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         InitSlicers();
 989         numberofsuccesulreads++;
 990       }
 991     }
 992   }
 993
 994   if (numberofsuccesulreads) {
 995     NOViewWidget->show();
 996     NEViewWidget->show();
 997     SOViewWidget->show();
 998     SEViewWidget->show();
 999     UpdateTree();
1000     InitDisplay();
1001     ShowLastImage();
1002
1003     // Try to guess default WindowLevel
1004     double range[2];
1005     mSlicerManagers.back()->GetImage()->GetFirstVTKImageData()->GetScalarRange(range);
1006     if ((range[0] == 0) && (range[1] == 1)) {
1007       presetComboBox->setCurrentIndex(WL_BINARY);// binary
1008     } else {
1009       // TODO
1010     }
1011   }
1012   QApplication::restoreOverrideCursor();
1013 }
1014 //------------------------------------------------------------------------------
1015
1016 //------------------------------------------------------------------------------
1017 void vvMainWindow::UpdateTree()
1018 {
1019   DataTree->resizeColumnToContents(COLUMN_TREE);
1020   DataTree->resizeColumnToContents(COLUMN_UL_VIEW);
1021   DataTree->resizeColumnToContents(COLUMN_UR_VIEW);
1022   DataTree->resizeColumnToContents(COLUMN_DL_VIEW);
1023   DataTree->resizeColumnToContents(COLUMN_DR_VIEW);
1024   DataTree->resizeColumnToContents(COLUMN_IMAGE_NAME);
1025   DataTree->resizeColumnToContents(COLUMN_CLOSE_IMAGE);
1026   DataTree->resizeColumnToContents(COLUMN_RELOAD_IMAGE);
1027 }
1028 //------------------------------------------------------------------------------
1029
1030 //------------------------------------------------------------------------------
1031 void vvMainWindow::CurrentImageChanged(std::string id)
1032 {
1033   if (id == mCurrentSelectedImageId) return; // Do nothing
1034   int selected = 0;
1035   for (int i = 0; i < DataTree->topLevelItemCount(); i++) {
1036     if (DataTree->topLevelItem(i)->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString().toStdString() == id) {
1037       selected = i;
1038     } else {
1039       DataTree->topLevelItem(i)->setSelected(0);
1040     }
1041     for (int child = 0; child < DataTree->topLevelItem(i)->childCount(); child++)
1042       DataTree->topLevelItem(i)->child(child)->setSelected(0);
1043
1044   }
1045   DataTree->topLevelItem(selected)->setSelected(1);
1046   mCurrentSelectedImageId = id;
1047
1048   landmarksPanel->SetCurrentLandmarks(mSlicerManagers[selected]->GetLandmarks(),
1049                                       mSlicerManagers[selected]->GetTSlice());
1050   landmarksPanel->SetCurrentPath(mInputPathName.toStdString());
1051   landmarksPanel->SetCurrentImage(mSlicerManagers[selected]->GetFileName().c_str());
1052
1053   emit SelectedImageHasChanged(mSlicerManagers[selected]);
1054 }
1055 //------------------------------------------------------------------------------
1056
1057 //------------------------------------------------------------------------------
1058 void vvMainWindow::CurrentPickedImageChanged(std::string id)
1059 {
1060   if (id == mCurrentPickedImageId) return; // Do nothing
1061   int selected = 0;
1062   for (int i = 0; i < DataTree->topLevelItemCount(); i++) {
1063     if (DataTree->topLevelItem(i)->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString().toStdString() == id) {
1064       selected = i;
1065     } else {
1066       DataTree->topLevelItem(i)->setSelected(0);
1067     }
1068     for (int child = 0; child < DataTree->topLevelItem(i)->childCount(); child++)
1069       DataTree->topLevelItem(i)->child(child)->setSelected(0);
1070
1071   }
1072   DataTree->topLevelItem(selected)->setSelected(1);
1073   mCurrentPickedImageId = id;
1074   mCurrentPickedImageIndex = selected;
1075 }
1076 //------------------------------------------------------------------------------
1077
1078 //------------------------------------------------------------------------------
1079 void vvMainWindow::ImageInfoChanged()
1080 {
1081   contextActions[6]->setEnabled(1);
1082   contextActions[5]->setEnabled(1);
1083   actionSave_As->setEnabled(1);
1084   actionAdd_VF_to_current_Image->setEnabled(1);
1085   actionAdd_fusion_image->setEnabled(1);
1086   actionAdd_wipe_image->setEnabled(1);
1087   actionAdd_overlay_image_to_current_image->setEnabled(1);
1088   actionAdd_USSequence_toCT->setEnabled(1);
1089   actionNorth_East_Window->setEnabled(1);
1090   actionNorth_West_Window->setEnabled(1);
1091   actionSouth_East_Window->setEnabled(1);
1092   actionSouth_West_Window->setEnabled(1);
1093   vvToolManager::GetInstance()->EnableToolsInMenu(this, true);
1094   inverseButton->setEnabled(1);
1095
1096   goToCursorPushButton->setEnabled(1);
1097
1098   if (DataTree->selectedItems().size()) {
1099     int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1100
1101     colorMapComboBox->setEnabled(1);
1102     for (int i = 0; i < DataTree->topLevelItem(index)->childCount(); i++) {
1103       if (DataTree->topLevelItem(index)->child(i)->data(1,Qt::UserRole).toString() == "overlay" ||
1104         DataTree->topLevelItem(index)->child(i)->data(1,Qt::UserRole).toString() == "fusion" ||
1105         DataTree->topLevelItem(index)->child(i)->data(1,Qt::UserRole).toString() == "fusionSequence") {
1106           colorMapComboBox->setEnabled(0);
1107           break;
1108       }
1109     }
1110
1111     std::vector<double> origin;
1112     std::vector<double> inputSpacing;
1113     std::vector<int> inputSize;
1114     std::vector<double> sizeMM;
1115     vtkSmartPointer<vtkMatrix4x4> transformation;
1116     int dimension=0;
1117     QString pixelType;
1118     QString inputSizeInBytes;
1119     QString image = DataTree->selectedItems()[0]->data(COLUMN_IMAGE_NAME,Qt::DisplayRole).toString();
1120
1121     int nframes = mSlicerManagers[index]->GetSlicer(0)->GetTMax();
1122
1123     if (nframes > 1 || playMode == 1) {
1124       playButton->setEnabled(1);
1125       frameRateLabel->setEnabled(1);
1126       frameRateSpinBox->setEnabled(1);
1127     } else {
1128       playButton->setEnabled(0);
1129       frameRateLabel->setEnabled(0);
1130       frameRateSpinBox->setEnabled(0);
1131     }
1132
1133     //read image header
1134     int NPixel = 1;
1135
1136     int tSlice = 0;
1137     vvImage::Pointer imageSelected;
1138     if (DataTree->topLevelItem(index) == DataTree->selectedItems()[0]) {
1139       imageSelected = mSlicerManagers[index]->GetSlicer(0)->GetImage();
1140       tSlice = mSlicerManagers[index]->GetSlicer(0)->GetTSlice();
1141     } else if (DataTree->selectedItems()[0]->data(1,Qt::UserRole).toString() == "vector") {
1142       imageSelected = mSlicerManagers[index]->GetSlicer(0)->GetVF();
1143       tSlice = mSlicerManagers[index]->GetSlicer(0)->GetOverlayTSlice();
1144     } else if (DataTree->selectedItems()[0]->data(1,Qt::UserRole).toString() == "overlay") {
1145       imageSelected = mSlicerManagers[index]->GetSlicer(0)->GetOverlay();
1146       tSlice = mSlicerManagers[index]->GetSlicer(0)->GetOverlayTSlice();
1147     } else if (DataTree->selectedItems()[0]->data(1,Qt::UserRole).toString() == "fusion") {
1148       imageSelected = mSlicerManagers[index]->GetSlicer(0)->GetFusion();
1149       tSlice = mSlicerManagers[index]->GetSlicer(0)->GetFusionTSlice();
1150     }
1151     else if (DataTree->selectedItems()[0]->data(1,Qt::UserRole).toString() == "fusionSequence") {
1152       imageSelected = mSlicerManagers[index]->GetSlicer(0)->GetFusion();
1153       tSlice = mSlicerManagers[index]->GetSlicer(0)->GetFusionTSlice();
1154     }
1155     else if (DataTree->selectedItems()[0]->data(1,Qt::UserRole).toString() == "contour") {
1156       imageSelected = mSlicerManagers[index]->GetSlicer(0)->GetImage();
1157       tSlice = mSlicerManagers[index]->GetSlicer(0)->GetTSlice();
1158     }
1159     else {
1160       imageSelected = mSlicerManagers[index]->GetSlicer(0)->GetImage();
1161       tSlice = mSlicerManagers[index]->GetSlicer(0)->GetTSlice();
1162     }
1163
1164     dimension = imageSelected->GetNumberOfDimensions();
1165     origin.resize(dimension);
1166     inputSpacing.resize(dimension);
1167     inputSize.resize(dimension);
1168     sizeMM.resize(dimension);
1169     pixelType = mSlicerManagers[index]->GetImage()->GetScalarTypeAsITKString().c_str();
1170     for (int i = 0; i < dimension; i++) {
1171       origin[i] = imageSelected->GetOrigin()[i];
1172       inputSpacing[i] = imageSelected->GetSpacing()[i];
1173       inputSize[i] = imageSelected->GetSize()[i];
1174       sizeMM[i] = inputSize[i]*inputSpacing[i];
1175       NPixel *= inputSize[i];
1176     }
1177     inputSizeInBytes = GetSizeInBytes(imageSelected->GetActualMemorySize()*1000);
1178
1179     QString dim = QString::number(dimension) + " (";
1180     dim += pixelType + ")";
1181
1182     infoPanel->setFileName(image);
1183     std::string creationImageTimeValue("No creation time");
1184     itk::ExposeMetaData< std::string > (*imageSelected->GetFirstMetaDataDictionary(), "creationImageTime", creationImageTimeValue);
1185     infoPanel->setImageCreationTime(QString(creationImageTimeValue.c_str()));
1186     infoPanel->setDimension(dim);
1187     infoPanel->setSizePixel(GetVectorIntAsString(inputSize));
1188     infoPanel->setSizeMM(GetVectorDoubleAsString(sizeMM));
1189     infoPanel->setOrigin(GetVectorDoubleAsString(origin));
1190     infoPanel->setSpacing(GetVectorDoubleAsString(inputSpacing));
1191     infoPanel->setNPixel(QString::number(NPixel)+" ("+inputSizeInBytes+")");
1192
1193     transformation = imageSelected->GetTransform()[tSlice]->GetMatrix();
1194     infoPanel->setTransformation(clitk::Get4x4MatrixDoubleAsString(transformation).c_str());
1195
1196     landmarksPanel->SetCurrentLandmarks(mSlicerManagers[index]->GetLandmarks(),
1197                                         mSlicerManagers[index]->GetTSlice());
1198     landmarksPanel->SetCurrentPath(mInputPathName.toStdString());
1199     landmarksPanel->SetCurrentImage(mSlicerManagers[index]->GetFileName().c_str());
1200
1201     overlayPanel->getCurrentImageName(mSlicerManagers[index]->GetFileName().c_str());
1202     for (int i = 0; i < 4; i++) {
1203       if (DataTree->selectedItems()[0]->data(i+1,Qt::CheckStateRole).toInt() > 0 || i == 3) {
1204         mSlicerManagers[index]->UpdateInfoOnCursorPosition(i);
1205         break;
1206       }
1207     }
1208
1209 //     infoPanel->setFileName(image);
1210 //     infoPanel->setDimension(dim);
1211 //     infoPanel->setSizePixel(GetVectorIntAsString(inputSize));
1212 //     infoPanel->setSizeMM(GetVectorDoubleAsString(sizeMM));
1213 //     infoPanel->setOrigin(GetVectorDoubleAsString(origin));
1214 //     infoPanel->setSpacing(GetVectorDoubleAsString(inputSpacing));
1215 //     infoPanel->setNPixel(QString::number(NPixel)+" ("+inputSizeInBytes+")");
1216 //
1217 //     landmarksPanel->SetCurrentLandmarks(mSlicerManagers[index]->GetLandmarks(),
1218 //                                         mSlicerManagers[index]->GetTSlice());
1219 //     landmarksPanel->SetCurrentPath(mInputPathName.toStdString());
1220 //     landmarksPanel->SetCurrentImage(mSlicerManagers[index]->GetFileName().c_str());
1221 //
1222 //     overlayPanel->getCurrentImageName(mSlicerManagers[index]->GetFileName().c_str());
1223 //     for (int i = 0; i < 4; i++) {
1224 //       if (DataTree->selectedItems()[0]->data(i+1,Qt::CheckStateRole).toInt() > 0 || i == 3) {
1225 //         mSlicerManagers[index]->UpdateInfoOnCursorPosition(i);
1226 //         break;
1227 //       }
1228 //     }
1229     WindowLevelChanged();
1230
1231     slicingPresetComboBox->setCurrentIndex(mSlicerManagers[index]->GetSlicingPreset());
1232
1233     if (mSlicerManagers[index]->GetSlicer(0)->GetVF()) {
1234       overlayPanel->getVFName(mSlicerManagers[index]->GetVFName().c_str());
1235       overlayPanel->getVFProperty(mSlicerManagers[index]->GetSlicer(0)->GetVFSubSampling(),
1236         mSlicerManagers[index]->GetSlicer(0)->GetVFScale(),
1237         mSlicerManagers[index]->GetSlicer(0)->GetVFLog());
1238     } else {
1239       overlayPanel->getVFName(mSlicerManagers[index]->GetVFName().c_str());
1240       overlayPanel->getVFProperty(-1,-1,-1);
1241     }
1242     if (mSlicerManagers[index]->GetSlicer(0)->GetOverlay()) {
1243       overlayPanel->getOverlayName(mSlicerManagers[index]->GetOverlayName().c_str());
1244     } else {
1245       overlayPanel->getOverlayName(mSlicerManagers[index]->GetOverlayName().c_str());
1246     }
1247
1248     if (mSlicerManagers[index]->GetSlicer(0)->GetFusion()) {
1249       overlayPanel->getFusionName(mSlicerManagers[index]->GetFusionName().c_str());
1250     } else {
1251       overlayPanel->getFusionName(mSlicerManagers[index]->GetFusionName().c_str());
1252     }
1253   }
1254 }
1255 //------------------------------------------------------------------------------
1256
1257 //------------------------------------------------------------------------------
1258 void vvMainWindow::ShowDocumentation()
1259 {
1260   documentation->show();
1261 }
1262 //------------------------------------------------------------------------------
1263
1264 //------------------------------------------------------------------------------
1265 void vvMainWindow::PopupRegisterForm(bool checkCanPush)
1266 {
1267   vvRegisterForm* registerForm = new vvRegisterForm(QUrl("http://www.creatis.insa-lyon.fr/~dsarrut/vvregister/write.php"), getVVSettingsPath(), getSettingsOptionFormat());
1268   if(!checkCanPush) {
1269     registerForm->show();
1270   } else {
1271     if(registerForm->canPush()) {
1272       registerForm->show();
1273       registerForm->acquitPushed();//too bad if there is not internet connection anymore.
