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 #include "clitkConfiguration.h"
  51
  52 // ITK include
  53 #include <itkImage.h>
  54 #include <itkImageFileReader.h>
  55 #include <itkByteSwapper.h>
  56 #include <itkCommand.h>
  57 #include <itkNumericSeriesFileNames.h>
  58
  59 // VTK include
  60 #include <vtkImageData.h>
  61 #include <vtkImageActor.h>
  62 #include <vtkCornerAnnotation.h>
  63 #include <vtkRenderWindow.h>
  64 #include <vtkRenderWindowInteractor.h>
  65 #include <vtkRenderer.h>
  66 #include <vtkRendererCollection.h>
  67 #include <vtkWindowToImageFilter.h>
  68 #include <vtkBMPWriter.h>
  69 #include <vtkTIFFWriter.h>
  70 #include <vtkPNMWriter.h>
  71 #include <vtkPNGWriter.h>
  72 #include <vtkJPEGWriter.h>
  73 #include <vtkGenericMovieWriter.h>
  74 #ifdef CLITK_EXPERIMENTAL
  75 #  include <vvAnimatedGIFWriter.h>
  76 #endif
  77 #ifdef VTK_USE_VIDEO_FOR_WINDOWS
  78 #  include <vtkAVIWriter.h>
  79 #endif
  80 #ifdef VTK_USE_FFMPEG_ENCODER
  81 #  include <vtkFFMPEGWriter.h>
  82 #endif
  83 #ifdef VTK_USE_MPEG2_ENCODER
  84 #  include <vtkMPEG2Writer.h>
  85 #endif
  86 #include <vtkMatrix4x4.h>
  87 #include <vtkTransform.h>
  88
  89 // Standard includes
  90 #include <iostream>
  91 #include <fstream>
  92 #include <sstream>
  93 #include <iomanip>
  94
  95 #define COLUMN_TREE 0
  96 #define COLUMN_UL_VIEW 1
  97 #define COLUMN_UR_VIEW 2
  98 #define COLUMN_DL_VIEW 3
  99 #define COLUMN_DR_VIEW 4
 100 #define COLUMN_CLOSE_IMAGE 5
 101 #define COLUMN_RELOAD_IMAGE 6
 102 #define COLUMN_IMAGE_NAME 7
 103
 104 #ifdef CLITK_PRIVATE_FEATURES
 105 #define EXTENSIONS "Images ( *.bmp *.png *.jpeg *.jpg *.tif *.mhd *.mha *.hdr *.vox *.his *.xdr *.SCAN *.nii *.nrrd *.nhdr *.refscan *.nii.gz *.usf *.svl)"
 106 #else
 107 #define EXTENSIONS "Images ( *.bmp *.png *.jpeg *.jpg *.tif *.mhd *.mha *.hdr *.vox *.his *.xdr *.SCAN *.nii *.nrrd *.nhdr *.refscan *.nii.gz)"
 108 #endif
 109
 110
 111 /*Data Tree values
 112 0,Qt::UserRole full filename
 113 1,Qt::CheckStateRole checkbutton UL View
 114 1,Qt::UserRole overlay, fusion or vector
 115 2,Qt::CheckStateRole checkbutton UR View
 116 3,Qt::CheckStateRole checkbutton DL View
 117 4,Qt::CheckStateRole checkbutton DR View
 118 5,0  short filename
 119 5,Qt::UserRole mSlicerManager id*/
 120
 121 //------------------------------------------------------------------------------
 122 vvMainWindow::vvMainWindow():vvMainWindowBase()
 123 {
 124   setupUi(this); // this sets up the GUI
 125
 126   mInputPathName = "";
 127   mMenuTools = menuTools;
 128   //  mMenuSegmentation = menuSegmentation;
 129   mContextMenu = &contextMenu;
 130   mMenuExperimentalTools = menuExperimental;
 131   mMainWidget = this;
 132   mCurrentTime = -1;
 133   mCurrentSelectedImageId = "";
 134   mCurrentPickedImageId = "";
 135   mCurrentPickedImageIndex = 0;
 136
 137   //Init the contextMenu
 138   this->setContextMenuPolicy(Qt::CustomContextMenu);
 139   contextActions.resize(0);
 140   QAction* actionOpen_new_image = contextMenu.addAction(QIcon(QString::fromUtf8(":/common/icons/fileopen.png")),
 141     tr("O&pen new Image"));
 142   actionOpen_new_image->setShortcut(QKeySequence(tr("Ctrl+O")));
 143   connect(actionOpen_new_image,SIGNAL(triggered()),this,SLOT(OpenImages()));
 144   contextActions.push_back(actionOpen_new_image);
 145   contextMenu.addSeparator();
 146
 147   QAction* actionClose_Image = contextMenu.addAction(QIcon(QString::fromUtf8(":/common/icons/exit.png")),
 148     tr("Close Current Image"));
 149   connect(actionClose_Image,SIGNAL(triggered()),this,SLOT(CloseImage()));
 150   contextActions.push_back(actionClose_Image);
 151
 152   QAction* actionReload_image = contextMenu.addAction(QIcon(QString::fromUtf8(":/common/icons/rotateright.png")),
 153     tr("Reload Current Image"));
 154   connect(actionReload_image,SIGNAL(triggered()),this,SLOT(ReloadImage()));
 155   contextActions.push_back(actionReload_image);
 156
 157   QAction* actionSave_image = contextMenu.addAction(QIcon(QString::fromUtf8(":/common/icons/filesave.png")),
 158     tr("Save Current Image"));
 159   connect(actionSave_image,SIGNAL(triggered()),this,SLOT(SaveAs()));
 160   contextActions.push_back(actionSave_image);
 161
 162   QAction* actionSave_state = contextMenu.addAction(QIcon(QString::fromUtf8(":/common/icons/filesave.png")),
 163     tr("Save Current State"));
 164   connect(actionSave_state,SIGNAL(triggered()),this,SLOT(SaveCurrentState()));
 165   contextActions.push_back(actionSave_state);
 166
 167   QAction* actionRead_state = contextMenu.addAction(QIcon(QString::fromUtf8(":/common/icons/filesave.png")),
 168     tr("Read Saved State"));
 169   connect(actionRead_state,SIGNAL(triggered()),this,SLOT(ReadSavedState()));
 170   contextActions.push_back(actionRead_state);
 171
 172   contextMenu.addSeparator();
 173
 174   contextMenu.addAction(actionAdd_VF_to_current_Image);
 175   contextActions.push_back(actionAdd_VF_to_current_Image);
 176
 177   //QAction* actionAdd_Overlay_to_current_Image = menuOverlay->addAction(QIcon(QString::fromUtf8(":/common/icons/GPSup.png")),
 178   //    tr("Add overlay image to current image"));
 179   contextMenu.addAction(actionAdd_overlay_image_to_current_image);
 180   contextActions.push_back(actionAdd_overlay_image_to_current_image);
 181
 182   contextMenu.addAction(actionAdd_fusion_image);
 183   contextActions.push_back(actionAdd_fusion_image);
 184
 185 #ifdef CLITK_EXPERIMENTAL
 186   contextMenu.addAction(actionAdd_USSequence_toCT);
 187   contextActions.push_back(actionAdd_USSequence_toCT);
 188 #endif
 189
 190
 191   contextMenu.addSeparator();
 192   QAction* actionResetMatrix = contextMenu.addAction(QIcon(QString::fromUtf8(":/common/icons/identity.png")),
 193     tr("Reset transformation to identity"));
 194   connect(actionResetMatrix, SIGNAL(triggered()), this,SLOT(ResetTransformationToIdentity()));
 195
 196   // TRIAL DS
 197   /*
 198   QMenu * m = new QMenu(menubar);
 199   m->setTitle("TOTO");
 200   //  m->setObjectName(QString::fromUtf8("TOTOTO"));
 201   contextMenu.addMenu(m);
 202   QAction * a = m->addAction(QIcon(QString::fromUtf8(":/common/icons/GPSup.png")),
 203   tr("BIDON"));
 204   QAction * b = m->addAction(QIcon(QString::fromUtf8(":/common/icons/GPSup.png")),
 205   tr("BIDON2"));
 206   m->addAction(a);
 207   m->addAction(b);
 208   connect(a,SIGNAL(triggered()),this,SLOT(AddFusionImage()));
 209   */
 210
 211   //init the DataTree
 212   mSlicerManagers.resize(0);
 213
 214   QStringList header;
 215   header.append("");
 216   header.append("TL");
 217   header.append("TR");
 218   header.append("BL");
 219   header.append("BR");
 220   header.append("");
 221   header.append("");
 222   header.append("Name");
 223
 224   DataTree->setHeaderLabels(header);
 225   DataTree->resizeColumnToContents(COLUMN_TREE);
 226   DataTree->resizeColumnToContents(COLUMN_UL_VIEW);
 227   DataTree->resizeColumnToContents(COLUMN_UR_VIEW);
 228   DataTree->resizeColumnToContents(COLUMN_DL_VIEW);
 229   DataTree->resizeColumnToContents(COLUMN_DR_VIEW);
 230   DataTree->resizeColumnToContents(COLUMN_CLOSE_IMAGE);
 231   DataTree->resizeColumnToContents(COLUMN_RELOAD_IMAGE);
 232   DataTree->resizeColumnToContents(COLUMN_IMAGE_NAME);
 233
 234   viewMode = 1;
 235   documentation = new vvDocumentation();
 236   help_dialog = new vvHelpDialog();
 237   dicomSeriesSelector = new vvDicomSeriesSelector();
 238
 239   inverseButton->setEnabled(0);
 240   actionAdd_overlay_image_to_current_image->setEnabled(0);
 241   actionSave_As->setEnabled(0);
 242   actionAdd_VF_to_current_Image->setEnabled(0);
 243   actionAdd_fusion_image->setEnabled(0);
 244   actionAdd_USSequence_toCT->setEnabled(0);
 245
 246   //init the sliders
 247   verticalSliders.push_back(NOVerticalSlider);
 248   verticalSliders.push_back(NEVerticalSlider);
 249   verticalSliders.push_back(SOVerticalSlider);
 250   verticalSliders.push_back(SEVerticalSlider);
