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
  27 // VV include
  28 #include "vvMainWindow.h"
  29 #include "vvHelpDialog.h"
  30 #include "vvRegisterForm.h"
  31 #include "vvDocumentation.h"
  32 #include "vvProgressDialog.h"
  33 #include "vvQDicomSeriesSelector.h"
  34 #include "vvSlicerManager.h"
  35 #include "clitkImageCommon.h"
  36 #include "vvSlicer.h"
  37 #include "vvInteractorStyleNavigator.h"
  38 #include "vvImageWriter.h"
  39 #include "vvSegmentationDialog.h"
  40 #include "vvSurfaceViewerDialog.h"
  41 #include "vvDeformationDialog.h"
  42 #include "vvImageWarp.h"
  43 #include "vvUtils.h"
  44 #include "vvMidPosition.h"
  45 #include "vvMesh.h"
  46 #include "vvStructSelector.h"
  47 #include "vvMeshReader.h"
  48 #include "vvSaveState.h"
  49 #include "vvReadState.h"
  50 #ifdef CLITK_USE_PACS_CONNECTION
  51 #include "vvQPacsConnection.h"
  52 #endif
  53 #include "clitkConfiguration.h"
  54 #include "clitkMatrix.h"
  55
  56 // ITK include
  57 #include <itkImage.h>
  58 #include <itkImageFileReader.h>
  59 #include <itkByteSwapper.h>
  60 #include <itkCommand.h>
  61 #include <itkNumericSeriesFileNames.h>
  62
  63 // VTK include
  64 #include <vtkImageData.h>
  65 #include <vtkImageActor.h>
  66 #include <vtkCornerAnnotation.h>
  67 #include <vtkRenderWindow.h>
  68 #include <vtkRenderWindowInteractor.h>
  69 #include <vtkRenderer.h>
  70 #include <vtkRendererCollection.h>
  71 #include <vtkWindowToImageFilter.h>
  72 #include <vtkBMPWriter.h>
  73 #include <vtkTIFFWriter.h>
  74 #include <vtkPNMWriter.h>
  75 #include <vtkPNGWriter.h>
  76 #include <vtkJPEGWriter.h>
  77 #include <vtkGenericMovieWriter.h>
  78 #ifdef CLITK_EXPERIMENTAL
  79 #  include <vvAnimatedGIFWriter.h>
  80 #endif
  81 #ifdef VTK_USE_VIDEO_FOR_WINDOWS
  82 #  include <vtkAVIWriter.h>
  83 #endif
  84 #ifdef VTK_USE_FFMPEG_ENCODER
  85 #  include <vtkFFMPEGWriter.h>
  86 #endif
  87 #ifdef VTK_USE_MPEG2_ENCODER
  88 #  include <vtkMPEG2Writer.h>
  89 #endif
  90 #include <vtkMatrix4x4.h>
  91 #include <vtkTransform.h>
  92
  93 // Standard includes
  94 #include <iostream>
  95 #include <fstream>
  96 #include <sstream>
  97 #include <iomanip>
  98
  99 #define COLUMN_TREE 0
 100 #define COLUMN_UL_VIEW 1
 101 #define COLUMN_UR_VIEW 2
 102 #define COLUMN_DL_VIEW 3
 103 #define COLUMN_DR_VIEW 4
 104 #define COLUMN_CLOSE_IMAGE 5
 105 #define COLUMN_RELOAD_IMAGE 6
 106 #define COLUMN_IMAGE_NAME 7
 107
 108 #ifdef CLITK_PRIVATE_FEATURES
 109 #define EXTENSIONS "Images ( *.bmp *.png *.jpeg *.jpg *.tif *.mhd *.mha *.hdr *.vox *.his *.xdr *.SCAN *.nii *.nrrd *.nhdr *.refscan *.nii.gz *.usf *.svl)"
 110 #else
 111 #define EXTENSIONS "Images ( *.bmp *.png *.jpeg *.jpg *.tif *.mhd *.mha *.hdr *.vox *.his *.xdr *.SCAN *.nii *.nrrd *.nhdr *.refscan *.nii.gz)"
 112 #endif
 113
 114
 115 /*Data Tree values
 116 0,Qt::UserRole full filename
 117 1,Qt::CheckStateRole checkbutton UL View
 118 1,Qt::UserRole overlay, fusion or vector
 119 2,Qt::CheckStateRole checkbutton UR View
 120 3,Qt::CheckStateRole checkbutton DL View
 121 4,Qt::CheckStateRole checkbutton DR View
 122 5,0  short filename
 123 5,Qt::UserRole mSlicerManager id*/
 124
 125 //------------------------------------------------------------------------------
 126 vvMainWindow::vvMainWindow():vvMainWindowBase()
 127 {
 128   setupUi(this); // this sets up the GUI
 129   setDicomClient();
 130   mInputPathName = "";
 131   mMenuTools = menuTools;
 132   //  mMenuSegmentation = menuSegmentation;
 133   mContextMenu = &contextMenu;
 134   mMenuExperimentalTools = menuExperimental;
 135   mMainWidget = this;
 136   mCurrentTime = -1;
 137   mCurrentSelectedImageId = "";
 138   mCurrentPickedImageId = "";
 139   mCurrentPickedImageIndex = 0;
 140
 141   //Init the contextMenu
 142   this->setContextMenuPolicy(Qt::CustomContextMenu);
 143   contextActions.resize(0);
 144   QAction* actionOpen_new_image = contextMenu.addAction(QIcon(QString::fromUtf8(":/common/icons/fileopen.png")),
 145     tr("O&pen new Image"));
 146   actionOpen_new_image->setShortcut(QKeySequence(tr("Ctrl+O")));
 147   connect(actionOpen_new_image,SIGNAL(triggered()),this,SLOT(OpenImages()));
 148   contextActions.push_back(actionOpen_new_image);
 149   contextMenu.addSeparator();
 150
 151   QAction* actionClose_Image = contextMenu.addAction(QIcon(QString::fromUtf8(":/common/icons/exit.png")),
 152     tr("Close Current Image"));
 153   connect(actionClose_Image,SIGNAL(triggered()),this,SLOT(CloseImage()));
 154   contextActions.push_back(actionClose_Image);
 155
 156   QAction* actionReload_image = contextMenu.addAction(QIcon(QString::fromUtf8(":/common/icons/rotateright.png")),
 157     tr("Reload Current Image"));
 158   connect(actionReload_image,SIGNAL(triggered()),this,SLOT(ReloadImage()));
 159   contextActions.push_back(actionReload_image);
 160
 161   QAction* actionSave_image = contextMenu.addAction(QIcon(QString::fromUtf8(":/common/icons/filesave.png")),
 162     tr("Save Current Image"));
 163   connect(actionSave_image,SIGNAL(triggered()),this,SLOT(SaveAs()));
 164   contextActions.push_back(actionSave_image);
 165
 166   QAction* actionSave_state = contextMenu.addAction(QIcon(QString::fromUtf8(":/common/icons/filesave.png")),
 167     tr("Save Current State"));
 168   connect(actionSave_state,SIGNAL(triggered()),this,SLOT(SaveCurrentState()));
 169   contextActions.push_back(actionSave_state);
 170
 171   QAction* actionRead_state = contextMenu.addAction(QIcon(QString::fromUtf8(":/common/icons/filesave.png")),
 172     tr("Read Saved State"));
 173   connect(actionRead_state,SIGNAL(triggered()),this,SLOT(ReadSavedState()));
 174   contextActions.push_back(actionRead_state);
 175
 176   contextMenu.addSeparator();
 177
 178   contextMenu.addAction(actionAdd_VF_to_current_Image);
 179   contextActions.push_back(actionAdd_VF_to_current_Image);
 180
 181   //QAction* actionAdd_Overlay_to_current_Image = menuOverlay->addAction(QIcon(QString::fromUtf8(":/common/icons/GPSup.png")),
 182   //    tr("Add overlay image to current image"));
 183   contextMenu.addAction(actionAdd_overlay_image_to_current_image);
 184   contextActions.push_back(actionAdd_overlay_image_to_current_image);
 185
 186   contextMenu.addAction(actionAdd_fusion_image);
 187   contextActions.push_back(actionAdd_fusion_image);
 188
 189 #ifdef CLITK_EXPERIMENTAL
 190   contextMenu.addAction(actionAdd_USSequence_toCT);
 191   contextActions.push_back(actionAdd_USSequence_toCT);
 192 #endif
 193
 194
 195   contextMenu.addSeparator();
 196   QAction* actionResetMatrix = contextMenu.addAction(QIcon(QString::fromUtf8(":/common/icons/identity.png")),
 197     tr("Reset transformation to identity"));
 198   connect(actionResetMatrix, SIGNAL(triggered()), this,SLOT(ResetTransformationToIdentity()));
 199
 200   // TRIAL DS
 201   /*
 202   QMenu * m = new QMenu(menubar);
 203   m->setTitle("TOTO");
 204   //  m->setObjectName(QString::fromUtf8("TOTOTO"));
 205   contextMenu.addMenu(m);
 206   QAction * a = m->addAction(QIcon(QString::fromUtf8(":/common/icons/GPSup.png")),
 207   tr("BIDON"));
 208   QAction * b = m->addAction(QIcon(QString::fromUtf8(":/common/icons/GPSup.png")),
 209   tr("BIDON2"));
 210   m->addAction(a);
 211   m->addAction(b);
 212   connect(a,SIGNAL(triggered()),this,SLOT(AddFusionImage()));
 213   */
 214
 215   //init the DataTree
 216   mSlicerManagers.resize(0);
 217
 218   QStringList header;
 219   header.append("");
 220   header.append("TL");
 221   header.append("TR");
 222   header.append("BL");
 223   header.append("BR");
 224   header.append("");
 225   header.append("");
 226   header.append("Name");
 227
 228   DataTree->setHeaderLabels(header);
 229   DataTree->resizeColumnToContents(COLUMN_TREE);
 230   DataTree->resizeColumnToContents(COLUMN_UL_VIEW);
 231   DataTree->resizeColumnToContents(COLUMN_UR_VIEW);
 232   DataTree->resizeColumnToContents(COLUMN_DL_VIEW);
 233   DataTree->resizeColumnToContents(COLUMN_DR_VIEW);
 234   DataTree->resizeColumnToContents(COLUMN_CLOSE_IMAGE);
 235   DataTree->resizeColumnToContents(COLUMN_RELOAD_IMAGE);
 236   DataTree->resizeColumnToContents(COLUMN_IMAGE_NAME);
 237
 238   viewMode = 1;
 239   documentation = new vvDocumentation();
 240   help_dialog = new vvHelpDialog();
 241   dicomSeriesSelector = new vvDicomSeriesSelector();
 242 #ifdef CLITK_USE_PACS_CONNECTION
 243      PacsConnection = new vvQPacsConnection();
 244 #endif
 245
 246   inverseButton->setEnabled(0);
 247   actionAdd_overlay_image_to_current_image->setEnabled(0);
 248   actionSave_As->setEnabled(0);
 249   actionAdd_VF_to_current_Image->setEnabled(0);
 250   actionAdd_fusion_image->setEnabled(0);
 251   actionAdd_USSequence_toCT->setEnabled(0);
 252
 253   //init the sliders
 254   verticalSliders.push_back(NOVerticalSlider);
 255   verticalSliders.push_back(NEVerticalSlider);
 256   verticalSliders.push_back(SOVerticalSlider);
 257   verticalSliders.push_back(SEVerticalSlider);
 258
 259   for (int i =0; i < 4; i++)
 260     verticalSliders[i]->hide();
 261
 262   horizontalSliders.push_back(NOHorizontalSlider);
 263   horizontalSliders.push_back(NEHorizontalSlider);
 264   horizontalSliders.push_back(SOHorizontalSlider);
 265   horizontalSliders.push_back(SEHorizontalSlider);
 266
 267   for (int i =0; i < 4; i++)
 268     horizontalSliders[i]->hide();
 269
 270
 271   connect(NOVerticalSlider,SIGNAL(valueChanged(int)),this,SLOT(NOVerticalSliderChanged()));
 272   connect(NEVerticalSlider,SIGNAL(valueChanged(int)),this,SLOT(NEVerticalSliderChanged()));
 273   connect(SOVerticalSlider,SIGNAL(valueChanged(int)),this,SLOT(SOVerticalSliderChanged()));
 274   connect(SEVerticalSlider,SIGNAL(valueChanged(int)),this,SLOT(SEVerticalSliderChanged()));
 275
 276   connect(NOHorizontalSlider,SIGNAL(valueChanged(int)),this,SLOT(NOHorizontalSliderMoved()));
 277   connect(NEHorizontalSlider,SIGNAL(valueChanged(int)),this,SLOT(NEHorizontalSliderMoved()));
 278   connect(SOHorizontalSlider,SIGNAL(valueChanged(int)),this,SLOT(SOHorizontalSliderMoved()));
 279   connect(SEHorizontalSlider,SIGNAL(valueChanged(int)),this,SLOT(SEHorizontalSliderMoved()));
 280
 281   //connect everything
 282   connect(actionCompute_mid_position_image,SIGNAL(triggered()),this,SLOT(ComputeMidPosition()));
 283   connect(actionDeformable_Registration,SIGNAL(triggered()),this,SLOT(ComputeDeformableRegistration()));
 284   connect(actionWarp_image_with_vector_field,SIGNAL(triggered()),this,SLOT(WarpImage()));
 285   connect(actionLoad_images,SIGNAL(triggered()),this,SLOT(OpenImages()));
 286   connect(actionOpen_Dicom,SIGNAL(triggered()),this,SLOT(OpenDicom()));
 287   #ifdef CLITK_USE_PACS_CONNECTION
 288 connect(actionConnect_Pacs,SIGNAL(triggered()),this,SLOT(ConnectPacs()));
 289 #endif
 290   //  connect(actionOpen_Dicom_Struct,SIGNAL(triggered()),this,SLOT(OpenDCStructContour()));
 291   connect(actionOpen_VTK_contour,SIGNAL(triggered()),this,SLOT(OpenVTKContour()));
 292   connect(actionOpen_Multiple_Images_As_One,SIGNAL(triggered()),this,SLOT(MergeImages()));
 293   connect(actionSlice_Image_As_Multiple_Images,SIGNAL(triggered()),this,SLOT(SliceImages()));
 294   connect(actionOpen_Image_With_Time,SIGNAL(triggered()),this,SLOT(OpenImageWithTime()));
 295   connect(actionMerge_images_as_n_dim_t, SIGNAL(triggered()), this, SLOT(MergeImagesWithTime()));
 296   connect(actionSave_As,SIGNAL(triggered()),this,SLOT(SaveAs()));
 297   connect(actionSave_current_state,SIGNAL(triggered()),this,SLOT(SaveCurrentState()));
 298   connect(actionRead_saved_state,SIGNAL(triggered()),this,SLOT(ReadSavedState()));
 299   connect(actionExit,SIGNAL(triggered()),this,SLOT(close()));
 300   connect(actionAdd_VF_to_current_Image,SIGNAL(triggered()),this,SLOT(OpenField()));
 301   connect(actionAdd_fusion_image,SIGNAL(triggered()),this,SLOT(SelectFusionImage()));
 302   connect(actionAdd_overlay_image_to_current_image,SIGNAL(triggered()), this,SLOT(SelectOverlayImage()));
 303   connect(actionAdd_USSequence_toCT,SIGNAL(triggered()), this,SLOT(SelectFusionSequence()));
 304   connect(actionNavigation_Help,SIGNAL(triggered()),this,SLOT(ShowHelpDialog()));
 305   connect(actionDocumentation,SIGNAL(triggered()),this,SLOT(ShowDocumentation()));
 306   connect(actionRegister_vv,SIGNAL(triggered()),this,SLOT(PopupRegisterForm()));
 307
 308   connect(overlayPanel, SIGNAL(FusionSequenceCorrespondancesButtonPressed()), this, SLOT(SelectFusionSequenceCorrespondances()));
 309
 310
 311   ///////////////////////////////////////////////
 312   connect(actionSegmentation,SIGNAL(triggered()),this,SLOT(SegmentationOnCurrentImage()));
 313   connect(actionSurface_Viewer,SIGNAL(triggered()),this,SLOT(SurfaceViewerLaunch()));
 314   ///////////////////////////////////////////////
 315
 316   actionNorth_East_Window->setEnabled(0);
 317   actionNorth_West_Window->setEnabled(0);
 318   actionSouth_East_Window->setEnabled(0);
 319   actionSouth_West_Window->setEnabled(0);
 320
 321   connect(actionNorth_East_Window,SIGNAL(triggered()),this,SLOT(SaveNEScreenshot()));
 322   connect(actionNorth_West_Window,SIGNAL(triggered()),this,SLOT(SaveNOScreenshot()));
 323   connect(actionSouth_East_Window,SIGNAL(triggered()),this,SLOT(SaveSEScreenshot()));
 324   connect(actionSouth_West_Window,SIGNAL(triggered()),this,SLOT(SaveSOScreenshot()));
 325   connect(actionSave_all_slices,SIGNAL(triggered()),this,SLOT(SaveScreenshotAllSlices()));
 326
 327   connect(DataTree,SIGNAL(itemSelectionChanged()),this,SLOT(ImageInfoChanged()));
 328   connect(DataTree,SIGNAL(itemClicked(QTreeWidgetItem*, int)),this,
 329     SLOT(DisplayChanged(QTreeWidgetItem*, int)));
 330
 331   connect(viewButton,SIGNAL(clicked()),this, SLOT(ChangeViewMode()) );
 332   connect(windowSpinBox,SIGNAL(editingFinished()),this,SLOT(WindowLevelEdited()));
 333   connect(levelSpinBox,SIGNAL(editingFinished()),this,SLOT(WindowLevelEdited()));
 334   connect(colorMapComboBox,SIGNAL(currentIndexChanged(int)),this,SLOT(UpdateColorMap()));
 335   connect(presetComboBox,SIGNAL(currentIndexChanged(int)),this,SLOT(UpdateWindowLevel()));
 336   connect(slicingPresetComboBox, SIGNAL(currentIndexChanged(int)),this,SLOT(UpdateSlicingPreset()));
 337   connect(inverseButton,SIGNAL(clicked()),this,SLOT(SwitchWindowLevel()));
 338   connect(applyWindowLevelToAllButton,SIGNAL(clicked()),this,SLOT(ApplyWindowLevelToAllImages()));
 339
 340   connect(this,SIGNAL(customContextMenuRequested(QPoint)),this,SLOT(ShowContextMenu(QPoint)));
 341
 342   connect(linkPanel,SIGNAL(addLink(QString,QString,bool)),this,SLOT(AddLink(QString,QString,bool)));
 343   connect(linkPanel,SIGNAL(removeLink(QString,QString)),this,SLOT(RemoveLink(QString,QString)));
 344   connect(overlayPanel,SIGNAL(VFPropertyUpdated(int,int,int,int,double,double,double)),this,SLOT(SetVFProperty(int,int,int,int,double,double,double)));
 345   connect(overlayPanel,SIGNAL(OverlayPropertyUpdated(int,int,double,double)),
 346     this,SLOT(SetOverlayProperty(int,int,double,double)));
 347   connect(overlayPanel,SIGNAL(FusionPropertyUpdated(int,int,int,double,double, bool)),
 348     this,SLOT(SetFusionProperty(int,int,int,double,double, bool)));
 349   connect(landmarksPanel,SIGNAL(UpdateRenderWindows()),this,SLOT(UpdateRenderWindows()));
 350   connect(landmarksPanel,SIGNAL(SelectedPointChanged()),this,SLOT(GoToLandmark()));
 351
 352   connect(overlayPanel,SIGNAL(FusionSequencePropertyUpdated(int, bool, unsigned int, bool)),
 353     this,SLOT(SetFusionSequenceProperty(int, bool,unsigned int, bool)));
 354
 355
 356   playMode = 0;//pause
 357   mFrameRate = 10;
 358   playButton->setEnabled(0);
 359   frameRateLabel->setEnabled(0);
 360   frameRateSpinBox->setEnabled(0);
 361   connect(playButton, SIGNAL(clicked()),this,SLOT(PlayPause()));
 362   connect(frameRateSpinBox, SIGNAL(valueChanged(int)),this,SLOT(ChangeFrameRate(int)));
 363
 364   goToCursorPushButton->setEnabled(0);
 365   connect(goToCursorPushButton, SIGNAL(clicked()),this,SLOT(GoToCursor()));
 366
 367   NOViewWidget->hide();
 368   NEViewWidget->hide();
 369   SOViewWidget->hide();
 370   SEViewWidget->hide();
 371
 372   //Recently opened files
 373   std::list<std::string> recent_files = GetRecentlyOpenedImages();
 374   recentlyOpenedFilesMenu=NULL;
 375   if ( !recent_files.empty() ) {
 376     createRecentlyOpenedFilesMenu();
 377     updateRecentlyOpenedFilesMenu(recent_files);
 378   }
 379
 380   // Adding all new tools (insertion in the menu)
 381   vvToolManager::GetInstance()->InsertToolsInMenu(this);
 382   vvToolManager::GetInstance()->EnableToolsInMenu(this, false);
 383
 384   if (!CLITK_EXPERIMENTAL)
 385     menuExperimental->menuAction()->setVisible(false);
 386
 387
 388   QTimer * timerMemory = new QTimer(this);
 389   //timerMemory->setInterval(5);
 390   connect(timerMemory, SIGNAL(timeout()), this, SLOT(UpdateMemoryUsage()));
 391   timerMemory->start(2000);
 392
 393 }
 394 //------------------------------------------------------------------------------
 395 void vvMainWindow::show()
 396 {
 397   vvMainWindowBase::show();
 398   PopupRegisterForm(true);
 399 }
 400 //------------------------------------------------------------------------------
 401 void vvMainWindow::UpdateMemoryUsage()
 402 {
 403   //  clitk::PrintMemory(true);
 404   if (clitk::GetMemoryUsageInMb() == 0) infoPanel->setMemoryInMb("NA");
 405   else infoPanel->setMemoryInMb(QString::number(clitk::GetMemoryUsageInMb())+" MiB");
 406 }
 407 //------------------------------------------------------------------------------
 408
 409
 410 //------------------------------------------------------------------------------
 411 void vvMainWindow::createRecentlyOpenedFilesMenu()
 412 {
 413   recentlyOpenedFilesMenu = new QMenu("Recently opened files...");
 414   recentlyOpenedFilesMenu->setIcon(QIcon(QString::fromUtf8(":/common/icons/open.png")));
 415   menuFile->insertMenu(actionOpen_Image_With_Time,recentlyOpenedFilesMenu);
 416   menuFile->insertSeparator(actionOpen_Image_With_Time);
 417 }
 418 //------------------------------------------------------------------------------
 419
 420
 421 //------------------------------------------------------------------------------
 422
 423 void vvMainWindow::updateRecentlyOpenedFilesMenu(const std::list<std::string> &recent_files)
 424 {
 425   if(recentlyOpenedFilesMenu==NULL) {
 426     createRecentlyOpenedFilesMenu();
 427   } else {
 428     recentlyOpenedFilesMenu->clear();
 429   }
 430   for (std::list<std::string>::const_iterator i = recent_files.begin(); i!=recent_files.end(); i++) {
 431     QAction* current=new QAction(QIcon(QString::fromUtf8(":/common/icons/open.png")), i->c_str(),this);
 432     recentlyOpenedFilesMenu->addAction(current);
 433     connect(current,SIGNAL(triggered()),this,SLOT(OpenRecentImage()));
 434   }
 435 }
 436 //------------------------------------------------------------------------------
 437
 438
 439 //------------------------------------------------------------------------------
 440 void vvMainWindow::ComputeMidPosition()
 441 {
 442   bool ok;
 443   int index=GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
 444   int ref = QInputDialog::getInteger(this,"Chose reference phase","Reference phase",0,0,\
 445     mSlicerManagers[index]->GetImage()->GetVTKImages().size()-1,1,&ok);
 446   if (ok) {
 447     vvMidPosition midp;
 448     midp.slicer_manager = mSlicerManagers[index];
 449     midp.reference_image_index = ref;
 450     QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
 451     midp.Update();
 452     if (midp.error)
 453       QMessageBox::warning(this, "Error computing midposition image",midp.error_message.c_str());
 454     else {
 455       QFileInfo info(midp.slicer_manager->GetFileName().c_str());
 456       AddImage(midp.output,info.path().toStdString()+"/"+info.completeBaseName().toStdString()+"_midposition.mhd");
 457     }
 458     QApplication::restoreOverrideCursor();
 459   }
 460 }
 461 //------------------------------------------------------------------------------
 462
 463
 464 //------------------------------------------------------------------------------
