needed for ImageContour ...
3115         //mSlicerManagers[i]->GetSlicer(0)->Render(); // <-- DS add this, needed for contour, seems ok ? not too slow ?
3116       }
3117       break;
3118     }
3119   }
3120 }
3121 //------------------------------------------------------------------------------
3122
3123
3124 //------------------------------------------------------------------------------
3125 void vvMainWindow::NEVerticalSliderChanged()
3126 {
3127   static int value=-1;
3128   if (value == NEVerticalSlider->value()) return;
3129   else value = NEVerticalSlider->value();
3130   //  int value = NEVerticalSlider->value();
3131   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
3132     if (DataTree->topLevelItem(i)->data(COLUMN_UR_VIEW,Qt::CheckStateRole).toInt() > 1) {
3133       if (mSlicerManagers[i]->GetSlicer(1)->GetSlice() != value) {
3134         mSlicerManagers[i]->GetSlicer(1)->SetSlice(value);
3135         mSlicerManagers[i]->VerticalSliderHasChanged(1, value);
3136         mSlicerManagers[i]->UpdateSlice(1);
3137         //mSlicerManagers[i]->GetSlicer(1)->Render(); // <-- DS add this, needed for contour, seems ok ? not too slow ?
3138       }
3139       break;
3140     }
3141   }
3142 }
3143 //------------------------------------------------------------------------------
3144
3145
3146 //------------------------------------------------------------------------------
3147 void vvMainWindow::SOVerticalSliderChanged()
3148 {
3149   static int value=-1;
3150   if (value == SOVerticalSlider->value()) return;
3151   else value = SOVerticalSlider->value();
3152   //int value = SOVerticalSlider->value();
3153   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
3154     if (DataTree->topLevelItem(i)->data(COLUMN_DL_VIEW,Qt::CheckStateRole).toInt() > 1) {
3155       if (mSlicerManagers[i]->GetSlicer(2)->GetSlice() != value) {
3156         mSlicerManagers[i]->GetSlicer(2)->SetSlice(value);
3157         mSlicerManagers[i]->VerticalSliderHasChanged(2, value);
3158         mSlicerManagers[i]->UpdateSlice(2);
3159         //mSlicerManagers[i]->GetSlicer(2)->Render(); // <-- DS add this, needed for contour, seems ok ? not too slow ?
3160       }
3161       // else { DD("avoid SOVerticalSlider slicer update"); }
3162       break;
3163     }
3164   }
3165 }
3166 //------------------------------------------------------------------------------
3167
3168
3169 //------------------------------------------------------------------------------
3170 void vvMainWindow::SEVerticalSliderChanged()
3171 {
3172   static int value=-1;
3173   if (value == SEVerticalSlider->value()) return;
3174   else value = SEVerticalSlider->value();
3175   // int value = SEVerticalSlider->value();
3176   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
3177     if (DataTree->topLevelItem(i)->data(COLUMN_DR_VIEW,Qt::CheckStateRole).toInt() > 1) {
3178       if (mSlicerManagers[i]->GetSlicer(3)->GetSlice() != value) {
3179         mSlicerManagers[i]->GetSlicer(3)->SetSlice(value);
3180         mSlicerManagers[i]->VerticalSliderHasChanged(3, value);
3181         mSlicerManagers[i]->UpdateSlice(3);
3182         //mSlicerManagers[i]->GetSlicer(3)->Render(); // <-- DS add this, needed for contour, seems ok ? not too slow ?