 251
 252   for (int i =0; i < 4; i++)
 253     verticalSliders[i]->hide();
 254
 255   horizontalSliders.push_back(NOHorizontalSlider);
 256   horizontalSliders.push_back(NEHorizontalSlider);
 257   horizontalSliders.push_back(SOHorizontalSlider);
 258   horizontalSliders.push_back(SEHorizontalSlider);
 259
 260   for (int i =0; i < 4; i++)
 261     horizontalSliders[i]->hide();
 262
 263
 264   connect(NOVerticalSlider,SIGNAL(valueChanged(int)),this,SLOT(NOVerticalSliderChanged()));
 265   connect(NEVerticalSlider,SIGNAL(valueChanged(int)),this,SLOT(NEVerticalSliderChanged()));
 266   connect(SOVerticalSlider,SIGNAL(valueChanged(int)),this,SLOT(SOVerticalSliderChanged()));
 267   connect(SEVerticalSlider,SIGNAL(valueChanged(int)),this,SLOT(SEVerticalSliderChanged()));
 268
 269   connect(NOHorizontalSlider,SIGNAL(valueChanged(int)),this,SLOT(NOHorizontalSliderMoved()));
 270   connect(NEHorizontalSlider,SIGNAL(valueChanged(int)),this,SLOT(NEHorizontalSliderMoved()));
 271   connect(SOHorizontalSlider,SIGNAL(valueChanged(int)),this,SLOT(SOHorizontalSliderMoved()));
 272   connect(SEHorizontalSlider,SIGNAL(valueChanged(int)),this,SLOT(SEHorizontalSliderMoved()));
 273
 274   //connect everything
 275   connect(actionCompute_mid_position_image,SIGNAL(triggered()),this,SLOT(ComputeMidPosition()));
 276   connect(actionDeformable_Registration,SIGNAL(triggered()),this,SLOT(ComputeDeformableRegistration()));
 277   connect(actionWarp_image_with_vector_field,SIGNAL(triggered()),this,SLOT(WarpImage()));
 278   connect(actionLoad_images,SIGNAL(triggered()),this,SLOT(OpenImages()));
 279   connect(actionOpen_Dicom,SIGNAL(triggered()),this,SLOT(OpenDicom()));
 280   connect(actionOpen_Dicom_Struct,SIGNAL(triggered()),this,SLOT(OpenDCStructContour()));
 281   connect(actionOpen_VTK_contour,SIGNAL(triggered()),this,SLOT(OpenVTKContour()));
 282   connect(actionOpen_Multiple_Images_As_One,SIGNAL(triggered()),this,SLOT(MergeImages()));
 283   connect(actionSlice_Image_As_Multiple_Images,SIGNAL(triggered()),this,SLOT(SliceImages()));
 284   connect(actionOpen_Image_With_Time,SIGNAL(triggered()),this,SLOT(OpenImageWithTime()));
 285   connect(actionMerge_images_as_n_dim_t, SIGNAL(triggered()), this, SLOT(MergeImagesWithTime()));
 286   connect(actionSave_As,SIGNAL(triggered()),this,SLOT(SaveAs()));
 287   connect(actionSave_current_state,SIGNAL(triggered()),this,SLOT(SaveCurrentState()));
 288   connect(actionRead_saved_state,SIGNAL(triggered()),this,SLOT(ReadSavedState()));
 289   connect(actionExit,SIGNAL(triggered()),this,SLOT(close()));
 290   connect(actionAdd_VF_to_current_Image,SIGNAL(triggered()),this,SLOT(OpenField()));
 291   connect(actionAdd_fusion_image,SIGNAL(triggered()),this,SLOT(SelectFusionImage()));
 292   connect(actionAdd_overlay_image_to_current_image,SIGNAL(triggered()), this,SLOT(SelectOverlayImage()));
 293   connect(actionAdd_USSequence_toCT,SIGNAL(triggered()), this,SLOT(SelectFusionSequence()));
 294   connect(actionNavigation_Help,SIGNAL(triggered()),this,SLOT(ShowHelpDialog()));
 295   connect(actionDocumentation,SIGNAL(triggered()),this,SLOT(ShowDocumentation()));
 296   connect(actionRegister_vv,SIGNAL(triggered()),this,SLOT(PopupRegisterForm()));
 297
 298   connect(overlayPanel, SIGNAL(FusionSequenceCorrespondancesButtonPressed()), this, SLOT(SelectFusionSequenceCorrespondances()));
 299
 300
 301   ///////////////////////////////////////////////
 302   connect(actionSegmentation,SIGNAL(triggered()),this,SLOT(SegmentationOnCurrentImage()));
 303   connect(actionSurface_Viewer,SIGNAL(triggered()),this,SLOT(SurfaceViewerLaunch()));
 304   ///////////////////////////////////////////////
 305
 306   actionNorth_East_Window->setEnabled(0);
 307   actionNorth_West_Window->setEnabled(0);
 308   actionSouth_East_Window->setEnabled(0);
 309   actionSouth_West_Window->setEnabled(0);
 310
 311   connect(actionNorth_East_Window,SIGNAL(triggered()),this,SLOT(SaveNEScreenshot()));
 312   connect(actionNorth_West_Window,SIGNAL(triggered()),this,SLOT(SaveNOScreenshot()));
 313   connect(actionSouth_East_Window,SIGNAL(triggered()),this,SLOT(SaveSEScreenshot()));
 314   connect(actionSouth_West_Window,SIGNAL(triggered()),this,SLOT(SaveSOScreenshot()));
 315   connect(actionSave_all_slices,SIGNAL(triggered()),this,SLOT(SaveScreenshotAllSlices()));
 316
 317   connect(DataTree,SIGNAL(itemSelectionChanged()),this,SLOT(ImageInfoChanged()));
 318   connect(DataTree,SIGNAL(itemClicked(QTreeWidgetItem*, int)),this,
 319     SLOT(DisplayChanged(QTreeWidgetItem*, int)));
 320
 321   connect(viewButton,SIGNAL(clicked()),this, SLOT(ChangeViewMode()) );
 322   connect(windowSpinBox,SIGNAL(editingFinished()),this,SLOT(WindowLevelEdited()));
 323   connect(levelSpinBox,SIGNAL(editingFinished()),this,SLOT(WindowLevelEdited()));
 324   connect(colorMapComboBox,SIGNAL(currentIndexChanged(int)),this,SLOT(UpdateColorMap()));
 325   connect(presetComboBox,SIGNAL(currentIndexChanged(int)),this,SLOT(UpdateWindowLevel()));
 326   connect(slicingPresetComboBox, SIGNAL(currentIndexChanged(int)),this,SLOT(UpdateSlicingPreset()));
 327   connect(inverseButton,SIGNAL(clicked()),this,SLOT(SwitchWindowLevel()));
 328   connect(applyWindowLevelToAllButton,SIGNAL(clicked()),this,SLOT(ApplyWindowLevelToAllImages()));
 329
 330   connect(this,SIGNAL(customContextMenuRequested(QPoint)),this,SLOT(ShowContextMenu(QPoint)));
 331
 332   connect(linkPanel,SIGNAL(addLink(QString,QString,bool)),this,SLOT(AddLink(QString,QString,bool)));
 333   connect(linkPanel,SIGNAL(removeLink(QString,QString)),this,SLOT(RemoveLink(QString,QString)));
 334   connect(overlayPanel,SIGNAL(VFPropertyUpdated(int,int,int,int,double,double,double)),this,SLOT(SetVFProperty(int,int,int,int,double,double,double)));
 335   connect(overlayPanel,SIGNAL(OverlayPropertyUpdated(int,int,double,double)),
 336     this,SLOT(SetOverlayProperty(int,int,double,double)));
 337   connect(overlayPanel,SIGNAL(FusionPropertyUpdated(int,int,int,double,double, bool)),
 338     this,SLOT(SetFusionProperty(int,int,int,double,double, bool)));
 339   connect(landmarksPanel,SIGNAL(UpdateRenderWindows()),this,SLOT(UpdateRenderWindows()));
 340   connect(landmarksPanel,SIGNAL(SelectedPointChanged()),this,SLOT(GoToLandmark()));
 341
 342   connect(overlayPanel,SIGNAL(FusionSequencePropertyUpdated(int, bool, unsigned int, bool)),
 343     this,SLOT(SetFusionSequenceProperty(int, bool,unsigned int, bool)));
 344
 345
 346   playMode = 0;//pause
 347   mFrameRate = 10;
 348   playButton->setEnabled(0);
 349   frameRateLabel->setEnabled(0);
 350   frameRateSpinBox->setEnabled(0);
 351   connect(playButton, SIGNAL(clicked()),this,SLOT(PlayPause()));
 352   connect(frameRateSpinBox, SIGNAL(valueChanged(int)),this,SLOT(ChangeFrameRate(int)));
 353
 354   goToCursorPushButton->setEnabled(0);
 355   connect(goToCursorPushButton, SIGNAL(clicked()),this,SLOT(GoToCursor()));
 356
 357   NOViewWidget->hide();
 358   NEViewWidget->hide();
 359   SOViewWidget->hide();
 360   SEViewWidget->hide();
 361
 362   //Recently opened files
 363   std::list<std::string> recent_files = GetRecentlyOpenedImages();
 364   recentlyOpenedFilesMenu=NULL;
 365   if ( !recent_files.empty() ) {
 366     createRecentlyOpenedFilesMenu();
 367     updateRecentlyOpenedFilesMenu(recent_files);
 368   }
 369
 370   // Adding all new tools (insertion in the menu)
 371   vvToolManager::GetInstance()->InsertToolsInMenu(this);
 372   vvToolManager::GetInstance()->EnableToolsInMenu(this, false);
 373
 374   if (!CLITK_EXPERIMENTAL)
 375     menuExperimental->menuAction()->setVisible(false);
 376
 377
 378   QTimer * timerMemory = new QTimer(this);
 379   //timerMemory->setInterval(5);
 380   connect(timerMemory, SIGNAL(timeout()), this, SLOT(UpdateMemoryUsage()));
 381   timerMemory->start(2000);
 382
 383 }
 384 //------------------------------------------------------------------------------
 385 void vvMainWindow::show()