 465 void vvMainWindow::AddContour(int image_index, vvMesh::Pointer contour, bool propagation)
 466 {
 467   QTreeWidgetItem *item = new QTreeWidgetItem();
 468   item->setData(0,Qt::UserRole,"filename.vtk");
 469   item->setData(1,Qt::UserRole,tr("contour"));
 470   QBrush brush;
 471   brush.setColor(QColor(contour->r*255,contour->g*255,contour->b*255));
 472   brush.setStyle(Qt::SolidPattern);
 473   item->setData(COLUMN_IMAGE_NAME,Qt::BackgroundRole,brush);
 474   //  item->setData(COLUMN_IMAGE_NAME,Qt::DisplayRole,contour->structure_name.c_str());
 475
 476   for (int j = 1; j <= 4; j++)
 477     item->setData(j,Qt::CheckStateRole,DataTree->topLevelItem(image_index)->data(j,Qt::CheckStateRole));
 478
 479   QTreePushButton* cButton = new QTreePushButton;
 480   cButton->setItem(item);
 481   cButton->setColumn(COLUMN_CLOSE_IMAGE);
 482   cButton->setToolTip(tr("close image"));
 483   cButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/exit.png")));
 484   connect(cButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
 485     this,SLOT(CloseImage(QTreeWidgetItem*, int)));
 486
 487   QTreePushButton* rButton = new QTreePushButton;
 488   rButton->setItem(item);
 489   rButton->setColumn(COLUMN_RELOAD_IMAGE);
 490   rButton->setToolTip(tr("reload image"));
 491   rButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/rotateright.png")));
 492   rButton->setEnabled(false);
 493   //Not implemented
 494   //connect(rButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
 495   //this,SLOT(ReloadImage(QTreeWidgetItem*, int)));
 496
 497   DataTree->topLevelItem(image_index)->setExpanded(1);
 498   DataTree->topLevelItem(image_index)->addChild(item);
 499   DataTree->setItemWidget(item, COLUMN_CLOSE_IMAGE, cButton);
 500   DataTree->setItemWidget(item, COLUMN_RELOAD_IMAGE, rButton);
 501   QString id = DataTree->topLevelItem(image_index)->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString();
 502   item->setData(COLUMN_IMAGE_NAME,Qt::UserRole,id.toStdString().c_str());
 503
 504   UpdateTree();
 505   mSlicerManagers[image_index]->AddContour(contour,propagation);
 506   mSlicerManagers[image_index]->Render();
 507 }
 508 //------------------------------------------------------------------------------
 509
 510
 511 //------------------------------------------------------------------------------
 512 void vvMainWindow::OpenVTKContour()
 513 {
 514   if (mSlicerManagers.size() > 0) {
 515     QString Extensions = "Images ( *.vtk *.obj)";
 516     Extensions += ";;All Files (*)";
 517     QString file = QFileDialog::getOpenFileName(this,tr("Open vtkPolyData"),mInputPathName,Extensions);
 518     if (file.isNull())
 519       return;
 520     QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
 521     int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
 522     vvMeshReader reader;
 523     reader.SetImage(mSlicerManagers[index]->GetImage());
 524     reader.SetModeToVTK();
 525     reader.SetFilename(file.toStdString());
 526     reader.Update();
 527     AddContour(index,reader.GetOutput()[0],false);
 528     QApplication::restoreOverrideCursor();
 529   }
 530 }
 531 //------------------------------------------------------------------------------
 532
 533
 534 //------------------------------------------------------------------------------
 535 void vvMainWindow::AddDCStructContour(int index, QString file)
 536 {
 537   vvMeshReader reader;
 538   reader.SetFilename(file.toStdString());
 539   vvStructSelector selector;
 540   selector.SetStructures(reader.GetROINames());
 541   if (!mSlicerManagers[index]->GetVF().IsNull())
 542     selector.EnablePropagationCheckBox();
 543   if (selector.exec()) {
 544     QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
 545     reader.SetSelectedItems(selector.getSelectedItems());
 546     reader.SetImage(mSlicerManagers[index]->GetImage());
 547     if (selector.PropagationEnabled())
 548       reader.SetPropagationVF(mSlicerManagers[index]->GetVF());
 549     reader.Update();
 550     std::vector<vvMesh::Pointer> contours=reader.GetOutput();
 551     for (std::vector<vvMesh::Pointer>::iterator i=contours.begin();
 552       i!=contours.end(); i++)
 553       AddContour(index,*i,selector.PropagationEnabled());
 554     QApplication::restoreOverrideCursor();
 555   }
 556 }
 557
 558 //------------------------------------------------------------------------------
 559 void vvMainWindow::OpenDCStructContour()
 560 {
 561   if (mSlicerManagers.size() > 0) {
 562     QString Extensions = "Dicom Files ( *.dcm RS*)";
 563     Extensions += ";;All Files (*)";
 564     QString file = QFileDialog::getOpenFileName(this,tr("Merge Images"),mInputPathName,Extensions);
 565     if (file.isNull())
 566       return;
 567     int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
 568     AddDCStructContour(index, file);
 569   }
 570 }
 571 //------------------------------------------------------------------------------
 572
 573
 574 //------------------------------------------------------------------------------
 575 void vvMainWindow::ComputeDeformableRegistration()
 576 {
 577   if (mSlicerManagers.size() > 0) {
 578     int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
 579     vvDeformationDialog dialog(index,mSlicerManagers);
 580     if (dialog.exec()) {
 581       std::string base_name=itksys::SystemTools::GetFilenameWithoutExtension(mSlicerManagers[dialog.GetInputFileIndex()]->GetFileName());
 582       AddField(dialog.GetOutput(),dialog.getFieldFile(),dialog.GetInputFileIndex());
 583       WarpImage(dialog.GetSelectedSlicer(),dialog.GetReferenceFrameIndex());
 584     } else
 585       std::cout << "Error or user cancellation while computing deformation field..." << std::endl;
 586   } else QMessageBox::information(this, "Need to open image","You must open an image first.");
 587 }
 588 //------------------------------------------------------------------------------
 589
 590
 591 //------------------------------------------------------------------------------
 592 void vvMainWindow::WarpImage()
 593 {
 594   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
 595   if (!mSlicerManagers[index]->GetVF().IsNull()) {
 596     bool ok;
 597     int ref = QInputDialog::getInteger(this,"Chose reference phase","Reference phase",0,0,\
 598       mSlicerManagers[index]->GetImage()->GetVTKImages().size()-1,1,&ok);
 599     if (ok) {
 600       WarpImage(mSlicerManagers[index],ref);
 601     }
 602   } else
 603     QMessageBox::warning(this,tr("No vector field"),tr("Sorry, can't warp without a vector field"));
 604 }
 605 //------------------------------------------------------------------------------
 606
 607
 608 //------------------------------------------------------------------------------
 609 void vvMainWindow::WarpImage(vvSlicerManager* selected_slicer,int reference_phase)
 610 {
 611   if (!selected_slicer->GetVF().IsNull()) {
 612     QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
 613     QFileInfo info(selected_slicer->GetFileName().c_str());
 614     vvImageWarp warp(selected_slicer->GetImage(),selected_slicer->GetVF(),
 615       reference_phase,this);
 616     if (warp.ComputeWarpedImage()) {
 617       AddImage(warp.GetWarpedImage(),info.path().toStdString()+"/"+info.completeBaseName().toStdString()+"_warped.mhd");
 618       AddImage(warp.GetDiffImage()  ,info.path().toStdString()+"/"+info.completeBaseName().toStdString()+"_diff.mhd");
 619       AddImage(warp.GetJacobianImage()  ,info.path().toStdString()+"/"+info.completeBaseName().toStdString()+"_jacobian.mhd");
 620       QApplication::restoreOverrideCursor();
 621     } else {
 622       QApplication::restoreOverrideCursor();
 623       QMessageBox::warning(this,tr("Different spacings"),tr("The vector field and image spacings must be the same in order to warp."));
 624     }
 625   } else
 626     QMessageBox::warning(this,tr("No vector field"),tr("Sorry, can't warp without a vector field."));
 627 }
 628 //------------------------------------------------------------------------------
 629
 630
 631 //------------------------------------------------------------------------------
 632 vvMainWindow::~vvMainWindow()
 633 {
 634   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
 635     if (mSlicerManagers[i] != NULL)
 636       delete mSlicerManagers[i];
 637   }
 638 }
 639 //------------------------------------------------------------------------------
 640
 641 //------------------------------------------------------------------------------
 642 QTabWidget * vvMainWindow::GetTab()
 643 {
 644   return tabWidget;
 645 }
 646 //------------------------------------------------------------------------------
 647
 648
 649 //------------------------------------------------------------------------------
 650 void vvMainWindow::MergeImages()
 651 {
 652   QString Extensions = EXTENSIONS;
 653   Extensions += ";;All Files (*)";
 654   QStringList files = QFileDialog::getOpenFileNames(this,tr("Merge Images"),mInputPathName,Extensions);
 655   if (files.isEmpty())
 656     return;
 657   mInputPathName = itksys::SystemTools::GetFilenamePath(files[0].toStdString()).c_str();
 658   std::vector<std::string> vector;
 659
 660   unsigned int currentDim = 0;
 661   std::vector<double> currentSpacing;
 662   std::vector<int> currentSize;
 663   std::vector<double> currentOrigin;
 664
 665   for (int i = 0; i < files.size(); i++) {
 666     itk::ImageIOBase::Pointer reader = itk::ImageIOFactory::CreateImageIO(
 667       files[i].toStdString().c_str(), itk::ImageIOFactory::ReadMode);
 668     reader->SetFileName(files[i].toStdString().c_str());
 669     reader->ReadImageInformation();
 670     if (reader)        {
 671       //NOViewWidget->hide();
 672       //NEViewWidget->hide();
 673       //SOViewWidget->hide();
 674       //SEViewWidget->hide();
 675       if (i == 0)
 676         currentDim = reader->GetNumberOfDimensions();
 677       bool IsOk = true;
 678       for (unsigned int j = 0; j < currentDim; j++) {
 679         if (i == 0) {
 680           if (j == 0) {
 681             currentSpacing.resize(currentDim);
 682             currentSize.resize(currentDim);
 683             currentOrigin.resize(currentDim);
 684           }
 685           currentOrigin[j] = reader->GetOrigin(j);
 686           currentSpacing[j] = reader->GetSpacing(j);
 687           currentSize[j] = reader->GetDimensions(j);
 688         } else if (currentDim != reader->GetNumberOfDimensions()
 689           || currentSpacing[j] != reader->GetSpacing(j)
 690           || currentSize[j] != (int)reader->GetDimensions(j)
 691           || currentOrigin[j] != reader->GetOrigin(j)) {
 692             QString error = "Cannot read file (too different from others ";
 693             error += files[i].toStdString().c_str();
 694             QMessageBox::information(this,tr("Reading problem"),error);
 695             IsOk = false;
 696             break;
 697         }
 698       }
 699       if (IsOk)
 700         vector.push_back(files[i].toStdString());
 701     }
 702   }
 703   if (vector.size() > 0)
 704     LoadImages(vector, vvImageReader::MERGED);
 705 }
 706 //------------------------------------------------------------------------------
 707
 708 //------------------------------------------------------------------------------
 709 void vvMainWindow::SliceImages()
 710 {
 711   QString Extensions = EXTENSIONS;
 712   Extensions += ";;All Files (*)";
 713
 714   QStringList files = QFileDialog::getOpenFileNames(this,tr("Slice Images"),mInputPathName,Extensions);
 715   if (files.isEmpty())
 716     return;
 717   mInputPathName = itksys::SystemTools::GetFilenamePath(files[0].toStdString()).c_str();
 718   std::vector<std::string> vector;
 719   for (int i = 0; i < files.size(); i++)
 720     vector.push_back(files[i].toStdString());
 721   LoadImages(vector, vvImageReader::SLICED);
 722 }
 723 //------------------------------------------------------------------------------
 724
 725 //------------------------------------------------------------------------------
 726 void vvMainWindow::MergeImagesWithTime()
 727 {
 728   QString Extensions = EXTENSIONS;
 729   Extensions += ";;All Files (*)";
 730   QStringList files = QFileDialog::getOpenFileNames(this,tr("Merge Images With Time"),mInputPathName,Extensions);
 731   if (files.isEmpty())
 732     return;
 733   mInputPathName = itksys::SystemTools::GetFilenamePath(files[0].toStdString()).c_str();
 734   std::vector<std::string> vector;
 735
 736   for (int i = 0; i < files.size(); i++)
 737     vector.push_back(files[i].toStdString());
 738   sort(vector.begin(),vector.end());
 739   if (vector.size() > 1)
 740     LoadImages(vector, vvImageReader::MERGEDWITHTIME);
 741   else
 742     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.");
 743 }
 744 //------------------------------------------------------------------------------
 745
 746
 747 //------------------------------------------------------------------------------
 748 void vvMainWindow::OpenDicom()
 749 {
 750   std::vector<std::string> files;
 751
 752   //std::cout << "dicomSeriesSelector " << std::endl;
 753   if (dicomSeriesSelector->exec() == QDialog::Accepted) {
 754     files = *(dicomSeriesSelector->GetFilenames());
 755     LoadImages(files, vvImageReader::DICOM);
 756   }
 757 }
 758 #ifdef CLITK_USE_PACS_CONNECTION
 759 void vvMainWindow::ConnectPacs()
 760 {
 761   std::vector<std::string> files;
 762
 763   //std::cout << "dicomSeriesSelector " << std::endl;
 764 if (PacsConnection->exec() == QDialog::Accepted) {
 765         files = PacsConnection->getFileNames();
 766     LoadImages(files, vvImageReader::DICOM);
 767         PacsConnection->clearMove();
 768   }
 769   }
 770
 771 #endif
 772 //------------------------------------------------------------------------------
 773
 774 //------------------------------------------------------------------------------
 775 void vvMainWindow::OpenImages()
 776 {
 777   QString Extensions = EXTENSIONS;
 778   Extensions += ";;All Files (*)";
 779
 780   QStringList files = QFileDialog::getOpenFileNames(this,tr("Load Images"),mInputPathName,Extensions);
 781   if (files.isEmpty())
 782     return;
 783   mInputPathName = itksys::SystemTools::GetFilenamePath(files[0].toStdString()).c_str();
 784   std::vector<std::string> vector;
 785   for (int i = 0; i < files.size(); i++)
 786     vector.push_back(files[i].toStdString());
 787   LoadImages(vector, vvImageReader::IMAGE);
 788 }
 789 //------------------------------------------------------------------------------
 790 void vvMainWindow::OpenRecentImage()
 791 {
 792   QAction * caller = qobject_cast<QAction*>(sender());
 793   std::vector<std::string> images;
 794   images.push_back(caller->text().toStdString());
 795   mInputPathName = itksys::SystemTools::GetFilenamePath(images[0]).c_str();
 796   LoadImages(images, vvImageReader::IMAGE);
 797 }
 798 //------------------------------------------------------------------------------
 799
 800
 801 //------------------------------------------------------------------------------
 802 void vvMainWindow::OpenImageWithTime()
 803 {
 804   QString Extensions = EXTENSIONS;
 805   Extensions += ";;All Files (*)";
 806
 807   QStringList files = QFileDialog::getOpenFileNames(this,tr("Load Images With Time"),mInputPathName,Extensions);
 808   if (files.isEmpty())
 809     return;
 810   mInputPathName = itksys::SystemTools::GetFilenamePath(files[0].toStdString()).c_str();
 811   std::vector<std::string> vector;
 812   for (int i = 0; i < files.size(); i++) {
 813     vector.push_back(files[i].toStdString());
 814   }
 815   LoadImages(vector, vvImageReader::IMAGEWITHTIME);
 816 }
 817 //------------------------------------------------------------------------------
 818
 819
 820 //------------------------------------------------------------------------------
 821 void vvMainWindow::LoadImages(std::vector<std::string> files, vvImageReader::LoadedImageType filetype)
 822 {
 823   //Separate the way to open images and dicoms
 824   int fileSize;
 825   if (filetype == vvImageReader::IMAGE || filetype == vvImageReader::IMAGEWITHTIME)
 826     fileSize = files.size();
 827   else
 828     fileSize = 1;
 829
 830   // For SLICED, we need the number of slices (ndim and #slices)
 831   std::vector<unsigned int> nSlices;
 832   nSlices.resize(files.size());
 833   std::fill(nSlices.begin(), nSlices.end(), 1);
 834   if (filetype == vvImageReader::SLICED) {
 835     for (int i = 0; i < fileSize; i++) {
 836       itk::ImageIOBase::Pointer header = clitk::readImageHeader(files[i]);
 837       QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
 838       if (!header) {
 839         nSlices[i] = 0;
 840         QString error = "Cannot open file \n";
 841         error += files[i].c_str();
 842         QMessageBox::information(this,tr("Reading problem"),error);
 843         return;
 844       }
 845       if (header->GetNumberOfDimensions() < 3) {
 846         nSlices[i] = 0;
 847         QString error = "Dimension problem. Cannot slice \n";
 848         error += files[i].c_str();
 849         QMessageBox::information(this,tr("Reading problem"),error);
 850         return;
 851       }
 852       nSlices[i] = header->GetDimensions( header->GetNumberOfDimensions()-1 );
 853     }
 854   }
 855
 856   //Only add to the list of recently opened files when a single file is opened,
 857   //to avoid polluting the list of recently opened files
 858   if (files.size() == 1) {
 859     QFileInfo finfo=tr(files[0].c_str());
 860     AddToRecentlyOpenedImages(finfo.absoluteFilePath().toStdString());
 861     updateRecentlyOpenedFilesMenu(GetRecentlyOpenedImages());
 862   }
 863   //init the progress events
 864   QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
 865   vvProgressDialog progress("Opening " + files[0],fileSize>1);
 866   qApp->processEvents();
 867
 868   int numberofsuccesulreads=0;
 869   //open images as 1 or multiples
 870   for (int i = 0; i < fileSize; i++) {
 871     progress.SetText("Opening " + files[i]);
 872     progress.SetProgress(i,fileSize);
 873     qApp->processEvents();
 874
 875     for (unsigned int j = 0; j < nSlices[i]; j++) {
 876       //read the image and put it in mSlicerManagers
 877       vvSlicerManager* imageManager = new vvSlicerManager(4);
 878       qApp->processEvents();
 879
 880       bool SetImageSucceed=false;
 881
 882       // Change filename if an image with the same already exist
 883       int number = GetImageDuplicateFilenameNumber(files[i] + std::string("_slice"));
 884
 885       if (filetype == vvImageReader::IMAGE || filetype == vvImageReader::IMAGEWITHTIME || filetype == vvImageReader::SLICED)
 886         SetImageSucceed = imageManager->SetImage(files[i],filetype, number, j);
 887       else {
 888         SetImageSucceed = imageManager->SetImages(files,filetype, number);
 889       }
 890
 891       if (!SetImageSucceed) {
 892         QApplication::restoreOverrideCursor();
 893         QString error = "Cannot open file \n";
 894         error += imageManager->GetLastError().c_str();
 895         QMessageBox::information(this,tr("Reading problem"),error);
 896         delete imageManager;
 897       } else {
 898         mSlicerManagers.push_back(imageManager);
 899
 900         //create an item in the tree with good settings
 901         QTreeWidgetItem *item = new QTreeWidgetItem();
 902         item->setData(0,Qt::UserRole,files[i].c_str());
 903         QFileInfo fileinfo(imageManager->GetFileName().c_str()); //Do not show the path
 904         item->setData(COLUMN_IMAGE_NAME,Qt::DisplayRole,fileinfo.fileName());
 905         item->setData(1,Qt::UserRole,tr("image"));
 906         item->setToolTip(COLUMN_IMAGE_NAME, imageManager->GetListOfAbsoluteFilePathInOneString("image").c_str());
 907         qApp->processEvents();
 908
 909         //Create the buttons for reload and close
 910         qApp->processEvents();
 911         QTreePushButton* cButton = new QTreePushButton;
 912         cButton->setItem(item);
 913         cButton->setColumn(COLUMN_CLOSE_IMAGE);