1274     }
1275   }
1276 }
1277 //------------------------------------------------------------------------------
1278
1279 //------------------------------------------------------------------------------
1280 void vvMainWindow::ShowHelpDialog()
1281 {
1282   help_dialog->show();
1283 }
1284 //------------------------------------------------------------------------------
1285
1286 //------------------------------------------------------------------------------
1287 void vvMainWindow::ChangeViewMode()
1288 {
1289   typedef struct _SIZE{
1290     QSplitter* splitter;
1291     QList<int> size1, size2;
1292     int cols[3];
1293   }SplitterSize;
1294   SplitterSize sizes[4];
1295   sizes[0].splitter = OSplitter;
1296   sizes[0].size1.push_back(1);
1297   sizes[0].size1.push_back(0);
1298   sizes[0].size2.push_back(1);
1299   sizes[0].size2.push_back(0);
1300   sizes[0].cols[0] = 2;
1301   sizes[0].cols[1] = 3;
1302   sizes[0].cols[2] = 4;
1303
1304   sizes[1].splitter = ESplitter;
1305   sizes[1].size1.push_back(0);
1306   sizes[1].size1.push_back(1);
1307   sizes[1].size2.push_back(1);
1308   sizes[1].size2.push_back(0);
1309   sizes[1].cols[0] = 1;
1310   sizes[1].cols[1] = 3;
1311   sizes[1].cols[2] = 4;
1312
1313   sizes[2].splitter = OSplitter;
1314   sizes[2].size1.push_back(1);
1315   sizes[2].size1.push_back(0);
1316   sizes[2].size2.push_back(0);
1317   sizes[2].size2.push_back(1);
1318   sizes[2].cols[0] = 1;
1319   sizes[2].cols[1] = 2;
1320   sizes[2].cols[2] = 4;
1321
1322   sizes[3].splitter = ESplitter;
1323   sizes[3].size1.push_back(0);
1324   sizes[3].size1.push_back(1);
1325   sizes[3].size2.push_back(0);
1326   sizes[3].size2.push_back(1);
1327   sizes[3].cols[0] = 1;
1328   sizes[3].cols[1] = 2;
1329   sizes[3].cols[2] = 3;
1330
1331   int slicer = mSlicerManagers[mCurrentPickedImageIndex]->GetSelectedSlicer();
1332   if (viewMode == 1) {
1333     if (slicer >= 0) {
1334       viewMode = 0;
1335       splitter_3->setSizes(sizes[slicer].size1);
1336       sizes[slicer].splitter->setSizes(sizes[slicer].size2);
1337       DataTree->setColumnHidden(sizes[slicer].cols[0],1);
1338       DataTree->setColumnHidden(sizes[slicer].cols[1],1);
1339       DataTree->setColumnHidden(sizes[slicer].cols[2],1);
1340     }
1341   } else {
1342     QList<int> size;
1343     if (slicer >= 0) {
1344       viewMode = 1;
1345       size.push_back(1);
1346       size.push_back(1);
1347       splitter_3->setSizes(size);
1348       sizes[slicer].splitter->setSizes(size);
1349       DataTree->setColumnHidden(sizes[slicer].cols[0],0);
1350       DataTree->setColumnHidden(sizes[slicer].cols[1],0);
1351       DataTree->setColumnHidden(sizes[slicer].cols[2],0);
1352     }
1353   }
1354   UpdateRenderWindows();
1355   /*
1356   ** I don't know why but for both resized QVTKWidget we also need to render
1357   ** the associated Slicer to redraw crosses.
1358   */
1359   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
1360     //     if (DataTree->topLevelItem(i)->data(COLUMN_UL_VIEW,Qt::CheckStateRole).toInt() > 1)
1361     mSlicerManagers[i]->GetSlicer(0)->Render();
1362     mSlicerManagers[i]->GetSlicer(1)->Render();
1363     //     if (DataTree->topLevelItem(i)->data(COLUMN_DL_VIEW,Qt::CheckStateRole).toInt() > 1)
1364     mSlicerManagers[i]->GetSlicer(2)->Render();
1365     mSlicerManagers[i]->GetSlicer(3)->Render();
1366   }
1367 }
1368 //------------------------------------------------------------------------------
1369
1370 //------------------------------------------------------------------------------
1371 QString vvMainWindow::GetSizeInBytes(unsigned long size)
1372 {
1373   QString result = "";// QString::number(size);
1374   //result += " bytes (";
1375   if (size > 1000000000) {
1376     size /= 1000000000;
1377     result += QString::number(size);
1378     result += "Gb";//)";
1379   } else if (size > 1000000) {
1380     size /= 1000000;
1381     result += QString::number(size);
1382     result += "Mb";//)";
1383   } else if (size > 1000) {
1384     size /= 1000;
1385     result += QString::number(size);
1386     result += "kb";//)";
1387   }
1388   return result;
1389 }
1390 //------------------------------------------------------------------------------
1391
1392 //------------------------------------------------------------------------------
1393 QString vvMainWindow::GetVectorDoubleAsString(std::vector<double> vectorDouble)
1394 {
1395   QString result;
1396   for (unsigned int i= 0; i < vectorDouble.size(); i++) {
1397     if (i != 0)
1398       result += " ";
1399     result += QString::number(vectorDouble[i]);
1400   }
1401   return result;
1402 }
1403 //------------------------------------------------------------------------------
1404
1405 //------------------------------------------------------------------------------
1406 QString vvMainWindow::GetVectorIntAsString(std::vector<int> vectorInt)
1407 {
1408   QString result;
1409   for (unsigned int i= 0; i < vectorInt.size(); i++) {
1410     if (i != 0)
1411       result += " ";
1412     result += QString::number(vectorInt[i]);
1413   }
1414   return result;
1415 }
1416 //------------------------------------------------------------------------------
1417
1418 //------------------------------------------------------------------------------
1419 //this actually returns the SlicerManager index!
1420 int vvMainWindow::GetSlicerIndexFromItem(QTreeWidgetItem* item)
1421 {
1422   QString id = item->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString();
1423   for (int i = 0; i < DataTree->topLevelItemCount(); i++) {
1424     if (DataTree->topLevelItem(i)->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString() == id)
1425       return i;
1426   }
1427   return -1;
1428 }
1429 //------------------------------------------------------------------------------
1430
1431 //------------------------------------------------------------------------------
1432 QTreeWidgetItem* vvMainWindow::GetItemFromSlicerManager(vvSlicerManager* sm)
1433 {
1434   QString id = sm->GetId().c_str();
1435   for (int i = 0; i < DataTree->topLevelItemCount(); i++) {
1436     if (DataTree->topLevelItem(i)->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString() == id)
1437       return DataTree->topLevelItem(i);
1438   }
1439   return NULL;
1440 }
1441 //------------------------------------------------------------------------------
1442
1443 //------------------------------------------------------------------------------
1444 void vvMainWindow::DisplayChanged(QTreeWidgetItem *clickedItem, int column)
1445 {
1446   if ( column >= COLUMN_CLOSE_IMAGE || column <= 0)
1447     return;
1448
1449   // Get parent information (might be the same item)
1450   int slicerManagerIndex = GetSlicerIndexFromItem(clickedItem);
1451   QTreeWidgetItem* clickedParentItem = DataTree->topLevelItem(slicerManagerIndex);
1452   vvSlicer* clickedSlicer = mSlicerManagers[slicerManagerIndex]->GetSlicer(column-1);
1453
1454   // Go over the complete item tree (only 2 levels, parents and children)
1455   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
1456     // Trick to avoid redoing twice the job for a key (sr)
1457     mSlicerManagers[i]->GetSlicer(column-1)->GetRenderWindow()->GetInteractor()->SetKeySym("Crap");
1458
1459     QTreeWidgetItem* currentParentItem = DataTree->topLevelItem(i);
1460     if(currentParentItem != clickedParentItem) {
1461       // Not the branch of the clicked item, uncheck all
1462
1463       // Parent
1464       currentParentItem->setData(column,Qt::CheckStateRole, 0);
1465       mSlicerManagers[i]->UpdateSlicer(column-1, false);
1466
1467       // Children
1468       for (int iChild = 0; iChild < currentParentItem->childCount(); iChild++) {
1469         currentParentItem->child(iChild)->setData(column,Qt::CheckStateRole, 0);
1470       }
1471     }
1472     else {
1473       // Branch of the clicked one: get check status from actor visibility in slicer
1474       // and toggle the clicked one
1475
1476       // Parent
1477       bool vis = clickedSlicer->GetActorVisibility("image", 0);
1478       bool draw = clickedSlicer->GetRenderer()->GetDraw();
1479
1480       // Update slicer (after getting visibility)
1481       mSlicerManagers[slicerManagerIndex]->UpdateSlicer(column-1, true);
1482       mSlicerManagers[slicerManagerIndex]->UpdateInfoOnCursorPosition(column-1);
1483       DisplaySliders(slicerManagerIndex, column-1);
1484       if(clickedParentItem == clickedItem) {
1485         // Toggle
1486         vis = !draw || !vis;
1487       }
1488       clickedSlicer->SetActorVisibility("image", 0, vis);
1489       clickedParentItem->setData(column, Qt::CheckStateRole, vis?2:0);
1490
1491       // Children
1492       std::map<std::string, int> actorTypeCounts;
1493       for (int iChild = 0; iChild < clickedParentItem->childCount(); iChild++) {
1494         QTreeWidgetItem* currentChildItem = clickedParentItem->child(iChild);
1495         std::string actorType = currentChildItem->data(1,Qt::UserRole).toString().toStdString();
1496         vis = clickedSlicer->GetActorVisibility(actorType, actorTypeCounts[actorType]);
1497         if(currentChildItem == clickedItem) {
1498           // Toggle or force visibility if it was not on this branch so far
1499           vis = !draw || !vis;
1500           clickedSlicer->SetActorVisibility(actorType, actorTypeCounts[actorType], vis);
1501         }
1502         currentChildItem->setData(column, Qt::CheckStateRole, vis?2:0);
1503         actorTypeCounts[actorType]++;
1504       }
1505     }
1506   }
1507
1508   clickedSlicer->Render();
1509 }
1510 //------------------------------------------------------------------------------
1511
1512 void vvMainWindow::InitSlicers()
1513 {
1514   if (mSlicerManagers.size()) {
1515     mSlicerManagers.back()->GenerateDefaultLookupTable();
1516     mSlicerManagers.back()->SetSlicerWindow(0,NOViewWidget->GetRenderWindow());
1517     mSlicerManagers.back()->SetSlicerWindow(1,NEViewWidget->GetRenderWindow());
1518     mSlicerManagers.back()->SetSlicerWindow(2,SOViewWidget->GetRenderWindow());
1519     mSlicerManagers.back()->SetSlicerWindow(3,SEViewWidget->GetRenderWindow());
1520 #if VTK_MAJOR_VERSION <= 5
1521     mSlicerManagers.back()->Render(); // SR: displayed #slice is wrong without this / TB: With VTK6 and multiple images, all slicers are updated, not only the first
1522 #endif
1523   }
1524 }
1525
1526 //------------------------------------------------------------------------------
1527 void vvMainWindow::InitDisplay()
1528 {
1529   if (mSlicerManagers.size()) {
1530     //BE CAREFUL : this is absolutely necessary to set the interactor style
1531     //in order to have the same style instanciation for all SlicerManagers in
1532     // a same window
1533     for (int j = 0; j < 4; j++) {
1534       vvInteractorStyleNavigator* style = vvInteractorStyleNavigator::New();
1535       style->SetAutoAdjustCameraClippingRange(1);
1536       bool AlreadySelected = false;
1537       for (int i = 0; i < DataTree->topLevelItemCount(); i++) {
1538         mSlicerManagers[i]->SetInteractorStyleNavigator(j,style);
1539         //select the image only if previous are not selected
1540         if (DataTree->topLevelItem(i)->data(j+1,Qt::CheckStateRole).toInt() > 1) {
1541           mSlicerManagers[i]->UpdateSlicer(j,1);
1542           AlreadySelected = true;
1543         } else if (i == DataTree->topLevelItemCount()-1 && !AlreadySelected) {
1544           if (DataTree->selectedItems().size() == 0) {
1545             DataTree->topLevelItem(i)->setSelected(1);
1546           }
1547           DataTree->topLevelItem(i)->setData(j+1,Qt::CheckStateRole,2);
1548           mSlicerManagers[i]->UpdateSlicer(j,1);
1549           DisplaySliders(i,j);
1550         } else {
1551           DataTree->topLevelItem(i)->setData(j+1,Qt::CheckStateRole,0);
1552           mSlicerManagers[i]->UpdateSlicer(j,0);
1553         }
1554       }
1555       style->Delete();
1556     }
1557   }
1558 }
1559 //------------------------------------------------------------------------------
1560
1561 //------------------------------------------------------------------------------
1562 void vvMainWindow::DisplaySliders(int slicer, int window)
1563 {
1564   if(!mSlicerManagers[slicer]->GetSlicer(window)->GetRenderer()->GetDraw())
1565     return;
1566
1567   int range[2];
1568   mSlicerManagers[slicer]->GetSlicer(window)->GetSliceRange(range);
1569   int position = mSlicerManagers[slicer]->GetSlicer(window)->GetSlice();
1570   if (range[1]>0)
1571     verticalSliders[window]->show();
1572   else
1573     verticalSliders[window]->hide();
1574   verticalSliders[window]->setRange(range[0],range[1]);
1575   verticalSliders[window]->setValue(position);
1576
1577   int tRange[2];
1578   tRange[0] = 0;
1579   tRange[1] = mSlicerManagers[slicer]->GetSlicer(window)->GetTMax();
1580   if (tRange[1]>0)
1581     horizontalSliders[window]->show();
1582   else
1583     horizontalSliders[window]->hide();
1584   horizontalSliders[window]->setRange(tRange[0],tRange[1]);
1585   int tPosition = mSlicerManagers[slicer]->GetSlicer(window)->GetMaxCurrentTSlice();
1586   horizontalSliders[window]->setValue(tPosition);
1587 }
1588 //------------------------------------------------------------------------------
1589
1590 //------------------------------------------------------------------------------
1591 void vvMainWindow::CloseImage(QTreeWidgetItem* item, int column)
1592 {
1593   int index = GetSlicerIndexFromItem(item);
1594
1595   if (DataTree->topLevelItem(index) != item) {
1596     QString warning = "Do you really want to close the overlay : ";
1597     warning += item->data(COLUMN_IMAGE_NAME,Qt::DisplayRole).toString();
1598     QMessageBox msgBox(QMessageBox::Warning, tr("Close Overlay"),
1599       warning, 0, this);
1600     msgBox.addButton(tr("Close"), QMessageBox::AcceptRole);
1601     msgBox.addButton(tr("Cancel"), QMessageBox::RejectRole);
1602     if (msgBox.exec() == QMessageBox::AcceptRole) {
1603       std::string overlay_type=item->data(1,Qt::UserRole).toString().toStdString();
1604       int overlay_index=0;
1605       for (int child = 0; child < DataTree->topLevelItem(index)->childCount(); child++) {
1606         if (DataTree->topLevelItem(index)->\
1607           child(child)->data(1,Qt::UserRole).toString().toStdString() == overlay_type)
1608           overlay_index++;
1609         if (DataTree->topLevelItem(index)->child(child) == item) break;
1610       }
1611       if (overlay_type=="fusionSequence") {
1612         //removing the overlay sequence in a fusion sequence visualization mode
1613         //reset the transforms
1614         overlayPanel->getFusionSequenceProperty(-1, false, 0, false);
1615
1616         //unlink and untie the slicer managers
1617         RemoveLink(mSlicerManagers[index]->GetId().c_str(), mSlicerManagers[mSlicerManagers[index]->GetFusionSequenceIndexOfLinkedManager()]->GetId().c_str());
1618         mSlicerManagers[index]->SetFusionSequenceInvolvmentCode(-1);
1619         mSlicerManagers[mSlicerManagers[index]->GetFusionSequenceIndexOfLinkedManager()]->SetFusionSequenceInvolvmentCode(-1);
1620         for (unsigned i=0 ; i<4 ; i++) {
1621             mSlicerManagers[index]->GetSlicer(i)->SetFusionSequenceCode(-1);
1622             mSlicerManagers[mSlicerManagers[index]->GetFusionSequenceIndexOfLinkedManager()]->GetSlicer(i)->SetFusionSequenceCode(-1);
1623         }
1624
1625       }
1626       mSlicerManagers[index]->RemoveActor(overlay_type, overlay_index-1);
1627       mSlicerManagers[index]->SetColorMap(0);
1628       DataTree->topLevelItem(index)->takeChild(DataTree->topLevelItem(index)->indexOfChild(item));
1629       mSlicerManagers[index]->Render();
1630     }
1631   } else if (DataTree->topLevelItemCount() <= 1) {
1632     QString warning = "Do you really want to close the image : ";
1633     warning += item->data(COLUMN_IMAGE_NAME,Qt::DisplayRole).toString();
1634     warning += "\nThis is the last image, you're about to close vv !!!";
1635     QMessageBox msgBox(QMessageBox::Warning, tr("Close Image"),
1636       warning, 0, this);
1637     msgBox.addButton(tr("Close vv"), QMessageBox::AcceptRole);
1638     msgBox.addButton(tr("Cancel"), QMessageBox::RejectRole);
1639     if (msgBox.exec() == QMessageBox::AcceptRole) {
1640       this->close();
1641     }
1642   } else {
1643     QString warning = "Do you really want to close the image : ";
1644     warning += item->data(COLUMN_IMAGE_NAME,Qt::DisplayRole).toString();
1645     QMessageBox msgBox(QMessageBox::Warning, tr("Close Image"),
1646       warning, 0, this);
1647     msgBox.addButton(tr("Close"), QMessageBox::AcceptRole);
1648     msgBox.addButton(tr("Cancel"), QMessageBox::RejectRole);
1649     if (msgBox.exec() == QMessageBox::AcceptRole) {
1650
1651       // Tell tools that we close an image
1652       emit AnImageIsBeingClosed(mSlicerManagers[index]);
1653
1654       std::vector<vvSlicerManager*>::iterator Manageriter = mSlicerManagers.begin();
1655       DataTree->takeTopLevelItem(index);
1656       for (int i = 0; i < index; i++) {
1657         Manageriter++;
1658       }
1659       //if the slicer manager was involved in a fusion sequence visualization...