 386 {
 387   vvMainWindowBase::show();
 388   PopupRegisterForm(true);
 389 }
 390 //------------------------------------------------------------------------------
 391 void vvMainWindow::UpdateMemoryUsage()
 392 {
 393   //  clitk::PrintMemory(true);
 394   if (clitk::GetMemoryUsageInMb() == 0) infoPanel->setMemoryInMb("NA");
 395   else infoPanel->setMemoryInMb(QString::number(clitk::GetMemoryUsageInMb())+" MiB");
 396 }
 397 //------------------------------------------------------------------------------
 398
 399
 400 //------------------------------------------------------------------------------
 401 void vvMainWindow::createRecentlyOpenedFilesMenu()
 402 {
 403   recentlyOpenedFilesMenu = new QMenu("Recently opened files...");
 404   recentlyOpenedFilesMenu->setIcon(QIcon(QString::fromUtf8(":/common/icons/open.png")));
 405   menuFile->insertMenu(actionOpen_Image_With_Time,recentlyOpenedFilesMenu);
 406   menuFile->insertSeparator(actionOpen_Image_With_Time);
 407 }
 408 //------------------------------------------------------------------------------
 409
 410
 411 //------------------------------------------------------------------------------
 412
 413 void vvMainWindow::updateRecentlyOpenedFilesMenu(const std::list<std::string> &recent_files)
 414 {
 415   if(recentlyOpenedFilesMenu==NULL) {
 416     createRecentlyOpenedFilesMenu();
 417   } else {
 418     recentlyOpenedFilesMenu->clear();
 419   }
 420   for (std::list<std::string>::const_iterator i = recent_files.begin(); i!=recent_files.end(); i++) {
 421     QAction* current=new QAction(QIcon(QString::fromUtf8(":/common/icons/open.png")), i->c_str(),this);
 422     recentlyOpenedFilesMenu->addAction(current);
 423     connect(current,SIGNAL(triggered()),this,SLOT(OpenRecentImage()));
 424   }
 425 }
 426 //------------------------------------------------------------------------------
 427
 428
 429 //------------------------------------------------------------------------------
 430 void vvMainWindow::ComputeMidPosition()
 431 {
 432   bool ok;
 433   int index=GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
 434   int ref = QInputDialog::getInteger(this,"Chose reference phase","Reference phase",0,0,\
 435     mSlicerManagers[index]->GetImage()->GetVTKImages().size()-1,1,&ok);
 436   if (ok) {
 437     vvMidPosition midp;
 438     midp.slicer_manager = mSlicerManagers[index];
 439     midp.reference_image_index = ref;
 440     QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
 441     midp.Update();
 442     if (midp.error)
 443       QMessageBox::warning(this, "Error computing midposition image",midp.error_message.c_str());
 444     else {
 445       QFileInfo info(midp.slicer_manager->GetFileName().c_str());
 446       AddImage(midp.output,info.path().toStdString()+"/"+info.completeBaseName().toStdString()+"_midposition.mhd");
 447     }
 448     QApplication::restoreOverrideCursor();
 449   }
 450 }
 451 //------------------------------------------------------------------------------
 452
 453
 454 //------------------------------------------------------------------------------
 455 void vvMainWindow::AddContour(int image_index, vvMesh::Pointer contour, bool propagation)
 456 {
 457   QTreeWidgetItem *item = new QTreeWidgetItem();
 458   item->setData(0,Qt::UserRole,"filename.vtk");
 459   item->setData(1,Qt::UserRole,tr("contour"));
 460   QBrush brush;
 461   brush.setColor(QColor(contour->r*255,contour->g*255,contour->b*255));
 462   brush.setStyle(Qt::SolidPattern);
 463   item->setData(COLUMN_IMAGE_NAME,Qt::BackgroundRole,brush);
 464   item->setData(COLUMN_IMAGE_NAME,Qt::DisplayRole,contour->structure_name.c_str());
 465
 466   for (int j = 1; j <= 4; j++)
 467     item->setData(j,Qt::CheckStateRole,DataTree->topLevelItem(image_index)->data(j,Qt::CheckStateRole));
 468
 469   QTreePushButton* cButton = new QTreePushButton;
 470   cButton->setItem(item);
 471   cButton->setColumn(COLUMN_CLOSE_IMAGE);
 472   cButton->setToolTip(tr("close image"));
 473   cButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/exit.png")));
 474   connect(cButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
 475     this,SLOT(CloseImage(QTreeWidgetItem*, int)));
 476
 477   QTreePushButton* rButton = new QTreePushButton;
 478   rButton->setItem(item);
 479   rButton->setColumn(COLUMN_RELOAD_IMAGE);
 480   rButton->setToolTip(tr("reload image"));
 481   rButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/rotateright.png")));
 482   rButton->setEnabled(false);
 483   //Not implemented
 484   //connect(rButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
 485   //this,SLOT(ReloadImage(QTreeWidgetItem*, int)));
 486
 487   DataTree->topLevelItem(image_index)->setExpanded(1);
 488   DataTree->topLevelItem(image_index)->addChild(item);
 489   DataTree->setItemWidget(item, COLUMN_CLOSE_IMAGE, cButton);
 490   DataTree->setItemWidget(item, COLUMN_RELOAD_IMAGE, rButton);
 491   QString id = DataTree->topLevelItem(image_index)->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString();
 492   item->setData(COLUMN_IMAGE_NAME,Qt::UserRole,id.toStdString().c_str());
 493
 494   UpdateTree();
 495   mSlicerManagers[image_index]->AddContour(contour,propagation);
 496   mSlicerManagers[image_index]->Render();
 497 }
 498 //------------------------------------------------------------------------------
 499
 500
 501 //------------------------------------------------------------------------------
 502 void vvMainWindow::OpenVTKContour()
 503 {
 504   if (mSlicerManagers.size() > 0) {
 505     QString Extensions = "Images ( *.vtk *.obj)";
 506     Extensions += ";;All Files (*)";
 507     QString file = QFileDialog::getOpenFileName(this,tr("Open vtkPolyData"),mInputPathName,Extensions);
 508     if (file.isNull())
 509       return;
 510     QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
 511     int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
 512     vvMeshReader reader;
 513     reader.SetImage(mSlicerManagers[index]->GetImage());
 514     reader.SetModeToVTK();
 515     reader.SetFilename(file.toStdString());
 516     reader.Update();
 517     AddContour(index,reader.GetOutput()[0],false);
 518     QApplication::restoreOverrideCursor();
 519   }
 520 }
 521 //------------------------------------------------------------------------------
 522
 523
 524 //------------------------------------------------------------------------------
 525 void vvMainWindow::AddDCStructContour(int index, QString file)
 526 {
 527   vvMeshReader reader;
 528   reader.SetFilename(file.toStdString());
 529   vvStructSelector selector;
 530   selector.SetStructures(reader.GetROINames());
 531   if (!mSlicerManagers[index]->GetVF().IsNull())
 532     selector.EnablePropagationCheckBox();
 533   if (selector.exec()) {
 534     QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
 535     reader.SetSelectedItems(selector.getSelectedItems());
 536     reader.SetImage(mSlicerManagers[index]->GetImage());
 537     if (selector.PropagationEnabled())
 538       reader.SetPropagationVF(mSlicerManagers[index]->GetVF());
 539     reader.Update();
 540     std::vector<vvMesh::Pointer> contours=reader.GetOutput();
 541     for (std::vector<vvMesh::Pointer>::iterator i=contours.begin();
 542       i!=contours.end(); i++)
 543       AddContour(index,*i,selector.PropagationEnabled());
 544     QApplication::restoreOverrideCursor();
 545   }
 546 }
 547
 548 //------------------------------------------------------------------------------
 549 void vvMainWindow::OpenDCStructContour()
 550 {
 551   if (mSlicerManagers.size() > 0) {
 552     QString Extensions = "Dicom Files ( *.dcm RS*)";
 553     Extensions += ";;All Files (*)";
 554     QString file = QFileDialog::getOpenFileName(this,tr("Merge Images"),mInputPathName,Extensions);
 555     if (file.isNull())
 556       return;
 557     int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