 914         cButton->setToolTip(tr("close image"));
 915         cButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/exit.png")));
 916         connect(cButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
 917           this,SLOT(CloseImage(QTreeWidgetItem*, int)));
 918
 919         QTreePushButton* rButton = new QTreePushButton;
 920         rButton->setItem(item);
 921         rButton->setColumn(COLUMN_RELOAD_IMAGE);
 922         rButton->setToolTip(tr("reload image"));
 923         rButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/rotateright.png")));
 924         connect(rButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
 925           this,SLOT(ReloadImage(QTreeWidgetItem*, int)));
 926
 927         DataTree->addTopLevelItem(item);
 928         DataTree->setItemWidget(item, COLUMN_CLOSE_IMAGE, cButton);
 929         DataTree->setItemWidget(item, COLUMN_RELOAD_IMAGE, rButton);
 930
 931         //set the id of the image
 932         QString id = QDir::current().absoluteFilePath(files[i].c_str()) + QString::number(mSlicerManagers.size()-1);
 933         item->setData(COLUMN_IMAGE_NAME,Qt::UserRole,id.toStdString().c_str());
 934         mSlicerManagers.back()->SetId(id.toStdString());
 935
 936         linkPanel->addImage(imageManager->GetFileName(), id.toStdString());
 937
 938         connect(mSlicerManagers.back(), SIGNAL(currentImageChanged(std::string)),
 939           this,SLOT(CurrentImageChanged(std::string)));
 940         connect(mSlicerManagers.back(), SIGNAL(currentPickedImageChanged(std::string)),
 941           this, SLOT(CurrentPickedImageChanged(std::string)));
 942         connect(mSlicerManagers.back(), SIGNAL(UpdatePosition(int, double, double, double, double, double, double, double)),
 943           this,SLOT(MousePositionChanged(int,double, double, double, double, double, double, double)));
 944         connect(mSlicerManagers.back(), SIGNAL(UpdateVector(int, double, double, double, double)),
 945           this, SLOT(VectorChanged(int,double,double,double, double)));
 946         connect(mSlicerManagers.back(), SIGNAL(UpdateOverlay(int, double, double)),
 947           this, SLOT(OverlayChanged(int,double,double)));
 948         connect(mSlicerManagers.back(), SIGNAL(UpdateFusion(int, double)),
 949           this, SLOT(FusionChanged(int,double)));
 950         connect(mSlicerManagers.back(), SIGNAL(WindowLevelChanged()),
 951           this,SLOT(WindowLevelChanged()));
 952         connect(mSlicerManagers.back(), SIGNAL(UpdateSlice(int,int)),
 953           this,SLOT(UpdateSlice(int,int)));
 954         connect(mSlicerManagers.back(), SIGNAL(UpdateTSlice(int, int, int)),
 955           this,SLOT(UpdateTSlice(int, int, int)));
 956         connect(mSlicerManagers.back(), SIGNAL(UpdateTSlice(int, int, int)),
 957           this,SLOT(ImageInfoChanged()));
 958         connect(mSlicerManagers.back(), SIGNAL(UpdateSliceRange(int,int,int,int,int)),
 959           this,SLOT(UpdateSliceRange(int,int,int,int,int)));
 960         connect(mSlicerManagers.back(), SIGNAL(UpdateLinkManager(std::string,int,double,double,double,int)),
 961           this,SLOT(UpdateLinkManager(std::string,int,double,double,double,int)));
 962         connect(mSlicerManagers.back(), SIGNAL(UpdateLinkedNavigation(std::string,vvSlicerManager*,vvSlicer*)),
 963           this,SLOT(UpdateLinkedNavigation(std::string,vvSlicerManager*,vvSlicer*)));
 964         connect(mSlicerManagers.back(), SIGNAL(ChangeImageWithIndexOffset(vvSlicerManager*,int,int)),
 965           this,SLOT(ChangeImageWithIndexOffset(vvSlicerManager*,int,int)));
 966         connect(mSlicerManagers.back(),SIGNAL(LandmarkAdded()),landmarksPanel,SLOT(AddPoint()));
 967
 968         InitSlicers();
 969         numberofsuccesulreads++;
 970       }
 971     }
 972   }
 973   if (numberofsuccesulreads) {
 974     NOViewWidget->show();
 975     NEViewWidget->show();
 976     SOViewWidget->show();
 977     SEViewWidget->show();
 978     UpdateTree();
 979     InitDisplay();
 980     ShowLastImage();
 981
 982     // Try to guess default WindowLevel
 983     double range[2];
 984     mSlicerManagers.back()->GetImage()->GetFirstVTKImageData()->GetScalarRange(range);
 985     if ((range[0] == 0) && (range[1] == 1)) {
 986       presetComboBox->setCurrentIndex(WL_BINARY);// binary
 987     } else {
 988       // TODO
 989     }
 990   }
 991   QApplication::restoreOverrideCursor();
 992 }
 993 //------------------------------------------------------------------------------
 994
 995 //------------------------------------------------------------------------------
 996 void vvMainWindow::UpdateTree()
 997 {
 998   DataTree->resizeColumnToContents(COLUMN_TREE);
 999   DataTree->resizeColumnToContents(COLUMN_UL_VIEW);
1000   DataTree->resizeColumnToContents(COLUMN_UR_VIEW);
1001   DataTree->resizeColumnToContents(COLUMN_DL_VIEW);
1002   DataTree->resizeColumnToContents(COLUMN_DR_VIEW);
1003   DataTree->resizeColumnToContents(COLUMN_IMAGE_NAME);
1004   DataTree->resizeColumnToContents(COLUMN_CLOSE_IMAGE);
1005   DataTree->resizeColumnToContents(COLUMN_RELOAD_IMAGE);
1006 }
1007 //------------------------------------------------------------------------------
1008
1009 //------------------------------------------------------------------------------
1010 void vvMainWindow::CurrentImageChanged(std::string id)
1011 {
1012   if (id == mCurrentSelectedImageId) return; // Do nothing
1013   int selected = 0;
1014   for (int i = 0; i < DataTree->topLevelItemCount(); i++) {
1015     if (DataTree->topLevelItem(i)->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString().toStdString() == id) {
1016       selected = i;
1017     } else {
1018       DataTree->topLevelItem(i)->setSelected(0);
1019     }
1020     for (int child = 0; child < DataTree->topLevelItem(i)->childCount(); child++)
1021       DataTree->topLevelItem(i)->child(child)->setSelected(0);
1022
1023   }
1024   DataTree->topLevelItem(selected)->setSelected(1);
1025   mCurrentSelectedImageId = id;
1026
1027   landmarksPanel->SetCurrentLandmarks(mSlicerManagers[selected]->GetLandmarks(),
1028                                       mSlicerManagers[selected]->GetTSlice());
1029   landmarksPanel->SetCurrentPath(mInputPathName.toStdString());
1030   landmarksPanel->SetCurrentImage(mSlicerManagers[selected]->GetFileName().c_str());
1031
1032   emit SelectedImageHasChanged(mSlicerManagers[selected]);
1033 }
1034 //------------------------------------------------------------------------------
1035
1036 //------------------------------------------------------------------------------
1037 void vvMainWindow::CurrentPickedImageChanged(std::string id)
1038 {
1039   if (id == mCurrentPickedImageId) return; // Do nothing
1040   int selected = 0;
1041   for (int i = 0; i < DataTree->topLevelItemCount(); i++) {
1042     if (DataTree->topLevelItem(i)->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString().toStdString() == id) {
1043       selected = i;
1044     } else {
1045       DataTree->topLevelItem(i)->setSelected(0);
1046     }
1047     for (int child = 0; child < DataTree->topLevelItem(i)->childCount(); child++)
1048       DataTree->topLevelItem(i)->child(child)->setSelected(0);
1049
1050   }
1051   DataTree->topLevelItem(selected)->setSelected(1);
1052   mCurrentPickedImageId = id;
1053   mCurrentPickedImageIndex = selected;
1054 }
1055 //------------------------------------------------------------------------------
1056
1057 //------------------------------------------------------------------------------
1058 void vvMainWindow::ImageInfoChanged()
1059 {
1060   contextActions[6]->setEnabled(1);
1061   contextActions[5]->setEnabled(1);
1062   actionSave_As->setEnabled(1);
1063   actionAdd_VF_to_current_Image->setEnabled(1);
1064   actionAdd_fusion_image->setEnabled(1);
1065   actionAdd_overlay_image_to_current_image->setEnabled(1);
1066   actionAdd_USSequence_toCT->setEnabled(1);
1067   actionNorth_East_Window->setEnabled(1);
1068   actionNorth_West_Window->setEnabled(1);
1069   actionSouth_East_Window->setEnabled(1);
1070   actionSouth_West_Window->setEnabled(1);
1071   vvToolManager::GetInstance()->EnableToolsInMenu(this, true);
1072   inverseButton->setEnabled(1);
1073
1074   goToCursorPushButton->setEnabled(1);
1075
1076   if (DataTree->selectedItems().size()) {
1077     int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1078
1079     colorMapComboBox->setEnabled(1);
1080     for (int i = 0; i < DataTree->topLevelItem(index)->childCount(); i++) {
1081       if (DataTree->topLevelItem(index)->child(i)->data(1,Qt::UserRole).toString() == "overlay" ||
1082         DataTree->topLevelItem(index)->child(i)->data(1,Qt::UserRole).toString() == "fusion" ||
1083         DataTree->topLevelItem(index)->child(i)->data(1,Qt::UserRole).toString() == "fusionSequence") {
1084           colorMapComboBox->setEnabled(0);
1085           break;
1086       }
1087     }
1088
1089     std::vector<double> origin;
1090     std::vector<double> inputSpacing;
1091     std::vector<int> inputSize;
1092     std::vector<double> sizeMM;
1093     vtkSmartPointer<vtkMatrix4x4> transformation;
1094     int dimension=0;
1095     QString pixelType;
1096     QString inputSizeInBytes;
1097     QString image = DataTree->selectedItems()[0]->data(COLUMN_IMAGE_NAME,Qt::DisplayRole).toString();
1098
1099     int nframes = mSlicerManagers[index]->GetSlicer(0)->GetTMax();
1100
1101     if (nframes > 1 || playMode == 1) {
1102       playButton->setEnabled(1);
1103       frameRateLabel->setEnabled(1);
1104       frameRateSpinBox->setEnabled(1);
1105     } else {
1106       playButton->setEnabled(0);
1107       frameRateLabel->setEnabled(0);
1108       frameRateSpinBox->setEnabled(0);
1109     }
1110
1111     //read image header
1112     int NPixel = 1;
1113
1114     int tSlice = 0;
1115     vvImage::Pointer imageSelected;
1116     if (DataTree->topLevelItem(index) == DataTree->selectedItems()[0]) {
1117       imageSelected = mSlicerManagers[index]->GetSlicer(0)->GetImage();
1118       tSlice = mSlicerManagers[index]->GetSlicer(0)->GetTSlice();
1119     } else if (DataTree->selectedItems()[0]->data(1,Qt::UserRole).toString() == "vector") {
1120       imageSelected = mSlicerManagers[index]->GetSlicer(0)->GetVF();
1121       tSlice = mSlicerManagers[index]->GetSlicer(0)->GetOverlayTSlice();
1122     } else if (DataTree->selectedItems()[0]->data(1,Qt::UserRole).toString() == "overlay") {
1123       imageSelected = mSlicerManagers[index]->GetSlicer(0)->GetOverlay();
1124       tSlice = mSlicerManagers[index]->GetSlicer(0)->GetOverlayTSlice();
1125     } else if (DataTree->selectedItems()[0]->data(1,Qt::UserRole).toString() == "fusion") {
1126       imageSelected = mSlicerManagers[index]->GetSlicer(0)->GetFusion();
1127       tSlice = mSlicerManagers[index]->GetSlicer(0)->GetFusionTSlice();
1128     }
1129     else if (DataTree->selectedItems()[0]->data(1,Qt::UserRole).toString() == "fusionSequence") {
1130       imageSelected = mSlicerManagers[index]->GetSlicer(0)->GetFusion();
1131       tSlice = mSlicerManagers[index]->GetSlicer(0)->GetFusionTSlice();
1132     }
1133     else if (DataTree->selectedItems()[0]->data(1,Qt::UserRole).toString() == "contour") {
1134       imageSelected = mSlicerManagers[index]->GetSlicer(0)->GetImage();
1135       tSlice = mSlicerManagers[index]->GetSlicer(0)->GetTSlice();
1136     }
1137     else {
1138       imageSelected = mSlicerManagers[index]->GetSlicer(0)->GetImage();
1139       tSlice = mSlicerManagers[index]->GetSlicer(0)->GetTSlice();
1140     }
1141
1142     dimension = imageSelected->GetNumberOfDimensions();
1143     origin.resize(dimension);
1144     inputSpacing.resize(dimension);
1145     inputSize.resize(dimension);
1146     sizeMM.resize(dimension);
1147     pixelType = mSlicerManagers[index]->GetImage()->GetScalarTypeAsITKString().c_str();
1148     for (int i = 0; i < dimension; i++) {
1149       origin[i] = imageSelected->GetOrigin()[i];
1150       inputSpacing[i] = imageSelected->GetSpacing()[i];
1151       inputSize[i] = imageSelected->GetSize()[i];
1152       sizeMM[i] = inputSize[i]*inputSpacing[i];
1153       NPixel *= inputSize[i];
1154     }
1155     inputSizeInBytes = GetSizeInBytes(imageSelected->GetActualMemorySize()*1000);
1156
1157     QString dim = QString::number(dimension) + " (";
1158     dim += pixelType + ")";
1159
1160     infoPanel->setFileName(image);
1161     std::string creationImageTimeValue("No creation time");
1162     itk::ExposeMetaData< std::string > (*imageSelected->GetFirstMetaDataDictionary(), "creationImageTime", creationImageTimeValue);
1163     infoPanel->setImageCreationTime(QString(creationImageTimeValue.c_str()));
1164     infoPanel->setDimension(dim);
1165     infoPanel->setSizePixel(GetVectorIntAsString(inputSize));
1166     infoPanel->setSizeMM(GetVectorDoubleAsString(sizeMM));
1167     infoPanel->setOrigin(GetVectorDoubleAsString(origin));
1168     infoPanel->setSpacing(GetVectorDoubleAsString(inputSpacing));
1169     infoPanel->setNPixel(QString::number(NPixel)+" ("+inputSizeInBytes+")");
1170
1171     transformation = imageSelected->GetTransform()[tSlice]->GetMatrix();
1172     infoPanel->setTransformation(clitk::Get4x4MatrixDoubleAsString(transformation).c_str());
1173
1174     landmarksPanel->SetCurrentLandmarks(mSlicerManagers[index]->GetLandmarks(),
1175                                         mSlicerManagers[index]->GetTSlice());
1176     landmarksPanel->SetCurrentPath(mInputPathName.toStdString());
1177     landmarksPanel->SetCurrentImage(mSlicerManagers[index]->GetFileName().c_str());
1178
1179     overlayPanel->getCurrentImageName(mSlicerManagers[index]->GetFileName().c_str());
1180     for (int i = 0; i < 4; i++) {
1181       if (DataTree->selectedItems()[0]->data(i+1,Qt::CheckStateRole).toInt() > 0 || i == 3) {
1182         mSlicerManagers[index]->UpdateInfoOnCursorPosition(i);
1183         break;
1184       }
1185     }
1186
1187 //     infoPanel->setFileName(image);
1188 //     infoPanel->setDimension(dim);
1189 //     infoPanel->setSizePixel(GetVectorIntAsString(inputSize));
1190 //     infoPanel->setSizeMM(GetVectorDoubleAsString(sizeMM));
1191 //     infoPanel->setOrigin(GetVectorDoubleAsString(origin));
1192 //     infoPanel->setSpacing(GetVectorDoubleAsString(inputSpacing));
1193 //     infoPanel->setNPixel(QString::number(NPixel)+" ("+inputSizeInBytes+")");
1194 //
1195 //     landmarksPanel->SetCurrentLandmarks(mSlicerManagers[index]->GetLandmarks(),
1196 //                                         mSlicerManagers[index]->GetTSlice());
1197 //     landmarksPanel->SetCurrentPath(mInputPathName.toStdString());
1198 //     landmarksPanel->SetCurrentImage(mSlicerManagers[index]->GetFileName().c_str());
1199 //
1200 //     overlayPanel->getCurrentImageName(mSlicerManagers[index]->GetFileName().c_str());
1201 //     for (int i = 0; i < 4; i++) {
1202 //       if (DataTree->selectedItems()[0]->data(i+1,Qt::CheckStateRole).toInt() > 0 || i == 3) {
1203 //         mSlicerManagers[index]->UpdateInfoOnCursorPosition(i);
1204 //         break;
1205 //       }
1206 //     }
1207     WindowLevelChanged();
1208
1209     slicingPresetComboBox->setCurrentIndex(mSlicerManagers[index]->GetSlicingPreset());
1210
1211     if (mSlicerManagers[index]->GetSlicer(0)->GetVF()) {
1212       overlayPanel->getVFName(mSlicerManagers[index]->GetVFName().c_str());
1213       overlayPanel->getVFProperty(mSlicerManagers[index]->GetSlicer(0)->GetVFSubSampling(),
1214         mSlicerManagers[index]->GetSlicer(0)->GetVFScale(),
1215         mSlicerManagers[index]->GetSlicer(0)->GetVFLog());
1216     } else {
1217       overlayPanel->getVFName(mSlicerManagers[index]->GetVFName().c_str());
1218       overlayPanel->getVFProperty(-1,-1,-1);
1219     }
1220     if (mSlicerManagers[index]->GetSlicer(0)->GetOverlay()) {
1221       overlayPanel->getOverlayName(mSlicerManagers[index]->GetOverlayName().c_str());
1222     } else {
1223       overlayPanel->getOverlayName(mSlicerManagers[index]->GetOverlayName().c_str());
1224     }
1225
1226     if (mSlicerManagers[index]->GetSlicer(0)->GetFusion()) {
1227       overlayPanel->getFusionName(mSlicerManagers[index]->GetFusionName().c_str());
1228     } else {
1229       overlayPanel->getFusionName(mSlicerManagers[index]->GetFusionName().c_str());
1230     }
1231   }
1232 }
1233 //------------------------------------------------------------------------------
1234
1235 //------------------------------------------------------------------------------
1236 void vvMainWindow::ShowDocumentation()
1237 {
1238   documentation->show();
1239 }
1240 //------------------------------------------------------------------------------
1241
1242 //------------------------------------------------------------------------------
1243 void vvMainWindow::PopupRegisterForm(bool checkCanPush)
1244 {
1245   vvRegisterForm* registerForm = new vvRegisterForm(QUrl("http://www.creatis.insa-lyon.fr/~dsarrut/vvregister/write.php"), getVVSettingsPath(), getSettingsOptionFormat());
1246   if(!checkCanPush) {
1247     registerForm->show();
1248   } else {
1249     if(registerForm->canPush()) {
1250       registerForm->show();
1251       registerForm->acquitPushed();//too bad if there is not internet connection anymore.
1252     }
1253   }
1254 }
1255 //------------------------------------------------------------------------------
1256
1257 //------------------------------------------------------------------------------
1258 void vvMainWindow::ShowHelpDialog()
1259 {
1260   help_dialog->show();
1261 }
1262 //------------------------------------------------------------------------------
1263
1264 //------------------------------------------------------------------------------
1265 void vvMainWindow::ChangeViewMode()
1266 {
1267   typedef struct _SIZE{
1268     QSplitter* splitter;
1269     QList<int> size1, size2;
1270     int cols[3];
1271   }SplitterSize;
1272   SplitterSize sizes[4];
1273   sizes[0].splitter = OSplitter;
1274   sizes[0].size1.push_back(1);
1275   sizes[0].size1.push_back(0);
1276   sizes[0].size2.push_back(1);
1277   sizes[0].size2.push_back(0);
1278   sizes[0].cols[0] = 2;
1279   sizes[0].cols[1] = 3;
1280   sizes[0].cols[2] = 4;
1281
1282   sizes[1].splitter = ESplitter;
1283   sizes[1].size1.push_back(0);
1284   sizes[1].size1.push_back(1);
1285   sizes[1].size2.push_back(1);
1286   sizes[1].size2.push_back(0);
1287   sizes[1].cols[0] = 1;
1288   sizes[1].cols[1] = 3;
1289   sizes[1].cols[2] = 4;
1290
1291   sizes[2].splitter = OSplitter;
1292   sizes[2].size1.push_back(1);
1293   sizes[2].size1.push_back(0);
1294   sizes[2].size2.push_back(0);
1295   sizes[2].size2.push_back(1);
1296   sizes[2].cols[0] = 1;
1297   sizes[2].cols[1] = 2;
1298   sizes[2].cols[2] = 4;
1299
1300   sizes[3].splitter = ESplitter;
1301   sizes[3].size1.push_back(0);
1302   sizes[3].size1.push_back(1);
1303   sizes[3].size2.push_back(0);
1304   sizes[3].size2.push_back(1);
1305   sizes[3].cols[0] = 1;
1306   sizes[3].cols[1] = 2;
1307   sizes[3].cols[2] = 3;
1308
1309   int slicer = mSlicerManagers[mCurrentPickedImageIndex]->GetSelectedSlicer();
1310   if (viewMode == 1) {
1311     if (slicer >= 0) {
1312       viewMode = 0;
1313       splitter_3->setSizes(sizes[slicer].size1);
1314       sizes[slicer].splitter->setSizes(sizes[slicer].size2);
1315       DataTree->setColumnHidden(sizes[slicer].cols[0],1);
1316       DataTree->setColumnHidden(sizes[slicer].cols[1],1);
1317       DataTree->setColumnHidden(sizes[slicer].cols[2],1);
1318     }
1319   } else {
1320     QList<int> size;
1321     if (slicer >= 0) {
1322       viewMode = 1;
1323       size.push_back(1);
1324       size.push_back(1);
1325       splitter_3->setSizes(size);
1326       sizes[slicer].splitter->setSizes(size);
1327       DataTree->setColumnHidden(sizes[slicer].cols[0],0);
1328       DataTree->setColumnHidden(sizes[slicer].cols[1],0);
1329       DataTree->setColumnHidden(sizes[slicer].cols[2],0);
1330     }
1331   }
1332   UpdateRenderWindows();
1333   /*
1334   ** I don't know why but for both resized QVTKWidget we also need to render
1335   ** the associated Slicer to redraw crosses.