3183       }
3184       break;
3185     }
3186   }
3187 }
3188 //------------------------------------------------------------------------------
3189
3190
3191 //------------------------------------------------------------------------------
3192 void vvMainWindow::UpdateSlice(int slicer, int slice)
3193 {
3194   // DD("vvMainWindow::UpdateSlice");
3195   //   DD(slicer);
3196   //   DD(slice);
3197   if (slicer == 0) {
3198     //    if (slice != NOVerticalSlider->value())
3199     NOVerticalSlider->setValue(slice);
3200   } else {
3201     if (slicer == 1)
3202       NEVerticalSlider->setValue(slice);
3203     else {
3204       if (slicer == 2)
3205         SOVerticalSlider->setValue(slice);
3206       else {
3207         if (slicer == 3)
3208           SEVerticalSlider->setValue(slice);
3209       }
3210     }
3211   }
3212   // DD("vvMainWindow:UpdateSlice END");
3213 }
3214 //------------------------------------------------------------------------------
3215
3216
3217 //------------------------------------------------------------------------------
3218 void vvMainWindow::UpdateTSlice(int slicer, int slice, int code)
3219 {
3220   //FusionSequence: the slider value should be updated for slicers which show the same sequence as requested
3221   bool doUpdate=false;
3222   if (code==-1) doUpdate=true;
3223   else {
3224     for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
3225       if (DataTree->topLevelItem(i)->data(slicer+1,Qt::CheckStateRole).toInt() > 1) {
3226         //i is the active SlicerManager
3227         if (mSlicerManagers[i]->GetFusionSequenceInvolvmentCode()==code) doUpdate=true;
3228         break;
3229       }
3230     }
3231   }
3232   if (!doUpdate) return;
3233
3234   switch (slicer) {
3235   case 0:
3236     if (NOHorizontalSlider->value()==slice) return;
3237     NOHorizontalSlider->setValue(slice);
3238     break;
3239   case 1:
3240     if (NEHorizontalSlider->value()==slice) return;
3241     NEHorizontalSlider->setValue(slice);
3242     break;
3243   case 2:
3244     if (SOHorizontalSlider->value()==slice) return;
3245     SOHorizontalSlider->setValue(slice);
3246     break;
3247   case 3:
3248     if (SEHorizontalSlider->value()==slice) return;
3249     SEHorizontalSlider->setValue(slice);
3250     break;
3251   }
3252 }
3253 //------------------------------------------------------------------------------
3254
3255
3256 //------------------------------------------------------------------------------
3257 void vvMainWindow::UpdateSliceRange(int slicer, int min, int max, int tmin, int tmax)
3258 {
3259   //int position = int((min+max)/2);
3260   int position = mSlicerManagers[mCurrentPickedImageIndex]->GetSlicer(slicer)->GetSlice();
3261   if (slicer == 0) {
3262     NOVerticalSlider->setRange(min,max);
3263     NOHorizontalSlider->setRange(tmin,tmax);
3264     NOVerticalSlider->setValue(position);
3265   } else if (slicer == 1) {
3266     NEVerticalSlider->setRange(min,max);
3267     NEHorizontalSlider->setRange(tmin,tmax);
3268     NEVerticalSlider->setValue(position);
3269   } else if (slicer == 2) {
3270     SOVerticalSlider->setRange(min,max);
3271     SOHorizontalSlider->setRange(tmin,tmax);
3272     SOVerticalSlider->setValue(position);
3273   } else if (slicer == 3) {
3274     SEVerticalSlider->setRange(min,max);
3275     SEHorizontalSlider->setRange(tmin,tmax);
3276     SEVerticalSlider->setValue(position);
3277   }
3278 }
3279 //------------------------------------------------------------------------------
3280
3281
3282 //------------------------------------------------------------------------------
3283 void vvMainWindow::SaveNOScreenshot()
3284 {
3285   SaveScreenshot(NOViewWidget);
3286 }
3287 //------------------------------------------------------------------------------
3288
3289
3290 //------------------------------------------------------------------------------
3291 void vvMainWindow::SaveNEScreenshot()
3292 {
3293   SaveScreenshot(NEViewWidget);
3294 }
3295 //------------------------------------------------------------------------------
3296
3297