 558     AddDCStructContour(index, file);
 559   }
 560 }
 561 //------------------------------------------------------------------------------
 562
 563
 564 //------------------------------------------------------------------------------
 565 void vvMainWindow::ComputeDeformableRegistration()
 566 {
 567   if (mSlicerManagers.size() > 0) {
 568     int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
 569     vvDeformationDialog dialog(index,mSlicerManagers);
 570     if (dialog.exec()) {
 571       std::string base_name=itksys::SystemTools::GetFilenameWithoutExtension(mSlicerManagers[dialog.GetInputFileIndex()]->GetFileName());
 572       AddField(dialog.GetOutput(),dialog.getFieldFile(),dialog.GetInputFileIndex());
 573       WarpImage(dialog.GetSelectedSlicer(),dialog.GetReferenceFrameIndex());
 574     } else
 575       std::cout << "Error or user cancellation while computing deformation field..." << std::endl;
 576   } else QMessageBox::information(this, "Need to open image","You must open an image first.");
 577 }
 578 //------------------------------------------------------------------------------
 579
 580
 581 //------------------------------------------------------------------------------
 582 void vvMainWindow::WarpImage()
 583 {
 584   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
 585   if (!mSlicerManagers[index]->GetVF().IsNull()) {
 586     bool ok;
 587     int ref = QInputDialog::getInteger(this,"Chose reference phase","Reference phase",0,0,\
 588       mSlicerManagers[index]->GetImage()->GetVTKImages().size()-1,1,&ok);
 589     if (ok) {
 590       WarpImage(mSlicerManagers[index],ref);
 591     }
 592   } else
 593     QMessageBox::warning(this,tr("No vector field"),tr("Sorry, can't warp without a vector field"));
 594 }
 595 //------------------------------------------------------------------------------
 596
 597
 598 //------------------------------------------------------------------------------
 599 void vvMainWindow::WarpImage(vvSlicerManager* selected_slicer,int reference_phase)
 600 {
 601   if (!selected_slicer->GetVF().IsNull()) {
 602     QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
 603     QFileInfo info(selected_slicer->GetFileName().c_str());
 604     vvImageWarp warp(selected_slicer->GetImage(),selected_slicer->GetVF(),
 605       reference_phase,this);
 606     if (warp.ComputeWarpedImage()) {
 607       AddImage(warp.GetWarpedImage(),info.path().toStdString()+"/"+info.completeBaseName().toStdString()+"_warped.mhd");
 608       AddImage(warp.GetDiffImage()  ,info.path().toStdString()+"/"+info.completeBaseName().toStdString()+"_diff.mhd");
 609       AddImage(warp.GetJacobianImage()  ,info.path().toStdString()+"/"+info.completeBaseName().toStdString()+"_jacobian.mhd");
 610       QApplication::restoreOverrideCursor();
 611     } else {
 612       QApplication::restoreOverrideCursor();
 613       QMessageBox::warning(this,tr("Different spacings"),tr("The vector field and image spacings must be the same in order to warp."));
 614     }
 615   } else
 616     QMessageBox::warning(this,tr("No vector field"),tr("Sorry, can't warp without a vector field."));
 617 }
 618 //------------------------------------------------------------------------------
 619
 620
 621 //------------------------------------------------------------------------------
 622 vvMainWindow::~vvMainWindow()
 623 {
 624   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
 625     if (mSlicerManagers[i] != NULL)
 626       delete mSlicerManagers[i];
 627   }
 628 }
 629 //------------------------------------------------------------------------------
 630
 631 //------------------------------------------------------------------------------
 632 QTabWidget * vvMainWindow::GetTab()
 633 {
 634   return tabWidget;
 635 }
 636 //------------------------------------------------------------------------------
 637
 638
 639 //------------------------------------------------------------------------------
 640 void vvMainWindow::MergeImages()
 641 {
 642   QString Extensions = EXTENSIONS;
 643   Extensions += ";;All Files (*)";
 644   QStringList files = QFileDialog::getOpenFileNames(this,tr("Merge Images"),mInputPathName,Extensions);
 645   if (files.isEmpty())
 646     return;
 647   mInputPathName = itksys::SystemTools::GetFilenamePath(files[0].toStdString()).c_str();
 648   std::vector<std::string> vector;
 649
 650   unsigned int currentDim = 0;
 651   std::vector<double> currentSpacing;
 652   std::vector<int> currentSize;
 653   std::vector<double> currentOrigin;
 654
 655   for (int i = 0; i < files.size(); i++) {
 656     itk::ImageIOBase::Pointer reader = itk::ImageIOFactory::CreateImageIO(
 657       files[i].toStdString().c_str(), itk::ImageIOFactory::ReadMode);
 658     reader->SetFileName(files[i].toStdString().c_str());
 659     reader->ReadImageInformation();
 660     if (reader)        {
 661       //NOViewWidget->hide();
 662       //NEViewWidget->hide();
 663       //SOViewWidget->hide();
 664       //SEViewWidget->hide();
 665       if (i == 0)
 666         currentDim = reader->GetNumberOfDimensions();
 667       bool IsOk = true;
 668       for (unsigned int j = 0; j < currentDim; j++) {
 669         if (i == 0) {
 670           if (j == 0) {
 671             currentSpacing.resize(currentDim);
 672             currentSize.resize(currentDim);
 673             currentOrigin.resize(currentDim);
 674           }
 675           currentOrigin[j] = reader->GetOrigin(j);
 676           currentSpacing[j] = reader->GetSpacing(j);
 677           currentSize[j] = reader->GetDimensions(j);
 678         } else if (currentDim != reader->GetNumberOfDimensions()
 679           || currentSpacing[j] != reader->GetSpacing(j)
 680           || currentSize[j] != (int)reader->GetDimensions(j)
 681           || currentOrigin[j] != reader->GetOrigin(j)) {
 682             QString error = "Cannot read file (too different from others ";
 683             error += files[i].toStdString().c_str();
 684             QMessageBox::information(this,tr("Reading problem"),error);
 685             IsOk = false;
 686             break;
 687         }
 688       }
 689       if (IsOk)
 690         vector.push_back(files[i].toStdString());
 691     }
 692   }
 693   if (vector.size() > 0)
 694     LoadImages(vector, vvImageReader::MERGED);
 695 }
 696 //------------------------------------------------------------------------------
 697
 698 //------------------------------------------------------------------------------
 699 void vvMainWindow::SliceImages()
 700 {
 701   QString Extensions = EXTENSIONS;
 702   Extensions += ";;All Files (*)";
 703
 704   QStringList files = QFileDialog::getOpenFileNames(this,tr("Slice Images"),mInputPathName,Extensions);
 705   if (files.isEmpty())
 706     return;
 707   mInputPathName = itksys::SystemTools::GetFilenamePath(files[0].toStdString()).c_str();
 708   std::vector<std::string> vector;
 709   for (int i = 0; i < files.size(); i++)
 710     vector.push_back(files[i].toStdString());
 711   LoadImages(vector, vvImageReader::SLICED);
 712 }
 713 //------------------------------------------------------------------------------
 714
 715 //------------------------------------------------------------------------------
 716 void vvMainWindow::MergeImagesWithTime()
 717 {
 718   QString Extensions = EXTENSIONS;
 719   Extensions += ";;All Files (*)";
 720   QStringList files = QFileDialog::getOpenFileNames(this,tr("Merge Images With Time"),mInputPathName,Extensions);
 721   if (files.isEmpty())
 722     return;
 723   mInputPathName = itksys::SystemTools::GetFilenamePath(files[0].toStdString()).c_str();
 724   std::vector<std::string> vector;
 725
 726   for (int i = 0; i < files.size(); i++)
 727     vector.push_back(files[i].toStdString());
 728   sort(vector.begin(),vector.end());
 729   if (vector.size() > 1)
 730     LoadImages(vector, vvImageReader::MERGEDWITHTIME);
 731   else
