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