3298 //------------------------------------------------------------------------------
3299 void vvMainWindow::SaveSOScreenshot()
3300 {
3301   SaveScreenshot(SOViewWidget);
3302 }
3303 //------------------------------------------------------------------------------
3304
3305
3306 //------------------------------------------------------------------------------
3307 void vvMainWindow::SaveSEScreenshot()
3308 {
3309   SaveScreenshot(SEViewWidget);
3310 }
3311 //------------------------------------------------------------------------------
3312
3313
3314 //------------------------------------------------------------------------------
3315 void vvMainWindow::SaveScreenshotAllSlices()
3316 {
3317   QVTKWidget *widget = NOViewWidget;
3318
3319   int index = 0;// GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
3320   vvSlicerManager * SM = mSlicerManagers[index];
3321   vvImage * image = SM->GetImage();
3322   vvSlicer * slicer = SM->GetSlicer(0);
3323   int orientation = slicer->GetOrientation();
3324   int nbSlices = image->GetSize()[orientation];
3325   vtkSmartPointer<vtkRenderWindow>  renderWindow = widget->GetRenderWindow();
3326
3327   // Select filename base
3328   QString filename = QFileDialog::getSaveFileName(this,
3329     tr("Save As (filename will be completed by slice number)"),
3330     itksys::SystemTools::GetFilenamePath(mSlicerManagers[index]->GetFileName()).c_str(),
3331     "Images( *.png);;Images( *.jpg)");
3332
3333   // Loop on slices
3334   for(int i=0; i<nbSlices; i++) {
3335     // Change the slice
3336     slicer->SetSlice(i); // -> change the slice of the current slicer
3337     SM->UpdateSlice(0); // --> this one emit UpdateSlice
3338     QCoreApplication::flush(); // -> needed to force display of contours
3339
3340     // Screenshot
3341     vtkSmartPointer<vtkWindowToImageFilter> windowToImageFilter = vtkSmartPointer<vtkWindowToImageFilter>::New();
3342     windowToImageFilter->SetInput(renderWindow);
3343     windowToImageFilter->SetMagnification(1);
3344     windowToImageFilter->SetInputBufferTypeToRGBA(); //also record the alpha (transparency) channel
3345     windowToImageFilter->Update();
3346
3347     vtkSmartPointer<vtkPNGWriter> writer = vtkSmartPointer<vtkPNGWriter>::New();
3348     std::string fn = itksys::SystemTools::GetFilenameWithoutLastExtension(filename.toStdString());
3349     std::string num = clitk::toString(i);
3350     if (i<10) num = "0"+num;
3351     if (i<100) num = "0"+num;
3352     if (i<1000) num = "0"+num;
3353
3354     fn = itksys::SystemTools::GetFilenamePath(filename.toStdString()) + "/"+ fn
3355       + "_" + num + itksys::SystemTools::GetFilenameLastExtension(filename.toStdString());
3356     writer->SetFileName(fn.c_str());
3357 #if VTK_MAJOR_VERSION <= 5
3358     writer->SetInput(windowToImageFilter->GetOutput());
3359 #else
3360     writer->SetInputConnection(windowToImageFilter->GetOutputPort());
3361 #endif
3362     writer->Write();
3363   }
3364 }
3365 //------------------------------------------------------------------------------
3366
3367
3368 //------------------------------------------------------------------------------
3369 void vvMainWindow::SaveScreenshot(QVTKWidget *widget)
3370 {
3371   QString Extensions = "Images( *.png);;";
3372   Extensions += "Images( *.jpg);;";
3373   Extensions += "Images( *.bmp);;";
3374   Extensions += "Images( *.tif);;";
3375   Extensions += "Images( *.ppm)";
3376 #if defined(VTK_USE_FFMPEG_ENCODER) || defined(VTK_USE_VIDEO_FOR_WINDOWS)
3377   Extensions += ";;Video( *.avi)";
3378 #endif
3379 #ifdef VTK_USE_MPEG2_ENCODER
3380   Extensions += ";;Video( *.mpg)";
3381 #endif
3382   Extensions += ";;Video( *.gif)";
3383
3384   int smIndex=GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
3385   QString fileName = QFileDialog::getSaveFileName(this,
3386     tr("Save As"),
3387     itksys::SystemTools::GetFilenamePath(mSlicerManagers[smIndex]->GetFileName()).c_str(),
3388     Extensions);
3389
3390   if (!fileName.isEmpty()) {
3391     vtkSmartPointer<vtkWindowToImageFilter> w2i = vtkSmartPointer<vtkWindowToImageFilter>::New();