1336   */
1337   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
1338     //     if (DataTree->topLevelItem(i)->data(COLUMN_UL_VIEW,Qt::CheckStateRole).toInt() > 1)
1339     mSlicerManagers[i]->GetSlicer(0)->Render();
1340     mSlicerManagers[i]->GetSlicer(1)->Render();
1341     //     if (DataTree->topLevelItem(i)->data(COLUMN_DL_VIEW,Qt::CheckStateRole).toInt() > 1)
1342     mSlicerManagers[i]->GetSlicer(2)->Render();
1343     mSlicerManagers[i]->GetSlicer(3)->Render();
1344   }
1345 }
1346 //------------------------------------------------------------------------------
1347
1348 //------------------------------------------------------------------------------
1349 QString vvMainWindow::GetSizeInBytes(unsigned long size)
1350 {
1351   QString result = "";// QString::number(size);
1352   //result += " bytes (";
1353   if (size > 1000000000) {
1354     size /= 1000000000;
1355     result += QString::number(size);
1356     result += "Gb";//)";
1357   } else if (size > 1000000) {
1358     size /= 1000000;
1359     result += QString::number(size);
1360     result += "Mb";//)";
1361   } else if (size > 1000) {
1362     size /= 1000;
1363     result += QString::number(size);
1364     result += "kb";//)";
1365   }
1366   return result;
1367 }
1368 //------------------------------------------------------------------------------
1369
1370 //------------------------------------------------------------------------------
1371 QString vvMainWindow::GetVectorDoubleAsString(std::vector<double> vectorDouble)
1372 {
1373   QString result;
1374   for (unsigned int i= 0; i < vectorDouble.size(); i++) {
1375     if (i != 0)
1376       result += " ";
1377     result += QString::number(vectorDouble[i]);
1378   }
1379   return result;
1380 }
1381 //------------------------------------------------------------------------------
1382
1383 //------------------------------------------------------------------------------
1384 QString vvMainWindow::GetVectorIntAsString(std::vector<int> vectorInt)
1385 {
1386   QString result;
1387   for (unsigned int i= 0; i < vectorInt.size(); i++) {
1388     if (i != 0)
1389       result += " ";
1390     result += QString::number(vectorInt[i]);
1391   }
1392   return result;
1393 }
1394 //------------------------------------------------------------------------------
1395
1396 //------------------------------------------------------------------------------
1397 //this actually returns the SlicerManager index!
1398 int vvMainWindow::GetSlicerIndexFromItem(QTreeWidgetItem* item)
1399 {
1400   QString id = item->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString();
1401   for (int i = 0; i < DataTree->topLevelItemCount(); i++) {
1402     if (DataTree->topLevelItem(i)->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString() == id)
1403       return i;
1404   }
1405   return -1;
1406 }
1407 //------------------------------------------------------------------------------
1408
1409 //------------------------------------------------------------------------------
1410 QTreeWidgetItem* vvMainWindow::GetItemFromSlicerManager(vvSlicerManager* sm)
1411 {
1412   QString id = sm->GetId().c_str();
1413   for (int i = 0; i < DataTree->topLevelItemCount(); i++) {
1414     if (DataTree->topLevelItem(i)->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString() == id)
1415       return DataTree->topLevelItem(i);
1416   }
1417   return NULL;
1418 }
1419 //------------------------------------------------------------------------------
1420
1421 //------------------------------------------------------------------------------
1422 void vvMainWindow::DisplayChanged(QTreeWidgetItem *clickedItem, int column)
1423 {
1424   if ( column >= COLUMN_CLOSE_IMAGE || column <= 0)
1425     return;
1426
1427   // Get parent information (might be the same item)
1428   int slicerManagerIndex = GetSlicerIndexFromItem(clickedItem);
1429   QTreeWidgetItem* clickedParentItem = DataTree->topLevelItem(slicerManagerIndex);
1430   vvSlicer* clickedSlicer = mSlicerManagers[slicerManagerIndex]->GetSlicer(column-1);
1431
1432   // Go over the complete item tree (only 2 levels, parents and children)
1433   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
1434     // Trick to avoid redoing twice the job for a key (sr)
1435     mSlicerManagers[i]->GetSlicer(column-1)->GetRenderWindow()->GetInteractor()->SetKeySym("Crap");
1436
1437     QTreeWidgetItem* currentParentItem = DataTree->topLevelItem(i);
1438     if(currentParentItem != clickedParentItem) {
1439       // Not the branch of the clicked item, uncheck all
1440
1441       // Parent
1442       currentParentItem->setData(column,Qt::CheckStateRole, 0);
1443       mSlicerManagers[i]->UpdateSlicer(column-1, false);
1444
1445       // Children
1446       for (int iChild = 0; iChild < currentParentItem->childCount(); iChild++) {
1447         currentParentItem->child(iChild)->setData(column,Qt::CheckStateRole, 0);
1448       }
1449     }
1450     else {
1451       // Branch of the clicked one: get check status from actor visibility in slicer
1452       // and toggle the clicked one
1453
1454       // Parent
1455       bool vis = clickedSlicer->GetActorVisibility("image", 0);
1456       bool draw = clickedSlicer->GetRenderer()->GetDraw();
1457
1458       // Update slicer (after getting visibility)
1459       mSlicerManagers[slicerManagerIndex]->UpdateSlicer(column-1, true);
1460       mSlicerManagers[slicerManagerIndex]->UpdateInfoOnCursorPosition(column-1);
1461       DisplaySliders(slicerManagerIndex, column-1);
1462       if(clickedParentItem == clickedItem) {
1463         // Toggle
1464         vis = !draw || !vis;
1465       }
1466       clickedSlicer->SetActorVisibility("image", 0, vis);
1467       clickedParentItem->setData(column, Qt::CheckStateRole, vis?2:0);
1468
1469       // Children
1470       std::map<std::string, int> actorTypeCounts;
1471       for (int iChild = 0; iChild < clickedParentItem->childCount(); iChild++) {
1472         QTreeWidgetItem* currentChildItem = clickedParentItem->child(iChild);
1473         std::string actorType = currentChildItem->data(1,Qt::UserRole).toString().toStdString();
1474         vis = clickedSlicer->GetActorVisibility(actorType, actorTypeCounts[actorType]);
1475         if(currentChildItem == clickedItem) {
1476           // Toggle or force visibility if it was not on this branch so far
1477           vis = !draw || !vis;
1478           clickedSlicer->SetActorVisibility(actorType, actorTypeCounts[actorType], vis);
1479         }
1480         currentChildItem->setData(column, Qt::CheckStateRole, vis?2:0);
1481         actorTypeCounts[actorType]++;
1482       }
1483     }
1484   }
1485
1486   clickedSlicer->Render();
1487 }
1488 //------------------------------------------------------------------------------
1489
1490 void vvMainWindow::InitSlicers()
1491 {
1492   if (mSlicerManagers.size()) {
1493     mSlicerManagers.back()->GenerateDefaultLookupTable();
1494
1495     mSlicerManagers.back()->SetSlicerWindow(0,NOViewWidget->GetRenderWindow());
1496     mSlicerManagers.back()->SetSlicerWindow(1,NEViewWidget->GetRenderWindow());
1497     mSlicerManagers.back()->SetSlicerWindow(2,SOViewWidget->GetRenderWindow());
1498     mSlicerManagers.back()->SetSlicerWindow(3,SEViewWidget->GetRenderWindow());
1499   }
1500 }
1501
1502 //------------------------------------------------------------------------------
1503 void vvMainWindow::InitDisplay()
1504 {
1505   if (mSlicerManagers.size()) {
1506     //BE CAREFUL : this is absolutely necessary to set the interactor style
1507     //in order to have the same style instanciation for all SlicerManagers in
1508     // a same window
1509     for (int j = 0; j < 4; j++) {
1510       vvInteractorStyleNavigator* style = vvInteractorStyleNavigator::New();
1511       style->SetAutoAdjustCameraClippingRange(1);
1512       bool AlreadySelected = false;
1513       for (int i = 0; i < DataTree->topLevelItemCount(); i++) {
1514         mSlicerManagers[i]->SetInteractorStyleNavigator(j,style);
1515
1516         //select the image only if previous are not selected
1517         if (DataTree->topLevelItem(i)->data(j+1,Qt::CheckStateRole).toInt() > 1) {
1518           mSlicerManagers[i]->UpdateSlicer(j,1);
1519           AlreadySelected = true;
1520         } else if (i == DataTree->topLevelItemCount()-1 && !AlreadySelected) {
1521           if (DataTree->selectedItems().size() == 0)
1522             DataTree->topLevelItem(i)->setSelected(1);
1523           DataTree->topLevelItem(i)->setData(j+1,Qt::CheckStateRole,2);
1524           mSlicerManagers[i]->UpdateSlicer(j,1);
1525           DisplaySliders(i,j);
1526         } else {
1527           DataTree->topLevelItem(i)->setData(j+1,Qt::CheckStateRole,0);
1528           mSlicerManagers[i]->UpdateSlicer(j,0);
1529         }
1530       }
1531       style->Delete();
1532     }
1533   }
1534 }
1535 //------------------------------------------------------------------------------
1536
1537 //------------------------------------------------------------------------------
1538 void vvMainWindow::DisplaySliders(int slicer, int window)
1539 {
1540   if(!mSlicerManagers[slicer]->GetSlicer(window)->GetRenderer()->GetDraw())
1541     return;
1542
1543   int range[2];
1544   mSlicerManagers[slicer]->GetSlicer(window)->GetSliceRange(range);
1545   int position = mSlicerManagers[slicer]->GetSlicer(window)->GetSlice();
1546   if (range[1]>0)
1547     verticalSliders[window]->show();
1548   else
1549     verticalSliders[window]->hide();
1550   verticalSliders[window]->setRange(range[0],range[1]);
1551   verticalSliders[window]->setValue(position);
1552
1553   int tRange[2];
1554   tRange[0] = 0;
1555   tRange[1] = mSlicerManagers[slicer]->GetSlicer(window)->GetTMax();
1556   if (tRange[1]>0)
1557     horizontalSliders[window]->show();
1558   else
1559     horizontalSliders[window]->hide();
1560   horizontalSliders[window]->setRange(tRange[0],tRange[1]);
1561   int tPosition = mSlicerManagers[slicer]->GetSlicer(window)->GetMaxCurrentTSlice();
1562   horizontalSliders[window]->setValue(tPosition);
1563 }
1564 //------------------------------------------------------------------------------
1565
1566 //------------------------------------------------------------------------------
1567 void vvMainWindow::CloseImage(QTreeWidgetItem* item, int column)
1568 {
1569   int index = GetSlicerIndexFromItem(item);
1570
1571   if (DataTree->topLevelItem(index) != item) {
1572     QString warning = "Do you really want to close the overlay : ";
1573     warning += item->data(COLUMN_IMAGE_NAME,Qt::DisplayRole).toString();
1574     QMessageBox msgBox(QMessageBox::Warning, tr("Close Overlay"),
1575       warning, 0, this);
1576     msgBox.addButton(tr("Close"), QMessageBox::AcceptRole);
1577     msgBox.addButton(tr("Cancel"), QMessageBox::RejectRole);
1578     if (msgBox.exec() == QMessageBox::AcceptRole) {
1579       std::string overlay_type=item->data(1,Qt::UserRole).toString().toStdString();
1580       int overlay_index=0;
1581       for (int child = 0; child < DataTree->topLevelItem(index)->childCount(); child++) {
1582         if (DataTree->topLevelItem(index)->\
1583           child(child)->data(1,Qt::UserRole).toString().toStdString() == overlay_type)
1584           overlay_index++;
1585         if (DataTree->topLevelItem(index)->child(child) == item) break;
1586       }
1587       if (overlay_type=="fusionSequence") {
1588         //removing the overlay sequence in a fusion sequence visualization mode
1589         //reset the transforms
1590         overlayPanel->getFusionSequenceProperty(-1, false, 0, false);
1591
1592         //unlink and untie the slicer managers
1593         RemoveLink(mSlicerManagers[index]->GetId().c_str(), mSlicerManagers[mSlicerManagers[index]->GetFusionSequenceIndexOfLinkedManager()]->GetId().c_str());
1594         mSlicerManagers[index]->SetFusionSequenceInvolvmentCode(-1);
1595         mSlicerManagers[mSlicerManagers[index]->GetFusionSequenceIndexOfLinkedManager()]->SetFusionSequenceInvolvmentCode(-1);
1596         for (unsigned i=0 ; i<4 ; i++) {
1597             mSlicerManagers[index]->GetSlicer(i)->SetFusionSequenceCode(-1);
1598             mSlicerManagers[mSlicerManagers[index]->GetFusionSequenceIndexOfLinkedManager()]->GetSlicer(i)->SetFusionSequenceCode(-1);
1599         }
1600
1601       }
1602       mSlicerManagers[index]->RemoveActor(overlay_type, overlay_index-1);
1603       mSlicerManagers[index]->SetColorMap(0);
1604       DataTree->topLevelItem(index)->takeChild(DataTree->topLevelItem(index)->indexOfChild(item));
1605       mSlicerManagers[index]->Render();
1606     }
1607   } else if (DataTree->topLevelItemCount() <= 1) {
1608     QString warning = "Do you really want to close the image : ";
1609     warning += item->data(COLUMN_IMAGE_NAME,Qt::DisplayRole).toString();
1610     warning += "\nThis is the last image, you're about to close vv !!!";
1611     QMessageBox msgBox(QMessageBox::Warning, tr("Close Image"),
1612       warning, 0, this);
1613     msgBox.addButton(tr("Close vv"), QMessageBox::AcceptRole);
1614     msgBox.addButton(tr("Cancel"), QMessageBox::RejectRole);
1615     if (msgBox.exec() == QMessageBox::AcceptRole) {
1616       this->close();
1617     }
1618   } else {
1619     QString warning = "Do you really want to close the image : ";
1620     warning += item->data(COLUMN_IMAGE_NAME,Qt::DisplayRole).toString();
1621     QMessageBox msgBox(QMessageBox::Warning, tr("Close Image"),
1622       warning, 0, this);
1623     msgBox.addButton(tr("Close"), QMessageBox::AcceptRole);
1624     msgBox.addButton(tr("Cancel"), QMessageBox::RejectRole);
1625     if (msgBox.exec() == QMessageBox::AcceptRole) {
1626
1627       // Tell tools that we close an image
1628       emit AnImageIsBeingClosed(mSlicerManagers[index]);
1629
1630       std::vector<vvSlicerManager*>::iterator Manageriter = mSlicerManagers.begin();
1631       DataTree->takeTopLevelItem(index);
1632       for (int i = 0; i < index; i++) {
1633         Manageriter++;
1634       }
1635       //if the slicer manager was involved in a fusion sequence visualization...
1636       if ( mSlicerManagers[index]->IsInvolvedInFusionSequence() ) {
1637         //in both cases, close the overlay: find it... and close it
1638         //ideally, I should duplicate the code, and avoid calling CloseImage, since this pops up another interactive box
1639         QTreeWidgetItem* overlayItem;
1640         if (mSlicerManagers[index]->IsMainSequenceOfFusionSequence()) {
1641           for (unsigned i=0 ; i<item->childCount() ; i++) {
1642             overlayItem = item->child(i);
1643             this->CloseImage( overlayItem, 0 );
1644           }
1645         }
1646         else {
1647           QTreeWidgetItem* linkedItem = this->GetItemFromSlicerManager( mSlicerManagers[mSlicerManagers[index]->GetFusionSequenceIndexOfLinkedManager()] );
1648           for (unsigned i=0 ; i<linkedItem->childCount() ; i++) {
1649             overlayItem = linkedItem->child(i);
1650             this->CloseImage( overlayItem, 0 );
1651           }
1652         }
1653
1654         /* -- this is normally already done when closing the overlay.
1655         //reset the transforms
1656         overlayPanel->getFusionSequenceProperty(-1, false, 0, false);
1657
1658         //unlink and untie the slicer managers
1659         RemoveLink(mSlicerManagers[index]->GetId().c_str(), mSlicerManagers[mSlicerManagers[index]->GetFusionSequenceIndexOfLinkedManager()]->GetId().c_str());
1660         mSlicerManagers[index]->SetFusionSequenceInvolvmentCode(-1);
1661         mSlicerManagers[mSlicerManagers[index]->GetFusionSequenceIndexOfLinkedManager()]->SetFusionSequenceInvolvmentCode(-1);
1662         for (unsigned i=0 ; i<4 ; i++) {
1663             mSlicerManagers[index]->GetSlicer(i)->SetFusionSequenceCode(-1);
1664             mSlicerManagers[mSlicerManagers[index]->GetFusionSequenceIndexOfLinkedManager()]->GetSlicer(i)->SetFusionSequenceCode(-1);
1665         }
1666         */
1667       }
1668
1669       linkPanel->removeImage(index);
1670       mSlicerManagers[index]->RemoveActors();
1671
1672       //remove the slicer manager
1673       delete mSlicerManagers[index];
1674       mSlicerManagers.erase(Manageriter);
1675
1676       //
1677       InitDisplay();
1678     }
1679   }
1680   ImageInfoChanged();
1681 }
1682 //------------------------------------------------------------------------------
1683
1684 //------------------------------------------------------------------------------
1685 void vvMainWindow::ReloadImage(QTreeWidgetItem* item, int column)
1686 {
1687   // int index = GetSlicerIndexFromItem(item);
1688   //   QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
1689   //   if (item->data(1,Qt::UserRole).toString() == "vector")
1690   //     mSlicerManagers[index]->ReloadVF();
1691   //   else
1692   //     mSlicerManagers[index]->Reload();
1693
1694   //   QApplication::restoreOverrideCursor();
1695   int index = GetSlicerIndexFromItem(item);
1696   QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
1697   QString role=item->data(1,Qt::UserRole).toString();
1698   if ( role == "vector") {
1699     mSlicerManagers[index]->ReloadVF();
1700   }
1701   else if (role == "overlay") {
1702     mSlicerManagers[index]->ReloadOverlay();
1703   }
1704   else if (role == "fusion") {
1705     mSlicerManagers[index]->ReloadFusion();
1706   }
1707   else if (role == "fusionSequence") {
1708     //both versions of the secondary sequence must be updated.
1709     mSlicerManagers[index]->ReloadFusionSequence();
1710     mSlicerManagers[mSlicerManagers[index]->GetFusionSequenceIndexOfLinkedManager()]->Reload();
1711   }
1712   else {
1713     mSlicerManagers[index]->Reload();
1714     //if we update the secondary sequence, then the overlay of the main sequence should also be updated
1715     if (mSlicerManagers[index]->IsSecondarySequenceOfFusionSequence()) mSlicerManagers[mSlicerManagers[index]->GetFusionSequenceIndexOfLinkedManager()]->ReloadFusionSequence();
1716   }
1717   // Update view and info
1718   ImageInfoChanged();
1719   mSlicerManagers[index]->Render();
1720   QApplication::restoreOverrideCursor();
1721 }
1722 //------------------------------------------------------------------------------
1723
1724 //------------------------------------------------------------------------------
1725 void vvMainWindow::MousePositionChanged(int visibility,double x, double y, double z, double X, double Y, double Z , double value)
1726 {
1727   infoPanel->setCurrentInfo(visibility,x,y,z,X,Y,Z,value);
1728 }
1729 //------------------------------------------------------------------------------
1730
1731 //------------------------------------------------------------------------------
1732 void vvMainWindow::VectorChanged(int visibility,double x, double y, double z, double value)
1733 {
1734   overlayPanel->getCurrentVectorInfo(visibility,x,y,z,value);
1735 }
1736 //------------------------------------------------------------------------------
1737
1738 //------------------------------------------------------------------------------
1739 void vvMainWindow::OverlayChanged(int visibility, double valueOver, double valueRef)
1740 {
1741   overlayPanel->getCurrentOverlayInfo(visibility,valueOver, valueRef);
1742 }
1743 //------------------------------------------------------------------------------
1744
1745 //------------------------------------------------------------------------------
1746 void vvMainWindow::FusionChanged(int visibility, double value)
1747 {
1748   overlayPanel->getCurrentFusionInfo(visibility,value);
1749 }
1750 //------------------------------------------------------------------------------
1751
1752 //------------------------------------------------------------------------------
1753 //called when AddOverlayImage, AddFusionSequence
1754 //or when UpdateWindowLevel() is called ; when slicerManager emits WindowLevelChanged
1755 //when ImageInfoChanged() is called
1756 void vvMainWindow::WindowLevelChanged()
1757 {
1758   // Base image
1759   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1760   if(index==-1) return;
1761   windowSpinBox->setValue(mSlicerManagers[index]->GetColorWindow());
1762   levelSpinBox->setValue(mSlicerManagers[index]->GetColorLevel());
1763   colorMapComboBox->setCurrentIndex(mSlicerManagers[index]->GetColorMap());
1764   presetComboBox->setCurrentIndex(mSlicerManagers[index]->GetPreset());
1765
1766   // Overlay image
1767   if (mSlicerManagers[index]->GetSlicer(0)->GetOverlay())
1768     overlayPanel->getOverlayProperty(mSlicerManagers[index]->GetOverlayColor(),
1769     mSlicerManagers[index]->GetLinkOverlayWindowLevel(),
1770     mSlicerManagers[index]->GetOverlayColorWindow(),
1771     mSlicerManagers[index]->GetOverlayColorLevel());
1772   else
1773     overlayPanel->getOverlayProperty(-1,0,0.,0.);
1774
1775   // Fusion & SequenceFusion image
1776   if (mSlicerManagers[index]->GetSlicer(0)->GetFusion()) {
1777     overlayPanel->getFusionProperty(mSlicerManagers[index]->GetFusionOpacity(),
1778       mSlicerManagers[index]->GetFusionThresholdOpacity(),
1779       mSlicerManagers[index]->GetFusionColorMap(),
1780       mSlicerManagers[index]->GetFusionWindow(),
1781       mSlicerManagers[index]->GetFusionLevel());
1782     if (mSlicerManagers[index]->IsMainSequenceOfFusionSequence()) {
1783       overlayPanel->getFusionSequenceProperty(mSlicerManagers[index]->GetFusionSequenceFrameIndex(),
1784         mSlicerManagers[index]->GetFusionSequenceSpatialSyncFlag(),
1785         mSlicerManagers[index]->GetFusionSequenceNbFrames(),
1786         mSlicerManagers[index]->GetFusionSequenceTemporalSyncFlag());
1787     }
1788   }
1789   else if ( mSlicerManagers[index]->IsSecondarySequenceOfFusionSequence() ) {
1790     //if the image is involved in a fusion sequence, preserve the overlay panel!