 732     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.");
 733 }
 734 //------------------------------------------------------------------------------
 735
 736
 737 //------------------------------------------------------------------------------
 738 void vvMainWindow::OpenDicom()
 739 {
 740   std::vector<std::string> files;
 741
 742   //std::cout << "dicomSeriesSelector " << std::endl;
 743   if (dicomSeriesSelector->exec() == QDialog::Accepted) {
 744     files = *(dicomSeriesSelector->GetFilenames());
 745     LoadImages(files, vvImageReader::DICOM);
 746   }
 747 }
 748 //------------------------------------------------------------------------------
 749
 750 //------------------------------------------------------------------------------
 751 void vvMainWindow::OpenImages()
 752 {
 753   QString Extensions = EXTENSIONS;
 754   Extensions += ";;All Files (*)";
 755
 756   QStringList files = QFileDialog::getOpenFileNames(this,tr("Load Images"),mInputPathName,Extensions);
 757   if (files.isEmpty())
 758     return;
 759   mInputPathName = itksys::SystemTools::GetFilenamePath(files[0].toStdString()).c_str();
 760   std::vector<std::string> vector;
 761   for (int i = 0; i < files.size(); i++)
 762     vector.push_back(files[i].toStdString());
 763   LoadImages(vector, vvImageReader::IMAGE);
 764 }
 765 //------------------------------------------------------------------------------
 766 void vvMainWindow::OpenRecentImage()
 767 {
 768   QAction * caller = qobject_cast<QAction*>(sender());
 769   std::vector<std::string> images;
 770   images.push_back(caller->text().toStdString());
 771   mInputPathName = itksys::SystemTools::GetFilenamePath(images[0]).c_str();
 772   LoadImages(images, vvImageReader::IMAGE);
 773 }
 774 //------------------------------------------------------------------------------
 775
 776
 777 //------------------------------------------------------------------------------
 778 void vvMainWindow::OpenImageWithTime()
 779 {
 780   QString Extensions = EXTENSIONS;
 781   Extensions += ";;All Files (*)";
 782
 783   QStringList files = QFileDialog::getOpenFileNames(this,tr("Load Images With Time"),mInputPathName,Extensions);
 784   if (files.isEmpty())
 785     return;
 786   mInputPathName = itksys::SystemTools::GetFilenamePath(files[0].toStdString()).c_str();
 787   std::vector<std::string> vector;
 788   for (int i = 0; i < files.size(); i++) {
 789     vector.push_back(files[i].toStdString());
 790   }
 791   LoadImages(vector, vvImageReader::IMAGEWITHTIME);
 792 }
 793 //------------------------------------------------------------------------------
 794
 795
 796 //------------------------------------------------------------------------------
 797 void vvMainWindow::LoadImages(std::vector<std::string> files, vvImageReader::LoadedImageType filetype)
 798 {
 799   //Separate the way to open images and dicoms
 800   int fileSize;
 801   if (filetype == vvImageReader::IMAGE || filetype == vvImageReader::IMAGEWITHTIME)
 802     fileSize = files.size();
 803   else
 804     fileSize = 1;
 805
 806   // For SLICED, we need the number of slices (ndim and #slices)
 807   std::vector<unsigned int> nSlices;
 808   nSlices.resize(files.size());
 809   std::fill(nSlices.begin(), nSlices.end(), 1);
 810   if (filetype == vvImageReader::SLICED) {
 811     for (int i = 0; i < fileSize; i++) {
 812       itk::ImageIOBase::Pointer header = clitk::readImageHeader(files[i]);
 813       QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
 814       if (!header) {
 815         nSlices[i] = 0;
 816         QString error = "Cannot open file \n";
 817         error += files[i].c_str();
 818         QMessageBox::information(this,tr("Reading problem"),error);
 819         return;
 820       }
 821       if (header->GetNumberOfDimensions() < 3) {
 822         nSlices[i] = 0;
 823         QString error = "Dimension problem. Cannot slice \n";
 824         error += files[i].c_str();
 825         QMessageBox::information(this,tr("Reading problem"),error);
 826         return;
 827       }
 828       nSlices[i] = header->GetDimensions( header->GetNumberOfDimensions()-1 );
 829     }
 830   }
 831
 832   //Only add to the list of recently opened files when a single file is opened,
 833   //to avoid polluting the list of recently opened files
 834   if (files.size() == 1) {
 835     QFileInfo finfo=tr(files[0].c_str());
 836     AddToRecentlyOpenedImages(finfo.absoluteFilePath().toStdString());
 837     updateRecentlyOpenedFilesMenu(GetRecentlyOpenedImages());
 838   }
 839   //init the progress events
 840   QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
 841   vvProgressDialog progress("Opening " + files[0],fileSize>1);
 842   qApp->processEvents();
 843
 844   int numberofsuccesulreads=0;
 845   //open images as 1 or multiples
 846   for (int i = 0; i < fileSize; i++) {
 847     progress.SetText("Opening " + files[i]);
 848     progress.SetProgress(i,fileSize);
 849     qApp->processEvents();
 850
 851     for (unsigned int j = 0; j < nSlices[i]; j++) {
 852       //read the image and put it in mSlicerManagers
 853       vvSlicerManager* imageManager = new vvSlicerManager(4);
 854       qApp->processEvents();
 855
 856       bool SetImageSucceed=false;
 857
 858       // Change filename if an image with the same already exist
 859       int number = GetImageDuplicateFilenameNumber(files[i] + std::string("_slice"));
 860
 861       if (filetype == vvImageReader::IMAGE || filetype == vvImageReader::IMAGEWITHTIME || filetype == vvImageReader::SLICED)
 862         SetImageSucceed = imageManager->SetImage(files[i],filetype, number, j);
 863       else {
 864         SetImageSucceed = imageManager->SetImages(files,filetype, number);
 865       }
 866
 867       if (!SetImageSucceed) {
 868         QApplication::restoreOverrideCursor();
 869         QString error = "Cannot open file \n";
 870         error += imageManager->GetLastError().c_str();
 871         QMessageBox::information(this,tr("Reading problem"),error);
 872         delete imageManager;
 873       } else {
 874         mSlicerManagers.push_back(imageManager);
 875
 876         //create an item in the tree with good settings
 877         QTreeWidgetItem *item = new QTreeWidgetItem();
 878         item->setData(0,Qt::UserRole,files[i].c_str());
 879         QFileInfo fileinfo(imageManager->GetFileName().c_str()); //Do not show the path
 880         item->setData(COLUMN_IMAGE_NAME,Qt::DisplayRole,fileinfo.fileName());
 881         item->setData(1,Qt::UserRole,tr("image"));
 882         item->setToolTip(COLUMN_IMAGE_NAME, imageManager->GetListOfAbsoluteFilePathInOneString("image").c_str());
 883         qApp->processEvents();
 884
 885         //Create the buttons for reload and close
 886         qApp->processEvents();
 887         QTreePushButton* cButton = new QTreePushButton;
 888         cButton->setItem(item);
 889         cButton->setColumn(COLUMN_CLOSE_IMAGE);
 890         cButton->setToolTip(tr("close image"));
 891         cButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/exit.png")));
 892         connect(cButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
 893           this,SLOT(CloseImage(QTreeWidgetItem*, int)));
 894
 895         QTreePushButton* rButton = new QTreePushButton;
 896         rButton->setItem(item);
 897         rButton->setColumn(COLUMN_RELOAD_IMAGE);
 898         rButton->setToolTip(tr("reload image"));
 899         rButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/rotateright.png")));
 900         connect(rButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
 901           this,SLOT(ReloadImage(QTreeWidgetItem*, int)));
 902
 903         DataTree->addTopLevelItem(item);
 904         DataTree->setItemWidget(item, COLUMN_CLOSE_IMAGE, cButton);
 905         DataTree->setItemWidget(item, COLUMN_RELOAD_IMAGE, rButton);
 906
 907         //set the id of the image