3392     w2i->SetInput(widget->GetRenderWindow());
3393     w2i->SetMagnification(1);
3394     w2i->SetInputBufferTypeToRGBA(); //also record the alpha (transparency) channel
3395     w2i->Update();
3396     vtkImageData *image = w2i->GetOutput();
3397
3398     std::string ext(itksys::SystemTools::GetFilenameLastExtension(fileName.toStdString()));
3399
3400     // Image
3401     vtkImageWriter *imgwriter = NULL;
3402     if (ext==".bmp")
3403       imgwriter = vtkBMPWriter::New();
3404     else if (ext==".tif")
3405       imgwriter = vtkTIFFWriter::New();
3406     else if (ext==".ppm")
3407       imgwriter = vtkPNMWriter::New();
3408     else if (ext==".png")
3409       imgwriter = vtkPNGWriter::New();
3410     else if (ext==".jpg")
3411       imgwriter = vtkJPEGWriter::New();
3412
3413     // Snapshot image if not null
3414     if(imgwriter!=NULL) {
3415 #if VTK_MAJOR_VERSION <= 5
3416       imgwriter->SetInput(image);
3417 #else
3418       imgwriter->SetInputConnection(w2i->GetOutputPort());
3419 #endif
3420       imgwriter->SetFileName(fileName.toStdString().c_str());
3421       imgwriter->Write();
3422       return;
3423     }
3424
3425     // Video
3426     vtkGenericMovieWriter *vidwriter = NULL;
3427     if (ext==".gif") {
3428       vvAnimatedGIFWriter *gif = vvAnimatedGIFWriter::New();
3429       vidwriter = gif;
3430
3431       // FPS
3432       bool ok;
3433       int fps = QInputDialog::getInt(this, tr("Number of frames per second"),
3434         tr("FPS:"), 5, 0, 1000, 1, &ok);
3435       if(ok)
3436         gif->SetRate(fps);
3437
3438       // Loops
3439       int loops = QInputDialog::getInt(this, tr("Loops"),
3440         tr("Number of loops (0 means infinite):"), 0, 0, 1000000000, 1, &ok);
3441       if(ok)
3442         gif->SetLoops(loops);
3443
3444       // Dithering
3445       QString msg = "Would you like to activate dithering?";
3446       QMessageBox msgBox(QMessageBox::Question, tr("Dithering"),msg, 0, this);
3447       msgBox.addButton(tr("Yes"), QMessageBox::AcceptRole);
3448       msgBox.addButton(tr("No"), QMessageBox::RejectRole);
3449       gif->SetDither(msgBox.exec() == QMessageBox::AcceptRole);
3450     }
3451 #ifdef VTK_USE_VIDEO_FOR_WINDOWS
3452     if (ext==".avi") {
3453       vtkAVIWriter *mpg = vtkAVIWriter::New();
3454       vidwriter = mpg;
3455       mpg->SetQuality(2);
3456       bool ok;
3457       int fps = QInputDialog::getInt(this, tr("Number of frames per second"),
3458         tr("FPS:"), 5, 0, 1024, 1, &ok);
3459       if(!ok)
3460         fps = 5;
3461       mpg->SetRate(fps);
3462     }
3463 #endif
3464 #ifdef VTK_USE_FFMPEG_ENCODER
3465     if (ext==".avi") {
3466       vtkFFMPEGWriter *mpg = vtkFFMPEGWriter::New();
3467       vidwriter = mpg;
3468       mpg->SetQuality(2);
3469       bool ok;
3470       int fps = QInputDialog::getInt(this, tr("Number of frames per second"),
3471         tr("FPS:"), 5, 0, 1024, 1, &ok);
3472       if(!ok)
3473         fps = 5;
3474       mpg->SetRate(fps);
3475       mpg->SetBitRateTolerance(int(ceil(12.0*1024*1024/fps)));
3476     }
3477 #endif
3478 #ifdef VTK_USE_MPEG2_ENCODER
3479     if (ext==".mpg") {
3480       vtkMPEG2Writer *mpg = vtkMPEG2Writer::New();
3481       vidwriter = mpg;
3482     }
3483 #endif
3484
3485     // Take video if not null
3486     if(vidwriter!=NULL){
3487 #if VTK_MAJOR_VERSION <= 5
3488       vidwriter->SetInput(image);
3489 #else
3490       vidwriter->SetInputConnection(w2i->GetOutputPort());
3491 #endif
3492       vidwriter->SetFileName(fileName.toStdString().c_str());
3493       vidwriter->Start();
3494       int nSlice = mSlicerManagers[smIndex]->GetSlicer(0)->GetTMax();
3495       for(int i=0; i<=nSlice; i++) {
3496         mSlicerManagers[smIndex]->SetNextTSlice(0);
3497         vtkSmartPointer<vtkWindowToImageFilter> w2i = vtkSmartPointer<vtkWindowToImageFilter>::New();
3498         w2i->SetInput(widget->GetRenderWindow());
3499         w2i->Update();
3500 #if VTK_MAJOR_VERSION <= 5
3501         vidwriter->SetInput(w2i->GetOutput());
3502 #else
3503         vidwriter->SetInputConnection(w2i->GetOutputPort());
3504 #endif