1660       if ( mSlicerManagers[index]->IsInvolvedInFusionSequence() ) {
1661         //in both cases, close the overlay: find it... and close it
1662         //ideally, I should duplicate the code, and avoid calling CloseImage, since this pops up another interactive box
1663         QTreeWidgetItem* overlayItem;
1664         if (mSlicerManagers[index]->IsMainSequenceOfFusionSequence()) {
1665           for (unsigned i=0 ; i<item->childCount() ; i++) {
1666             overlayItem = item->child(i);
1667             this->CloseImage( overlayItem, 0 );
1668           }
1669         }
1670         else {
1671           QTreeWidgetItem* linkedItem = this->GetItemFromSlicerManager( mSlicerManagers[mSlicerManagers[index]->GetFusionSequenceIndexOfLinkedManager()] );
1672           for (unsigned i=0 ; i<linkedItem->childCount() ; i++) {
1673             overlayItem = linkedItem->child(i);
1674             this->CloseImage( overlayItem, 0 );
1675           }
1676         }
1677
1678         /* -- this is normally already done when closing the overlay.
1679         //reset the transforms
1680         overlayPanel->getFusionSequenceProperty(-1, false, 0, false);
1681
1682         //unlink and untie the slicer managers
1683         RemoveLink(mSlicerManagers[index]->GetId().c_str(), mSlicerManagers[mSlicerManagers[index]->GetFusionSequenceIndexOfLinkedManager()]->GetId().c_str());
1684         mSlicerManagers[index]->SetFusionSequenceInvolvmentCode(-1);
1685         mSlicerManagers[mSlicerManagers[index]->GetFusionSequenceIndexOfLinkedManager()]->SetFusionSequenceInvolvmentCode(-1);
1686         for (unsigned i=0 ; i<4 ; i++) {
1687             mSlicerManagers[index]->GetSlicer(i)->SetFusionSequenceCode(-1);
1688             mSlicerManagers[mSlicerManagers[index]->GetFusionSequenceIndexOfLinkedManager()]->GetSlicer(i)->SetFusionSequenceCode(-1);
1689         }
1690         */
1691       }
1692
1693       linkPanel->removeImage(index);
1694       mSlicerManagers[index]->RemoveActors();
1695
1696       //remove the slicer manager
1697       delete mSlicerManagers[index];
1698       mSlicerManagers.erase(Manageriter);
1699
1700       //
1701       InitDisplay();
1702     }
1703   }
1704   ImageInfoChanged();
1705 }
1706 //------------------------------------------------------------------------------
1707
1708 //------------------------------------------------------------------------------
1709 void vvMainWindow::ReloadImage(QTreeWidgetItem* item, int column)
1710 {
1711   // int index = GetSlicerIndexFromItem(item);
1712   //   QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
1713   //   if (item->data(1,Qt::UserRole).toString() == "vector")
1714   //     mSlicerManagers[index]->ReloadVF();
1715   //   else
1716   //     mSlicerManagers[index]->Reload();
1717
1718   //   QApplication::restoreOverrideCursor();
1719   int index = GetSlicerIndexFromItem(item);
1720   QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
1721   QString role=item->data(1,Qt::UserRole).toString();
1722   if ( role == "vector") {
1723     mSlicerManagers[index]->ReloadVF();
1724   }
1725   else if (role == "overlay") {
1726     mSlicerManagers[index]->ReloadOverlay();
1727   }
1728   else if (role == "fusion") {
1729     mSlicerManagers[index]->ReloadFusion();
1730   }
1731   else if (role == "fusionSequence") {
1732     //both versions of the secondary sequence must be updated.
1733     mSlicerManagers[index]->ReloadFusionSequence();
1734     mSlicerManagers[mSlicerManagers[index]->GetFusionSequenceIndexOfLinkedManager()]->Reload();
1735   }
1736   else {
1737     mSlicerManagers[index]->Reload();
1738     //if we update the secondary sequence, then the overlay of the main sequence should also be updated
1739     if (mSlicerManagers[index]->IsSecondarySequenceOfFusionSequence()) mSlicerManagers[mSlicerManagers[index]->GetFusionSequenceIndexOfLinkedManager()]->ReloadFusionSequence();
1740   }
1741   // Update view and info
1742   ImageInfoChanged();
1743   mSlicerManagers[index]->Render();
1744   QApplication::restoreOverrideCursor();
1745 }
1746 //------------------------------------------------------------------------------
1747
1748 //------------------------------------------------------------------------------
1749 void vvMainWindow::MousePositionChanged(int visibility,double x, double y, double z, double X, double Y, double Z , double value)
1750 {
1751   infoPanel->setCurrentInfo(visibility,x,y,z,X,Y,Z,value);
1752 }
1753 //------------------------------------------------------------------------------
1754
1755 //------------------------------------------------------------------------------
1756 void vvMainWindow::VectorChanged(int visibility,double x, double y, double z, double value)
1757 {
1758   overlayPanel->getCurrentVectorInfo(visibility,x,y,z,value);
1759 }
1760 //------------------------------------------------------------------------------
1761
1762 //------------------------------------------------------------------------------
1763 void vvMainWindow::OverlayChanged(int visibility, double valueOver, double valueRef)
1764 {
1765   overlayPanel->getCurrentOverlayInfo(visibility,valueOver, valueRef);
1766 }
1767 //------------------------------------------------------------------------------
1768
1769 //------------------------------------------------------------------------------
1770 void vvMainWindow::FusionChanged(int visibility, double value)
1771 {
1772   overlayPanel->getCurrentFusionInfo(visibility,value);
1773 }
1774 //------------------------------------------------------------------------------
1775
1776 //------------------------------------------------------------------------------
1777 //called when AddOverlayImage, AddFusionSequence
1778 //or when UpdateWindowLevel() is called ; when slicerManager emits WindowLevelChanged
1779 //when ImageInfoChanged() is called
1780 void vvMainWindow::WindowLevelChanged()
1781 {
1782   // Base image
1783   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1784   if(index==-1) return;
1785   windowSpinBox->setValue(mSlicerManagers[index]->GetColorWindow());
1786   levelSpinBox->setValue(mSlicerManagers[index]->GetColorLevel());
1787   colorMapComboBox->setCurrentIndex(mSlicerManagers[index]->GetColorMap());
1788   presetComboBox->setCurrentIndex(mSlicerManagers[index]->GetPreset());
1789
1790   // Overlay image
1791   if (mSlicerManagers[index]->GetSlicer(0)->GetOverlay())
1792     overlayPanel->getOverlayProperty(mSlicerManagers[index]->GetOverlayColor(),
1793     mSlicerManagers[index]->GetLinkOverlayWindowLevel(),
1794     mSlicerManagers[index]->GetOverlayColorWindow(),
1795     mSlicerManagers[index]->GetOverlayColorLevel());
1796   else
1797     overlayPanel->getOverlayProperty(-1,0,0.,0.);
1798
1799   // Fusion & SequenceFusion image
1800   if (mSlicerManagers[index]->GetSlicer(0)->GetFusion()) {
1801     overlayPanel->getFusionProperty(mSlicerManagers[index]->GetFusionOpacity(),
1802       mSlicerManagers[index]->GetFusionThresholdOpacity(),
1803       mSlicerManagers[index]->GetFusionColorMap(),
1804       mSlicerManagers[index]->GetFusionWindow(),
1805       mSlicerManagers[index]->GetFusionLevel());
1806     if (mSlicerManagers[index]->IsMainSequenceOfFusionSequence()) {
1807       overlayPanel->getFusionSequenceProperty(mSlicerManagers[index]->GetFusionSequenceFrameIndex(),
1808         mSlicerManagers[index]->GetFusionSequenceSpatialSyncFlag(),
1809         mSlicerManagers[index]->GetFusionSequenceNbFrames(),
1810         mSlicerManagers[index]->GetFusionSequenceTemporalSyncFlag());
1811     }
1812   }
1813   else if ( mSlicerManagers[index]->IsSecondarySequenceOfFusionSequence() ) {
1814     //if the image is involved in a fusion sequence, preserve the overlay panel!
1815     int ind = mSlicerManagers[index]->GetFusionSequenceIndexOfLinkedManager();
1816     overlayPanel->getFusionProperty(mSlicerManagers[ind]->GetFusionOpacity(),
1817       mSlicerManagers[ind]->GetFusionThresholdOpacity(),
1818       mSlicerManagers[ind]->GetFusionColorMap(),
1819       mSlicerManagers[ind]->GetFusionWindow(),
1820       mSlicerManagers[ind]->GetFusionLevel());
1821     overlayPanel->getFusionSequenceProperty(mSlicerManagers[ind]->GetFusionSequenceFrameIndex(),
1822       mSlicerManagers[ind]->GetFusionSequenceSpatialSyncFlag(),
1823       mSlicerManagers[ind]->GetFusionSequenceNbFrames(),
1824       mSlicerManagers[ind]->GetFusionSequenceTemporalSyncFlag());
1825   }
1826   else
1827   {
1828     overlayPanel->getFusionProperty(-1, -1, -1, -1, -1);
1829     overlayPanel->getFusionSequenceProperty(-1, false, 0, false);
1830   }
1831 }
1832 //------------------------------------------------------------------------------
1833
1834 //------------------------------------------------------------------------------
1835 void vvMainWindow::WindowLevelEdited()
1836 {
1837   presetComboBox->setCurrentIndex(WL_USER);
1838   UpdateWindowLevel();
1839 }
1840 //------------------------------------------------------------------------------
1841
1842 //------------------------------------------------------------------------------
1843 void vvMainWindow::SetWindowLevel(double w, double l)
1844 {
1845   windowSpinBox->setValue(w);
1846   levelSpinBox->setValue(l);
1847   presetComboBox->setCurrentIndex(WL_USER);
1848   colorMapComboBox->setCurrentIndex(0);
1849   UpdateWindowLevel();
1850 }
1851 //------------------------------------------------------------------------------
1852
1853 //------------------------------------------------------------------------------
1854 void vvMainWindow::UpdateWindowLevel()
1855 {
1856   if (DataTree->selectedItems().size()) {
1857     if (presetComboBox->currentIndex() == WL_VENTILATION) //For ventilation
1858       colorMapComboBox->setCurrentIndex(5);
1859     int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1860     mSlicerManagers[index]->SetColorWindow(windowSpinBox->value());
1861     mSlicerManagers[index]->SetColorLevel(levelSpinBox->value());
1862     mSlicerManagers[index]->SetPreset(presetComboBox->currentIndex());
1863     mSlicerManagers[index]->Render();
1864     WindowLevelChanged();
1865   }
1866 }
1867 //------------------------------------------------------------------------------
1868
1869 //------------------------------------------------------------------------------
1870 void vvMainWindow::UpdateSlicingPreset()
1871 {
1872   if (DataTree->selectedItems().size()) {
1873     int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1874     mSlicerManagers[index]->SetSlicingPreset(vvSlicerManager::SlicingPresetType(slicingPresetComboBox->currentIndex()));
1875   }
1876 }
1877 //------------------------------------------------------------------------------
1878
1879 //------------------------------------------------------------------------------
1880 void vvMainWindow::UpdateColorMap()
1881 {
1882   if (DataTree->selectedItems().size()) {
1883     int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1884     mSlicerManagers[index]->SetColorMap(colorMapComboBox->currentIndex());
1885     mSlicerManagers[index]->Render();
1886   }
1887 }
1888 //------------------------------------------------------------------------------
1889 void vvMainWindow::SwitchWindowLevel()
1890 {
1891   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1892   int window = mSlicerManagers[index]->GetColorWindow();
1893   presetComboBox->setCurrentIndex(WL_USER);
1894   windowSpinBox->setValue(-window);
1895   UpdateWindowLevel();
1896 }
1897 //------------------------------------------------------------------------------
1898
1899 //------------------------------------------------------------------------------
1900 void vvMainWindow::ApplyWindowLevelToAllImages()
1901 {
1902   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1903   if(index==-1) return;
1904   double window = mSlicerManagers[index]->GetColorWindow();
1905   double level = mSlicerManagers[index]->GetColorLevel();
1906
1907   double fusWindow = mSlicerManagers[index]->GetFusionWindow();
1908   double fusLevel = mSlicerManagers[index]->GetFusionLevel();
1909
1910   double overWindow = mSlicerManagers[index]->GetOverlayColorWindow();
1911   double overLevel = mSlicerManagers[index]->GetOverlayColorLevel();
1912
1913   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
1914     if (mSlicerManagers[i] == NULL)
1915       continue;
1916     mSlicerManagers[i]->SetColorWindow(window);
1917     mSlicerManagers[i]->SetColorLevel(level);
1918     mSlicerManagers[i]->SetPreset(WL_USER);
1919     mSlicerManagers[i]->SetFusionWindow(fusWindow);
1920     mSlicerManagers[i]->SetFusionLevel(fusLevel);
1921     mSlicerManagers[i]->SetOverlayColorWindow(overWindow);
1922     mSlicerManagers[i]->SetOverlayColorLevel(overLevel);
1923     mSlicerManagers[i]->Render();
1924   }
1925 }
1926 //------------------------------------------------------------------------------
1927
1928 //------------------------------------------------------------------------------
1929 void vvMainWindow::ApplyWindowToSetOfImages(double window, unsigned int indexMin, unsigned int indexMax)
1930 {
1931   for (unsigned int i = indexMin; i <= indexMax && i < mSlicerManagers.size(); i++) {
1932     if (mSlicerManagers[i] == NULL)
1933       continue;
1934     SetWindowLevel(window, mSlicerManagers[i]->GetColorLevel());
1935     mSlicerManagers[i]->SetColorWindow(window);
1936     mSlicerManagers[i]->SetPreset(WL_USER);
1937     mSlicerManagers[i]->Render();
1938   }
1939 }
1940 //------------------------------------------------------------------------------
1941
1942 //------------------------------------------------------------------------------
1943 void vvMainWindow::ApplyLevelToSetOfImages(double level, unsigned int indexMin, unsigned int indexMax)
1944 {
1945   for (unsigned int i = indexMin; i <= indexMax && i < mSlicerManagers.size(); i++) {
1946     if (mSlicerManagers[i] == NULL)
1947       continue;
1948     SetWindowLevel(mSlicerManagers[i]->GetColorWindow(), level);
1949     mSlicerManagers[i]->SetColorLevel(level);
1950     mSlicerManagers[i]->SetPreset(WL_USER);
1951     mSlicerManagers[i]->Render();
1952   }
1953 }
1954 //------------------------------------------------------------------------------
1955
1956 //------------------------------------------------------------------------------
1957 void vvMainWindow::UpdateLinkManager(std::string id, int slicer, double x, double y, double z, int temps)
1958 {
1959   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
1960     if (mSlicerManagers[i]->GetId() == id) {
1961       mSlicerManagers[i]->GetSlicer(slicer)->SetCurrentPosition(x,y,z,temps);
1962       mSlicerManagers[i]->UpdateViews(0,slicer);
1963       break;
1964     }
1965   }
1966 }
1967 //------------------------------------------------------------------------------
1968
1969 //------------------------------------------------------------------------------
1970 void vvMainWindow::UpdateLinkedNavigation(std::string id, vvSlicerManager * sm, vvSlicer* refSlicer)
1971 {
1972   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
1973     if (id == mSlicerManagers[i]->GetId()) {
1974       mSlicerManagers[i]->UpdateLinkedNavigation(refSlicer);
1975     }
1976   }
1977 }
1978 //------------------------------------------------------------------------------
1979
1980 //------------------------------------------------------------------------------
1981 void vvMainWindow::ShowContextMenu(QPoint point)
1982 {
1983   if (!DataTree->selectedItems().size()) {
1984     contextActions[1]->setEnabled(0);
1985     contextActions[2]->setEnabled(0);
1986     contextActions[3]->setEnabled(0);
1987     contextActions[4]->setEnabled(0);
1988     contextActions[5]->setEnabled(0);
1989     contextActions[6]->setEnabled(0);
1990   } else {
1991     int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1992     contextActions[1]->setEnabled(1);
1993     contextActions[2]->setEnabled(
1994       DataTree->itemWidget(DataTree->selectedItems()[0],
1995       COLUMN_RELOAD_IMAGE)->isEnabled());
1996     contextActions[3]->setEnabled(1);
1997     contextActions[5]->setEnabled(1);
1998     contextActions[6]->setEnabled(1);
1999
2000     if (mSlicerManagers[index]->GetDimension() < 3)
2001       contextActions[4]->setEnabled(0);
2002     else
2003       contextActions[4]->setEnabled(1);
2004   }
2005   contextMenu.exec(QCursor::pos());
2006 }
2007 //------------------------------------------------------------------------------
2008
2009 //------------------------------------------------------------------------------
2010 void vvMainWindow::CloseImage()
2011 {