1791     int ind = mSlicerManagers[index]->GetFusionSequenceIndexOfLinkedManager();
1792     overlayPanel->getFusionProperty(mSlicerManagers[ind]->GetFusionOpacity(),
1793       mSlicerManagers[ind]->GetFusionThresholdOpacity(),
1794       mSlicerManagers[ind]->GetFusionColorMap(),
1795       mSlicerManagers[ind]->GetFusionWindow(),
1796       mSlicerManagers[ind]->GetFusionLevel());
1797     overlayPanel->getFusionSequenceProperty(mSlicerManagers[ind]->GetFusionSequenceFrameIndex(),
1798       mSlicerManagers[ind]->GetFusionSequenceSpatialSyncFlag(),
1799       mSlicerManagers[ind]->GetFusionSequenceNbFrames(),
1800       mSlicerManagers[ind]->GetFusionSequenceTemporalSyncFlag());
1801   }
1802   else
1803   {
1804     overlayPanel->getFusionProperty(-1, -1, -1, -1, -1);
1805     overlayPanel->getFusionSequenceProperty(-1, false, 0, false);
1806   }
1807 }
1808 //------------------------------------------------------------------------------
1809
1810 //------------------------------------------------------------------------------
1811 void vvMainWindow::WindowLevelEdited()
1812 {
1813   presetComboBox->setCurrentIndex(WL_USER);
1814   UpdateWindowLevel();
1815 }
1816 //------------------------------------------------------------------------------
1817
1818 //------------------------------------------------------------------------------
1819 void vvMainWindow::SetWindowLevel(double w, double l)
1820 {
1821   windowSpinBox->setValue(w);
1822   levelSpinBox->setValue(l);
1823   presetComboBox->setCurrentIndex(WL_USER);
1824   colorMapComboBox->setCurrentIndex(0);
1825   UpdateWindowLevel();
1826 }
1827 //------------------------------------------------------------------------------
1828
1829 //------------------------------------------------------------------------------
1830 void vvMainWindow::UpdateWindowLevel()
1831 {
1832   if (DataTree->selectedItems().size()) {
1833     if (presetComboBox->currentIndex() == WL_VENTILATION) //For ventilation
1834       colorMapComboBox->setCurrentIndex(5);
1835     int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1836     mSlicerManagers[index]->SetColorWindow(windowSpinBox->value());
1837     mSlicerManagers[index]->SetColorLevel(levelSpinBox->value());
1838     mSlicerManagers[index]->SetPreset(presetComboBox->currentIndex());
1839     mSlicerManagers[index]->Render();
1840     WindowLevelChanged();
1841   }
1842 }
1843 //------------------------------------------------------------------------------
1844
1845 //------------------------------------------------------------------------------
1846 void vvMainWindow::UpdateSlicingPreset()
1847 {
1848   if (DataTree->selectedItems().size()) {
1849     int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1850     mSlicerManagers[index]->SetSlicingPreset(vvSlicerManager::SlicingPresetType(slicingPresetComboBox->currentIndex()));
1851   }
1852 }
1853 //------------------------------------------------------------------------------
1854
1855 //------------------------------------------------------------------------------
1856 void vvMainWindow::UpdateColorMap()
1857 {
1858   if (DataTree->selectedItems().size()) {
1859     int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1860     mSlicerManagers[index]->SetColorMap(colorMapComboBox->currentIndex());
1861     mSlicerManagers[index]->Render();
1862   }
1863 }
1864 //------------------------------------------------------------------------------
1865 void vvMainWindow::SwitchWindowLevel()
1866 {
1867   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1868   int window = mSlicerManagers[index]->GetColorWindow();
1869   presetComboBox->setCurrentIndex(WL_USER);
1870   windowSpinBox->setValue(-window);
1871   UpdateWindowLevel();
1872 }
1873 //------------------------------------------------------------------------------
1874
1875 //------------------------------------------------------------------------------
1876 void vvMainWindow::ApplyWindowLevelToAllImages()
1877 {
1878   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1879   if(index==-1) return;
1880   double window = mSlicerManagers[index]->GetColorWindow();
1881   double level = mSlicerManagers[index]->GetColorLevel();
1882
1883   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
1884     if (mSlicerManagers[i] == NULL)
1885       continue;
1886     mSlicerManagers[i]->SetColorWindow(window);
1887     mSlicerManagers[i]->SetColorLevel(level);
1888     mSlicerManagers[i]->SetPreset(WL_USER);
1889     mSlicerManagers[i]->Render();
1890   }
1891 }
1892 //------------------------------------------------------------------------------
1893
1894 //------------------------------------------------------------------------------
1895 void vvMainWindow::ApplyWindowToSetOfImages(double window, unsigned int indexMin, unsigned int indexMax)
1896 {
1897   for (unsigned int i = indexMin; i <= indexMax && i < mSlicerManagers.size(); i++) {
1898     if (mSlicerManagers[i] == NULL)
1899       continue;
1900     mSlicerManagers[i]->SetColorWindow(window);
1901     mSlicerManagers[i]->SetPreset(WL_USER);
1902     mSlicerManagers[i]->Render();
1903   }
1904 }
1905 //------------------------------------------------------------------------------
1906
1907 //------------------------------------------------------------------------------
1908 void vvMainWindow::ApplyLevelToSetOfImages(double level, unsigned int indexMin, unsigned int indexMax)
1909 {
1910   for (unsigned int i = indexMin; i <= indexMax && i < mSlicerManagers.size(); i++) {
1911     if (mSlicerManagers[i] == NULL)
1912       continue;
1913     mSlicerManagers[i]->SetColorLevel(level);
1914     mSlicerManagers[i]->SetPreset(WL_USER);
1915     mSlicerManagers[i]->Render();
1916   }
1917 }
1918 //------------------------------------------------------------------------------
1919
1920 //------------------------------------------------------------------------------
1921 void vvMainWindow::UpdateLinkManager(std::string id, int slicer, double x, double y, double z, int temps)
1922 {
1923   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
1924     if (mSlicerManagers[i]->GetId() == id) {
1925       mSlicerManagers[i]->GetSlicer(slicer)->SetCurrentPosition(x,y,z,temps);
1926       mSlicerManagers[i]->UpdateViews(0,slicer);
1927       break;
1928     }
1929   }
1930 }
1931 //------------------------------------------------------------------------------
1932
1933 //------------------------------------------------------------------------------
1934 void vvMainWindow::UpdateLinkedNavigation(std::string id, vvSlicerManager * sm, vvSlicer* refSlicer)
1935 {
1936   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
1937     if (id == mSlicerManagers[i]->GetId()) {
1938       mSlicerManagers[i]->UpdateLinkedNavigation(refSlicer);
1939     }
1940   }
1941 }
1942 //------------------------------------------------------------------------------
1943
1944 //------------------------------------------------------------------------------
1945 void vvMainWindow::ShowContextMenu(QPoint point)
1946 {
1947   if (!DataTree->selectedItems().size()) {
1948     contextActions[1]->setEnabled(0);
1949     contextActions[2]->setEnabled(0);
1950     contextActions[3]->setEnabled(0);
1951     contextActions[4]->setEnabled(0);
1952     contextActions[5]->setEnabled(0);
1953     contextActions[6]->setEnabled(0);
1954   } else {
1955     int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1956     contextActions[1]->setEnabled(1);
1957     contextActions[2]->setEnabled(
1958       DataTree->itemWidget(DataTree->selectedItems()[0],
1959       COLUMN_RELOAD_IMAGE)->isEnabled());
1960     contextActions[3]->setEnabled(1);
1961     contextActions[5]->setEnabled(1);
1962     contextActions[6]->setEnabled(1);
1963
1964     if (mSlicerManagers[index]->GetDimension() < 3)
1965       contextActions[4]->setEnabled(0);
1966     else
1967       contextActions[4]->setEnabled(1);
1968   }
1969   contextMenu.exec(QCursor::pos());
1970 }
1971 //------------------------------------------------------------------------------
1972
1973 //------------------------------------------------------------------------------
1974 void vvMainWindow::CloseImage()
1975 {
1976   CloseImage(DataTree->selectedItems()[0],0);
1977 }
1978 //------------------------------------------------------------------------------
1979
1980 //------------------------------------------------------------------------------
1981 void vvMainWindow::ReloadImage()
1982 {
1983   ReloadImage(DataTree->selectedItems()[0],0);
1984 }
1985 //------------------------------------------------------------------------------
1986
1987 //------------------------------------------------------------------------------
1988 void vvMainWindow::SelectOverlayImage()
1989 {
1990   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1991
1992   //check if one overlay image is added
1993   for (int child = 0; child < DataTree->topLevelItem(index)->childCount(); child++)
1994     if (DataTree->topLevelItem(index)->child(child)->data(1,Qt::UserRole).toString() == "overlay") {
1995       QString error = "Cannot add more than one compared image\n";
1996       error += "Please remove first ";
1997       error += DataTree->topLevelItem(index)->child(child)->data(COLUMN_IMAGE_NAME,Qt::DisplayRole).toString();
1998       QMessageBox::information(this,tr("Problem adding compared image !"),error);
1999       return;
2000     }
2001
2002     QString Extensions = EXTENSIONS;
2003     Extensions += ";;All Files (*)";
2004     QStringList files = QFileDialog::getOpenFileNames(this,tr("Load Overlay image"),mInputPathName,Extensions);
2005     if (files.isEmpty())
2006       return;
2007
2008     std::vector<std::string> vecFileNames;
2009     for (int i = 0; i < files.size(); i++) {
2010       vecFileNames.push_back(files[i].toStdString());
2011     }
2012     AddOverlayImage(index,vecFileNames,vvImageReader::IMAGE);
2013 }
2014 //------------------------------------------------------------------------------
2015
2016 //------------------------------------------------------------------------------
2017 void vvMainWindow::AddOverlayImage(int index, std::vector<std::string> fileNames, vvImageReader::LoadedImageType type)
2018 {
2019   QString file(fileNames[0].c_str());
2020   if (QFile::exists(file))
2021   {
2022     mInputPathName = itksys::SystemTools::GetFilenamePath(file.toStdString()).c_str();
2023     itk::ImageIOBase::Pointer reader = itk::ImageIOFactory::CreateImageIO(
2024       file.toStdString().c_str(), itk::ImageIOFactory::ReadMode);
2025     reader->SetFileName(fileNames[0].c_str());
2026     reader->ReadImageInformation();
2027     std::string component = reader->GetComponentTypeAsString(reader->GetComponentType());
2028     int dimension = reader->GetNumberOfDimensions();
2029     QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
2030     vvProgressDialog progress("Opening " + file.toStdString());
2031     qApp->processEvents();
2032
2033     std::string filename = itksys::SystemTools::GetFilenameWithoutExtension(file.toStdString()).c_str();
2034     if (mSlicerManagers[index]->SetOverlay(fileNames,dimension, component,type)) {
2035       //create an item in the tree with good settings
2036       QTreeWidgetItem *item = new QTreeWidgetItem();
2037       item->setData(0,Qt::UserRole,file.toStdString().c_str());
2038       item->setData(1,Qt::UserRole,tr("overlay"));
2039       QFileInfo fileinfo(file); //Do not show the path
2040       item->setData(COLUMN_IMAGE_NAME,Qt::DisplayRole,fileinfo.fileName());
2041       item->setToolTip(COLUMN_IMAGE_NAME, mSlicerManagers[index]->GetListOfAbsoluteFilePathInOneString("overlay").c_str());
2042       qApp->processEvents();
2043
2044       for (int j = 1; j <= 4; j++) {
2045         item->setData(j,Qt::CheckStateRole,DataTree->topLevelItem(index)->data(j,Qt::CheckStateRole));
2046       }
2047
2048       //Create the buttons for reload and close
2049       qApp->processEvents();
2050       QTreePushButton* cButton = new QTreePushButton;
2051       cButton->setItem(item);
2052       cButton->setColumn(COLUMN_CLOSE_IMAGE);
2053       cButton->setToolTip(tr("close image"));
2054       cButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/exit.png")));
2055       connect(cButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
2056         this,SLOT(CloseImage(QTreeWidgetItem*, int)));
2057
2058       QTreePushButton* rButton = new QTreePushButton;
2059       rButton->setItem(item);
2060       rButton->setColumn(COLUMN_RELOAD_IMAGE);
2061       rButton->setToolTip(tr("reload image"));
2062       rButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/rotateright.png")));
2063       connect(rButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
2064         this,SLOT(ReloadImage(QTreeWidgetItem*, int)));
2065
2066       DataTree->topLevelItem(index)->setExpanded(1);
2067       DataTree->topLevelItem(index)->addChild(item);
2068       DataTree->setItemWidget(item, COLUMN_CLOSE_IMAGE, cButton);
2069       DataTree->setItemWidget(item, COLUMN_RELOAD_IMAGE, rButton);
2070
2071       //set the id of the image
2072       QString id = DataTree->topLevelItem(index)->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString();
2073       item->setData(COLUMN_IMAGE_NAME,Qt::UserRole,id.toStdString().c_str());
2074       UpdateTree();
2075       qApp->processEvents();
2076       ImageInfoChanged();
2077       QApplication::restoreOverrideCursor();
2078
2079       // Update the display to update, e.g., the sliders
2080       for(int i=0; i<4; i++)
2081         DisplaySliders(index, i);
2082     } else {
2083       QApplication::restoreOverrideCursor();
2084       QString error = "Cannot import the new image.\n";
2085       error += mSlicerManagers[index]->GetLastError().c_str();
2086       QMessageBox::information(this,tr("Problem reading image !"),error);
2087     }
2088     WindowLevelChanged();
2089   }
2090   else
2091     QMessageBox::information(this,tr("Problem reading Overlay !"),"File doesn't exist!");
2092 }
2093 //------------------------------------------------------------------------------
2094
2095
2096 //------------------------------------------------------------------------------
2097 void vvMainWindow::AddROI(int index, QString file)
2098 {
2099   /*
2100   // Get slice manager
2101
2102   // Load image
2103
2104   vvImageReader * mReader = new vvImageReader;
2105   mReader->SetInputFilename(filename.toStdString());
2106   mReader->Update(IMAGE);
2107   if (mReader->GetLastError().size() != 0) {
2108   std::cerr << "Error while reading " << filename.toStdString() << std::endl;
2109   QString error = "Cannot open file \n";
2110   error += mReader->GetLastError().c_str();
2111   QMessageBox::information(this,tr("Reading problem"),error);
2112   delete mReader;
2113   return;
2114   }
2115   vvImage::Pointer roi = mReader->GetOutput();
2116
2117   // Create roi in new tool
2118   vvToolStructureSetManager::AddImage(mCurrentSlicerManager, roi);
2119   */
2120 }
2121 //------------------------------------------------------------------------------
2122
2123 //------------------------------------------------------------------------------
2124 void vvMainWindow::SelectFusionImage()
2125 {
2126   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2127
2128   //check if one fusion image is added
2129   for (int child = 0; child < DataTree->topLevelItem(index)->childCount(); child++)
2130     if ( (DataTree->topLevelItem(index)->child(child)->data(1,Qt::UserRole).toString() == "fusion") ||
2131       (DataTree->topLevelItem(index)->child(child)->data(1,Qt::UserRole).toString() == "fusionSequence") ) {
2132         QString error = "Cannot add more than one fusion image\n";
2133         error += "Please remove first ";
2134         error += DataTree->topLevelItem(index)->child(child)->data(COLUMN_IMAGE_NAME,Qt::DisplayRole).toString();
2135         QMessageBox::information(this,tr("Problem adding fusion image !"),error);
2136         return;
2137     }
2138
2139     QString Extensions = EXTENSIONS;
2140     Extensions += ";;All Files (*)";
2141     QStringList files = QFileDialog::getOpenFileNames(this,tr("Load Fusion image"),mInputPathName,Extensions);
2142     if (files.isEmpty())
2143       return;
2144
2145     std::vector<std::string> vecFileNames;
2146     for (int i = 0; i < files.size(); i++) {
2147       vecFileNames.push_back(files[i].toStdString());
2148     }
2149     AddFusionImage(index,vecFileNames,vvImageReader::IMAGE);
2150 }
2151 //------------------------------------------------------------------------------
2152
2153 //------------------------------------------------------------------------------
2154 void vvMainWindow::ResetTransformationToIdentity()
2155 {
2156   std::string actorType = DataTree->selectedItems()[0]->data(1,Qt::UserRole).toString().toStdString();
2157   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2158   mSlicerManagers[index]->ResetTransformationToIdentity(actorType);
2159   ImageInfoChanged();
2160 }
2161 //------------------------------------------------------------------------------
2162
2163 //------------------------------------------------------------------------------
2164 void vvMainWindow::AddFusionImage(int index, std::vector<std::string> fileNames, vvImageReader::LoadedImageType type)
2165 {
2166   QString file(fileNames[0].c_str());
2167   if (QFile::exists(file))
2168   {
2169     mInputPathName = itksys::SystemTools::GetFilenamePath(file.toStdString()).c_str();
2170     itk::ImageIOBase::Pointer reader = itk::ImageIOFactory::CreateImageIO(
2171       file.toStdString().c_str(), itk::ImageIOFactory::ReadMode);
2172     reader->SetFileName(fileNames[0].c_str());
2173     reader->ReadImageInformation();
2174     std::string component = reader->GetComponentTypeAsString(reader->GetComponentType());
2175     int dimension = reader->GetNumberOfDimensions();
2176     QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
2177     vvProgressDialog progress("Opening fusion");
2178     qApp->processEvents();
2179
2180     std::string filename = itksys::SystemTools::GetFilenameWithoutExtension(file.toStdString()).c_str();
2181     if (mSlicerManagers[index]->SetFusion(fileNames,dimension, component,type)) {
2182       //create an item in the tree with good settings
2183       QTreeWidgetItem *item = new QTreeWidgetItem();
2184       item->setData(0,Qt::UserRole,file.toStdString().c_str());
2185       item->setData(1,Qt::UserRole,tr("fusion"));
2186       QFileInfo fileinfo(file); //Do not show the path
2187           item->setData(COLUMN_IMAGE_NAME,Qt::DisplayRole,fileinfo.fileName());
2188           item->setToolTip(COLUMN_IMAGE_NAME, mSlicerManagers[index]->GetListOfAbsoluteFilePathInOneString("fusion").c_str());
2189           qApp->processEvents();
2190
2191       for (int j = 1; j <= 4; j++) {
2192         item->setData(j,Qt::CheckStateRole,DataTree->topLevelItem(index)->data(j,Qt::CheckStateRole));
2193       }
2194
2195       //Create the buttons for reload and close
2196       qApp->processEvents();
2197       QTreePushButton* cButton = new QTreePushButton;
2198       cButton->setItem(item);
2199       cButton->setColumn(COLUMN_CLOSE_IMAGE);
2200       cButton->setToolTip(tr("close image"));
2201       cButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/exit.png")));
2202       connect(cButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
2203         this,SLOT(CloseImage(QTreeWidgetItem*, int)));
2204
2205       QTreePushButton* rButton = new QTreePushButton;
2206       rButton->setItem(item);
2207       rButton->setColumn(COLUMN_RELOAD_IMAGE);
2208       rButton->setToolTip(tr("reload image"));
2209       rButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/rotateright.png")));
2210       connect(rButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
2211         this,SLOT(ReloadImage(QTreeWidgetItem*, int)));
2212
2213       DataTree->topLevelItem(index)->setExpanded(1);
2214       DataTree->topLevelItem(index)->addChild(item);
2215       DataTree->setItemWidget(item, COLUMN_CLOSE_IMAGE, cButton);
2216       DataTree->setItemWidget(item, COLUMN_RELOAD_IMAGE, rButton);
2217
2218       //set the id of the image
2219       QString id = DataTree->topLevelItem(index)->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString();
2220       item->setData(COLUMN_IMAGE_NAME,Qt::UserRole,id.toStdString().c_str());
2221       UpdateTree();
2222       qApp->processEvents();
2223       ImageInfoChanged();
2224       QApplication::restoreOverrideCursor();
2225
2226       // Update the display to update, e.g., the sliders
2227       for(int i=0; i<4; i++)
2228         DisplaySliders(index, i);
2229     } else {
2230       QApplication::restoreOverrideCursor();
2231       QString error = "Cannot import the new image.\n";
2232       error += mSlicerManagers[index]->GetLastError().c_str();
2233       QMessageBox::information(this,tr("Problem reading image !"),error);
2234     }
2235     WindowLevelChanged();
2236   }
2237   else
2238     QMessageBox::information(this,tr("Problem reading Fusion !"),"File doesn't exist!");
2239 }
2240 //------------------------------------------------------------------------------
2241 //------------------------------------------------------------------------------
2242 void vvMainWindow::AddLandmarks(int index, std::vector<std::string> files)
2243 {
2244     if (!landmarksPanel->LoadFromFile(files))
2245       QMessageBox::information(this,tr("Problem reading Landmarks !"),"File doesn't exist!");
2246
2247     landmarksPanel->SetCurrentPath(mInputPathName.toStdString());
2248     landmarksPanel->SetCurrentImage(mSlicerManagers[index]->GetFileName().c_str());
2249 }
2250
2251 //------------------------------------------------------------------------------
2252 void vvMainWindow::OpenField()
2253 {
2254   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2255   //check if a vector field has already been added
2256   for (int child = 0; child < DataTree->topLevelItem(index)->childCount(); child++)
2257     if (DataTree->topLevelItem(index)->child(child)->data(1,Qt::UserRole).toString() == "vector") {
2258       QString error = "Cannot add more than one vector field\n";
2259       error += "Please remove first ";
2260       error += DataTree->topLevelItem(index)->child(child)->data(COLUMN_IMAGE_NAME,Qt::DisplayRole).toString();
2261       QMessageBox::information(this,tr("Problem adding vector field!"),error);
2262       return;
2263     }
2264
2265     QString Extensions = "Images ( *.mhd)";
2266     Extensions += ";;Images ( *.mha)";
2267     Extensions += ";;VF Images ( *.vf)";
2268     Extensions += ";;nii Images ( *.nii)";
2269     Extensions += ";;nrrd Images ( *.nrrd)";
2270     Extensions += ";;nhdr Images ( *.nhdr)";