3505         vidwriter->Write();
3506       }
3507       vidwriter->End();
3508       vidwriter->Delete();
3509       return;
3510     }
3511
3512     QMessageBox::information(this,tr("Problem saving screenshot !"),tr("Cannot save image.\nPlease set a file extension !!!"));
3513   }
3514 }
3515 //------------------------------------------------------------------------------
3516
3517
3518 //------------------------------------------------------------------------------
3519 void vvMainWindow::GoToCursor()
3520 {
3521   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
3522   for (int column = 1; column < 5; column++) {
3523     if (DataTree->selectedItems()[0]->data(column,Qt::CheckStateRole).toInt() > 1) {
3524       double* cursorPos = mSlicerManagers[index]->GetSlicer(column-1)->GetCursorPosition();
3525       mSlicerManagers[index]->GetSlicer(column-1)->SetCurrentPosition(
3526         cursorPos[0],cursorPos[1],cursorPos[2],cursorPos[3]);
3527       mSlicerManagers[index]->UpdateViews(1,column-1);
3528       mSlicerManagers[index]->UpdateLinked(column-1);
3529       break;
3530     }
3531   }
3532 }
3533 //------------------------------------------------------------------------------
3534
3535 //------------------------------------------------------------------------------
3536 void vvMainWindow::GoToLandmark()
3537 {
3538   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
3539   for (int column = 1; column < 5; column++) {
3540     if (DataTree->selectedItems()[0]->data(column,Qt::CheckStateRole).toInt() > 1) {
3541       double* cursorPos = landmarksPanel->GetSelectedPoint();
3542       mSlicerManagers[index]->GetSlicer(column-1)->SetCurrentPosition(
3543         cursorPos[0],cursorPos[1],cursorPos[2],cursorPos[3]);
3544       mSlicerManagers[index]->UpdateViews(1,column-1);
3545       mSlicerManagers[index]->UpdateLinked(column-1);
3546       break;
3547     }
3548   }
3549 }
3550 //------------------------------------------------------------------------------
3551
3552 //------------------------------------------------------------------------------
3553 void vvMainWindow::PlayPause()
3554 {
3555   if (playMode) {
3556     playMode = 0;
3557     playButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/player_play.png")));
3558     ImageInfoChanged();
3559     return;
3560   } else {
3561     int image_number=DataTree->topLevelItemCount();
3562     bool has_temporal;
3563     for (int i=0; i<image_number; i++)
3564       if (mSlicerManagers[i]->GetSlicer(0)->GetTMax() > 0) {
3565         has_temporal=true;
3566         break;
3567       }
3568       if (has_temporal) {
3569         playMode = 1;
3570         playButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/player_pause.png")));
3571         QTimer::singleShot(1000/mFrameRate, this, SLOT(PlayNext()));
3572       }
3573   }
3574 }
3575 //------------------------------------------------------------------------------
3576
3577 //------------------------------------------------------------------------------
3578 void vvMainWindow::PlayNext()
3579 {
3580   if (playMode && !this->isHidden()) {
3581     int image_number=DataTree->topLevelItemCount();
3582     ///Only play one slicer per SM, and only if the SM is being displayed
3583     for (int i=0; i<image_number; i++)
3584       for (int j=0; j<4; j++)
3585         if (mSlicerManagers[i]->GetSlicer(0)->GetTMax() > 0 &&
3586           DataTree->topLevelItem(i)->data(j+1,Qt::CheckStateRole).toInt() > 0) {
3587             mSlicerManagers[i]->SetNextTSlice(j);
3588             break;
3589         }
3590         QTimer::singleShot(1000/mFrameRate, this, SLOT(PlayNext()));
3591   }
3592 }
3593 //------------------------------------------------------------------------------
3594
3595 void vvMainWindow::ShowLastImage()
3596 {
3597   if (mSlicerManagers.size() > 1) {
3598     QTreeWidgetItem * item=DataTree->topLevelItem(DataTree->topLevelItemCount()-1);
3599     CurrentImageChanged(mSlicerManagers.back()->GetId()); //select new image
3600     item->setData(1,Qt::CheckStateRole,2); //show the new image in the first panel
