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