2271     Extensions += ";;All Files (*)";
2272     QString file = QFileDialog::getOpenFileName(this,tr("Load deformation field"),mInputPathName,Extensions);
2273     if (!file.isEmpty())
2274       AddField(file,index);
2275 }
2276 //------------------------------------------------------------------------------
2277
2278
2279 //------------------------------------------------------------------------------
2280 void vvMainWindow::AddFieldEntry(QString filename,int index,bool from_disk)
2281 {
2282   //create an item in the tree with good settings
2283   QTreeWidgetItem *item = new QTreeWidgetItem();
2284   item->setData(0,Qt::UserRole,filename.toStdString().c_str());
2285   item->setData(1,Qt::UserRole,tr("vector"));
2286   QFileInfo fileinfo(filename); //Do not show the path
2287   item->setData(COLUMN_IMAGE_NAME,Qt::DisplayRole,fileinfo.fileName());
2288   item->setToolTip(COLUMN_IMAGE_NAME, mSlicerManagers[index]->GetListOfAbsoluteFilePathInOneString("vector").c_str());
2289   qApp->processEvents();
2290
2291   for (int j = 1; j <= 4; j++) {
2292     item->setData(j,Qt::CheckStateRole,DataTree->topLevelItem(index)->data(j,Qt::CheckStateRole));
2293   }
2294
2295   //Create the buttons for reload and close
2296   qApp->processEvents();
2297   QTreePushButton* cButton = new QTreePushButton;
2298   cButton->setItem(item);
2299   cButton->setColumn(COLUMN_CLOSE_IMAGE);
2300   cButton->setToolTip(tr("close vector field"));
2301   cButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/exit.png")));
2302   connect(cButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
2303     this,SLOT(CloseImage(QTreeWidgetItem*, int)));
2304
2305   QTreePushButton* rButton = new QTreePushButton;
2306   rButton->setItem(item);
2307   rButton->setColumn(COLUMN_RELOAD_IMAGE);
2308   rButton->setToolTip(tr("reload vector field"));
2309   rButton->setEnabled(from_disk);
2310   rButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/rotateright.png")));
2311   connect(rButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
2312     this,SLOT(ReloadImage(QTreeWidgetItem*, int)));
2313
2314   DataTree->topLevelItem(index)->setExpanded(1);
2315   DataTree->topLevelItem(index)->addChild(item);
2316   DataTree->setItemWidget(item, COLUMN_RELOAD_IMAGE, rButton);
2317   DataTree->setItemWidget(item, COLUMN_CLOSE_IMAGE, cButton);
2318
2319   //set the id of the image
2320   QString id = DataTree->topLevelItem(index)->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString();
2321   item->setData(COLUMN_IMAGE_NAME,Qt::UserRole,id.toStdString().c_str());
2322   UpdateTree();
2323   qApp->processEvents();
2324   ImageInfoChanged();
2325   QApplication::restoreOverrideCursor();
2326 }
2327 //------------------------------------------------------------------------------
2328
2329
2330 //------------------------------------------------------------------------------
2331 void vvMainWindow::AddField(vvImage::Pointer vf,QString file,int index)
2332 {
2333   QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
2334   vvSlicerManager* imageManager = mSlicerManagers[index];
2335   if (imageManager->SetVF(vf,file.toStdString())) {
2336     AddFieldEntry(file,index,false);
2337   } else {
2338     QString error = "Cannot import the vector field for this image.\n";
2339     error += imageManager->GetLastError().c_str();
2340     QMessageBox::information(this,tr("Problem reading VF !"),error);
2341   }
2342   QApplication::restoreOverrideCursor();
2343 }
2344 //------------------------------------------------------------------------------
2345
2346
2347 //------------------------------------------------------------------------------
2348 void vvMainWindow::AddField(QString file,int index)
2349 {
2350   if (QFile::exists(file)) {
2351     mInputPathName = itksys::SystemTools::GetFilenamePath(file.toStdString()).c_str();
2352
2353     //init the progress events
2354     QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
2355     vvProgressDialog progress("Opening " + file.toStdString());
2356     qApp->processEvents();
2357
2358     //read the vector and put it in the current mSlicerManager
2359     vvSlicerManager* imageManager = mSlicerManagers[index];
2360     qApp->processEvents();
2361
2362     std::string filename = itksys::SystemTools::GetFilenameWithoutExtension(file.toStdString()).c_str();
2363     if (imageManager->SetVF(file.toStdString())) {
2364       imageManager->Render();
2365       AddFieldEntry(file,index,true);
2366     } else {
2367       QApplication::restoreOverrideCursor();
2368       QString error = "Cannot import the vector field for this image.\n";
2369       error += imageManager->GetLastError().c_str();
2370       QMessageBox::information(this,tr("Problem reading VF !"),error);
2371     }
2372   } else
2373     QMessageBox::information(this,tr("Problem reading VF !"),"File doesn't exist!");
2374
2375 }
2376 //------------------------------------------------------------------------------
2377
2378
2379 //------------------------------------------------------------------------------
2380 void vvMainWindow::SetVFProperty(int subsampling, int scale, int log, int width, double r, double g, double b)
2381 {
2382   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2383   if (mSlicerManagers[index]->GetSlicer(0)->GetVF()) {
2384     for (int i = 0; i < 4; i++) {
2385       mSlicerManagers[index]->GetSlicer(i)->SetVFSubSampling(subsampling);
2386       mSlicerManagers[index]->GetSlicer(i)->SetVFScale(scale);
2387       mSlicerManagers[index]->GetSlicer(i)->SetVFWidth(width);
2388       mSlicerManagers[index]->GetSlicer(i)->SetVFColor(r,g,b);
2389       if (log > 0)
2390         mSlicerManagers[index]->GetSlicer(i)->SetVFLog(1);
2391       else
2392         mSlicerManagers[index]->GetSlicer(i)->SetVFLog(0);
2393     }
2394   }
2395 }
2396 //------------------------------------------------------------------------------
2397
2398
2399 //------------------------------------------------------------------------------
2400 void vvMainWindow::SetOverlayProperty(int color, int linked, double window, double level)
2401 {
2402   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2403   if (mSlicerManagers[index]->GetSlicer(0)->GetOverlay()) {
2404     mSlicerManagers[index]->SetOverlayColor(color);
2405     mSlicerManagers[index]->SetColorMap(0);
2406     mSlicerManagers[index]->SetLinkOverlayWindowLevel(linked);
2407     mSlicerManagers[index]->SetOverlayColorWindow(window);
2408     mSlicerManagers[index]->SetOverlayColorLevel(level);
2409     mSlicerManagers[index]->Render();
2410   }
2411 }
2412 //------------------------------------------------------------------------------
2413
2414 //------------------------------------------------------------------------------
2415 void vvMainWindow::SetFusionProperty(int opacity, int thresOpacity, int colormap,double window, double level, bool showLegend)
2416 {
2417   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2418   if (mSlicerManagers[index]->GetSlicer(0)->GetFusion()) {
2419     mSlicerManagers[index]->SetFusionColorMap(colormap);
2420     mSlicerManagers[index]->SetFusionOpacity(opacity);
2421     mSlicerManagers[index]->SetFusionThresholdOpacity(thresOpacity);
2422     mSlicerManagers[index]->SetFusionWindow(window);
2423     mSlicerManagers[index]->SetFusionLevel(level);
2424     mSlicerManagers[index]->SetFusionShowLegend(showLegend);
2425     mSlicerManagers[index]->SetColorMap(0);
2426     mSlicerManagers[index]->Render();
2427   }
2428 }
2429 //------------------------------------------------------------------------------
2430
2431
2432 //------------------------------------------------------------------------------
2433 void vvMainWindow::SelectFusionSequence()
2434 {
2435   //get the index of the slicer manager of the main sequence (CT)
2436   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2437   //check if one overlay image is already associated
2438   for (int child = 0; child < DataTree->topLevelItem(index)->childCount(); child++)
2439     if ( (DataTree->topLevelItem(index)->child(child)->data(1,Qt::UserRole).toString() == "fusion") ||
2440       (DataTree->topLevelItem(index)->child(child)->data(1,Qt::UserRole).toString() == "fusionSequence") ) {
2441         QString error = "Cannot add more than one compared image\n";
2442         error += "Please remove first ";
2443         error += DataTree->topLevelItem(index)->child(child)->data(COLUMN_IMAGE_NAME,Qt::DisplayRole).toString();
2444         QMessageBox::information(this,tr("Problem adding compared image !"),error);
2445         return;
2446     }
2447
2448     QString Extensions = EXTENSIONS;
2449     Extensions += ";;All Files (*)";
2450     QStringList files = QFileDialog::getOpenFileNames(this,tr("Load Overlay image sequence"),mInputPathName,Extensions);
2451     if (files.isEmpty())
2452       return;
2453
2454     std::vector<std::string> vecFileNames;
2455     for (int i = 0; i < files.size(); i++) {
2456       vecFileNames.push_back(files[i].toStdString());
2457     }
2458
2459     //associate the secondary sequence (US) to the main one
2460     AddFusionSequence(index,vecFileNames,vvImageReader::MERGEDWITHTIME);
2461 }
2462 //------------------------------------------------------------------------------
2463
2464
2465 //------------------------------------------------------------------------------
2466 void vvMainWindow::SelectFusionSequenceCorrespondances() {
2467
2468   //make sure the index is right?
2469   //in the end, I should attach the temporal data to the right sequence!
2470   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2471   //in case the other sequence got selected, make sure we select the primary sequence
2472   if ( (!mSlicerManagers[index]->GetSlicer(0)->GetFusion()) && mSlicerManagers[index]->GetFusionSequenceIndexOfLinkedManager()>=0 ) {
2473     index = mSlicerManagers[index]->GetFusionSequenceIndexOfLinkedManager();
2474   }
2475
2476   //open a dialog box to find a file
2477   //QString Extensions = EXTENSIONS;
2478   QString Extensions = ";;All Files (*)";
2479   QString fileName = QFileDialog::getOpenFileName(this,tr("Load respiratory signal for fused sequence"),mInputPathName,Extensions);
2480   if (fileName.isNull())
2481     return;
2482
2483   //read it as a vector of values
2484   vnl_vector<double> tmpVect;
2485
2486   std::ifstream file;
2487   file.open(fileName.toStdString().c_str());
2488   tmpVect.read_ascii(file);
2489   file.close();
2490
2491   //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
2492   bool signalOK = true;
2493   unsigned nbFrameMain = mSlicerManagers[index]->GetImage()->GetTransform().size();
2494   unsigned nbFrameSecondary = mSlicerManagers[index]->GetFusionSequenceNbFrames();
2495 std::cout<<"nbFrameMain = "<<nbFrameMain<<", nbFrameSecondary= "<<nbFrameSecondary<<", signal size: "<<tmpVect.size()<<std::endl;
2496   std::vector<unsigned> temporalCorrespondances;
2497   if ( tmpVect.size() == nbFrameMain + nbFrameSecondary ) {
2498     for (unsigned i=0 ; i<tmpVect.size() ; i++) {
2499       if (i<nbFrameMain) { //first part of the file: i -> index in secondary seq.
2500         if ( tmpVect(i)<nbFrameSecondary ) temporalCorrespondances.push_back(tmpVect(i));
2501         else { signalOK=false; break; } //pointing outside the secondary sequence...
2502       }
2503       else { //first part of the file -> index in secondary seq.
2504         if ( tmpVect(i)<nbFrameMain ) temporalCorrespondances.push_back(tmpVect(i));
2505         else { signalOK=false; break; } //pointing outside the secondary sequence...
2506       }
2507     }
2508   }
2509   else {signalOK=false;}
2510   if (!signalOK) {//else, send a message to signal the failure...
2511     QString error = "The provided temporal correspondances is invalid - check tooltip.\n";
2512     error += "Ignoring file: " + fileName;
2513     QMessageBox::information(this,tr("Problem adding temporal correspondances!"),error);
2514     return;
2515   }
2516   else {
2517     //for convenience, associate this sequence to both the current slicer manager, and to the linked one
2518     mSlicerManagers[index]->SetFusionSequenceCorrespondances(temporalCorrespondances);
2519     mSlicerManagers[ mSlicerManagers[index]->GetFusionSequenceIndexOfLinkedManager() ]->SetFusionSequenceCorrespondances(temporalCorrespondances);
2520     overlayPanel->enableFusionSequenceTemporalSync();
2521   }
2522
2523 }
2524 //------------------------------------------------------------------------------
2525
2526
2527 //------------------------------------------------------------------------------
2528 //when this function is called index is the slicer manager index corresponding to the main sequence (CT)
2529 //the files behind fileNames points to the data for the secondary sequence
2530 void vvMainWindow::AddFusionSequence(int index, std::vector<std::string> fileNames, vvImageReader::LoadedImageType type)
2531 {
2532   QString file(fileNames[0].c_str());
2533   if (QFile::exists(file))
2534   {
2535     mInputPathName = itksys::SystemTools::GetFilenamePath(file.toStdString()).c_str();
2536     itk::ImageIOBase::Pointer reader = itk::ImageIOFactory::CreateImageIO(
2537       file.toStdString().c_str(), itk::ImageIOFactory::ReadMode);
2538     std::sort (fileNames.begin(), fileNames.end());//make sure the files are sorted.
2539     reader->SetFileName(fileNames[0].c_str());
2540     reader->ReadImageInformation();
2541     std::string component = reader->GetComponentTypeAsString(reader->GetComponentType());
2542     int dimension = reader->GetNumberOfDimensions();
2543     QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
2544     vvProgressDialog progress("Opening " + file.toStdString());
2545     qApp->processEvents();
2546
2547     std::string filename = itksys::SystemTools::GetFilenameWithoutExtension(file.toStdString()).c_str();
2548
2549     if (mSlicerManagers[index]->SetFusionSequence(fileNames,dimension, component,type)) {
2550       //create an item in the tree with good settings
2551       QTreeWidgetItem *item = new QTreeWidgetItem();
2552       item->setData(0,Qt::UserRole,file.toStdString().c_str());
2553       item->setData(1,Qt::UserRole,tr("fusionSequence"));
2554
2555       QFileInfo fileinfo(file); //Do not show the path
2556       item->setData(COLUMN_IMAGE_NAME,Qt::DisplayRole,fileinfo.fileName());
2557       item->setToolTip(COLUMN_IMAGE_NAME, mSlicerManagers[index]->GetListOfAbsoluteFilePathInOneString("fusionSequence").c_str());
2558       qApp->processEvents();
2559       for (int j = 1; j <= 4; j++) {
2560         item->setData(j,Qt::CheckStateRole,DataTree->topLevelItem(index)->data(j,Qt::CheckStateRole));
2561       }
2562
2563       //Create the buttons for reload and close
2564       qApp->processEvents();
2565       QTreePushButton* cButton = new QTreePushButton;
2566       cButton->setItem(item);
2567       cButton->setColumn(COLUMN_CLOSE_IMAGE);
2568       cButton->setToolTip(tr("close image"));
2569       cButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/exit.png")));
2570       connect(cButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
2571         this,SLOT(CloseImage(QTreeWidgetItem*, int)));
2572
2573       QTreePushButton* rButton = new QTreePushButton;
2574       rButton->setItem(item);
2575       rButton->setColumn(COLUMN_RELOAD_IMAGE);
2576       rButton->setToolTip(tr("reload image"));
2577       rButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/rotateright.png")));
2578       connect(rButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
2579         this,SLOT(ReloadImage(QTreeWidgetItem*, int)));
2580
2581       DataTree->topLevelItem(index)->setExpanded(1);
2582       DataTree->topLevelItem(index)->addChild(item);
2583       DataTree->setItemWidget(item, COLUMN_CLOSE_IMAGE, cButton);
2584       DataTree->setItemWidget(item, COLUMN_RELOAD_IMAGE, rButton);
2585
2586       //store the original transform matrix
2587       int indexParent = GetSlicerIndexFromItem( DataTree->topLevelItem(index) );
2588       mSlicerManagers[indexParent]->SetFusionSequenceMainTransformMatrix( mSlicerManagers[indexParent]->GetSlicer(0)->GetImage()->GetTransform()[0]->GetMatrix() );
2589
2590       //set the id of the image
2591       QString id = DataTree->topLevelItem(index)->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString();
2592       item->setData(COLUMN_IMAGE_NAME,Qt::UserRole,id.toStdString().c_str());
2593       UpdateTree();
2594       qApp->processEvents();
2595
2596       //ImageInfoChanged();
2597
2598       QApplication::restoreOverrideCursor();
2599       // Update the display to update, e.g., the sliders
2600       for(int i=0; i<4; i++)
2601         DisplaySliders(index, i);
2602
2603
2604       //This loads the secondary sequence (US) as an independent sequence
2605       LoadImages(fileNames, type);
2606       //reset the transforms to identity
2607       //FIX -- and set the thickness of the US slices to a large value (necessary for visualization purposes...)
2608       double sp_x, sp_y, sp_z;
2609       mSlicerManagers[indexParent]->GetImage()->GetVTKImages()[0]->GetSpacing(sp_x, sp_y, sp_z);
2610       sp_z = std::max(sp_x, std::max(sp_y, sp_z)) + 0.5; //
2611       for (unsigned i=0 ; i<mSlicerManagers.back()->GetImage()->GetTransform().size() ; i++) {
2612         sp_x = mSlicerManagers.back()->GetImage()->GetVTKImages()[i]->GetSpacing()[0];
2613         sp_y = mSlicerManagers.back()->GetImage()->GetVTKImages()[i]->GetSpacing()[1];
2614         mSlicerManagers.back()->GetImage()->GetVTKImages()[i]->SetSpacing( sp_x, sp_y, sp_z);
2615         mSlicerManagers.back()->GetImage()->GetTransform()[i]->Identity();
2616         mSlicerManagers.back()->GetImage()->GetTransform()[i]->Update();
2617       }
2618
2619       //automatically link both images...
2620       AddLink(mSlicerManagers[indexParent]->GetId().c_str(), mSlicerManagers.back()->GetId().c_str(), false);
2621
2622       //tie the main and secondary sequences by raising flags and informing each another of their respective SlicerManager indices
2623       mSlicerManagers[indexParent]->SetFusionSequenceIndexOfLinkedManager(mSlicerManagers.size()-1);
2624       mSlicerManagers[indexParent]->SetFusionSequenceInvolvmentCode(0); //main sequence
2625       mSlicerManagers.back()->SetFusionSequenceIndexOfLinkedManager(indexParent);
2626       mSlicerManagers.back()->SetFusionSequenceInvolvmentCode(1); //secondary sequence
2627       for (unsigned i=0 ; i<4 ; i++) {
2628         mSlicerManagers.back()->GetSlicer(i)->SetFusionSequenceCode(1); //flag the slicers of the secondary sequence
2629       }
2630
2631     } else {
2632       QApplication::restoreOverrideCursor();
2633       QString error = "Cannot import the new image.\n";
2634       error += mSlicerManagers[index]->GetLastError().c_str();
2635       QMessageBox::information(this,tr("Problem reading image !"),error);
2636     }
2637     WindowLevelChanged();
2638     ImageInfoChanged(); //this internally calls WindowLevelChanged...
2639   }
2640   else {
2641     QMessageBox::information(this,tr("Problem reading fusion sequence !"),"File doesn't exist!");
2642     return;
2643   }
2644
2645 }
2646 //------------------------------------------------------------------------------
2647
2648
2649 //------------------------------------------------------------------------------
2650 //fusionSequenceFrameIndex and fusionSequenceNbFrames are relative to the secondary sequence (US)
2651 void vvMainWindow::SetFusionSequenceProperty(int fusionSequenceFrameIndex, bool spatialSyncFlag, unsigned int fusionSequenceNbFrames, bool temporalSyncFlag)
2652 {
2653   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2654
2655   if (!mSlicerManagers[index]->IsInvolvedInFusionSequence()) return;
2656
2657   //check if the focus moved to the linked sequence, and in this case, select the master sequence instead
2658   if (!mSlicerManagers[index]->IsMainSequenceOfFusionSequence()) {
2659     index = mSlicerManagers[index]->GetFusionSequenceIndexOfLinkedManager();
2660   }
2661   int secondaryIndex = mSlicerManagers[index]->GetFusionSequenceIndexOfLinkedManager();
2662   if (secondaryIndex==-1) return; //this should never happen
2663   if ( (!mSlicerManagers[index]->IsMainSequenceOfFusionSequence()) ||
2664     (!mSlicerManagers[secondaryIndex]->IsSecondarySequenceOfFusionSequence()) )
2665   {return;} //this should never happen, raise an exception?
2666
2667   if (mSlicerManagers[index]->GetSlicer(0)->GetFusion()) {
2668
2669     //First, if the spatialSync button is unchecked, then reposition the parent sequence (CT) in its original coordinate frame
2670     if ( (!spatialSyncFlag) && (mSlicerManagers[index]->GetFusionSequenceSpatialSyncFlag()) ) {
2671       for ( unsigned i=0 ; i<mSlicerManagers[index]->GetSlicer(0)->GetImage()->GetTransform().size() ; i++ ) {
2672         mSlicerManagers[index]->GetSlicer(0)->GetImage()->GetTransform()[i]->SetMatrix( mSlicerManagers[index]->GetFusionSequenceMainTransformMatrix() );
2673         mSlicerManagers[index]->GetSlicer(0)->GetImage()->GetTransform()[i]->Update();
2674       }
2675
2676       for (int i=0; i<mSlicerManagers[index]->GetNumberOfSlicers(); i++) {
2677         mSlicerManagers[index]->GetSlicer(i)->ForceUpdateDisplayExtent();
2678         mSlicerManagers[index]->GetSlicer(i)->Render();
2679       }
2680     }
2681
2682     //then, update the property values in the slicer manager
2683     mSlicerManagers[index]->SetFusionSequenceLength(fusionSequenceNbFrames);
2684     mSlicerManagers[index]->SetFusionSequenceSpatialSyncFlag(spatialSyncFlag);
2685     mSlicerManagers[index]->SetFusionSequenceTemporalSyncFlag(temporalSyncFlag);
2686     mSlicerManagers[index]->SetFusionSequenceFrameIndex(fusionSequenceFrameIndex);
2687
2688     //select the right frame of the US sequence
2689     mSlicerManagers[index]->SetFusionSequenceTSlice(fusionSequenceFrameIndex); //here, I should only update the overlayed sequence
2690     mSlicerManagers[secondaryIndex]->SetTSlice(fusionSequenceFrameIndex, false); //this should update the secondary sequence (individual version)
2691
2692     //update the horizontal sliders of the main window
2693     overlayPanel->updateFusionSequenceSliderValueFromWindow(fusionSequenceFrameIndex, false);
2694
2695     if (spatialSyncFlag) { //reslice the CT
2696
2697       if (temporalSyncFlag) { //do the temporal synchronisation
2698         int mainSequenceFrameIndex=0;
2699         //estimate the TSlice to set to the CT
2700         unsigned nbFramesMain = mSlicerManagers[index]->GetImage()->GetTransform().size();
2701         mainSequenceFrameIndex = mSlicerManagers[index]->GetFusionSequenceCorrespondances()[ nbFramesMain + fusionSequenceFrameIndex];
2702         //and set it!