3601     //mSlicerManagers[GetSlicerIndexFromItem(item)]->GetSlicer(0)->SetActorVisibility("image", 0, 1); //Set the Last Image visibles
3602     DisplayChanged(item,1);
3603   }
3604 }
3605
3606 //------------------------------------------------------------------------------
3607 void vvMainWindow::UpdateRenderWindows()
3608 {
3609   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
3610       for (unsigned int j = 0; j < 4; ++j) {
3611         mSlicerManagers[i]->GetSlicer(j)->RemoveLandmarks();
3612         mSlicerManagers[i]->GetSlicer(j)->DisplayLandmarks();
3613       }
3614   }
3615   if (NOViewWidget->GetRenderWindow()) NOViewWidget->GetRenderWindow()->Render();
3616   if (NEViewWidget->GetRenderWindow()) NEViewWidget->GetRenderWindow()->Render();
3617   if (SOViewWidget->GetRenderWindow()) SOViewWidget->GetRenderWindow()->Render();
3618   if (SEViewWidget->GetRenderWindow()) SEViewWidget->GetRenderWindow()->Render();
3619 }
3620 //------------------------------------------------------------------------------
3621
3622 //------------------------------------------------------------------------------
3623 void vvMainWindow::SegmentationOnCurrentImage()
3624 {
3625   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
3626
3627   vvSegmentationDialog segmentation;
3628   segmentation.SetImage(mSlicerManagers[index]->GetSlicer(0)->GetImage());
3629   segmentation.exec();
3630 }
3631 //------------------------------------------------------------------------------
3632
3633 void vvMainWindow::SurfaceViewerLaunch()
3634 {
3635   vvSurfaceViewerDialog surfaceViewer;
3636   surfaceViewer.exec();
3637 }
3638 //------------------------------------------------------------------------------
3639
3640
3641 //------------------------------------------------------------------------------
3642 int vvMainWindow::GetImageDuplicateFilenameNumber(std::string filename)
3643 {
3644   int number=0;
3645   for(unsigned int l=0; l<mSlicerManagers.size(); l++) {
3646     vvSlicerManager * v = mSlicerManagers[l];
3647     if (v->GetBaseFileName() ==
3648       vtksys::SystemTools::GetFilenameName(vtksys::SystemTools::GetFilenameWithoutLastExtension(filename))) {
3649         number = std::max(number, v->GetBaseFileNameNumber()+1);
3650     }
3651   }
3652   return number;
3653 }
3654 //------------------------------------------------------------------------------
3655
3656
3657 //------------------------------------------------------------------------------
3658 vvSlicerManager* vvMainWindow::AddImage(vvImage::Pointer image,std::string filename)
3659 {
3660   // Change filename if another image exist with the same name
3661   int number = GetImageDuplicateFilenameNumber(filename);
3662
3663   // Create new SliceManager
3664   vvSlicerManager* slicer_manager = new vvSlicerManager(4);
3665   slicer_manager->SetImage(image);//, IMAGE, number);
3666   //  filename = filename+"_"+clitk::toString(number);
3667   slicer_manager->SetFilename(filename, number);
3668   mSlicerManagers.push_back(slicer_manager);
3669
3670   //create an item in the tree with good settings
3671   QTreeWidgetItem *item = new QTreeWidgetItem();
3672   item->setData(0,Qt::UserRole,slicer_manager->GetFileName().c_str());//files[i].c_str());
3673   item->setData(1,Qt::UserRole,tr("image"));
3674   item->setData(COLUMN_IMAGE_NAME,Qt::DisplayRole,slicer_manager->GetFileName().c_str());//filename.c_str());
3675   qApp->processEvents();
3676
3677   for (int j = 1; j <= 4; j++) item->setData(j,Qt::CheckStateRole,1);
3678
3679   //Create the buttons for reload and close
3680   qApp->processEvents();
3681   QTreePushButton* cButton = new QTreePushButton;
3682   cButton->setItem(item);
3683   cButton->setColumn(COLUMN_CLOSE_IMAGE);
3684   cButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/exit.png")));
3685   connect(cButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
3686     this,SLOT(CloseImage(QTreeWidgetItem*, int)));
3687
3688   QTreePushButton* rButton = new QTreePushButton;
3689   rButton->setItem(item);
3690   rButton->setColumn(COLUMN_RELOAD_IMAGE);