2012   CloseImage(DataTree->selectedItems()[0],0);
2013 }
2014 //------------------------------------------------------------------------------
2015
2016 //------------------------------------------------------------------------------
2017 void vvMainWindow::ReloadImage()
2018 {
2019   ReloadImage(DataTree->selectedItems()[0],0);
2020 }
2021 //------------------------------------------------------------------------------
2022
2023 //------------------------------------------------------------------------------
2024 void vvMainWindow::SelectOverlayImage()
2025 {
2026   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2027
2028   if (!(CheckAddedImage(index, "overlay")))
2029     return;
2030
2031   QString Extensions = EXTENSIONS;
2032   Extensions += ";;All Files (*)";
2033   QStringList files = QFileDialog::getOpenFileNames(this,tr("Load Overlay image"),mInputPathName,Extensions);
2034   if (files.isEmpty())
2035     return;
2036
2037   std::vector<std::string> vecFileNames;
2038   for (int i = 0; i < files.size(); i++) {
2039     vecFileNames.push_back(files[i].toStdString());
2040   }
2041
2042   AddOverlayImage(index,vecFileNames,vvImageReader::IMAGE);
2043 }
2044 //------------------------------------------------------------------------------
2045
2046 //------------------------------------------------------------------------------
2047 bool vvMainWindow::CheckAddedImage(int index, QString imageType)
2048 {
2049   //check if one overlay image is added
2050   for (int child = 0; child < DataTree->topLevelItem(index)->childCount(); child++)
2051     if (DataTree->topLevelItem(index)->child(child)->data(1,Qt::UserRole).toString().compare(imageType) == 0) {
2052       QString error = "Cannot add more than one compared image\n";
2053       error += "Please remove first ";
2054       error += DataTree->topLevelItem(index)->child(child)->data(COLUMN_IMAGE_NAME,Qt::DisplayRole).toString();
2055       QMessageBox::information(this,tr("Problem adding compared image !"),error);
2056       return false;
2057     }
2058     return true;
2059 }
2060 //------------------------------------------------------------------------------
2061
2062 //------------------------------------------------------------------------------
2063 void vvMainWindow::AddOverlayImage(int index, std::vector<std::string> fileNames, vvImageReader::LoadedImageType type)
2064 {
2065   QString file(fileNames[0].c_str());
2066   if (QFile::exists(file))
2067   {
2068     mInputPathName = itksys::SystemTools::GetFilenamePath(file.toStdString()).c_str();
2069     itk::ImageIOBase::Pointer reader = itk::ImageIOFactory::CreateImageIO(
2070       file.toStdString().c_str(), itk::ImageIOFactory::ReadMode);
2071     reader->SetFileName(fileNames[0].c_str());
2072     reader->ReadImageInformation();
2073     std::string component = reader->GetComponentTypeAsString(reader->GetComponentType());
2074     int dimension = reader->GetNumberOfDimensions();
2075     QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
2076     vvProgressDialog progress("Opening " + file.toStdString());
2077     qApp->processEvents();
2078
2079     std::string filename = itksys::SystemTools::GetFilenameWithoutExtension(file.toStdString()).c_str();
2080     if (mSlicerManagers[index]->SetOverlay(fileNames,dimension, component,type)) {
2081       //create an item in the tree with good settings
2082       QTreeWidgetItem *item = new QTreeWidgetItem();
2083       item->setData(0,Qt::UserRole,file.toStdString().c_str());
2084       item->setData(1,Qt::UserRole,tr("overlay"));
2085       QFileInfo fileinfo(file); //Do not show the path
2086       item->setData(COLUMN_IMAGE_NAME,Qt::DisplayRole,fileinfo.fileName());
2087       item->setToolTip(COLUMN_IMAGE_NAME, mSlicerManagers[index]->GetListOfAbsoluteFilePathInOneString("overlay").c_str());
2088       qApp->processEvents();
2089 #if VTK_MAJOR_VERSION > 5
2090       for ( unsigned int i = 0; i < mSlicerManagers[index]->GetNumberOfSlicers(); i++)
2091         mSlicerManagers[index]->GetSlicer(i)->ForceUpdateDisplayExtent();
2092 #endif
2093
2094       for (int j = 1; j <= 4; j++) {
2095         item->setData(j,Qt::CheckStateRole,DataTree->topLevelItem(index)->data(j,Qt::CheckStateRole));
2096       }
2097
2098       //Create the buttons for reload and close
2099       qApp->processEvents();
2100       QTreePushButton* cButton = new QTreePushButton;
2101       cButton->setItem(item);
2102       cButton->setColumn(COLUMN_CLOSE_IMAGE);
2103       cButton->setToolTip(tr("close image"));
2104       cButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/exit.png")));
2105       connect(cButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
2106         this,SLOT(CloseImage(QTreeWidgetItem*, int)));
2107
2108       QTreePushButton* rButton = new QTreePushButton;
2109       rButton->setItem(item);
2110       rButton->setColumn(COLUMN_RELOAD_IMAGE);
2111       rButton->setToolTip(tr("reload image"));
2112       rButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/rotateright.png")));
2113       connect(rButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
2114         this,SLOT(ReloadImage(QTreeWidgetItem*, int)));
2115
2116       DataTree->topLevelItem(index)->setExpanded(1);
2117       DataTree->topLevelItem(index)->addChild(item);
2118       DataTree->setItemWidget(item, COLUMN_CLOSE_IMAGE, cButton);
2119       DataTree->setItemWidget(item, COLUMN_RELOAD_IMAGE, rButton);
2120
2121       //set the id of the image
2122       QString id = DataTree->topLevelItem(index)->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString();
2123       item->setData(COLUMN_IMAGE_NAME,Qt::UserRole,id.toStdString().c_str());
2124       UpdateTree();
2125       qApp->processEvents();
2126       ImageInfoChanged();
2127       QApplication::restoreOverrideCursor();
2128
2129       // Update the display to update, e.g., the sliders
2130       for(int i=0; i<4; i++)
2131         DisplaySliders(index, i);
2132     } else {
2133       QApplication::restoreOverrideCursor();
2134       QString error = "Cannot import the new image.\n";
2135       error += mSlicerManagers[index]->GetLastError().c_str();
2136       QMessageBox::information(this,tr("Problem reading image !"),error);
2137     }
2138     WindowLevelChanged();
2139   }
2140   else
2141     QMessageBox::information(this,tr("Problem reading Overlay !"),"File doesn't exist!");
2142 }
2143 //------------------------------------------------------------------------------
2144
2145
2146 //------------------------------------------------------------------------------
2147 void vvMainWindow::AddROI(int index, QString file)
2148 {
2149   /*
2150   // Get slice manager
2151
2152   // Load image
2153
2154   vvImageReader * mReader = new vvImageReader;
2155   mReader->SetInputFilename(filename.toStdString());
2156   mReader->Update(IMAGE);
2157   if (mReader->GetLastError().size() != 0) {
2158   std::cerr << "Error while reading " << filename.toStdString() << std::endl;
2159   QString error = "Cannot open file \n";
2160   error += mReader->GetLastError().c_str();
2161   QMessageBox::information(this,tr("Reading problem"),error);
2162   delete mReader;
2163   return;
2164   }
2165   vvImage::Pointer roi = mReader->GetOutput();
2166
2167   // Create roi in new tool
2168   vvToolStructureSetManager::AddImage(mCurrentSlicerManager, roi);
2169   */
2170 }
2171 //------------------------------------------------------------------------------
2172
2173 //------------------------------------------------------------------------------
2174 void vvMainWindow::SelectWipeImage()
2175 {
2176   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2177
2178
2179   if (!(CheckAddedImage(index, "wipe")))
2180     return;
2181
2182   vvWipeImage::Pointer wipeImage = vvWipeImage::New();
2183   wipeImage->Initialize(mInputPathName, mSlicerManagers);
2184   wipeImage->selectWipeImage(index, GetTree());
2185   QTreeWidgetItem *item = DataTree->itemAt(index, COLUMN_CLOSE_IMAGE);
2186   //connect(item,SIGNAL(clickedInto(QTreeWidgetItem*, int)), this,SLOT(CloseImage(QTreeWidgetItem*, int)));
2187   UpdateTree();
2188   ImageInfoChanged();
2189   for(int i=0; i<4; i++)
2190         DisplaySliders(index, i);
2191   WindowLevelChanged();
2192
2193   /*QString Extensions = EXTENSIONS;
2194   Extensions += ";;All Files (*)";
2195   QStringList files = QFileDialog::getOpenFileNames(this,tr("Load Wipe image"),mInputPathName,Extensions);
2196   if (files.isEmpty())
2197     return;
2198
2199   std::vector<std::string> vecFileNames;
2200   for (int i = 0; i < files.size(); i++) {
2201     vecFileNames.push_back(files[i].toStdString());
2202   }*/
2203
2204   //AddWipeImage(index,vecFileNames,vvImageReader::IMAGE);
2205 }
2206 //------------------------------------------------------------------------------
2207
2208
2209 //------------------------------------------------------------------------------
2210 void vvMainWindow::SelectFusionImage()
2211 {
2212   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2213
2214   if (!(CheckAddedImage(index, "fusion")) || !(CheckAddedImage(index, "fusionSequence")))
2215     return;
2216
2217   QString Extensions = EXTENSIONS;
2218   Extensions += ";;All Files (*)";
2219   QStringList files = QFileDialog::getOpenFileNames(this,tr("Load Fusion image"),mInputPathName,Extensions);
2220   if (files.isEmpty())
2221     return;
2222
2223   std::vector<std::string> vecFileNames;
2224   for (int i = 0; i < files.size(); i++) {
2225     vecFileNames.push_back(files[i].toStdString());
2226   }
2227   AddFusionImage(index,vecFileNames,vvImageReader::IMAGE);
2228 }
2229 //------------------------------------------------------------------------------
2230
2231 //------------------------------------------------------------------------------
2232 void vvMainWindow::ResetTransformationToIdentity()
2233 {
2234   std::string actorType = DataTree->selectedItems()[0]->data(1,Qt::UserRole).toString().toStdString();
2235   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2236   mSlicerManagers[index]->ResetTransformationToIdentity(actorType);
2237   ImageInfoChanged();
2238 }
2239 //------------------------------------------------------------------------------
2240
2241 //------------------------------------------------------------------------------
2242 void vvMainWindow::AddFusionImage(int index, std::vector<std::string> fileNames, vvImageReader::LoadedImageType type)
2243 {
2244   QString file(fileNames[0].c_str());
2245   if (QFile::exists(file))
2246   {
2247     mInputPathName = itksys::SystemTools::GetFilenamePath(file.toStdString()).c_str();
2248     itk::ImageIOBase::Pointer reader = itk::ImageIOFactory::CreateImageIO(
2249       file.toStdString().c_str(), itk::ImageIOFactory::ReadMode);
2250     reader->SetFileName(fileNames[0].c_str());
2251     reader->ReadImageInformation();
2252     std::string component = reader->GetComponentTypeAsString(reader->GetComponentType());
2253     int dimension = reader->GetNumberOfDimensions();
2254     QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
2255     vvProgressDialog progress("Opening fusion");
2256     qApp->processEvents();
2257
2258     std::string filename = itksys::SystemTools::GetFilenameWithoutExtension(file.toStdString()).c_str();
2259     if (mSlicerManagers[index]->SetFusion(fileNames,dimension, component,type)) {
2260       //create an item in the tree with good settings
2261       QTreeWidgetItem *item = new QTreeWidgetItem();
2262       item->setData(0,Qt::UserRole,file.toStdString().c_str());
2263       item->setData(1,Qt::UserRole,tr("fusion"));
2264       QFileInfo fileinfo(file); //Do not show the path
2265           item->setData(COLUMN_IMAGE_NAME,Qt::DisplayRole,fileinfo.fileName());
2266           item->setToolTip(COLUMN_IMAGE_NAME, mSlicerManagers[index]->GetListOfAbsoluteFilePathInOneString("fusion").c_str());
2267           qApp->processEvents();
2268 #if VTK_MAJOR_VERSION > 5
2269       for ( unsigned int i = 0; i < mSlicerManagers[index]->GetNumberOfSlicers(); i++)
2270         mSlicerManagers[index]->GetSlicer(i)->ForceUpdateDisplayExtent();
2271 #endif
2272       for (int j = 1; j <= 4; j++) {
2273         item->setData(j,Qt::CheckStateRole,DataTree->topLevelItem(index)->data(j,Qt::CheckStateRole));
2274       }
2275
2276       //Create the buttons for reload and close
2277       qApp->processEvents();
2278       QTreePushButton* cButton = new QTreePushButton;
2279       cButton->setItem(item);
2280       cButton->setColumn(COLUMN_CLOSE_IMAGE);
2281       cButton->setToolTip(tr("close image"));
2282       cButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/exit.png")));
2283       connect(cButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
2284         this,SLOT(CloseImage(QTreeWidgetItem*, int)));
2285
2286       QTreePushButton* rButton = new QTreePushButton;
2287       rButton->setItem(item);
2288       rButton->setColumn(COLUMN_RELOAD_IMAGE);
2289       rButton->setToolTip(tr("reload image"));
2290       rButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/rotateright.png")));
2291       connect(rButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
2292         this,SLOT(ReloadImage(QTreeWidgetItem*, int)));
2293
2294       DataTree->topLevelItem(index)->setExpanded(1);
2295       DataTree->topLevelItem(index)->addChild(item);
2296       DataTree->setItemWidget(item, COLUMN_CLOSE_IMAGE, cButton);
2297       DataTree->setItemWidget(item, COLUMN_RELOAD_IMAGE, rButton);
2298
2299       //set the id of the image
2300       QString id = DataTree->topLevelItem(index)->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString();
2301       item->setData(COLUMN_IMAGE_NAME,Qt::UserRole,id.toStdString().c_str());
2302       UpdateTree();
2303       qApp->processEvents();
2304       ImageInfoChanged();
2305       QApplication::restoreOverrideCursor();
2306
2307       // Update the display to update, e.g., the sliders
2308       for(int i=0; i<4; i++)
2309         DisplaySliders(index, i);
2310     } else {
2311       QApplication::restoreOverrideCursor();
2312       QString error = "Cannot import the new image.\n";
2313       error += mSlicerManagers[index]->GetLastError().c_str();
2314       QMessageBox::information(this,tr("Problem reading image !"),error);
2315     }
2316     WindowLevelChanged();
2317   }
2318   else
2319     QMessageBox::information(this,tr("Problem reading Fusion !"),"File doesn't exist!");
2320 }
2321 //------------------------------------------------------------------------------
2322 //------------------------------------------------------------------------------
2323 void vvMainWindow::AddLandmarks(int index, std::vector<std::string> files)
2324 {
2325     if (!landmarksPanel->LoadFromFile(files))
2326       QMessageBox::information(this,tr("Problem reading Landmarks !"),"File doesn't exist!");
2327
2328     landmarksPanel->SetCurrentPath(mInputPathName.toStdString());
2329     landmarksPanel->SetCurrentImage(mSlicerManagers[index]->GetFileName().c_str());
2330 }
2331
2332 //------------------------------------------------------------------------------
2333 void vvMainWindow::OpenField()
2334 {
2335   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2336
2337   if (!(CheckAddedImage(index, "vector")))
2338     return;
2339
2340   QString Extensions = "Images ( *.mhd *.mha *.vf *.nii *.nrrd *.nhdr)";
2341   // Extensions += ";;Images ( *.mha)";
2342   // Extensions += ";;VF Images ( *.vf)";
2343   // Extensions += ";;nii Images ( *.nii)";
2344   // Extensions += ";;nrrd Images ( *.nrrd)";
2345   // Extensions += ";;nhdr Images ( *.nhdr)";
2346   Extensions += ";;All Files (*)";
2347   QString file = QFileDialog::getOpenFileName(this,tr("Load deformation field"),mInputPathName,Extensions);
2348   if (!file.isEmpty())
2349     AddField(file,index);
2350 }
2351 //------------------------------------------------------------------------------
2352
2353
2354 //------------------------------------------------------------------------------
2355 void vvMainWindow::AddFieldEntry(QString filename,int index,bool from_disk)
2356 {
2357   //create an item in the tree with good settings
2358   QTreeWidgetItem *item = new QTreeWidgetItem();
2359   item->setData(0,Qt::UserRole,filename.toStdString().c_str());
2360   item->setData(1,Qt::UserRole,tr("vector"));
2361   QFileInfo fileinfo(filename); //Do not show the path
2362   item->setData(COLUMN_IMAGE_NAME,Qt::DisplayRole,fileinfo.fileName());
2363   item->setToolTip(COLUMN_IMAGE_NAME, mSlicerManagers[index]->GetListOfAbsoluteFilePathInOneString("vector").c_str());
2364   qApp->processEvents();