 908         QString id = QDir::current().absoluteFilePath(files[i].c_str()) + QString::number(mSlicerManagers.size()-1);
 909         item->setData(COLUMN_IMAGE_NAME,Qt::UserRole,id.toStdString().c_str());
 910         mSlicerManagers.back()->SetId(id.toStdString());
 911
 912         linkPanel->addImage(imageManager->GetFileName(), id.toStdString());
 913
 914         connect(mSlicerManagers.back(), SIGNAL(currentImageChanged(std::string)),
 915           this,SLOT(CurrentImageChanged(std::string)));
 916         connect(mSlicerManagers.back(), SIGNAL(currentPickedImageChanged(std::string)),
 917           this, SLOT(CurrentPickedImageChanged(std::string)));
 918         connect(mSlicerManagers.back(), SIGNAL(UpdatePosition(int, double, double, double, double, double, double, double)),
 919           this,SLOT(MousePositionChanged(int,double, double, double, double, double, double, double)));
 920         connect(mSlicerManagers.back(), SIGNAL(UpdateVector(int, double, double, double, double)),
 921           this, SLOT(VectorChanged(int,double,double,double, double)));
 922         connect(mSlicerManagers.back(), SIGNAL(UpdateOverlay(int, double, double)),
 923           this, SLOT(OverlayChanged(int,double,double)));
 924         connect(mSlicerManagers.back(), SIGNAL(UpdateFusion(int, double)),
 925           this, SLOT(FusionChanged(int,double)));
 926         connect(mSlicerManagers.back(), SIGNAL(WindowLevelChanged()),
 927           this,SLOT(WindowLevelChanged()));
 928         connect(mSlicerManagers.back(), SIGNAL(UpdateSlice(int,int)),
 929           this,SLOT(UpdateSlice(int,int)));
 930         connect(mSlicerManagers.back(), SIGNAL(UpdateTSlice(int, int, int)),
 931           this,SLOT(UpdateTSlice(int, int, int)));
 932         connect(mSlicerManagers.back(), SIGNAL(UpdateTSlice(int, int, int)),
 933           this,SLOT(ImageInfoChanged()));
 934         connect(mSlicerManagers.back(), SIGNAL(UpdateSliceRange(int,int,int,int,int)),
 935           this,SLOT(UpdateSliceRange(int,int,int,int,int)));
 936         connect(mSlicerManagers.back(), SIGNAL(UpdateLinkManager(std::string,int,double,double,double,int)),
 937           this,SLOT(UpdateLinkManager(std::string,int,double,double,double,int)));
 938         connect(mSlicerManagers.back(), SIGNAL(UpdateLinkedNavigation(std::string,vvSlicerManager*,vvSlicer*)),
 939           this,SLOT(UpdateLinkedNavigation(std::string,vvSlicerManager*,vvSlicer*)));
 940         connect(mSlicerManagers.back(), SIGNAL(ChangeImageWithIndexOffset(vvSlicerManager*,int,int)),
 941           this,SLOT(ChangeImageWithIndexOffset(vvSlicerManager*,int,int)));
 942         connect(mSlicerManagers.back(),SIGNAL(LandmarkAdded()),landmarksPanel,SLOT(AddPoint()));
 943
 944         InitSlicers();
 945         numberofsuccesulreads++;
 946       }
 947     }
 948   }
 949   if (numberofsuccesulreads) {
 950     NOViewWidget->show();
 951     NEViewWidget->show();
 952     SOViewWidget->show();
 953     SEViewWidget->show();
 954     UpdateTree();
 955     InitDisplay();
 956     ShowLastImage();
 957
 958     // Try to guess default WindowLevel
 959     double range[2];
 960     mSlicerManagers.back()->GetImage()->GetFirstVTKImageData()->GetScalarRange(range);
 961     if ((range[0] == 0) && (range[1] == 1)) {
 962       presetComboBox->setCurrentIndex(WL_BINARY);// binary
 963     } else {
 964       // TODO
 965     }
 966   }
 967   QApplication::restoreOverrideCursor();
 968 }
 969 //------------------------------------------------------------------------------
 970
 971 //------------------------------------------------------------------------------
 972 void vvMainWindow::UpdateTree()
 973 {
 974   DataTree->resizeColumnToContents(COLUMN_TREE);
 975   DataTree->resizeColumnToContents(COLUMN_UL_VIEW);
 976   DataTree->resizeColumnToContents(COLUMN_UR_VIEW);
 977   DataTree->resizeColumnToContents(COLUMN_DL_VIEW);
 978   DataTree->resizeColumnToContents(COLUMN_DR_VIEW);
 979   DataTree->resizeColumnToContents(COLUMN_IMAGE_NAME);
 980   DataTree->resizeColumnToContents(COLUMN_CLOSE_IMAGE);
 981   DataTree->resizeColumnToContents(COLUMN_RELOAD_IMAGE);
 982 }
 983 //------------------------------------------------------------------------------
 984
 985 //------------------------------------------------------------------------------
 986 void vvMainWindow::CurrentImageChanged(std::string id)
 987 {
 988   if (id == mCurrentSelectedImageId) return; // Do nothing
 989   int selected = 0;
 990   for (int i = 0; i < DataTree->topLevelItemCount(); i++) {
 991     if (DataTree->topLevelItem(i)->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString().toStdString() == id) {
 992       selected = i;
 993     } else {
 994       DataTree->topLevelItem(i)->setSelected(0);
 995     }
 996     for (int child = 0; child < DataTree->topLevelItem(i)->childCount(); child++)
 997       DataTree->topLevelItem(i)->child(child)->setSelected(0);
 998
 999   }
1000   DataTree->topLevelItem(selected)->setSelected(1);
1001   mCurrentSelectedImageId = id;
1002
1003   landmarksPanel->SetCurrentLandmarks(mSlicerManagers[selected]->GetLandmarks(),
1004                                       mSlicerManagers[selected]->GetTSlice());
1005   landmarksPanel->SetCurrentPath(mInputPathName.toStdString());
1006   landmarksPanel->SetCurrentImage(mSlicerManagers[selected]->GetFileName().c_str());
1007
1008   emit SelectedImageHasChanged(mSlicerManagers[selected]);
1009 }
1010 //------------------------------------------------------------------------------
1011
1012 //------------------------------------------------------------------------------
1013 void vvMainWindow::CurrentPickedImageChanged(std::string id)
1014 {
1015   if (id == mCurrentPickedImageId) return; // Do nothing
1016   int selected = 0;
1017   for (int i = 0; i < DataTree->topLevelItemCount(); i++) {
1018     if (DataTree->topLevelItem(i)->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString().toStdString() == id) {
1019       selected = i;
1020     } else {
1021       DataTree->topLevelItem(i)->setSelected(0);
1022     }
1023     for (int child = 0; child < DataTree->topLevelItem(i)->childCount(); child++)
1024       DataTree->topLevelItem(i)->child(child)->setSelected(0);
1025
1026   }
1027   DataTree->topLevelItem(selected)->setSelected(1);
1028   mCurrentPickedImageId = id;
1029   mCurrentPickedImageIndex = selected;
1030 }
1031 //------------------------------------------------------------------------------
1032
1033 //------------------------------------------------------------------------------
1034 void vvMainWindow::ImageInfoChanged()
1035 {
1036   contextActions[6]->setEnabled(1);
1037   contextActions[5]->setEnabled(1);
1038   actionSave_As->setEnabled(1);
1039   actionAdd_VF_to_current_Image->setEnabled(1);
1040   actionAdd_fusion_image->setEnabled(1);
1041   actionAdd_overlay_image_to_current_image->setEnabled(1);
1042   actionAdd_USSequence_toCT->setEnabled(1);
1043   actionNorth_East_Window->setEnabled(1);
1044   actionNorth_West_Window->setEnabled(1);
1045   actionSouth_East_Window->setEnabled(1);
1046   actionSouth_West_Window->setEnabled(1);
1047   vvToolManager::GetInstance()->EnableToolsInMenu(this, true);
1048   inverseButton->setEnabled(1);
1049
1050   goToCursorPushButton->setEnabled(1);
1051
1052   if (DataTree->selectedItems().size()) {
1053     int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1054
1055     colorMapComboBox->setEnabled(1);
1056     for (int i = 0; i < DataTree->topLevelItem(index)->childCount(); i++) {
1057       if (DataTree->topLevelItem(index)->child(i)->data(1,Qt::UserRole).toString() == "overlay" ||
1058         DataTree->topLevelItem(index)->child(i)->data(1,Qt::UserRole).toString() == "fusion" ||
1059         DataTree->topLevelItem(index)->child(i)->data(1,Qt::UserRole).toString() == "fusionSequence") {
1060           colorMapComboBox->setEnabled(0);
1061           break;
1062       }
1063     }
1064