2703         mSlicerManagers[index]->SetTSlice(mainSequenceFrameIndex, false);
2704         //warning, there is a loopback, and modification of the TSlice in main sequence forces an update of the TSlice in secondary, etc...
2705       }
2706
2707
2708       //Set the transform matrix of the parent sequence (typically CT / 4DCT)
2709       vtkSmartPointer<vtkMatrix4x4> tmpMat = vtkSmartPointer<vtkMatrix4x4>::New();
2710       vtkMatrix4x4::Invert( mSlicerManagers[index]->GetFusionSequenceInitialTransformMatrixAtFrame(fusionSequenceFrameIndex), tmpMat );
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]->PreMultiply();
2714         mSlicerManagers[index]->GetSlicer(0)->GetImage()->GetTransform()[i]->Concatenate( tmpMat );
2715         mSlicerManagers[index]->GetSlicer(0)->GetImage()->GetTransform()[i]->Update();
2716       }
2717
2718       for (int i=0; i<mSlicerManagers[index]->GetNumberOfSlicers(); i++) {
2719         mSlicerManagers[index]->GetSlicer(i)->ForceUpdateDisplayExtent();
2720         mSlicerManagers[index]->GetSlicer(i)->Render();
2721       }
2722
2723     }
2724
2725   }
2726 }
2727 //------------------------------------------------------------------------------
2728
2729
2730 //------------------------------------------------------------------------------
2731 void vvMainWindow::SaveAs()
2732 {
2733   if (DataTree->selectedItems()[0]->data(1,Qt::UserRole).toString() == "vector") {
2734     QMessageBox::warning(this,tr("Unsupported type"),tr("Sorry, saving a vector field is unsupported for the moment"));
2735     return;
2736   }
2737
2738   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2739   int dimension = mSlicerManagers[index]->GetDimension();
2740   QStringList OutputListeFormat;
2741   OutputListeFormat.clear();
2742   if (dimension == 1) {
2743     OutputListeFormat.push_back(".mhd");
2744     OutputListeFormat.push_back(".mha");
2745   }
2746   if (dimension == 2) {
2747     OutputListeFormat.push_back(".bmp");
2748     OutputListeFormat.push_back(".png");
2749     OutputListeFormat.push_back(".jpeg");
2750     OutputListeFormat.push_back(".tif");
2751     OutputListeFormat.push_back(".mhd");
2752     OutputListeFormat.push_back(".mha");
2753     OutputListeFormat.push_back(".hdr");
2754     OutputListeFormat.push_back(".vox");
2755   } else if (dimension == 3) {
2756     OutputListeFormat.push_back(".mhd");
2757     OutputListeFormat.push_back(".mha");
2758     OutputListeFormat.push_back(".nii");
2759     OutputListeFormat.push_back(".nrrd");
2760     OutputListeFormat.push_back(".nhdr");
2761     OutputListeFormat.push_back(".hdr");
2762     OutputListeFormat.push_back(".vox");
2763   } else if (dimension == 4) {
2764     OutputListeFormat.push_back(".mhd");
2765     OutputListeFormat.push_back(".mha");
2766     OutputListeFormat.push_back(".nii");
2767     OutputListeFormat.push_back(".nrrd");
2768     OutputListeFormat.push_back(".nhdr");
2769   }
2770   QString Extensions = "AllFiles(*.*)";
2771   for (int i = 0; i < OutputListeFormat.count(); i++) {
2772     Extensions += ";;Images ( *";
2773     Extensions += OutputListeFormat[i];
2774     Extensions += ")";
2775   }
2776   QString fileName = QFileDialog::getSaveFileName(this,
2777     tr("Save As"),
2778     mSlicerManagers[index]->GetFileName().c_str(),
2779     Extensions);
2780   if (!fileName.isEmpty()) {
2781     std::string fileformat = itksys::SystemTools::GetFilenameLastExtension(fileName.toStdString());
2782     if (OutputListeFormat.contains(
2783       fileformat.c_str())) {
2784         QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
2785         std::string action = "Saving";
2786         vvProgressDialog progress("Saving "+fileName.toStdString());
2787         qApp->processEvents();
2788         vvImageWriter::Pointer writer = vvImageWriter::New();
2789         writer->SetOutputFileName(fileName.toStdString());
2790         writer->SetInput(mSlicerManagers[index]->GetImage());
2791
2792         // Check on transform and prompt user
2793         writer->SetSaveTransform(false);
2794         bool bId = true;
2795         for(int i=0; i<4; i++)
2796           for(int j=0; j<4; j++) {
2797             // TODO SR and BP: check on the list of transforms and not the first only
2798             double elt = mSlicerManagers[index]->GetImage()->GetTransform()[0]->GetMatrix()->GetElement(i,j);
2799             if(i==j && elt!=1.)
2800               bId = false;
2801             if(i!=j && elt!=0.)
2802               bId = false;
2803           }
2804           if( !bId ) {
2805             QString warning = "The image has an associated linear transform. Do you want to save it along?";
2806             QMessageBox msgBox(QMessageBox::Warning, tr("Save transform"), warning, 0, this);
2807             msgBox.addButton(tr("Yes"), QMessageBox::AcceptRole);
2808             msgBox.addButton(tr("No"), QMessageBox::RejectRole);
2809             if (msgBox.exec() == QMessageBox::AcceptRole)
2810               writer->SetSaveTransform(true);
2811           }
2812
2813           writer->Update();
2814           QApplication::restoreOverrideCursor();
2815           if (writer->GetLastError().size()) {
2816             QString error = "Saving did not succeed\n";
2817             error += writer->GetLastError().c_str();
2818             QMessageBox::information(this,tr("Saving Problem"),error);
2819             SaveAs();
2820           }
2821     } else {
2822       QString error = fileformat.c_str();
2823       if (error.isEmpty())
2824         error += "no file format specified !";
2825       else
2826         error += " format unknown !!!\n";
2827       QMessageBox::information(this,tr("Saving Problem"),error);
2828       SaveAs();
2829     }
2830   }
2831 }
2832 //------------------------------------------------------------------------------
2833
2834 //------------------------------------------------------------------------------
2835 void vvMainWindow::SaveCurrentState()
2836 {
2837   QString Extensions = "XML Files(*.xml)";
2838   QString fileName = QFileDialog::getSaveFileName(this,
2839     tr("Save Current Window State"),
2840     "",
2841     Extensions);
2842
2843   SaveCurrentStateAs(fileName.toStdString());
2844 }
2845 //------------------------------------------------------------------------------
2846
2847 //------------------------------------------------------------------------------
2848 void vvMainWindow::SaveCurrentStateAs(const std::string& stateFile)
2849 {
2850   vvSaveState save_state;
2851   save_state.Run(this, stateFile);
2852 }
2853
2854 //------------------------------------------------------------------------------
2855 void vvMainWindow::ReadSavedState()
2856 {
2857   QString Extensions = "XML Files(*.xml)";
2858   QString fileName = QFileDialog::getOpenFileName(this,
2859     tr("Load Window State"),
2860     "",
2861     Extensions);
2862
2863   ReadSavedStateFile(fileName.toStdString());
2864 }
2865 //------------------------------------------------------------------------------
2866
2867 //------------------------------------------------------------------------------
2868 void vvMainWindow::ReadSavedStateFile(const std::string& stateFile)
2869 {
2870   vvReadState read_state;
2871   read_state.Run(this, stateFile);
2872 }
2873 //------------------------------------------------------------------------------
2874
2875 //------------------------------------------------------------------------------
2876 void vvMainWindow::LinkAllImages()
2877 {
2878   linkPanel->linkAll();
2879 }
2880
2881 //------------------------------------------------------------------------------
2882 void vvMainWindow::AddLink(QString image1,QString image2,bool fromPanel)
2883 {
2884   if (!fromPanel) {
2885     // delegate to linkPanel if call came from elsewhere...
2886     linkPanel->addLinkFromIds(image1, image2);
2887     return;
2888   }
2889
2890   unsigned int sm1 = 0;
2891   unsigned int sm2 = 0;
2892
2893   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
2894     if (image1.toStdString() == mSlicerManagers[i]->GetId()) {
2895       mSlicerManagers[i]->AddLink(image2.toStdString());
2896       sm1 = i;
2897     }
2898     if (image2.toStdString() == mSlicerManagers[i]->GetId()) {
2899       mSlicerManagers[i]->AddLink(image1.toStdString());
2900       sm2 = i;
2901     }
2902   }
2903
2904   if (linkPanel->isLinkAll())   {
2905     emit UpdateLinkedNavigation(mSlicerManagers[sm1]->GetId(), mSlicerManagers[mCurrentPickedImageIndex], mSlicerManagers[mCurrentPickedImageIndex]->GetSlicer(0));
2906     emit UpdateLinkedNavigation(mSlicerManagers[sm2]->GetId(), mSlicerManagers[mCurrentPickedImageIndex], mSlicerManagers[mCurrentPickedImageIndex]->GetSlicer(0));
2907   } else {
2908     emit UpdateLinkedNavigation(mSlicerManagers[sm2]->GetId(), mSlicerManagers[sm1], mSlicerManagers[sm1]->GetSlicer(0));
2909   }
2910 }
2911
2912 //------------------------------------------------------------------------------
2913
2914
2915 //------------------------------------------------------------------------------
2916 void vvMainWindow::RemoveLink(QString image1,QString image2)
2917 {
2918   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
2919     if (image1.toStdString() == mSlicerManagers[i]->GetId()) {
2920       mSlicerManagers[i]->RemoveLink(image2.toStdString());
2921     }
2922     if (image2.toStdString() == mSlicerManagers[i]->GetId()) {
2923       mSlicerManagers[i]->RemoveLink(image1.toStdString());
2924     }
2925   }
2926 }
2927 //------------------------------------------------------------------------------
2928
2929 //------------------------------------------------------------------------------
2930 void vvMainWindow::ChangeImageWithIndexOffset(vvSlicerManager *sm, int slicer, int offset)
2931 {
2932   if(mSlicerManagers.size()==1)
2933     return;
2934
2935   int index = 0;
2936   while(sm != mSlicerManagers[index])
2937     index++;
2938   index = (index+offset+mSlicerManagers.size()) % mSlicerManagers.size();
2939
2940   QTreeWidgetItem* item = GetItemFromSlicerManager(mSlicerManagers[index]);
2941   item->setData(slicer+1,Qt::CheckStateRole,2);         //change checkbox
2942   CurrentImageChanged(mSlicerManagers[index]->GetId()); //select new image
2943   DisplayChanged(item,slicer+1);
2944 }
2945 //------------------------------------------------------------------------------
2946 void vvMainWindow::HorizontalSliderMoved(int value,int column, int slicer_index)
2947 {
2948   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
2949     if (DataTree->topLevelItem(i)->data(column,Qt::CheckStateRole).toInt() > 1) {
2950       //i is the SlicerManager that is in charge of this slicer.
2951       if (mSlicerManagers[i]->IsInvolvedInFusionSequence()) {
2952         //if the slicerManager is involved in a fusionSequence as the secondary sequence, then update the slider position in the overlay panel and everything accordingly
2953         if (mSlicerManagers[i]->IsSecondarySequenceOfFusionSequence()) {
2954           overlayPanel->updateFusionSequenceSliderValueFromWindow(value, true);
2955         }
2956         else { //if this is the primary sequence that has been modified
2957           if (mSlicerManagers[i]->GetFusionSequenceTemporalSyncFlag()) {
2958             //WARNING: for some obscure reason, there are problems when accessing mSlicerManagers[mSlicerManagers[i]->GetFusionSequenceIndexOfLinkedManager()]->GetFusionSequenceFrameIndex();
2959
2960             int estimatedValue=0;
2961             //estimate a corresponding time index for the secondary (US) sequence, and update it accordingly.
2962             estimatedValue = mSlicerManagers[i]->GetFusionSequenceCorrespondances()[ value ];
2963             //TODO: at the moment, there is a loop in TSlice modifications
2964             //modifying sequence 1 causes seq 2 to update, which in turns update seq1...
2965             //I disable control on seq1 at the moment.
2966             //overlayPanel->updateFusionSequenceSliderValueFromWindow(estimatedValue, true);
2967           }
2968         }
2969       }
2970
2971       for (int j = 0; j < 4; j++) {
2972         mSlicerManagers[i]->SetTSliceInSlicer(value,j);
2973       }
2974       mSlicerManagers[i]->GetSlicer(slicer_index)->Render();
2975       break;
2976     }
2977   }
2978 }
2979 //------------------------------------------------------------------------------
2980
2981
2982 //------------------------------------------------------------------------------
2983 void vvMainWindow::NOHorizontalSliderMoved()
2984 {
2985   // if (mCurrentTime == NOHorizontalSlider->value()) return;
2986   HorizontalSliderMoved(NOHorizontalSlider->value(),COLUMN_UL_VIEW,0);
2987   //  mCurrentTime = NOHorizontalSlider->value();
2988 }
2989 //------------------------------------------------------------------------------
2990
2991
2992 //------------------------------------------------------------------------------
2993 void vvMainWindow::NEHorizontalSliderMoved()
2994 {
2995   // if (mCurrentTime == NEHorizontalSlider->value()) return;
2996   HorizontalSliderMoved(NEHorizontalSlider->value(),COLUMN_UR_VIEW,1);
2997   //  mCurrentTime = NEHorizontalSlider->value();
2998 }
2999 //------------------------------------------------------------------------------
3000
3001
3002 //------------------------------------------------------------------------------
3003 void vvMainWindow::SOHorizontalSliderMoved()
3004 {
3005   // if (mCurrentTime == SOHorizontalSlider->value()) return;
3006   HorizontalSliderMoved(SOHorizontalSlider->value(),COLUMN_DL_VIEW,2);
3007   // mCurrentTime = SOHorizontalSlider->value();
3008 }
3009 //------------------------------------------------------------------------------
3010
3011
3012 //------------------------------------------------------------------------------
3013 void vvMainWindow::SEHorizontalSliderMoved()
3014 {
3015   // if (mCurrentTime == SEHorizontalSlider->value()) return;
3016   HorizontalSliderMoved(SEHorizontalSlider->value(),COLUMN_DR_VIEW,3);
3017   // mCurrentTime = SEHorizontalSlider->value();
3018 }
3019 //------------------------------------------------------------------------------
3020
3021 //------------------------------------------------------------------------------
3022 void vvMainWindow::NOVerticalSliderChanged()
3023 {
3024   static int value=-1;
3025   if (value == NOVerticalSlider->value()) return;
3026   else value = NOVerticalSlider->value();
3027   //  int value = NOVerticalSlider->value();
3028   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
3029     if (DataTree->topLevelItem(i)->data(COLUMN_UL_VIEW,Qt::CheckStateRole).toInt() > 1) {
3030       if (mSlicerManagers[i]->GetSlicer(0)->GetSlice() != value) {
3031         mSlicerManagers[i]->GetSlicer(0)->SetSlice(value);
3032         mSlicerManagers[i]->VerticalSliderHasChanged(0, value);
3033
3034         // If nor Update/Render -> slider not work
3035         // only render = ok navigation, but for contour Update needed but slower ?
3036
3037         mSlicerManagers[i]->UpdateSlice(0);  // <-- DS add this. Not too much update ? YES. but needed for ImageContour ...
3038         //mSlicerManagers[i]->GetSlicer(0)->Render(); // <-- DS add this, needed for contour, seems ok ? not too slow ?
3039       }
3040       break;
3041     }
3042   }
3043 }
3044 //------------------------------------------------------------------------------
3045
3046
3047 //------------------------------------------------------------------------------
3048 void vvMainWindow::NEVerticalSliderChanged()
3049 {
3050   static int value=-1;
3051   if (value == NEVerticalSlider->value()) return;
3052   else value = NEVerticalSlider->value();
3053   //  int value = NEVerticalSlider->value();
3054   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
3055     if (DataTree->topLevelItem(i)->data(COLUMN_UR_VIEW,Qt::CheckStateRole).toInt() > 1) {
3056       if (mSlicerManagers[i]->GetSlicer(1)->GetSlice() != value) {
3057         mSlicerManagers[i]->GetSlicer(1)->SetSlice(value);
3058         mSlicerManagers[i]->VerticalSliderHasChanged(1, value);
3059         mSlicerManagers[i]->UpdateSlice(1);
3060         //mSlicerManagers[i]->GetSlicer(1)->Render(); // <-- DS add this, needed for contour, seems ok ? not too slow ?
3061       }
3062       break;
3063     }
3064   }
3065 }
3066 //------------------------------------------------------------------------------
3067
3068
3069 //------------------------------------------------------------------------------
3070 void vvMainWindow::SOVerticalSliderChanged()
3071 {
3072   static int value=-1;
3073   if (value == SOVerticalSlider->value()) return;
3074   else value = SOVerticalSlider->value();
3075   //int value = SOVerticalSlider->value();
3076   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
3077     if (DataTree->topLevelItem(i)->data(COLUMN_DL_VIEW,Qt::CheckStateRole).toInt() > 1) {
3078       if (mSlicerManagers[i]->GetSlicer(2)->GetSlice() != value) {
3079         mSlicerManagers[i]->GetSlicer(2)->SetSlice(value);
3080         mSlicerManagers[i]->VerticalSliderHasChanged(2, value);
3081         mSlicerManagers[i]->UpdateSlice(2);
3082         //mSlicerManagers[i]->GetSlicer(2)->Render(); // <-- DS add this, needed for contour, seems ok ? not too slow ?
3083       }
3084       // else { DD("avoid SOVerticalSlider slicer update"); }
3085       break;
3086     }
3087   }
3088 }
3089 //------------------------------------------------------------------------------
3090
3091
3092 //------------------------------------------------------------------------------
3093 void vvMainWindow::SEVerticalSliderChanged()
3094 {
3095   static int value=-1;
3096   if (value == SEVerticalSlider->value()) return;
3097   else value = SEVerticalSlider->value();
3098   // int value = SEVerticalSlider->value();
3099   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
3100     if (DataTree->topLevelItem(i)->data(COLUMN_DR_VIEW,Qt::CheckStateRole).toInt() > 1) {
3101       if (mSlicerManagers[i]->GetSlicer(3)->GetSlice() != value) {
3102         mSlicerManagers[i]->GetSlicer(3)->SetSlice(value);
3103         mSlicerManagers[i]->VerticalSliderHasChanged(3, value);
3104         mSlicerManagers[i]->UpdateSlice(3);
3105         //mSlicerManagers[i]->GetSlicer(3)->Render(); // <-- DS add this, needed for contour, seems ok ? not too slow ?