2365
2366   for (int j = 1; j <= 4; j++) {
2367     item->setData(j,Qt::CheckStateRole,DataTree->topLevelItem(index)->data(j,Qt::CheckStateRole));
2368   }
2369
2370   //Create the buttons for reload and close
2371   qApp->processEvents();
2372   QTreePushButton* cButton = new QTreePushButton;
2373   cButton->setItem(item);
2374   cButton->setColumn(COLUMN_CLOSE_IMAGE);
2375   cButton->setToolTip(tr("close vector field"));
2376   cButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/exit.png")));
2377   connect(cButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
2378     this,SLOT(CloseImage(QTreeWidgetItem*, int)));
2379
2380   QTreePushButton* rButton = new QTreePushButton;
2381   rButton->setItem(item);
2382   rButton->setColumn(COLUMN_RELOAD_IMAGE);
2383   rButton->setToolTip(tr("reload vector field"));
2384   rButton->setEnabled(from_disk);
2385   rButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/rotateright.png")));
2386   connect(rButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
2387     this,SLOT(ReloadImage(QTreeWidgetItem*, int)));
2388
2389   DataTree->topLevelItem(index)->setExpanded(1);
2390   DataTree->topLevelItem(index)->addChild(item);
2391   DataTree->setItemWidget(item, COLUMN_RELOAD_IMAGE, rButton);
2392   DataTree->setItemWidget(item, COLUMN_CLOSE_IMAGE, cButton);
2393
2394   //set the id of the image
2395   QString id = DataTree->topLevelItem(index)->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString();
2396   item->setData(COLUMN_IMAGE_NAME,Qt::UserRole,id.toStdString().c_str());
2397   UpdateTree();
2398   qApp->processEvents();
2399   ImageInfoChanged();
2400   QApplication::restoreOverrideCursor();
2401 }
2402 //------------------------------------------------------------------------------
2403
2404
2405 //------------------------------------------------------------------------------
2406 void vvMainWindow::AddField(vvImage::Pointer vf,QString file,int index)
2407 {
2408   QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
2409   vvSlicerManager* imageManager = mSlicerManagers[index];
2410   if (imageManager->SetVF(vf,file.toStdString())) {
2411     AddFieldEntry(file,index,false);
2412 #if VTK_MAJOR_VERSION > 5
2413       for ( unsigned int i = 0; i < mSlicerManagers[index]->GetNumberOfSlicers(); i++)
2414         mSlicerManagers[index]->GetSlicer(i)->ForceUpdateDisplayExtent();
2415 #endif
2416   } else {
2417     QString error = "Cannot import the vector field for this image.\n";
2418     error += imageManager->GetLastError().c_str();
2419     QMessageBox::information(this,tr("Problem reading VF !"),error);
2420   }
2421   QApplication::restoreOverrideCursor();
2422 }
2423 //------------------------------------------------------------------------------
2424
2425
2426 //------------------------------------------------------------------------------
2427 void vvMainWindow::AddField(QString file,int index)
2428 {
2429   if (QFile::exists(file)) {
2430     mInputPathName = itksys::SystemTools::GetFilenamePath(file.toStdString()).c_str();
2431
2432     //init the progress events
2433     QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
2434     vvProgressDialog progress("Opening " + file.toStdString());
2435     qApp->processEvents();
2436
2437     //read the vector and put it in the current mSlicerManager
2438     vvSlicerManager* imageManager = mSlicerManagers[index];
2439     qApp->processEvents();
2440
2441     std::string filename = itksys::SystemTools::GetFilenameWithoutExtension(file.toStdString()).c_str();
2442     if (imageManager->SetVF(file.toStdString())) {
2443       imageManager->Render();
2444       AddFieldEntry(file,index,true);
2445     } else {
2446       QApplication::restoreOverrideCursor();
2447       QString error = "Cannot import the vector field for this image.\n";
2448       error += imageManager->GetLastError().c_str();
2449       QMessageBox::information(this,tr("Problem reading VF !"),error);
2450     }
2451   } else
2452     QMessageBox::information(this,tr("Problem reading VF !"),"File doesn't exist!");
2453
2454 }
2455 //------------------------------------------------------------------------------
2456
2457
2458 //------------------------------------------------------------------------------
2459 void vvMainWindow::SetVFProperty(int subsampling, int scale, int log, int width, double r, double g, double b)
2460 {
2461   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2462   if (mSlicerManagers[index]->GetSlicer(0)->GetVF()) {
2463     for (int i = 0; i < 4; i++) {
2464       mSlicerManagers[index]->GetSlicer(i)->SetVFSubSampling(subsampling);
2465       mSlicerManagers[index]->GetSlicer(i)->SetVFScale(scale);
2466       mSlicerManagers[index]->GetSlicer(i)->SetVFWidth(width);
2467       mSlicerManagers[index]->GetSlicer(i)->SetVFColor(r,g,b);
2468       if (log > 0)
2469         mSlicerManagers[index]->GetSlicer(i)->SetVFLog(1);
2470       else
2471         mSlicerManagers[index]->GetSlicer(i)->SetVFLog(0);
2472     }
2473   }
2474 }
2475 //------------------------------------------------------------------------------
2476
2477
2478 //------------------------------------------------------------------------------
2479 void vvMainWindow::SetOverlayProperty(int color, int linked, double window, double level)
2480 {
2481   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2482   if (mSlicerManagers[index]->GetSlicer(0)->GetOverlay()) {
2483     mSlicerManagers[index]->SetOverlayColor(color);
2484     mSlicerManagers[index]->SetColorMap(0);
2485     mSlicerManagers[index]->SetLinkOverlayWindowLevel(linked);
2486     mSlicerManagers[index]->SetOverlayColorWindow(window);
2487     mSlicerManagers[index]->SetOverlayColorLevel(level);
2488     mSlicerManagers[index]->Render();
2489   }
2490 }
2491 //------------------------------------------------------------------------------
2492
2493 //------------------------------------------------------------------------------
2494 void vvMainWindow::SetFusionProperty(int opacity, int thresOpacity, int colormap,double window, double level, bool showLegend)
2495 {
2496   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2497   if (mSlicerManagers[index]->GetSlicer(0)->GetFusion()) {
2498     mSlicerManagers[index]->SetFusionColorMap(colormap);
2499     mSlicerManagers[index]->SetFusionOpacity(opacity);
2500     mSlicerManagers[index]->SetFusionThresholdOpacity(thresOpacity);
2501     mSlicerManagers[index]->SetFusionWindow(window);
2502     mSlicerManagers[index]->SetFusionLevel(level);
2503     mSlicerManagers[index]->SetFusionShowLegend(showLegend);
2504     mSlicerManagers[index]->SetColorMap(0);
2505     mSlicerManagers[index]->Render();
2506   }
2507 }
2508 //------------------------------------------------------------------------------
2509
2510
2511 //------------------------------------------------------------------------------
2512 void vvMainWindow::SelectFusionSequence()
2513 {
2514   //get the index of the slicer manager of the main sequence (CT)
2515   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2516
2517   if (!(CheckAddedImage(index, "fusion")) || !(CheckAddedImage(index, "fusionSequence")))
2518     return;
2519
2520   QString Extensions = EXTENSIONS;
2521   Extensions += ";;All Files (*)";
2522   QStringList files = QFileDialog::getOpenFileNames(this,tr("Load Overlay image sequence"),mInputPathName,Extensions);
2523   if (files.isEmpty())
2524     return;
2525
2526   std::vector<std::string> vecFileNames;
2527   for (int i = 0; i < files.size(); i++) {
2528     vecFileNames.push_back(files[i].toStdString());
2529   }
2530
2531   //associate the secondary sequence (US) to the main one
2532   AddFusionSequence(index,vecFileNames,vvImageReader::MERGEDWITHTIME);
2533 }
2534 //------------------------------------------------------------------------------
2535
2536
2537 //------------------------------------------------------------------------------
2538 void vvMainWindow::SelectFusionSequenceCorrespondances()
2539 {
2540   //make sure the index is right?
2541   //in the end, I should attach the temporal data to the right sequence!
2542   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2543   //in case the other sequence got selected, make sure we select the primary sequence
2544   if ( (!mSlicerManagers[index]->GetSlicer(0)->GetFusion()) && mSlicerManagers[index]->GetFusionSequenceIndexOfLinkedManager()>=0 ) {
2545     index = mSlicerManagers[index]->GetFusionSequenceIndexOfLinkedManager();
2546   }
2547
2548   //open a dialog box to find a file
2549   //QString Extensions = EXTENSIONS;
2550   QString Extensions = ";;All Files (*)";
2551   QString fileName = QFileDialog::getOpenFileName(this,tr("Load respiratory signal for fused sequence"),mInputPathName,Extensions);
2552   if (fileName.isNull())
2553     return;
2554
2555   //read it as a vector of values
2556   vnl_vector<double> tmpVect;
2557
2558   std::ifstream file;
2559   file.open(fileName.toStdString().c_str());
2560   tmpVect.read_ascii(file);
2561   file.close();
2562
2563   //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
2564   bool signalOK = true;
2565   unsigned nbFrameMain = mSlicerManagers[index]->GetImage()->GetTransform().size();
2566   unsigned nbFrameSecondary = mSlicerManagers[index]->GetFusionSequenceNbFrames();
2567   std::cout<<"nbFrameMain = "<<nbFrameMain<<", nbFrameSecondary= "<<nbFrameSecondary<<", signal size: "<<tmpVect.size()<<std::endl;
2568   std::vector<unsigned> temporalCorrespondances;
2569   if ( tmpVect.size() == nbFrameMain + nbFrameSecondary ) {
2570     for (unsigned i=0 ; i<tmpVect.size() ; i++) {
2571       if (i<nbFrameMain) { //first part of the file: i -> index in secondary seq.
2572         if ( tmpVect(i)<nbFrameSecondary ) temporalCorrespondances.push_back(tmpVect(i));
2573         else { signalOK=false; break; } //pointing outside the secondary sequence...
2574       }
2575       else { //first part of the file -> index in secondary seq.
2576         if ( tmpVect(i)<nbFrameMain ) temporalCorrespondances.push_back(tmpVect(i));
2577         else { signalOK=false; break; } //pointing outside the secondary sequence...
2578       }
2579     }
2580   }
2581   else {signalOK=false;}
2582   if (!signalOK) {//else, send a message to signal the failure...
2583     QString error = "The provided temporal correspondances is invalid - check tooltip.\n";
2584     error += "Ignoring file: " + fileName;
2585     QMessageBox::information(this,tr("Problem adding temporal correspondances!"),error);
2586     return;
2587   }
2588   else {
2589     //for convenience, associate this sequence to both the current slicer manager, and to the linked one
2590     mSlicerManagers[index]->SetFusionSequenceCorrespondances(temporalCorrespondances);
2591     mSlicerManagers[ mSlicerManagers[index]->GetFusionSequenceIndexOfLinkedManager() ]->SetFusionSequenceCorrespondances(temporalCorrespondances);
2592     overlayPanel->enableFusionSequenceTemporalSync();
2593   }
2594
2595 }
2596 //------------------------------------------------------------------------------
2597
2598
2599 //------------------------------------------------------------------------------
2600 //when this function is called index is the slicer manager index corresponding to the main sequence (CT)
2601 //the files behind fileNames points to the data for the secondary sequence
2602 void vvMainWindow::AddFusionSequence(int index, std::vector<std::string> fileNames, vvImageReader::LoadedImageType type)
2603 {
2604   QString file(fileNames[0].c_str());
2605   if (QFile::exists(file))
2606   {
2607     mInputPathName = itksys::SystemTools::GetFilenamePath(file.toStdString()).c_str();
2608     itk::ImageIOBase::Pointer reader = itk::ImageIOFactory::CreateImageIO(
2609       file.toStdString().c_str(), itk::ImageIOFactory::ReadMode);
2610     std::sort (fileNames.begin(), fileNames.end());//make sure the files are sorted.
2611     reader->SetFileName(fileNames[0].c_str());
2612     reader->ReadImageInformation();
2613     std::string component = reader->GetComponentTypeAsString(reader->GetComponentType());
2614     int dimension = reader->GetNumberOfDimensions();
2615     QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
2616     vvProgressDialog progress("Opening " + file.toStdString());
2617     qApp->processEvents();
2618
2619     std::string filename = itksys::SystemTools::GetFilenameWithoutExtension(file.toStdString()).c_str();
2620
2621     if (mSlicerManagers[index]->SetFusionSequence(fileNames,dimension, component,type)) {
2622       //create an item in the tree with good settings
2623       QTreeWidgetItem *item = new QTreeWidgetItem();
2624       item->setData(0,Qt::UserRole,file.toStdString().c_str());
2625       item->setData(1,Qt::UserRole,tr("fusionSequence"));
2626
2627       QFileInfo fileinfo(file); //Do not show the path
2628       item->setData(COLUMN_IMAGE_NAME,Qt::DisplayRole,fileinfo.fileName());
2629       item->setToolTip(COLUMN_IMAGE_NAME, mSlicerManagers[index]->GetListOfAbsoluteFilePathInOneString("fusionSequence").c_str());
2630       qApp->processEvents();
2631 #if VTK_MAJOR_VERSION > 5
2632       for ( unsigned int i = 0; i < mSlicerManagers[index]->GetNumberOfSlicers(); i++)
2633         mSlicerManagers[index]->GetSlicer(i)->ForceUpdateDisplayExtent();
2634 #endif
2635       for (int j = 1; j <= 4; j++) {
2636         item->setData(j,Qt::CheckStateRole,DataTree->topLevelItem(index)->data(j,Qt::CheckStateRole));
2637       }
2638
2639       //Create the buttons for reload and close
2640       qApp->processEvents();
2641       QTreePushButton* cButton = new QTreePushButton;
2642       cButton->setItem(item);
2643       cButton->setColumn(COLUMN_CLOSE_IMAGE);
2644       cButton->setToolTip(tr("close image"));
2645       cButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/exit.png")));
2646       connect(cButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
2647         this,SLOT(CloseImage(QTreeWidgetItem*, int)));
2648
2649       QTreePushButton* rButton = new QTreePushButton;
2650       rButton->setItem(item);
2651       rButton->setColumn(COLUMN_RELOAD_IMAGE);
2652       rButton->setToolTip(tr("reload image"));
2653       rButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/rotateright.png")));
2654       connect(rButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
2655         this,SLOT(ReloadImage(QTreeWidgetItem*, int)));
2656
2657       DataTree->topLevelItem(index)->setExpanded(1);
2658       DataTree->topLevelItem(index)->addChild(item);
2659       DataTree->setItemWidget(item, COLUMN_CLOSE_IMAGE, cButton);
2660       DataTree->setItemWidget(item, COLUMN_RELOAD_IMAGE, rButton);
2661
2662       //store the original transform matrix
2663       int indexParent = GetSlicerIndexFromItem( DataTree->topLevelItem(index) );
2664       mSlicerManagers[indexParent]->SetFusionSequenceMainTransformMatrix( mSlicerManagers[indexParent]->GetSlicer(0)->GetImage()->GetTransform()[0]->GetMatrix() );
2665
2666       //set the id of the image
2667       QString id = DataTree->topLevelItem(index)->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString();
2668       item->setData(COLUMN_IMAGE_NAME,Qt::UserRole,id.toStdString().c_str());
2669       UpdateTree();
2670       qApp->processEvents();
2671
2672       //ImageInfoChanged();
2673
2674       QApplication::restoreOverrideCursor();
2675       // Update the display to update, e.g., the sliders
2676       for(int i=0; i<4; i++)
2677         DisplaySliders(index, i);
2678
2679
2680       //This loads the secondary sequence (US) as an independent sequence
2681       LoadImages(fileNames, type);
2682       //reset the transforms to identity
2683       //FIX -- and set the thickness of the US slices to a large value (necessary for visualization purposes...)
2684       double sp_x, sp_y, sp_z;
2685       mSlicerManagers[indexParent]->GetImage()->GetVTKImages()[0]->GetSpacing(sp_x, sp_y, sp_z);
2686       sp_z = std::max(sp_x, std::max(sp_y, sp_z)) + 0.5; //
2687       for (unsigned i=0 ; i<mSlicerManagers.back()->GetImage()->GetTransform().size() ; i++) {
2688         sp_x = mSlicerManagers.back()->GetImage()->GetVTKImages()[i]->GetSpacing()[0];
2689         sp_y = mSlicerManagers.back()->GetImage()->GetVTKImages()[i]->GetSpacing()[1];
2690         mSlicerManagers.back()->GetImage()->GetVTKImages()[i]->SetSpacing( sp_x, sp_y, sp_z);
2691         mSlicerManagers.back()->GetImage()->GetTransform()[i]->Identity();
2692         mSlicerManagers.back()->GetImage()->GetTransform()[i]->Update();
2693       }
2694
2695       //automatically link both images...