3691   rButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/rotateright.png")));
3692   rButton->setEnabled(0);
3693   connect(rButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
3694     this,SLOT(ReloadImage(QTreeWidgetItem*, int)));
3695
3696   DataTree->addTopLevelItem(item);
3697   DataTree->setItemWidget(item, COLUMN_CLOSE_IMAGE, cButton);
3698   DataTree->setItemWidget(item, COLUMN_RELOAD_IMAGE, rButton);
3699
3700   //set the id of the image
3701   QString id = QDir::current().absoluteFilePath(slicer_manager->GetFileName().c_str()) + QString::number(mSlicerManagers.size()-1);
3702   item->setData(COLUMN_IMAGE_NAME,Qt::UserRole,id.toStdString().c_str());
3703   mSlicerManagers.back()->SetId(id.toStdString());
3704
3705   linkPanel->addImage(slicer_manager->GetFileName().c_str()// filename
3706     , id.toStdString());
3707
3708   connect(mSlicerManagers.back(), SIGNAL(currentImageChanged(std::string)),
3709     this, SLOT(CurrentImageChanged(std::string)));
3710   connect(mSlicerManagers.back(), SIGNAL(currentPickedImageChanged(std::string)),
3711     this, SLOT(CurrentPickedImageChanged(std::string)));
3712   connect(mSlicerManagers.back(), SIGNAL(UpdatePosition(int, double, double, double, double, double, double, double)),
3713     this, SLOT(MousePositionChanged(int,double, double, double, double, double, double, double)));
3714   connect(mSlicerManagers.back(), SIGNAL(UpdateVector(int, double, double, double, double)),
3715     this, SLOT(VectorChanged(int,double,double,double, double)));
3716   connect(mSlicerManagers.back(), SIGNAL(UpdateOverlay(int, double, double)),
3717     this, SLOT(OverlayChanged(int,double,double)));
3718   connect(mSlicerManagers.back(), SIGNAL(UpdateFusion(int, double)),
3719     this, SLOT(FusionChanged(int,double)));
3720   //connect(mSlicerManagers.back(), SIGNAL(UpdateFusionSequence(int, bool, unsigned int)),
3721   //  this, SLOT(FusionSequenceChanged(int, bool, unsigned int)));
3722   connect(mSlicerManagers.back(), SIGNAL(WindowLevelChanged()),
3723     this,SLOT(WindowLevelChanged()));
3724   connect(mSlicerManagers.back(), SIGNAL(UpdateSlice(int,int)),
3725     this,SLOT(UpdateSlice(int,int)));
3726   connect(mSlicerManagers.back(), SIGNAL(UpdateTSlice(int, int, int)),
3727     this,SLOT(UpdateTSlice(int, int, int)));
3728   connect(mSlicerManagers.back(), SIGNAL(UpdateTSlice(int, int, int)),
3729     this,SLOT(ImageInfoChanged()));
3730   connect(mSlicerManagers.back(), SIGNAL(UpdateSliceRange(int,int,int,int,int)),
3731     this,SLOT(UpdateSliceRange(int,int,int,int,int)));
3732   connect(mSlicerManagers.back(), SIGNAL(UpdateLinkManager(std::string,int,double,double,double,int)),
3733     this,SLOT(UpdateLinkManager(std::string,int,double,double,double,int)));
3734   connect(mSlicerManagers.back(), SIGNAL(UpdateLinkedNavigation(std::string,vvSlicerManager*,vvSlicer*)),
3735     this,SLOT(UpdateLinkedNavigation(std::string,vvSlicerManager*,vvSlicer*)));
3736   connect(mSlicerManagers.back(), SIGNAL(ChangeImageWithIndexOffset(vvSlicerManager*,int,int)),
3737     this,SLOT(ChangeImageWithIndexOffset(vvSlicerManager*,int,int)));
3738   connect(mSlicerManagers.back(), SIGNAL(LandmarkAdded()),landmarksPanel,SLOT(AddPoint()));
3739   connect(landmarksPanel,SIGNAL(UpdateLandmarkTransform()), mSlicerManagers.back(), SLOT(UpdateLandmark()));
3740
3741
3742
3743   InitSlicers();
3744   UpdateTree();
3745   qApp->processEvents();
3746   InitDisplay();
3747   ShowLastImage();
3748   qApp->processEvents();
3749   // End
3750   ImageInfoChanged();
3751   return slicer_manager;
3752 }
3753 //------------------------------------------------------------------------------
3754
3755
3756 //------------------------------------------------------------------------------
3757 void vvMainWindow::UpdateCurrentSlicer()
3758 {
3759   int index = -1;
3760   if (DataTree->selectedItems().size() > 0) {
3761     index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
3762   }
3763   mSlicerManagerCurrentIndex = index;
3764 }
3765 //------------------------------------------------------------------------------