3106       }
3107       break;
3108     }
3109   }
3110 }
3111 //------------------------------------------------------------------------------
3112
3113
3114 //------------------------------------------------------------------------------
3115 void vvMainWindow::UpdateSlice(int slicer, int slice)
3116 {
3117   // DD("vvMainWindow::UpdateSlice");
3118   //   DD(slicer);
3119   //   DD(slice);
3120   if (slicer == 0) {
3121     //    if (slice != NOVerticalSlider->value())
3122     NOVerticalSlider->setValue(slice);
3123   } else {
3124     if (slicer == 1)
3125       NEVerticalSlider->setValue(slice);
3126     else {
3127       if (slicer == 2)
3128         SOVerticalSlider->setValue(slice);
3129       else {
3130         if (slicer == 3)
3131           SEVerticalSlider->setValue(slice);
3132       }
3133     }
3134   }
3135   // DD("vvMainWindow:UpdateSlice END");
3136 }
3137 //------------------------------------------------------------------------------
3138
3139
3140 //------------------------------------------------------------------------------
3141 void vvMainWindow::UpdateTSlice(int slicer, int slice, int code)
3142 {
3143   //FusionSequence: the slider value should be updated for slicers which show the same sequence as requested
3144   bool doUpdate=false;
3145   if (code==-1) doUpdate=true;
3146   else {
3147     for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
3148       if (DataTree->topLevelItem(i)->data(slicer+1,Qt::CheckStateRole).toInt() > 1) {
3149         //i is the active SlicerManager
3150         if (mSlicerManagers[i]->GetFusionSequenceInvolvmentCode()==code) doUpdate=true;
3151         break;
3152       }
3153     }
3154   }
3155   if (!doUpdate) return;
3156
3157   switch (slicer) {
3158   case 0:
3159     if (NOHorizontalSlider->value()==slice) return;
3160     NOHorizontalSlider->setValue(slice);
3161     break;
3162   case 1:
3163     if (NEHorizontalSlider->value()==slice) return;
3164     NEHorizontalSlider->setValue(slice);
3165     break;
3166   case 2:
3167     if (SOHorizontalSlider->value()==slice) return;
3168     SOHorizontalSlider->setValue(slice);
3169     break;
3170   case 3:
3171     if (SEHorizontalSlider->value()==slice) return;
3172     SEHorizontalSlider->setValue(slice);
3173     break;
3174   }
3175 }
3176 //------------------------------------------------------------------------------
3177
3178
3179 //------------------------------------------------------------------------------
3180 void vvMainWindow::UpdateSliceRange(int slicer, int min, int max, int tmin, int tmax)
3181 {
3182   //int position = int((min+max)/2);
3183   int position = mSlicerManagers[mCurrentPickedImageIndex]->GetSlicer(slicer)->GetSlice();
3184   if (slicer == 0) {
3185     NOVerticalSlider->setRange(min,max);
3186     NOHorizontalSlider->setRange(tmin,tmax);
3187     NOVerticalSlider->setValue(position);
3188   } else if (slicer == 1) {
3189     NEVerticalSlider->setRange(min,max);
3190     NEHorizontalSlider->setRange(tmin,tmax);
3191     NEVerticalSlider->setValue(position);
3192   } else if (slicer == 2) {
3193     SOVerticalSlider->setRange(min,max);
3194     SOHorizontalSlider->setRange(tmin,tmax);
3195     SOVerticalSlider->setValue(position);
3196   } else if (slicer == 3) {
3197     SEVerticalSlider->setRange(min,max);
3198     SEHorizontalSlider->setRange(tmin,tmax);
3199     SEVerticalSlider->setValue(position);
3200   }
3201 }
3202 //------------------------------------------------------------------------------
3203
3204
3205 //------------------------------------------------------------------------------
3206 void vvMainWindow::SaveNOScreenshot()
3207 {
3208   SaveScreenshot(NOViewWidget);
3209 }
3210 //------------------------------------------------------------------------------
3211
3212
3213 //------------------------------------------------------------------------------
3214 void vvMainWindow::SaveNEScreenshot()
3215 {
3216   SaveScreenshot(NEViewWidget);
3217 }
3218 //------------------------------------------------------------------------------
3219
3220
3221 //------------------------------------------------------------------------------
3222 void vvMainWindow::SaveSOScreenshot()
3223 {
3224   SaveScreenshot(SOViewWidget);
3225 }
3226 //------------------------------------------------------------------------------
3227
3228
3229 //------------------------------------------------------------------------------
3230 void vvMainWindow::SaveSEScreenshot()
3231 {
3232   SaveScreenshot(SEViewWidget);
3233 }
3234 //------------------------------------------------------------------------------
3235
3236
3237 //------------------------------------------------------------------------------
3238 void vvMainWindow::SaveScreenshotAllSlices()
3239 {
3240   QVTKWidget *widget = NOViewWidget;
3241
3242   int index = 0;// GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
3243   vvSlicerManager * SM = mSlicerManagers[index];
3244   vvImage * image = SM->GetImage();
3245   vvSlicer * slicer = SM->GetSlicer(0);
3246   int orientation = slicer->GetOrientation();
3247   int nbSlices = image->GetSize()[orientation];
3248   vtkSmartPointer<vtkRenderWindow>  renderWindow = widget->GetRenderWindow();
3249
3250   // Select filename base
3251   QString filename = QFileDialog::getSaveFileName(this,
3252     tr("Save As (filename will be completed by slice number)"),
3253     itksys::SystemTools::GetFilenamePath(mSlicerManagers[index]->GetFileName()).c_str(),
3254     "Images( *.png);;Images( *.jpg)");
3255
3256   // Loop on slices
3257   for(int i=0; i<nbSlices; i++) {
3258     // Change the slice
3259     slicer->SetSlice(i); // -> change the slice of the current slicer
3260     SM->UpdateSlice(0); // --> this one emit UpdateSlice
3261     QCoreApplication::flush(); // -> needed to force display of contours
3262
3263     // Screenshot
3264     vtkSmartPointer<vtkWindowToImageFilter> windowToImageFilter = vtkSmartPointer<vtkWindowToImageFilter>::New();
3265     windowToImageFilter->SetInput(renderWindow);
3266     windowToImageFilter->SetMagnification(1);
3267     windowToImageFilter->SetInputBufferTypeToRGBA(); //also record the alpha (transparency) channel
3268     windowToImageFilter->Update();
3269
3270     vtkSmartPointer<vtkPNGWriter> writer = vtkSmartPointer<vtkPNGWriter>::New();
3271     std::string fn = itksys::SystemTools::GetFilenameWithoutLastExtension(filename.toStdString());
3272     std::string num = clitk::toString(i);
3273     if (i<10) num = "0"+num;
3274     if (i<100) num = "0"+num;
3275     if (i<1000) num = "0"+num;
3276
3277     fn = itksys::SystemTools::GetFilenamePath(filename.toStdString()) + "/"+ fn
3278       + "_" + num + itksys::SystemTools::GetFilenameLastExtension(filename.toStdString());
3279     writer->SetFileName(fn.c_str());
3280     writer->SetInput(windowToImageFilter->GetOutput());
3281     writer->Write();
3282   }
3283 }
3284 //------------------------------------------------------------------------------
3285
3286
3287 //------------------------------------------------------------------------------
3288 void vvMainWindow::SaveScreenshot(QVTKWidget *widget)
3289 {
3290   QString Extensions = "Images( *.png);;";
3291   Extensions += "Images( *.jpg);;";
3292   Extensions += "Images( *.bmp);;";
3293   Extensions += "Images( *.tif);;";
3294   Extensions += "Images( *.ppm)";
3295 #if defined(VTK_USE_FFMPEG_ENCODER) || defined(VTK_USE_VIDEO_FOR_WINDOWS)
3296   Extensions += ";;Video( *.avi)";
3297 #endif
3298 #ifdef VTK_USE_MPEG2_ENCODER
3299   Extensions += ";;Video( *.mpg)";
3300 #endif
3301 #ifdef CLITK_EXPERIMENTAL
3302   Extensions += ";;Video( *.gif)";
3303 #endif
3304
3305   int smIndex=GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
3306   QString fileName = QFileDialog::getSaveFileName(this,
3307     tr("Save As"),
3308     itksys::SystemTools::GetFilenamePath(mSlicerManagers[smIndex]->GetFileName()).c_str(),
3309     Extensions);
3310
3311   if (!fileName.isEmpty()) {
3312     vtkSmartPointer<vtkWindowToImageFilter> w2i = vtkSmartPointer<vtkWindowToImageFilter>::New();
3313     w2i->SetInput(widget->GetRenderWindow());
3314     w2i->Update();
3315     vtkImageData *image = w2i->GetOutput();
3316
3317     std::string ext(itksys::SystemTools::GetFilenameLastExtension(fileName.toStdString()));
3318
3319     // Image
3320     vtkImageWriter *imgwriter = NULL;
3321     if (ext==".bmp")
3322       imgwriter = vtkBMPWriter::New();
3323     else if (ext==".tif")
3324       imgwriter = vtkTIFFWriter::New();
3325     else if (ext==".ppm")
3326       imgwriter = vtkPNMWriter::New();
3327     else if (ext==".png")
3328       imgwriter = vtkPNGWriter::New();
3329     else if (ext==".jpg")
3330       imgwriter = vtkJPEGWriter::New();
3331
3332     // Snapshot image if not null
3333     if(imgwriter!=NULL) {
3334       imgwriter->SetInput(image);
3335       imgwriter->SetFileName(fileName.toStdString().c_str());
3336       imgwriter->Write();
3337       return;
3338     }
3339
3340     // Video
3341     vtkGenericMovieWriter *vidwriter = NULL;
3342 #if CLITK_EXPERIMENTAL == 1
3343     if (ext==".gif") {
3344       vvAnimatedGIFWriter *gif = vvAnimatedGIFWriter::New();
3345       vidwriter = gif;
3346
3347       // FPS
3348       bool ok;
3349       int fps = QInputDialog::getInteger(this, tr("Number of frames per second"),
3350         tr("FPS:"), 5, 0, 1000, 1, &ok);
3351       if(ok)
3352         gif->SetRate(fps);
3353
3354       // Loops
3355       int loops = QInputDialog::getInteger(this, tr("Loops"),
3356         tr("Number of loops (0 means infinite):"), 0, 0, 1000000000, 1, &ok);
3357       if(ok)
3358         gif->SetLoops(loops);
3359
3360       // Dithering
3361       QString msg = "Would you like to activate dithering?";
3362       QMessageBox msgBox(QMessageBox::Question, tr("Dithering"),msg, 0, this);
3363       msgBox.addButton(tr("Yes"), QMessageBox::AcceptRole);
3364       msgBox.addButton(tr("No"), QMessageBox::RejectRole);
3365       gif->SetDither(msgBox.exec() == QMessageBox::AcceptRole);
3366     }
3367 #endif
3368 #ifdef VTK_USE_VIDEO_FOR_WINDOWS
3369     if (ext==".avi") {
3370       vtkAVIWriter *mpg = vtkAVIWriter::New();
3371       vidwriter = mpg;
3372       mpg->SetQuality(2);
3373       bool ok;
3374       int fps = QInputDialog::getInteger(this, tr("Number of frames per second"),
3375         tr("FPS:"), 5, 0, 1024, 1, &ok);
3376       if(!ok)
3377         fps = 5;
3378       mpg->SetRate(fps);
3379     }
3380 #endif
3381 #ifdef VTK_USE_FFMPEG_ENCODER
3382     if (ext==".avi") {
3383       vtkFFMPEGWriter *mpg = vtkFFMPEGWriter::New();
3384       vidwriter = mpg;
3385       mpg->SetQuality(2);
3386       bool ok;
3387       int fps = QInputDialog::getInteger(this, tr("Number of frames per second"),
3388         tr("FPS:"), 5, 0, 1024, 1, &ok);
3389       if(!ok)
3390         fps = 5;
3391       mpg->SetRate(fps);
3392       mpg->SetBitRateTolerance(int(ceil(12.0*1024*1024/fps)));
3393     }
3394 #endif
3395 #ifdef VTK_USE_MPEG2_ENCODER
3396     if (ext==".mpg") {
3397       vtkMPEG2Writer *mpg = vtkMPEG2Writer::New();
3398       vidwriter = mpg;
3399     }
3400 #endif
3401
3402     // Take video if not null
3403     if(vidwriter!=NULL){
3404       vidwriter->SetInput(image);
3405       vidwriter->SetFileName(fileName.toStdString().c_str());
3406       vidwriter->Start();
3407       int nSlice = mSlicerManagers[smIndex]->GetSlicer(0)->GetTMax();
3408       for(int i=0; i<=nSlice; i++) {
3409         mSlicerManagers[smIndex]->SetNextTSlice(0);
3410         vtkSmartPointer<vtkWindowToImageFilter> w2i = vtkSmartPointer<vtkWindowToImageFilter>::New();
3411         w2i->SetInput(widget->GetRenderWindow());
3412         w2i->Update();
3413         vidwriter->SetInput(w2i->GetOutput());
3414         vidwriter->Write();
3415       }
3416       vidwriter->End();
3417       vidwriter->Delete();
3418       return;
3419     }
3420
3421     QMessageBox::information(this,tr("Problem saving screenshot !"),tr("Cannot save image.\nPlease set a file extension !!!"));
3422   }
3423 }
3424 //------------------------------------------------------------------------------
3425
3426
3427 //------------------------------------------------------------------------------
3428 void vvMainWindow::GoToCursor()
3429 {
3430   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
3431   for (int column = 1; column < 5; column++) {
3432     if (DataTree->selectedItems()[0]->data(column,Qt::CheckStateRole).toInt() > 1) {
3433       double* cursorPos = mSlicerManagers[index]->GetSlicer(column-1)->GetCursorPosition();
3434       mSlicerManagers[index]->GetSlicer(column-1)->SetCurrentPosition(
3435         cursorPos[0],cursorPos[1],cursorPos[2],cursorPos[3]);
3436       mSlicerManagers[index]->UpdateViews(1,column-1);
3437       mSlicerManagers[index]->UpdateLinked(column-1);
3438       break;
3439     }
3440   }
3441 }
3442 //------------------------------------------------------------------------------
3443
3444 //------------------------------------------------------------------------------
3445 void vvMainWindow::GoToLandmark()
3446 {
3447   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
3448   for (int column = 1; column < 5; column++) {
3449     if (DataTree->selectedItems()[0]->data(column,Qt::CheckStateRole).toInt() > 1) {
3450       double* cursorPos = landmarksPanel->GetSelectedPoint();
3451       mSlicerManagers[index]->GetSlicer(column-1)->SetCurrentPosition(
3452         cursorPos[0],cursorPos[1],cursorPos[2],cursorPos[3]);
3453       mSlicerManagers[index]->UpdateViews(1,column-1);
3454       mSlicerManagers[index]->UpdateLinked(column-1);
3455       break;
3456     }
3457   }
3458 }
3459 //------------------------------------------------------------------------------
3460
3461 //------------------------------------------------------------------------------
3462 void vvMainWindow::PlayPause()
3463 {
3464   if (playMode) {
3465     playMode = 0;
3466     playButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/player_play.png")));
3467     ImageInfoChanged();
3468     return;
3469   } else {
3470     int image_number=DataTree->topLevelItemCount();
3471     bool has_temporal;
3472     for (int i=0; i<image_number; i++)
3473       if (mSlicerManagers[i]->GetSlicer(0)->GetTMax() > 0) {
3474         has_temporal=true;
3475         break;
3476       }
3477       if (has_temporal) {
3478         playMode = 1;
3479         playButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/player_pause.png")));
3480         QTimer::singleShot(1000/mFrameRate, this, SLOT(PlayNext()));
3481       }
3482   }
3483 }
3484 //------------------------------------------------------------------------------
3485
3486 //------------------------------------------------------------------------------
3487 void vvMainWindow::PlayNext()
3488 {
3489   if (playMode && !this->isHidden()) {
3490     int image_number=DataTree->topLevelItemCount();
3491     ///Only play one slicer per SM, and only if the SM is being displayed
3492     for (int i=0; i<image_number; i++)
3493       for (int j=0; j<4; j++)
3494         if (mSlicerManagers[i]->GetSlicer(0)->GetTMax() > 0 &&
3495           DataTree->topLevelItem(i)->data(j+1,Qt::CheckStateRole).toInt() > 0) {
3496             mSlicerManagers[i]->SetNextTSlice(j);
3497             break;
3498         }
3499         QTimer::singleShot(1000/mFrameRate, this, SLOT(PlayNext()));
3500   }
3501 }
3502 //------------------------------------------------------------------------------
3503
3504 void vvMainWindow::ShowLastImage()
3505 {
3506   if (mSlicerManagers.size() > 1) {
3507     QTreeWidgetItem * item=DataTree->topLevelItem(DataTree->topLevelItemCount()-1);
3508     CurrentImageChanged(mSlicerManagers.back()->GetId()); //select new image
3509     item->setData(1,Qt::CheckStateRole,2); //show the new image in the first panel
3510     DisplayChanged(item,1);
3511   }
3512 }
3513
3514 //------------------------------------------------------------------------------
3515 void vvMainWindow::UpdateRenderWindows()
3516 {
3517   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
3518     mSlicerManagers[i]->GetSlicer(0)->UpdateLandmarks();
3519     mSlicerManagers[i]->GetSlicer(1)->UpdateLandmarks();
3520     mSlicerManagers[i]->GetSlicer(2)->UpdateLandmarks();
3521     mSlicerManagers[i]->GetSlicer(3)->UpdateLandmarks();
3522   }
3523   if (NOViewWidget->GetRenderWindow()) NOViewWidget->GetRenderWindow()->Render();
3524   if (NEViewWidget->GetRenderWindow()) NEViewWidget->GetRenderWindow()->Render();
3525   if (SOViewWidget->GetRenderWindow()) SOViewWidget->GetRenderWindow()->Render();
3526   if (SEViewWidget->GetRenderWindow()) SEViewWidget->GetRenderWindow()->Render();
3527 }
3528 //------------------------------------------------------------------------------
3529
3530 //------------------------------------------------------------------------------
3531 void vvMainWindow::SegmentationOnCurrentImage()
3532 {
3533   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
3534
3535   vvSegmentationDialog segmentation;
3536   segmentation.SetImage(mSlicerManagers[index]->GetSlicer(0)->GetImage());
3537   segmentation.exec();
3538 }
3539 //------------------------------------------------------------------------------
3540
3541 void vvMainWindow::SurfaceViewerLaunch()
3542 {
3543   vvSurfaceViewerDialog surfaceViewer;
3544   surfaceViewer.exec();
3545 }
3546 //------------------------------------------------------------------------------
3547
3548
3549 //------------------------------------------------------------------------------
3550 int vvMainWindow::GetImageDuplicateFilenameNumber(std::string filename)
3551 {
3552   int number=0;
3553   for(unsigned int l=0; l<mSlicerManagers.size(); l++) {
3554     vvSlicerManager * v = mSlicerManagers[l];
3555     if (v->GetBaseFileName() ==
3556       vtksys::SystemTools::GetFilenameName(vtksys::SystemTools::GetFilenameWithoutLastExtension(filename))) {
3557         number = std::max(number, v->GetBaseFileNameNumber()+1);
3558     }
3559   }
3560   return number;
3561 }
3562 //------------------------------------------------------------------------------
3563
3564
3565 //------------------------------------------------------------------------------
3566 vvSlicerManager* vvMainWindow::AddImage(vvImage::Pointer image,std::string filename)
3567 {
3568   // Change filename if another image exist with the same name
3569   int number = GetImageDuplicateFilenameNumber(filename);
3570
3571   // Create new SliceManager
3572   vvSlicerManager* slicer_manager = new vvSlicerManager(4);
3573   slicer_manager->SetImage(image);//, IMAGE, number);
3574   //  filename = filename+"_"+clitk::toString(number);
3575   slicer_manager->SetFilename(filename, number);
3576   mSlicerManagers.push_back(slicer_manager);
3577
3578   //create an item in the tree with good settings
3579   QTreeWidgetItem *item = new QTreeWidgetItem();
3580   item->setData(0,Qt::UserRole,slicer_manager->GetFileName().c_str());//files[i].c_str());
3581   item->setData(1,Qt::UserRole,tr("image"));
3582   item->setData(COLUMN_IMAGE_NAME,Qt::DisplayRole,slicer_manager->GetFileName().c_str());//filename.c_str());
3583   qApp->processEvents();
3584
3585   for (int j = 1; j <= 4; j++) item->setData(j,Qt::CheckStateRole,1);
3586
3587   //Create the buttons for reload and close
3588   qApp->processEvents();
3589   QTreePushButton* cButton = new QTreePushButton;
3590   cButton->setItem(item);
3591   cButton->setColumn(COLUMN_CLOSE_IMAGE);
3592   cButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/exit.png")));
3593   connect(cButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
3594     this,SLOT(CloseImage(QTreeWidgetItem*, int)));
3595
3596   QTreePushButton* rButton = new QTreePushButton;
3597   rButton->setItem(item);
3598   rButton->setColumn(COLUMN_RELOAD_IMAGE);
3599   rButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/rotateright.png")));
3600   rButton->setEnabled(0);
3601   connect(rButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
3602     this,SLOT(ReloadImage(QTreeWidgetItem*, int)));
3603
3604   DataTree->addTopLevelItem(item);
3605   DataTree->setItemWidget(item, COLUMN_CLOSE_IMAGE, cButton);
3606   DataTree->setItemWidget(item, COLUMN_RELOAD_IMAGE, rButton);
3607
3608   //set the id of the image
3609   QString id = QDir::current().absoluteFilePath(slicer_manager->GetFileName().c_str()) + QString::number(mSlicerManagers.size()-1);
3610   item->setData(COLUMN_IMAGE_NAME,Qt::UserRole,id.toStdString().c_str());
3611   mSlicerManagers.back()->SetId(id.toStdString());
3612
3613   linkPanel->addImage(slicer_manager->GetFileName().c_str()// filename
3614     , id.toStdString());
3615
3616   connect(mSlicerManagers.back(), SIGNAL(currentImageChanged(std::string)),
3617     this, SLOT(CurrentImageChanged(std::string)));
3618   connect(mSlicerManagers.back(), SIGNAL(currentPickedImageChanged(std::string)),
3619     this, SLOT(CurrentPickedImageChanged(std::string)));
3620   connect(mSlicerManagers.back(), SIGNAL(UpdatePosition(int, double, double, double, double, double, double, double)),
3621     this, SLOT(MousePositionChanged(int,double, double, double, double, double, double, double)));
3622   connect(mSlicerManagers.back(), SIGNAL(UpdateVector(int, double, double, double, double)),
3623     this, SLOT(VectorChanged(int,double,double,double, double)));
3624   connect(mSlicerManagers.back(), SIGNAL(UpdateOverlay(int, double, double)),
3625     this, SLOT(OverlayChanged(int,double,double)));
3626   connect(mSlicerManagers.back(), SIGNAL(UpdateFusion(int, double)),
3627     this, SLOT(FusionChanged(int,double)));
3628   //connect(mSlicerManagers.back(), SIGNAL(UpdateFusionSequence(int, bool, unsigned int)),
3629   //  this, SLOT(FusionSequenceChanged(int, bool, unsigned int)));
3630   connect(mSlicerManagers.back(), SIGNAL(WindowLevelChanged()),
3631     this,SLOT(WindowLevelChanged()));
3632   connect(mSlicerManagers.back(), SIGNAL(UpdateSlice(int,int)),
3633     this,SLOT(UpdateSlice(int,int)));
3634   connect(mSlicerManagers.back(), SIGNAL(UpdateTSlice(int, int, int)),
3635     this,SLOT(UpdateTSlice(int, int, int)));
3636   connect(mSlicerManagers.back(), SIGNAL(UpdateTSlice(int, int, int)),
3637     this,SLOT(ImageInfoChanged()));
3638   connect(mSlicerManagers.back(), SIGNAL(UpdateSliceRange(int,int,int,int,int)),
3639     this,SLOT(UpdateSliceRange(int,int,int,int,int)));
3640   connect(mSlicerManagers.back(), SIGNAL(UpdateLinkManager(std::string,int,double,double,double,int)),
3641     this,SLOT(UpdateLinkManager(std::string,int,double,double,double,int)));
3642   connect(mSlicerManagers.back(), SIGNAL(UpdateLinkedNavigation(std::string,vvSlicerManager*,vvSlicer*)),
3643     this,SLOT(UpdateLinkedNavigation(std::string,vvSlicerManager*,vvSlicer*)));
3644   connect(mSlicerManagers.back(), SIGNAL(ChangeImageWithIndexOffset(vvSlicerManager*,int,int)),
3645     this,SLOT(ChangeImageWithIndexOffset(vvSlicerManager*,int,int)));
3646   connect(mSlicerManagers.back(), SIGNAL(LandmarkAdded()),landmarksPanel,SLOT(AddPoint()));
3647
3648
3649   UpdateTree();
3650   qApp->processEvents();
3651   InitSlicers();
3652   ShowLastImage();
3653   InitDisplay();
3654   qApp->processEvents();
3655
3656   // End
3657   ImageInfoChanged();
3658   return slicer_manager;
3659 }
3660 //------------------------------------------------------------------------------
3661
3662
3663 //------------------------------------------------------------------------------
3664 void vvMainWindow::UpdateCurrentSlicer()
3665 {
3666   int index = -1;
3667   if (DataTree->selectedItems().size() > 0) {
3668     index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
3669   }
3670   mSlicerManagerCurrentIndex = index;
3671 }
3672 //------------------------------------------------------------------------------
3673