2696       AddLink(mSlicerManagers[indexParent]->GetId().c_str(), mSlicerManagers.back()->GetId().c_str(), false);
2697
2698       //tie the main and secondary sequences by raising flags and informing each another of their respective SlicerManager indices
2699       mSlicerManagers[indexParent]->SetFusionSequenceIndexOfLinkedManager(mSlicerManagers.size()-1);
2700       mSlicerManagers[indexParent]->SetFusionSequenceInvolvmentCode(0); //main sequence
2701       mSlicerManagers.back()->SetFusionSequenceIndexOfLinkedManager(indexParent);
2702       mSlicerManagers.back()->SetFusionSequenceInvolvmentCode(1); //secondary sequence
2703       for (unsigned i=0 ; i<4 ; i++) {
2704         mSlicerManagers.back()->GetSlicer(i)->SetFusionSequenceCode(1); //flag the slicers of the secondary sequence
2705       }
2706
2707     } else {
2708       QApplication::restoreOverrideCursor();
2709       QString error = "Cannot import the new image.\n";
2710       error += mSlicerManagers[index]->GetLastError().c_str();
2711       QMessageBox::information(this,tr("Problem reading image !"),error);
2712     }
2713     WindowLevelChanged();
2714     ImageInfoChanged(); //this internally calls WindowLevelChanged...
2715   }
2716   else {
2717     QMessageBox::information(this,tr("Problem reading fusion sequence !"),"File doesn't exist!");
2718     return;
2719   }
2720
2721 }
2722 //------------------------------------------------------------------------------
2723
2724
2725 //------------------------------------------------------------------------------
2726 //fusionSequenceFrameIndex and fusionSequenceNbFrames are relative to the secondary sequence (US)
2727 void vvMainWindow::SetFusionSequenceProperty(int fusionSequenceFrameIndex, bool spatialSyncFlag, unsigned int fusionSequenceNbFrames, bool temporalSyncFlag)
2728 {
2729   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2730
2731   if (!mSlicerManagers[index]->IsInvolvedInFusionSequence()) return;
2732
2733   //check if the focus moved to the linked sequence, and in this case, select the master sequence instead
2734   if (!mSlicerManagers[index]->IsMainSequenceOfFusionSequence()) {
2735     index = mSlicerManagers[index]->GetFusionSequenceIndexOfLinkedManager();
2736   }
2737   int secondaryIndex = mSlicerManagers[index]->GetFusionSequenceIndexOfLinkedManager();
2738   if (secondaryIndex==-1) return; //this should never happen
2739   if ( (!mSlicerManagers[index]->IsMainSequenceOfFusionSequence()) ||
2740     (!mSlicerManagers[secondaryIndex]->IsSecondarySequenceOfFusionSequence()) )
2741   {return;} //this should never happen, raise an exception?
2742
2743   if (mSlicerManagers[index]->GetSlicer(0)->GetFusion()) {
2744
2745     //First, if the spatialSync button is unchecked, then reposition the parent sequence (CT) in its original coordinate frame
2746     if ( (!spatialSyncFlag) && (mSlicerManagers[index]->GetFusionSequenceSpatialSyncFlag()) ) {
2747       for ( unsigned i=0 ; i<mSlicerManagers[index]->GetSlicer(0)->GetImage()->GetTransform().size() ; i++ ) {
2748         mSlicerManagers[index]->GetSlicer(0)->GetImage()->GetTransform()[i]->SetMatrix( mSlicerManagers[index]->GetFusionSequenceMainTransformMatrix() );
2749         mSlicerManagers[index]->GetSlicer(0)->GetImage()->GetTransform()[i]->Update();
2750       }
2751
2752       for (int i=0; i<mSlicerManagers[index]->GetNumberOfSlicers(); i++) {
2753         mSlicerManagers[index]->GetSlicer(i)->ForceUpdateDisplayExtent();
2754         mSlicerManagers[index]->GetSlicer(i)->Render();
2755       }
2756     }
2757
2758     //then, update the property values in the slicer manager
2759     mSlicerManagers[index]->SetFusionSequenceLength(fusionSequenceNbFrames);
2760     mSlicerManagers[index]->SetFusionSequenceSpatialSyncFlag(spatialSyncFlag);
2761     mSlicerManagers[index]->SetFusionSequenceTemporalSyncFlag(temporalSyncFlag);
2762     mSlicerManagers[index]->SetFusionSequenceFrameIndex(fusionSequenceFrameIndex);
2763
2764     //select the right frame of the US sequence
2765     mSlicerManagers[index]->SetFusionSequenceTSlice(fusionSequenceFrameIndex); //here, I should only update the overlayed sequence
2766     mSlicerManagers[secondaryIndex]->SetTSlice(fusionSequenceFrameIndex, false); //this should update the secondary sequence (individual version)
2767
2768     //update the horizontal sliders of the main window
2769     overlayPanel->updateFusionSequenceSliderValueFromWindow(fusionSequenceFrameIndex, false);
2770
2771     if (spatialSyncFlag) { //reslice the CT
2772
2773       if (temporalSyncFlag) { //do the temporal synchronisation
2774         int mainSequenceFrameIndex=0;
2775         //estimate the TSlice to set to the CT
2776         unsigned nbFramesMain = mSlicerManagers[index]->GetImage()->GetTransform().size();
2777         mainSequenceFrameIndex = mSlicerManagers[index]->GetFusionSequenceCorrespondances()[ nbFramesMain + fusionSequenceFrameIndex];
2778         //and set it!
2779         mSlicerManagers[index]->SetTSlice(mainSequenceFrameIndex, false);
2780         //warning, there is a loopback, and modification of the TSlice in main sequence forces an update of the TSlice in secondary, etc...
2781       }
2782
2783
2784       //Set the transform matrix of the parent sequence (typically CT / 4DCT)
2785       vtkSmartPointer<vtkMatrix4x4> tmpMat = vtkSmartPointer<vtkMatrix4x4>::New();
2786       vtkMatrix4x4::Invert( mSlicerManagers[index]->GetFusionSequenceInitialTransformMatrixAtFrame(fusionSequenceFrameIndex), tmpMat );
2787       for ( unsigned i=0 ; i<mSlicerManagers[index]->GetSlicer(0)->GetImage()->GetTransform().size() ; i++ ) {
2788         mSlicerManagers[index]->GetSlicer(0)->GetImage()->GetTransform()[i]->SetMatrix( mSlicerManagers[index]->GetFusionSequenceMainTransformMatrix() );
2789         mSlicerManagers[index]->GetSlicer(0)->GetImage()->GetTransform()[i]->PreMultiply();
2790         mSlicerManagers[index]->GetSlicer(0)->GetImage()->GetTransform()[i]->Concatenate( tmpMat );
2791         mSlicerManagers[index]->GetSlicer(0)->GetImage()->GetTransform()[i]->Update();
2792       }
2793
2794       for (int i=0; i<mSlicerManagers[index]->GetNumberOfSlicers(); i++) {
2795         mSlicerManagers[index]->GetSlicer(i)->ForceUpdateDisplayExtent();
2796         mSlicerManagers[index]->GetSlicer(i)->Render();
2797       }
2798
2799     }
2800
2801   }
2802 }
2803 //------------------------------------------------------------------------------
2804
2805
2806 //------------------------------------------------------------------------------
2807 void vvMainWindow::SaveAs()
2808 {
2809   if (DataTree->selectedItems()[0]->data(1,Qt::UserRole).toString() == "vector") {
2810     QMessageBox::warning(this,tr("Unsupported type"),tr("Sorry, saving a vector field is unsupported for the moment"));
2811     return;
2812   }
2813
2814   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2815   int dimension = mSlicerManagers[index]->GetDimension();
2816   QStringList OutputListeFormat;
2817   OutputListeFormat.clear();
2818   if (dimension == 1) {
2819     OutputListeFormat.push_back(".mhd");
2820     OutputListeFormat.push_back(".mha");
2821   }
2822   if (dimension == 2) {
2823     OutputListeFormat.push_back(".bmp");
2824     OutputListeFormat.push_back(".png");
2825     OutputListeFormat.push_back(".jpeg");
2826     OutputListeFormat.push_back(".tif");
2827     OutputListeFormat.push_back(".mhd");
2828     OutputListeFormat.push_back(".mha");
2829     OutputListeFormat.push_back(".hdr");
2830     OutputListeFormat.push_back(".vox");
2831   } else if (dimension == 3) {
2832     OutputListeFormat.push_back(".mhd");
2833     OutputListeFormat.push_back(".mha");
2834     OutputListeFormat.push_back(".nii");
2835     OutputListeFormat.push_back(".nrrd");
2836     OutputListeFormat.push_back(".nhdr");
2837     OutputListeFormat.push_back(".hdr");
2838     OutputListeFormat.push_back(".vox");
2839   } else if (dimension == 4) {
2840     OutputListeFormat.push_back(".mhd");
2841     OutputListeFormat.push_back(".mha");
2842     OutputListeFormat.push_back(".nii");
2843     OutputListeFormat.push_back(".nrrd");
2844     OutputListeFormat.push_back(".nhdr");
2845   }
2846   QString Extensions = "AllFiles(*.*)";
2847   for (int i = 0; i < OutputListeFormat.count(); i++) {
2848     Extensions += ";;Images ( *";
2849     Extensions += OutputListeFormat[i];
2850     Extensions += ")";
2851   }
2852   QString fileName = QFileDialog::getSaveFileName(this,
2853     tr("Save As"),
2854     mSlicerManagers[index]->GetFileName().c_str(),
2855     Extensions);
2856   if (!fileName.isEmpty()) {
2857     std::string fileformat = itksys::SystemTools::GetFilenameLastExtension(fileName.toStdString());
2858     if (OutputListeFormat.contains(
2859       fileformat.c_str())) {
2860         QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
2861         std::string action = "Saving";
2862         vvProgressDialog progress("Saving "+fileName.toStdString());
2863         qApp->processEvents();
2864         vvImageWriter::Pointer writer = vvImageWriter::New();
2865         writer->SetOutputFileName(fileName.toStdString());
2866         writer->SetInput(mSlicerManagers[index]->GetImage());
2867
2868         // Check on transform and prompt user
2869         writer->SetSaveTransform(false);
2870         bool bId = true;
2871         for(int i=0; i<4; i++)
2872           for(int j=0; j<4; j++) {
2873             // TODO SR and BP: check on the list of transforms and not the first only
2874             double elt = mSlicerManagers[index]->GetImage()->GetTransform()[0]->GetMatrix()->GetElement(i,j);
2875             if(i==j && elt!=1.)
2876               bId = false;
2877             if(i!=j && elt!=0.)
2878               bId = false;
2879           }
2880           if( !bId ) {
2881             QString warning = "The image has an associated linear transform. Do you want to save it along?";
2882             QMessageBox msgBox(QMessageBox::Warning, tr("Save transform"), warning, 0, this);
2883             msgBox.addButton(tr("Yes"), QMessageBox::AcceptRole);
2884             msgBox.addButton(tr("No"), QMessageBox::RejectRole);
2885             if (msgBox.exec() == QMessageBox::AcceptRole)
2886               writer->SetSaveTransform(true);
2887           }
2888
2889           writer->Update();
2890           QApplication::restoreOverrideCursor();
2891           if (writer->GetLastError().size()) {
2892             QString error = "Saving did not succeed\n";
2893             error += writer->GetLastError().c_str();
2894             QMessageBox::information(this,tr("Saving Problem"),error);
2895             SaveAs();
2896           }
2897     } else {
2898       QString error = fileformat.c_str();
2899       if (error.isEmpty())
2900         error += "no file format specified !";
2901       else
2902         error += " format unknown !!!\n";
2903       QMessageBox::information(this,tr("Saving Problem"),error);
2904       SaveAs();
2905     }
2906   }
2907 }
2908 //------------------------------------------------------------------------------
2909
2910 //------------------------------------------------------------------------------
2911 void vvMainWindow::SaveCurrentState()
2912 {
2913   QString Extensions = "XML Files(*.xml)";
2914   QString fileName = QFileDialog::getSaveFileName(this,
2915     tr("Save Current Window State"),
2916     "",
2917     Extensions);
2918
2919   SaveCurrentStateAs(fileName.toStdString());
2920 }
2921 //------------------------------------------------------------------------------
2922
2923 //------------------------------------------------------------------------------
2924 void vvMainWindow::SaveCurrentStateAs(const std::string& stateFile)
2925 {
2926   vvSaveState save_state;
2927   save_state.Run(this, stateFile);
2928 }
2929
2930 //------------------------------------------------------------------------------
2931 void vvMainWindow::ReadSavedState()
2932 {
2933   QString Extensions = "XML Files(*.xml)";
2934   QString fileName = QFileDialog::getOpenFileName(this,
2935     tr("Load Window State"),
2936     "",
2937     Extensions);
2938
2939   ReadSavedStateFile(fileName.toStdString());
2940 }
2941 //------------------------------------------------------------------------------
2942
2943 //------------------------------------------------------------------------------
2944 void vvMainWindow::ReadSavedStateFile(const std::string& stateFile)
2945 {
2946   vvReadState read_state;
2947   read_state.Run(this, stateFile);
2948 }
2949 //------------------------------------------------------------------------------
2950
2951 //------------------------------------------------------------------------------
2952 void vvMainWindow::LinkAllImages()
2953 {
2954   linkPanel->linkAll();
2955 }
2956
2957 //------------------------------------------------------------------------------
2958 void vvMainWindow::AddLink(QString image1,QString image2,bool fromPanel)
2959 {
2960   if (!fromPanel) {
2961     // delegate to linkPanel if call came from elsewhere...
2962     linkPanel->addLinkFromIds(image1, image2);
2963     return;
2964   }
2965
2966   unsigned int sm1 = 0;
2967   unsigned int sm2 = 0;
2968
2969   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
2970     if (image1.toStdString() == mSlicerManagers[i]->GetId()) {
2971       mSlicerManagers[i]->AddLink(image2.toStdString());
2972       sm1 = i;
2973     }
2974     if (image2.toStdString() == mSlicerManagers[i]->GetId()) {
2975       mSlicerManagers[i]->AddLink(image1.toStdString());
2976       sm2 = i;
2977     }
2978   }
2979
2980   if (linkPanel->isLinkAll())   {
2981     emit UpdateLinkedNavigation(mSlicerManagers[sm1]->GetId(), mSlicerManagers[mCurrentPickedImageIndex], mSlicerManagers[mCurrentPickedImageIndex]->GetSlicer(0));
2982     emit UpdateLinkedNavigation(mSlicerManagers[sm2]->GetId(), mSlicerManagers[mCurrentPickedImageIndex], mSlicerManagers[mCurrentPickedImageIndex]->GetSlicer(0));
2983   } else {
2984     emit UpdateLinkedNavigation(mSlicerManagers[sm2]->GetId(), mSlicerManagers[sm1], mSlicerManagers[sm1]->GetSlicer(0));
2985   }
2986 }
2987
2988 //------------------------------------------------------------------------------
2989
2990
2991 //------------------------------------------------------------------------------
2992 void vvMainWindow::RemoveLink(QString image1,QString image2)
2993 {
2994   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
2995     if (image1.toStdString() == mSlicerManagers[i]->GetId()) {
2996       mSlicerManagers[i]->RemoveLink(image2.toStdString());
2997     }
2998     if (image2.toStdString() == mSlicerManagers[i]->GetId()) {
2999       mSlicerManagers[i]->RemoveLink(image1.toStdString());
3000     }
3001   }
3002 }
3003 //------------------------------------------------------------------------------
3004
3005 //------------------------------------------------------------------------------
3006 void vvMainWindow::ChangeImageWithIndexOffset(vvSlicerManager *sm, int slicer, int offset)
3007 {
3008   if(mSlicerManagers.size()==1)
3009     return;
3010
3011   int index = 0;
3012   while(sm != mSlicerManagers[index])
3013     index++;
3014   index = (index+offset+mSlicerManagers.size()) % mSlicerManagers.size();
3015
3016   QTreeWidgetItem* item = GetItemFromSlicerManager(mSlicerManagers[index]);
3017   item->setData(slicer+1,Qt::CheckStateRole,2);         //change checkbox
3018   CurrentImageChanged(mSlicerManagers[index]->GetId()); //select new image
3019   DisplayChanged(item,slicer+1);
3020 }
3021 //------------------------------------------------------------------------------
3022 void vvMainWindow::HorizontalSliderMoved(int value,int column, int slicer_index)
3023 {
3024   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
3025     if (DataTree->topLevelItem(i)->data(column,Qt::CheckStateRole).toInt() > 1) {
3026       //i is the SlicerManager that is in charge of this slicer.
3027       if (mSlicerManagers[i]->IsInvolvedInFusionSequence()) {
3028         //if the slicerManager is involved in a fusionSequence as the secondary sequence, then update the slider position in the overlay panel and everything accordingly
3029         if (mSlicerManagers[i]->IsSecondarySequenceOfFusionSequence()) {
3030           overlayPanel->updateFusionSequenceSliderValueFromWindow(value, true);
3031         }
3032         else { //if this is the primary sequence that has been modified
3033           if (mSlicerManagers[i]->GetFusionSequenceTemporalSyncFlag()) {
3034             //WARNING: for some obscure reason, there are problems when accessing mSlicerManagers[mSlicerManagers[i]->GetFusionSequenceIndexOfLinkedManager()]->GetFusionSequenceFrameIndex();
3035
3036             int estimatedValue=0;
3037             //estimate a corresponding time index for the secondary (US) sequence, and update it accordingly.
