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