1065     std::vector<double> origin;
1066     std::vector<double> inputSpacing;
1067     std::vector<int> inputSize;
1068     std::vector<double> sizeMM;
1069     vtkSmartPointer<vtkMatrix4x4> transformation;
1070     int dimension=0;
1071     QString pixelType;
1072     QString inputSizeInBytes;
1073     QString image = DataTree->selectedItems()[0]->data(COLUMN_IMAGE_NAME,Qt::DisplayRole).toString();
1074
1075     int nframes = mSlicerManagers[index]->GetSlicer(0)->GetTMax();
1076
1077     if (nframes > 1 || playMode == 1) {
1078       playButton->setEnabled(1);
1079       frameRateLabel->setEnabled(1);
1080       frameRateSpinBox->setEnabled(1);
1081     } else {
1082       playButton->setEnabled(0);
1083       frameRateLabel->setEnabled(0);
1084       frameRateSpinBox->setEnabled(0);
1085     }
1086
1087     //read image header
1088     int NPixel = 1;
1089
1090     int tSlice = 0;
1091     vvImage::Pointer imageSelected;
1092     if (DataTree->topLevelItem(index) == DataTree->selectedItems()[0]) {
1093       imageSelected = mSlicerManagers[index]->GetSlicer(0)->GetImage();
1094       tSlice = mSlicerManagers[index]->GetSlicer(0)->GetTSlice();
1095     } else if (DataTree->selectedItems()[0]->data(1,Qt::UserRole).toString() == "vector") {
1096       imageSelected = mSlicerManagers[index]->GetSlicer(0)->GetVF();
1097       tSlice = mSlicerManagers[index]->GetSlicer(0)->GetOverlayTSlice();
1098     } else if (DataTree->selectedItems()[0]->data(1,Qt::UserRole).toString() == "overlay") {
1099       imageSelected = mSlicerManagers[index]->GetSlicer(0)->GetOverlay();
1100       tSlice = mSlicerManagers[index]->GetSlicer(0)->GetOverlayTSlice();
1101     } else if (DataTree->selectedItems()[0]->data(1,Qt::UserRole).toString() == "fusion") {
1102       imageSelected = mSlicerManagers[index]->GetSlicer(0)->GetFusion();
1103       tSlice = mSlicerManagers[index]->GetSlicer(0)->GetFusionTSlice();
1104     }
1105     else if (DataTree->selectedItems()[0]->data(1,Qt::UserRole).toString() == "fusionSequence") {
1106       imageSelected = mSlicerManagers[index]->GetSlicer(0)->GetFusion();
1107       tSlice = mSlicerManagers[index]->GetSlicer(0)->GetFusionTSlice();
1108     }
1109     else if (DataTree->selectedItems()[0]->data(1,Qt::UserRole).toString() == "contour") {
1110       imageSelected = mSlicerManagers[index]->GetSlicer(0)->GetImage();
1111       tSlice = mSlicerManagers[index]->GetSlicer(0)->GetTSlice();
1112     }
1113     else {
1114       imageSelected = mSlicerManagers[index]->GetSlicer(0)->GetImage();
1115       tSlice = mSlicerManagers[index]->GetSlicer(0)->GetTSlice();
1116     }
1117
1118     dimension = imageSelected->GetNumberOfDimensions();
1119     origin.resize(dimension);
1120     inputSpacing.resize(dimension);
1121     inputSize.resize(dimension);
1122     sizeMM.resize(dimension);
1123     pixelType = mSlicerManagers[index]->GetImage()->GetScalarTypeAsITKString().c_str();
1124     for (int i = 0; i < dimension; i++) {
1125       origin[i] = imageSelected->GetOrigin()[i];
1126       inputSpacing[i] = imageSelected->GetSpacing()[i];
1127       inputSize[i] = imageSelected->GetSize()[i];
1128       sizeMM[i] = inputSize[i]*inputSpacing[i];
1129       NPixel *= inputSize[i];
1130     }
1131     inputSizeInBytes = GetSizeInBytes(imageSelected->GetActualMemorySize()*1000);
1132
1133     QString dim = QString::number(dimension) + " (";
1134     dim += pixelType + ")";
1135
1136     infoPanel->setFileName(image);
1137     std::string creationImageTimeValue("No creation time");
1138     itk::ExposeMetaData< std::string > (*imageSelected->GetFirstMetaDataDictionary(), "creationImageTime", creationImageTimeValue);
1139     infoPanel->setImageCreationTime(QString(creationImageTimeValue.c_str()));
1140     infoPanel->setDimension(dim);
1141     infoPanel->setSizePixel(GetVectorIntAsString(inputSize));
1142     infoPanel->setSizeMM(GetVectorDoubleAsString(sizeMM));
1143     infoPanel->setOrigin(GetVectorDoubleAsString(origin));
1144     infoPanel->setSpacing(GetVectorDoubleAsString(inputSpacing));
1145     infoPanel->setNPixel(QString::number(NPixel)+" ("+inputSizeInBytes+")");
1146
1147     transformation = imageSelected->GetTransform()[tSlice]->GetMatrix();
1148     infoPanel->setTransformation(Get4x4MatrixDoubleAsString(transformation));
1149
1150     landmarksPanel->SetCurrentLandmarks(mSlicerManagers[index]->GetLandmarks(),
1151                                         mSlicerManagers[index]->GetTSlice());
1152     landmarksPanel->SetCurrentPath(mInputPathName.toStdString());
1153     landmarksPanel->SetCurrentImage(mSlicerManagers[index]->GetFileName().c_str());
1154
1155     overlayPanel->getCurrentImageName(mSlicerManagers[index]->GetFileName().c_str());
1156     for (int i = 0; i < 4; i++) {
1157       if (DataTree->selectedItems()[0]->data(i+1,Qt::CheckStateRole).toInt() > 0 || i == 3) {
1158         mSlicerManagers[index]->UpdateInfoOnCursorPosition(i);
1159         break;
1160       }
1161     }
1162
1163 //     infoPanel->setFileName(image);
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 //     landmarksPanel->SetCurrentLandmarks(mSlicerManagers[index]->GetLandmarks(),
1172 //                                         mSlicerManagers[index]->GetTSlice());
1173 //     landmarksPanel->SetCurrentPath(mInputPathName.toStdString());
1174 //     landmarksPanel->SetCurrentImage(mSlicerManagers[index]->GetFileName().c_str());
1175 //
1176 //     overlayPanel->getCurrentImageName(mSlicerManagers[index]->GetFileName().c_str());
1177 //     for (int i = 0; i < 4; i++) {
1178 //       if (DataTree->selectedItems()[0]->data(i+1,Qt::CheckStateRole).toInt() > 0 || i == 3) {
1179 //         mSlicerManagers[index]->UpdateInfoOnCursorPosition(i);
1180 //         break;
1181 //       }
1182 //     }
1183     WindowLevelChanged();
1184
1185     slicingPresetComboBox->setCurrentIndex(mSlicerManagers[index]->GetSlicingPreset());
1186
1187     if (mSlicerManagers[index]->GetSlicer(0)->GetVF()) {
1188       overlayPanel->getVFName(mSlicerManagers[index]->GetVFName().c_str());
1189       overlayPanel->getVFProperty(mSlicerManagers[index]->GetSlicer(0)->GetVFSubSampling(),
1190         mSlicerManagers[index]->GetSlicer(0)->GetVFScale(),
1191         mSlicerManagers[index]->GetSlicer(0)->GetVFLog());
1192     } else {
1193       overlayPanel->getVFName(mSlicerManagers[index]->GetVFName().c_str());
1194       overlayPanel->getVFProperty(-1,-1,-1);
1195     }
1196     if (mSlicerManagers[index]->GetSlicer(0)->GetOverlay()) {
1197       overlayPanel->getOverlayName(mSlicerManagers[index]->GetOverlayName().c_str());
1198     } else {
1199       overlayPanel->getOverlayName(mSlicerManagers[index]->GetOverlayName().c_str());
1200     }
1201
1202     if (mSlicerManagers[index]->GetSlicer(0)->GetFusion()) {
1203       overlayPanel->getFusionName(mSlicerManagers[index]->GetFusionName().c_str());
1204     } else {
1205       overlayPanel->getFusionName(mSlicerManagers[index]->GetFusionName().c_str());
1206     }
1207   }
1208 }
1209 //------------------------------------------------------------------------------
1210
1211 //------------------------------------------------------------------------------
1212 void vvMainWindow::ShowDocumentation()
1213 {
1214   documentation->show();
1215 }
1216 //------------------------------------------------------------------------------
1217
1218 //------------------------------------------------------------------------------
1219 void vvMainWindow::PopupRegisterForm(bool checkCanPush)
1220 {
1221   vvRegisterForm* registerForm = new vvRegisterForm(QUrl("http://www.creatis.insa-lyon.fr/~dsarrut/vvregister/write.php"), getVVSettingsPath(), getSettingsOptionFormat());
1222   if(!checkCanPush) {
1223     registerForm->show();
1224   } else {
1225     if(registerForm->canPush()) {
1226       registerForm->show();
1227       registerForm->acquitPushed();//too bad if there is not internet connection anymore.