3038             estimatedValue = mSlicerManagers[i]->GetFusionSequenceCorrespondances()[ value ];
3039             //TODO: at the moment, there is a loop in TSlice modifications
3040             //modifying sequence 1 causes seq 2 to update, which in turns update seq1...
3041             //I disable control on seq1 at the moment.
3042             //overlayPanel->updateFusionSequenceSliderValueFromWindow(estimatedValue, true);
3043           }
3044         }
3045       }
3046
3047       for (int j = 0; j < 4; j++) {
3048         mSlicerManagers[i]->SetTSliceInSlicer(value,j);
3049       }
3050       mSlicerManagers[i]->GetSlicer(slicer_index)->Render();
3051       break;
3052     }
3053   }
3054 }
3055 //------------------------------------------------------------------------------
3056
3057
3058 //------------------------------------------------------------------------------
3059 void vvMainWindow::NOHorizontalSliderMoved()
3060 {
3061   // if (mCurrentTime == NOHorizontalSlider->value()) return;
3062   HorizontalSliderMoved(NOHorizontalSlider->value(),COLUMN_UL_VIEW,0);
3063   //  mCurrentTime = NOHorizontalSlider->value();
3064 }
3065 //------------------------------------------------------------------------------
3066
3067
3068 //------------------------------------------------------------------------------
3069 void vvMainWindow::NEHorizontalSliderMoved()
3070 {
3071   // if (mCurrentTime == NEHorizontalSlider->value()) return;
3072   HorizontalSliderMoved(NEHorizontalSlider->value(),COLUMN_UR_VIEW,1);
3073   //  mCurrentTime = NEHorizontalSlider->value();
3074 }
3075 //------------------------------------------------------------------------------
3076
3077
3078 //------------------------------------------------------------------------------
3079 void vvMainWindow::SOHorizontalSliderMoved()
3080 {
3081   // if (mCurrentTime == SOHorizontalSlider->value()) return;
3082   HorizontalSliderMoved(SOHorizontalSlider->value(),COLUMN_DL_VIEW,2);
3083   // mCurrentTime = SOHorizontalSlider->value();
3084 }
3085 //------------------------------------------------------------------------------
3086
3087
3088 //------------------------------------------------------------------------------
3089 void vvMainWindow::SEHorizontalSliderMoved()
3090 {
3091   // if (mCurrentTime == SEHorizontalSlider->value()) return;
3092   HorizontalSliderMoved(SEHorizontalSlider->value(),COLUMN_DR_VIEW,3);
3093   // mCurrentTime = SEHorizontalSlider->value();
3094 }
3095 //------------------------------------------------------------------------------
3096
3097 //------------------------------------------------------------------------------
3098 void vvMainWindow::NOVerticalSliderChanged()
3099 {
3100   static int value=-1;
3101   if (value == NOVerticalSlider->value()) return;
3102   else value = NOVerticalSlider->value();
3103   //  int value = NOVerticalSlider->value();
3104   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
3105     if (DataTree->topLevelItem(i)->data(COLUMN_UL_VIEW,Qt::CheckStateRole).toInt() > 1) {
3106       if (mSlicerManagers[i]->GetSlicer(0)->GetSlice() != value) {
3107         mSlicerManagers[i]->GetSlicer(0)->SetSlice(value);
3108         mSlicerManagers[i]->VerticalSliderHasChanged(0, value);
3109
3110         // If nor Update/Render -> slider not work
3111         // only render = ok navigation, but for contour Update needed but slower ?
3112
3113         mSlicerManagers[i]->UpdateSlice(0);  // <-- DS add this. Not too much update ? YES. but needed for ImageContour ...
3114         //mSlicerManagers[i]->GetSlicer(0)->Render(); // <-- DS add this, needed for contour, seems ok ? not too slow ?
3115       }
3116       break;
3117     }
3118   }
3119 }
3120 //------------------------------------------------------------------------------
3121
3122
3123 //------------------------------------------------------------------------------
3124 void vvMainWindow::NEVerticalSliderChanged()
3125 {
3126   static int value=-1;
3127   if (value == NEVerticalSlider->value()) return;
3128   else value = NEVerticalSlider->value();
3129   //  int value = NEVerticalSlider->value();
3130   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
3131     if (DataTree->topLevelItem(i)->data(COLUMN_UR_VIEW,Qt::CheckStateRole).toInt() > 1) {
3132       if (mSlicerManagers[i]->GetSlicer(1)->GetSlice() != value) {
3133         mSlicerManagers[i]->GetSlicer(1)->SetSlice(value);
3134         mSlicerManagers[i]->VerticalSliderHasChanged(1, value);
3135         mSlicerManagers[i]->UpdateSlice(1);
3136         //mSlicerManagers[i]->GetSlicer(1)->Render(); // <-- DS add this, needed for contour, seems ok ? not too slow ?
3137       }
3138       break;
3139     }
3140   }
3141 }
3142 //------------------------------------------------------------------------------
3143
3144
3145 //------------------------------------------------------------------------------
3146 void vvMainWindow::SOVerticalSliderChanged()
3147 {
3148   static int value=-1;
3149   if (value == SOVerticalSlider->value()) return;
3150   else value = SOVerticalSlider->value();
3151   //int value = SOVerticalSlider->value();
3152   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
3153     if (DataTree->topLevelItem(i)->data(COLUMN_DL_VIEW,Qt::CheckStateRole).toInt() > 1) {
3154       if (mSlicerManagers[i]->GetSlicer(2)->GetSlice() != value) {
3155         mSlicerManagers[i]->GetSlicer(2)->SetSlice(value);
3156         mSlicerManagers[i]->VerticalSliderHasChanged(2, value);
3157         mSlicerManagers[i]->UpdateSlice(2);
3158         //mSlicerManagers[i]->GetSlicer(2)->Render(); // <-- DS add this, needed for contour, seems ok ? not too slow ?
3159       }
3160       // else { DD("avoid SOVerticalSlider slicer update"); }
3161       break;
3162     }
3163   }
3164 }
3165 //------------------------------------------------------------------------------
3166
3167
3168 //------------------------------------------------------------------------------
3169 void vvMainWindow::SEVerticalSliderChanged()
3170 {
3171   static int value=-1;
3172   if (value == SEVerticalSlider->value()) return;
3173   else value = SEVerticalSlider->value();
3174   // int value = SEVerticalSlider->value();
3175   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
3176     if (DataTree->topLevelItem(i)->data(COLUMN_DR_VIEW,Qt::CheckStateRole).toInt() > 1) {
3177       if (mSlicerManagers[i]->GetSlicer(3)->GetSlice() != value) {
3178         mSlicerManagers[i]->GetSlicer(3)->SetSlice(value);
3179         mSlicerManagers[i]->VerticalSliderHasChanged(3, value);
3180         mSlicerManagers[i]->UpdateSlice(3);
3181         //mSlicerManagers[i]->GetSlicer(3)->Render(); // <-- DS add this, needed for contour, seems ok ? not too slow ?
3182       }
3183       break;
3184     }
3185   }
3186 }
3187 //------------------------------------------------------------------------------
3188
3189
3190 //------------------------------------------------------------------------------
3191 void vvMainWindow::UpdateSlice(int slicer, int slice)
3192 {
3193   // DD("vvMainWindow::UpdateSlice");
3194   //   DD(slicer);
3195   //   DD(slice);
3196   if (slicer == 0) {
3197     //    if (slice != NOVerticalSlider->value())
3198     NOVerticalSlider->setValue(slice);
3199   } else {
3200     if (slicer == 1)
3201       NEVerticalSlider->setValue(slice);
3202     else {
3203       if (slicer == 2)
3204         SOVerticalSlider->setValue(slice);
3205       else {
3206         if (slicer == 3)
3207           SEVerticalSlider->setValue(slice);
3208       }
3209     }
3210   }
3211   // DD("vvMainWindow:UpdateSlice END");
3212 }
3213 //------------------------------------------------------------------------------
3214
3215
3216 //------------------------------------------------------------------------------
3217 void vvMainWindow::UpdateTSlice(int slicer, int slice, int code)
3218 {
3219   //FusionSequence: the slider value should be updated for slicers which show the same sequence as requested
3220   bool doUpdate=false;
3221   if (code==-1) doUpdate=true;
3222   else {
3223     for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
3224       if (DataTree->topLevelItem(i)->data(slicer+1,Qt::CheckStateRole).toInt() > 1) {
3225         //i is the active SlicerManager
3226         if (mSlicerManagers[i]->GetFusionSequenceInvolvmentCode()==code) doUpdate=true;
3227         break;
3228       }
3229     }
3230   }
3231   if (!doUpdate) return;
3232
3233   switch (slicer) {
3234   case 0:
3235     if (NOHorizontalSlider->value()==slice) return;
3236     NOHorizontalSlider->setValue(slice);
3237     break;
3238   case 1:
3239     if (NEHorizontalSlider->value()==slice) return;
3240     NEHorizontalSlider->setValue(slice);
3241     break;
3242   case 2:
3243     if (SOHorizontalSlider->value()==slice) return;
3244     SOHorizontalSlider->setValue(slice);
3245     break;
3246   case 3:
3247     if (SEHorizontalSlider->value()==slice) return;
3248     SEHorizontalSlider->setValue(slice);
3249     break;
3250   }
3251 }
3252 //------------------------------------------------------------------------------
3253
3254
3255 //------------------------------------------------------------------------------
3256 void vvMainWindow::UpdateSliceRange(int slicer, int min, int max, int tmin, int tmax)
3257 {
3258   //int position = int((min+max)/2);
3259   int position = mSlicerManagers[mCurrentPickedImageIndex]->GetSlicer(slicer)->GetSlice();
3260   if (slicer == 0) {
3261     NOVerticalSlider->setRange(min,max);
3262     NOHorizontalSlider->setRange(tmin,tmax);
3263     NOVerticalSlider->setValue(position);
3264   } else if (slicer == 1) {
3265     NEVerticalSlider->setRange(min,max);
3266     NEHorizontalSlider->setRange(tmin,tmax);
3267     NEVerticalSlider->setValue(position);
3268   } else if (slicer == 2) {
3269     SOVerticalSlider->setRange(min,max);
3270     SOHorizontalSlider->setRange(tmin,tmax);
3271     SOVerticalSlider->setValue(position);
3272   } else if (slicer == 3) {
3273     SEVerticalSlider->setRange(min,max);
3274     SEHorizontalSlider->setRange(tmin,tmax);
3275     SEVerticalSlider->setValue(position);
3276   }
3277 }
3278 //------------------------------------------------------------------------------
3279
3280
3281 //------------------------------------------------------------------------------
3282 void vvMainWindow::SaveNOScreenshot()
3283 {
3284   SaveScreenshot(NOViewWidget);
3285 }
3286 //------------------------------------------------------------------------------
3287
3288
3289 //------------------------------------------------------------------------------
3290 void vvMainWindow::SaveNEScreenshot()
3291 {
3292   SaveScreenshot(NEViewWidget);
3293 }
3294 //------------------------------------------------------------------------------
3295
3296
3297 //------------------------------------------------------------------------------
3298 void vvMainWindow::SaveSOScreenshot()
3299 {
3300   SaveScreenshot(SOViewWidget);
3301 }
3302 //------------------------------------------------------------------------------
3303
3304
3305 //------------------------------------------------------------------------------
3306 void vvMainWindow::SaveSEScreenshot()
3307 {
3308   SaveScreenshot(SEViewWidget);
3309 }
3310 //------------------------------------------------------------------------------
3311
3312
3313 //------------------------------------------------------------------------------
3314 void vvMainWindow::SaveScreenshotAllSlices()
3315 {
3316   QVTKWidget *widget = NOViewWidget;
3317
3318   int index = 0;// GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
3319   vvSlicerManager * SM = mSlicerManagers[index];
3320   vvImage * image = SM->GetImage();
3321   vvSlicer * slicer = SM->GetSlicer(0);
3322   int orientation = slicer->GetOrientation();
3323   int nbSlices = image->GetSize()[orientation];
3324   vtkSmartPointer<vtkRenderWindow>  renderWindow = widget->GetRenderWindow();
3325
3326   // Select filename base
3327   QString filename = QFileDialog::getSaveFileName(this,
3328     tr("Save As (filename will be completed by slice number)"),
3329     itksys::SystemTools::GetFilenamePath(mSlicerManagers[index]->GetFileName()).c_str(),
3330     "Images( *.png);;Images( *.jpg)");
3331
3332   // Loop on slices
3333   for(int i=0; i<nbSlices; i++) {
3334     // Change the slice
3335     slicer->SetSlice(i); // -> change the slice of the current slicer
3336     SM->UpdateSlice(0); // --> this one emit UpdateSlice
3337     QCoreApplication::flush(); // -> needed to force display of contours
3338
3339     // Screenshot
3340     vtkSmartPointer<vtkWindowToImageFilter> windowToImageFilter = vtkSmartPointer<vtkWindowToImageFilter>::New();
3341     windowToImageFilter->SetInput(renderWindow);
3342     windowToImageFilter->SetMagnification(1);
3343     windowToImageFilter->SetInputBufferTypeToRGBA(); //also record the alpha (transparency) channel
3344     windowToImageFilter->Update();
3345
3346     vtkSmartPointer<vtkPNGWriter> writer = vtkSmartPointer<vtkPNGWriter>::New();
3347     std::string fn = itksys::SystemTools::GetFilenameWithoutLastExtension(filename.toStdString());
3348     std::string num = clitk::toString(i);
3349     if (i<10) num = "0"+num;
3350     if (i<100) num = "0"+num;
3351     if (i<1000) num = "0"+num;
3352
3353     fn = itksys::SystemTools::GetFilenamePath(filename.toStdString()) + "/"+ fn
3354       + "_" + num + itksys::SystemTools::GetFilenameLastExtension(filename.toStdString());
3355     writer->SetFileName(fn.c_str());
3356 #if VTK_MAJOR_VERSION <= 5
3357     writer->SetInput(windowToImageFilter->GetOutput());
3358 #else
3359     writer->SetInputConnection(windowToImageFilter->GetOutputPort());
3360 #endif
3361     writer->Write();
3362   }
3363 }
3364 //------------------------------------------------------------------------------
3365
3366
3367 //------------------------------------------------------------------------------
3368 void vvMainWindow::SaveScreenshot(QVTKWidget *widget)
3369 {
3370   QString Extensions = "Images( *.png);;";
3371   Extensions += "Images( *.jpg);;";
3372   Extensions += "Images( *.bmp);;";
3373   Extensions += "Images( *.tif);;";
3374   Extensions += "Images( *.ppm)";
3375 #if defined(VTK_USE_FFMPEG_ENCODER) || defined(VTK_USE_VIDEO_FOR_WINDOWS)
3376   Extensions += ";;Video( *.avi)";
3377 #endif
3378 #ifdef VTK_USE_MPEG2_ENCODER
3379   Extensions += ";;Video( *.mpg)";
3380 #endif
3381   Extensions += ";;Video( *.gif)";
3382
3383   int smIndex=GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
3384   QString fileName = QFileDialog::getSaveFileName(this,
3385     tr("Save As"),
3386     itksys::SystemTools::GetFilenamePath(mSlicerManagers[smIndex]->GetFileName()).c_str(),
3387     Extensions);
3388
3389   if (!fileName.isEmpty()) {
3390     vtkSmartPointer<vtkWindowToImageFilter> w2i = vtkSmartPointer<vtkWindowToImageFilter>::New();
3391     w2i->SetInput(widget->GetRenderWindow());
3392     w2i->SetMagnification(1);
3393     w2i->SetInputBufferTypeToRGBA(); //also record the alpha (transparency) channel
3394     w2i->Update();
3395     vtkImageData *image = w2i->GetOutput();
3396
3397     std::string ext(itksys::SystemTools::GetFilenameLastExtension(fileName.toStdString()));
3398
3399     // Image
3400     vtkImageWriter *imgwriter = NULL;
3401     if (ext==".bmp")
3402       imgwriter = vtkBMPWriter::New();
3403     else if (ext==".tif")
3404       imgwriter = vtkTIFFWriter::New();
3405     else if (ext==".ppm")
3406       imgwriter = vtkPNMWriter::New();
3407     else if (ext==".png")
3408       imgwriter = vtkPNGWriter::New();
3409     else if (ext==".jpg")
3410       imgwriter = vtkJPEGWriter::New();
3411
3412     // Snapshot image if not null
3413     if(imgwriter!=NULL) {
3414 #if VTK_MAJOR_VERSION <= 5
3415       imgwriter->SetInput(image);
3416 #else
3417       imgwriter->SetInputConnection(w2i->GetOutputPort());
3418 #endif
3419       imgwriter->SetFileName(fileName.toStdString().c_str());
3420       imgwriter->Write();
3421       return;
3422     }
3423
3424     // Video
3425     vtkGenericMovieWriter *vidwriter = NULL;
3426     if (ext==".gif") {
3427       vvAnimatedGIFWriter *gif = vvAnimatedGIFWriter::New();
3428       vidwriter = gif;
3429
3430       // FPS
3431       bool ok;
3432       int fps = QInputDialog::getInt(this, tr("Number of frames per second"),
3433         tr("FPS:"), 5, 0, 1000, 1, &ok);
3434       if(ok)
3435         gif->SetRate(fps);
3436
3437       // Loops
3438       int loops = QInputDialog::getInt(this, tr("Loops"),
3439         tr("Number of loops (0 means infinite):"), 0, 0, 1000000000, 1, &ok);
3440       if(ok)
3441         gif->SetLoops(loops);
3442
3443       // Dithering
3444       QString msg = "Would you like to activate dithering?";
3445       QMessageBox msgBox(QMessageBox::Question, tr("Dithering"),msg, 0, this);
3446       msgBox.addButton(tr("Yes"), QMessageBox::AcceptRole);
3447       msgBox.addButton(tr("No"), QMessageBox::RejectRole);
3448       gif->SetDither(msgBox.exec() == QMessageBox::AcceptRole);
3449     }
3450 #ifdef VTK_USE_VIDEO_FOR_WINDOWS
3451     if (ext==".avi") {
3452       vtkAVIWriter *mpg = vtkAVIWriter::New();
3453       vidwriter = mpg;
3454       mpg->SetQuality(2);
3455       bool ok;
3456       int fps = QInputDialog::getInt(this, tr("Number of frames per second"),
3457         tr("FPS:"), 5, 0, 1024, 1, &ok);
3458       if(!ok)
3459         fps = 5;
3460       mpg->SetRate(fps);
3461     }
3462 #endif
3463 #ifdef VTK_USE_FFMPEG_ENCODER
3464     if (ext==".avi") {
3465       vtkFFMPEGWriter *mpg = vtkFFMPEGWriter::New();
3466       vidwriter = mpg;
3467       mpg->SetQuality(2);
3468       bool ok;
3469       int fps = QInputDialog::getInt(this, tr("Number of frames per second"),
3470         tr("FPS:"), 5, 0, 1024, 1, &ok);
3471       if(!ok)
3472         fps = 5;
3473       mpg->SetRate(fps);
3474       mpg->SetBitRateTolerance(int(ceil(12.0*1024*1024/fps)));
3475     }
3476 #endif
3477 #ifdef VTK_USE_MPEG2_ENCODER
3478     if (ext==".mpg") {
3479       vtkMPEG2Writer *mpg = vtkMPEG2Writer::New();
3480       vidwriter = mpg;
3481     }
3482 #endif
3483
3484     // Take video if not null
3485     if(vidwriter!=NULL){
3486 #if VTK_MAJOR_VERSION <= 5
3487       vidwriter->SetInput(image);
3488 #else
3489       vidwriter->SetInputConnection(w2i->GetOutputPort());
3490 #endif
3491       vidwriter->SetFileName(fileName.toStdString().c_str());
3492       vidwriter->Start();
3493       int nSlice = mSlicerManagers[smIndex]->GetSlicer(0)->GetTMax();
3494       for(int i=0; i<=nSlice; i++) {
3495         mSlicerManagers[smIndex]->SetNextTSlice(0);
3496         vtkSmartPointer<vtkWindowToImageFilter> w2i = vtkSmartPointer<vtkWindowToImageFilter>::New();
3497         w2i->SetInput(widget->GetRenderWindow());
3498         w2i->Update();
3499 #if VTK_MAJOR_VERSION <= 5
3500         vidwriter->SetInput(w2i->GetOutput());
3501 #else
3502         vidwriter->SetInputConnection(w2i->GetOutputPort());
3503 #endif
3504         vidwriter->Write();
3505       }
3506       vidwriter->End();
3507       vidwriter->Delete();
3508       return;
3509     }
3510
3511     QMessageBox::information(this,tr("Problem saving screenshot !"),tr("Cannot save image.\nPlease set a file extension !!!"));
3512   }
3513 }
3514 //------------------------------------------------------------------------------
3515
3516
3517 //------------------------------------------------------------------------------
3518 void vvMainWindow::GoToCursor()
3519 {
3520   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
3521   for (int column = 1; column < 5; column++) {
3522     if (DataTree->selectedItems()[0]->data(column,Qt::CheckStateRole).toInt() > 1) {
3523       double* cursorPos = mSlicerManagers[index]->GetSlicer(column-1)->GetCursorPosition();
3524       mSlicerManagers[index]->GetSlicer(column-1)->SetCurrentPosition(
3525         cursorPos[0],cursorPos[1],cursorPos[2],cursorPos[3]);
3526       mSlicerManagers[index]->UpdateViews(1,column-1);
3527       mSlicerManagers[index]->UpdateLinked(column-1);
3528       break;
3529     }
3530   }
3531 }
3532 //------------------------------------------------------------------------------
3533
3534 //------------------------------------------------------------------------------
3535 void vvMainWindow::GoToLandmark()
3536 {
3537   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
3538   for (int column = 1; column < 5; column++) {
3539     if (DataTree->selectedItems()[0]->data(column,Qt::CheckStateRole).toInt() > 1) {
3540       double* cursorPos = landmarksPanel->GetSelectedPoint();
3541       mSlicerManagers[index]->GetSlicer(column-1)->SetCurrentPosition(
3542         cursorPos[0],cursorPos[1],cursorPos[2],cursorPos[3]);
3543       mSlicerManagers[index]->UpdateViews(1,column-1);
3544       mSlicerManagers[index]->UpdateLinked(column-1);
3545       break;
3546     }
3547   }
3548 }
3549 //------------------------------------------------------------------------------
3550
3551 //------------------------------------------------------------------------------
3552 void vvMainWindow::PlayPause()
3553 {
3554   if (playMode) {
3555     playMode = 0;
3556     playButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/player_play.png")));
3557     ImageInfoChanged();
3558     return;
3559   } else {
3560     int image_number=DataTree->topLevelItemCount();
3561     bool has_temporal;
3562     for (int i=0; i<image_number; i++)
3563       if (mSlicerManagers[i]->GetSlicer(0)->GetTMax() > 0) {
3564         has_temporal=true;
3565         break;
3566       }
3567       if (has_temporal) {
3568         playMode = 1;
3569         playButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/player_pause.png")));
3570         QTimer::singleShot(1000/mFrameRate, this, SLOT(PlayNext()));
3571       }
3572   }
3573 }
3574 //------------------------------------------------------------------------------
3575
3576 //------------------------------------------------------------------------------
3577 void vvMainWindow::PlayNext()
3578 {
3579   if (playMode && !this->isHidden()) {
3580     int image_number=DataTree->topLevelItemCount();
3581     ///Only play one slicer per SM, and only if the SM is being displayed
3582     for (int i=0; i<image_number; i++)
3583       for (int j=0; j<4; j++)
3584         if (mSlicerManagers[i]->GetSlicer(0)->GetTMax() > 0 &&
3585           DataTree->topLevelItem(i)->data(j+1,Qt::CheckStateRole).toInt() > 0) {
3586             mSlicerManagers[i]->SetNextTSlice(j);
3587             break;
3588         }
3589         QTimer::singleShot(1000/mFrameRate, this, SLOT(PlayNext()));
3590   }
3591 }
3592 //------------------------------------------------------------------------------
3593
3594 void vvMainWindow::ShowLastImage()
3595 {
3596   if (mSlicerManagers.size() > 1) {
3597     QTreeWidgetItem * item=DataTree->topLevelItem(DataTree->topLevelItemCount()-1);
3598     CurrentImageChanged(mSlicerManagers.back()->GetId()); //select new image
3599     item->setData(1,Qt::CheckStateRole,2); //show the new image in the first panel
3600     //mSlicerManagers[GetSlicerIndexFromItem(item)]->GetSlicer(0)->SetActorVisibility("image", 0, 1); //Set the Last Image visibles
3601     DisplayChanged(item,1);
3602   }
3603 }
3604
3605 //------------------------------------------------------------------------------
3606 void vvMainWindow::UpdateRenderWindows()
3607 {
3608   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
3609       for (unsigned int j = 0; j < 4; ++j) {
3610         mSlicerManagers[i]->GetSlicer(j)->RemoveLandmarks();
3611         mSlicerManagers[i]->GetSlicer(j)->DisplayLandmarks();
3612       }
3613   }
3614   if (NOViewWidget->GetRenderWindow()) NOViewWidget->GetRenderWindow()->Render();
3615   if (NEViewWidget->GetRenderWindow()) NEViewWidget->GetRenderWindow()->Render();
3616   if (SOViewWidget->GetRenderWindow()) SOViewWidget->GetRenderWindow()->Render();
3617   if (SEViewWidget->GetRenderWindow()) SEViewWidget->GetRenderWindow()->Render();
3618 }
3619 //------------------------------------------------------------------------------
3620
3621 //------------------------------------------------------------------------------
3622 void vvMainWindow::SegmentationOnCurrentImage()
3623 {
3624   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
3625
3626   vvSegmentationDialog segmentation;
3627   segmentation.SetImage(mSlicerManagers[index]->GetSlicer(0)->GetImage());
3628   segmentation.exec();
3629 }
3630 //------------------------------------------------------------------------------
3631
3632 void vvMainWindow::SurfaceViewerLaunch()
3633 {
3634   vvSurfaceViewerDialog surfaceViewer;
3635   surfaceViewer.exec();
3636 }
3637 //------------------------------------------------------------------------------
3638
3639
3640 //------------------------------------------------------------------------------
3641 int vvMainWindow::GetImageDuplicateFilenameNumber(std::string filename)
3642 {
3643   int number=0;
3644   for(unsigned int l=0; l<mSlicerManagers.size(); l++) {
3645     vvSlicerManager * v = mSlicerManagers[l];
3646     if (v->GetBaseFileName() ==
3647       vtksys::SystemTools::GetFilenameName(vtksys::SystemTools::GetFilenameWithoutLastExtension(filename))) {
3648         number = std::max(number, v->GetBaseFileNameNumber()+1);
3649     }
3650   }
3651   return number;
3652 }
3653 //------------------------------------------------------------------------------
3654
3655
3656 //------------------------------------------------------------------------------
3657 vvSlicerManager* vvMainWindow::AddImage(vvImage::Pointer image,std::string filename)
3658 {
3659   // Change filename if another image exist with the same name
3660   int number = GetImageDuplicateFilenameNumber(filename);
3661
3662   // Create new SliceManager
3663   vvSlicerManager* slicer_manager = new vvSlicerManager(4);
3664   slicer_manager->SetImage(image);//, IMAGE, number);
3665   //  filename = filename+"_"+clitk::toString(number);
3666   slicer_manager->SetFilename(filename, number);
3667   mSlicerManagers.push_back(slicer_manager);
3668
3669   //create an item in the tree with good settings
3670   QTreeWidgetItem *item = new QTreeWidgetItem();
3671   item->setData(0,Qt::UserRole,slicer_manager->GetFileName().c_str());//files[i].c_str());
3672   item->setData(1,Qt::UserRole,tr("image"));
3673   item->setData(COLUMN_IMAGE_NAME,Qt::DisplayRole,slicer_manager->GetFileName().c_str());//filename.c_str());
3674   qApp->processEvents();
3675
3676   for (int j = 1; j <= 4; j++) item->setData(j,Qt::CheckStateRole,1);
3677
3678   //Create the buttons for reload and close
3679   qApp->processEvents();
3680   QTreePushButton* cButton = new QTreePushButton;
3681   cButton->setItem(item);
3682   cButton->setColumn(COLUMN_CLOSE_IMAGE);
3683   cButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/exit.png")));
3684   connect(cButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
3685     this,SLOT(CloseImage(QTreeWidgetItem*, int)));
3686
3687   QTreePushButton* rButton = new QTreePushButton;
3688   rButton->setItem(item);
3689   rButton->setColumn(COLUMN_RELOAD_IMAGE);
3690   rButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/rotateright.png")));
3691   rButton->setEnabled(0);
3692   connect(rButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
3693     this,SLOT(ReloadImage(QTreeWidgetItem*, int)));
3694
3695   DataTree->addTopLevelItem(item);
3696   DataTree->setItemWidget(item, COLUMN_CLOSE_IMAGE, cButton);
3697   DataTree->setItemWidget(item, COLUMN_RELOAD_IMAGE, rButton);
3698
3699   //set the id of the image
3700   QString id = QDir::current().absoluteFilePath(slicer_manager->GetFileName().c_str()) + QString::number(mSlicerManagers.size()-1);
3701   item->setData(COLUMN_IMAGE_NAME,Qt::UserRole,id.toStdString().c_str());
3702   mSlicerManagers.back()->SetId(id.toStdString());
3703
3704   linkPanel->addImage(slicer_manager->GetFileName().c_str()// filename
3705     , id.toStdString());
3706
3707   connect(mSlicerManagers.back(), SIGNAL(currentImageChanged(std::string)),
3708     this, SLOT(CurrentImageChanged(std::string)));
3709   connect(mSlicerManagers.back(), SIGNAL(currentPickedImageChanged(std::string)),
3710     this, SLOT(CurrentPickedImageChanged(std::string)));
3711   connect(mSlicerManagers.back(), SIGNAL(UpdatePosition(int, double, double, double, double, double, double, double)),
3712     this, SLOT(MousePositionChanged(int,double, double, double, double, double, double, double)));
3713   connect(mSlicerManagers.back(), SIGNAL(UpdateVector(int, double, double, double, double)),
3714     this, SLOT(VectorChanged(int,double,double,double, double)));
3715   connect(mSlicerManagers.back(), SIGNAL(UpdateOverlay(int, double, double)),
3716     this, SLOT(OverlayChanged(int,double,double)));
3717   connect(mSlicerManagers.back(), SIGNAL(UpdateFusion(int, double)),
3718     this, SLOT(FusionChanged(int,double)));
3719   //connect(mSlicerManagers.back(), SIGNAL(UpdateFusionSequence(int, bool, unsigned int)),
3720   //  this, SLOT(FusionSequenceChanged(int, bool, unsigned int)));
3721   connect(mSlicerManagers.back(), SIGNAL(WindowLevelChanged()),
3722     this,SLOT(WindowLevelChanged()));
3723   connect(mSlicerManagers.back(), SIGNAL(UpdateSlice(int,int)),
3724     this,SLOT(UpdateSlice(int,int)));
3725   connect(mSlicerManagers.back(), SIGNAL(UpdateTSlice(int, int, int)),
3726     this,SLOT(UpdateTSlice(int, int, int)));
3727   connect(mSlicerManagers.back(), SIGNAL(UpdateTSlice(int, int, int)),
3728     this,SLOT(ImageInfoChanged()));
3729   connect(mSlicerManagers.back(), SIGNAL(UpdateSliceRange(int,int,int,int,int)),
3730     this,SLOT(UpdateSliceRange(int,int,int,int,int)));
3731   connect(mSlicerManagers.back(), SIGNAL(UpdateLinkManager(std::string,int,double,double,double,int)),
3732     this,SLOT(UpdateLinkManager(std::string,int,double,double,double,int)));
3733   connect(mSlicerManagers.back(), SIGNAL(UpdateLinkedNavigation(std::string,vvSlicerManager*,vvSlicer*)),
3734     this,SLOT(UpdateLinkedNavigation(std::string,vvSlicerManager*,vvSlicer*)));
3735   connect(mSlicerManagers.back(), SIGNAL(ChangeImageWithIndexOffset(vvSlicerManager*,int,int)),
3736     this,SLOT(ChangeImageWithIndexOffset(vvSlicerManager*,int,int)));
3737   connect(mSlicerManagers.back(), SIGNAL(LandmarkAdded()),landmarksPanel,SLOT(AddPoint()));
3738
3739
3740
3741   InitSlicers();
3742   UpdateTree();
3743   qApp->processEvents();
3744   InitDisplay();
3745   ShowLastImage();
3746   qApp->processEvents();
3747   // End
3748   ImageInfoChanged();
3749   return slicer_manager;
3750 }
3751 //------------------------------------------------------------------------------
3752
3753
3754 //------------------------------------------------------------------------------
3755 void vvMainWindow::UpdateCurrentSlicer()
3756 {
3757   int index = -1;
3758   if (DataTree->selectedItems().size() > 0) {
3759     index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
3760   }
3761   mSlicerManagerCurrentIndex = index;
3762 }
3763 //------------------------------------------------------------------------------