1228     }
1229   }
1230 }
1231 //------------------------------------------------------------------------------
1232
1233 //------------------------------------------------------------------------------
1234 void vvMainWindow::ShowHelpDialog()
1235 {
1236   help_dialog->show();
1237 }
1238 //------------------------------------------------------------------------------
1239
1240 //------------------------------------------------------------------------------
1241 void vvMainWindow::ChangeViewMode()
1242 {
1243   typedef struct _SIZE{
1244     QSplitter* splitter;
1245     QList<int> size1, size2;
1246     int cols[3];
1247   }SplitterSize;
1248   SplitterSize sizes[4];
1249   sizes[0].splitter = OSplitter;
1250   sizes[0].size1.push_back(1);
1251   sizes[0].size1.push_back(0);
1252   sizes[0].size2.push_back(1);
1253   sizes[0].size2.push_back(0);
1254   sizes[0].cols[0] = 2;
1255   sizes[0].cols[1] = 3;
1256   sizes[0].cols[2] = 4;
1257
1258   sizes[1].splitter = ESplitter;
1259   sizes[1].size1.push_back(0);
1260   sizes[1].size1.push_back(1);
1261   sizes[1].size2.push_back(1);
1262   sizes[1].size2.push_back(0);
1263   sizes[1].cols[0] = 1;
1264   sizes[1].cols[1] = 3;
1265   sizes[1].cols[2] = 4;
1266
1267   sizes[2].splitter = OSplitter;
1268   sizes[2].size1.push_back(1);
1269   sizes[2].size1.push_back(0);
1270   sizes[2].size2.push_back(0);
1271   sizes[2].size2.push_back(1);
1272   sizes[2].cols[0] = 1;
1273   sizes[2].cols[1] = 2;
1274   sizes[2].cols[2] = 4;
1275
1276   sizes[3].splitter = ESplitter;
1277   sizes[3].size1.push_back(0);
1278   sizes[3].size1.push_back(1);
1279   sizes[3].size2.push_back(0);
1280   sizes[3].size2.push_back(1);
1281   sizes[3].cols[0] = 1;
1282   sizes[3].cols[1] = 2;
1283   sizes[3].cols[2] = 3;
1284
1285   int slicer = mSlicerManagers[mCurrentPickedImageIndex]->GetSelectedSlicer();
1286   if (viewMode == 1) {
1287     if (slicer >= 0) {
1288       viewMode = 0;
1289       splitter_3->setSizes(sizes[slicer].size1);
1290       sizes[slicer].splitter->setSizes(sizes[slicer].size2);
1291       DataTree->setColumnHidden(sizes[slicer].cols[0],1);
1292       DataTree->setColumnHidden(sizes[slicer].cols[1],1);
1293       DataTree->setColumnHidden(sizes[slicer].cols[2],1);
1294     }
1295   } else {
1296     QList<int> size;
1297     if (slicer >= 0) {
1298       viewMode = 1;
1299       size.push_back(1);
1300       size.push_back(1);
1301       splitter_3->setSizes(size);
1302       sizes[slicer].splitter->setSizes(size);
1303       DataTree->setColumnHidden(sizes[slicer].cols[0],0);
1304       DataTree->setColumnHidden(sizes[slicer].cols[1],0);
1305       DataTree->setColumnHidden(sizes[slicer].cols[2],0);
1306     }
1307   }
1308   UpdateRenderWindows();
1309   /*
1310   ** I don't know why but for both resized QVTKWidget we also need to render
1311   ** the associated Slicer to redraw crosses.
1312   */
1313   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
1314     //     if (DataTree->topLevelItem(i)->data(COLUMN_UL_VIEW,Qt::CheckStateRole).toInt() > 1)
1315     mSlicerManagers[i]->GetSlicer(0)->Render();
1316     mSlicerManagers[i]->GetSlicer(1)->Render();
1317     //     if (DataTree->topLevelItem(i)->data(COLUMN_DL_VIEW,Qt::CheckStateRole).toInt() > 1)
1318     mSlicerManagers[i]->GetSlicer(2)->Render();
1319     mSlicerManagers[i]->GetSlicer(3)->Render();
1320   }
1321 }
1322 //------------------------------------------------------------------------------
1323
1324 //------------------------------------------------------------------------------
1325 QString vvMainWindow::GetSizeInBytes(unsigned long size)
1326 {
1327   QString result = "";// QString::number(size);
1328   //result += " bytes (";
1329   if (size > 1000000000) {
1330     size /= 1000000000;
1331     result += QString::number(size);
1332     result += "Gb";//)";
1333   } else if (size > 1000000) {
1334     size /= 1000000;
1335     result += QString::number(size);
1336     result += "Mb";//)";
1337   } else if (size > 1000) {
1338     size /= 1000;
1339     result += QString::number(size);
1340     result += "kb";//)";
1341   }
1342   return result;
1343 }
1344 //------------------------------------------------------------------------------
1345
1346 //------------------------------------------------------------------------------
1347 QString vvMainWindow::Get4x4MatrixDoubleAsString(vtkSmartPointer<vtkMatrix4x4> matrix, const int precision)
1348 {
1349   std::ostringstream strmatrix;
1350
1351   // Figure out the number of digits of the integer part of the largest absolute value
1352   // for each column
1353   unsigned width[4];
1354   for (unsigned int j = 0; j < 4; j++){
1355     double absmax = 0.;
1356     for (unsigned int i = 0; i < 4; i++)
1357       absmax = std::max(absmax, vnl_math_abs(matrix->GetElement(i, j)));
1358     unsigned ndigits = (unsigned)std::max(0.,std::log10(absmax))+1;
1359     width[j] = precision+ndigits+3;
1360   }
1361
1362   // Output with correct width, aligned to the right
1363   for (unsigned int i = 0; i < 4; i++) {
1364     for (unsigned int j = 0; j < 4; j++) {
1365       strmatrix.setf(ios::fixed,ios::floatfield);
1366       strmatrix.precision(precision);
1367       strmatrix.fill(' ');
1368       strmatrix.width(width[j]);
1369       strmatrix << std::right << matrix->GetElement(i, j);
1370     }
1371     strmatrix << std::endl;
1372   }
1373   QString result = strmatrix.str().c_str();
1374   return result;
1375 }
1376 //------------------------------------------------------------------------------
1377
1378 //------------------------------------------------------------------------------
1379 QString vvMainWindow::GetVectorDoubleAsString(std::vector<double> vectorDouble)
1380 {
1381   QString result;
1382   for (unsigned int i= 0; i < vectorDouble.size(); i++) {
1383     if (i != 0)
1384       result += " ";
1385     result += QString::number(vectorDouble[i]);
1386   }
1387   return result;
1388 }
1389 //------------------------------------------------------------------------------
1390
1391 //------------------------------------------------------------------------------
1392 QString vvMainWindow::GetVectorIntAsString(std::vector<int> vectorInt)
1393 {
1394   QString result;
1395   for (unsigned int i= 0; i < vectorInt.size(); i++) {
1396     if (i != 0)
1397       result += " ";
1398     result += QString::number(vectorInt[i]);
1399   }
1400   return result;
1401 }
1402 //------------------------------------------------------------------------------
1403
1404 //------------------------------------------------------------------------------
1405 //this actually returns the SlicerManager index!
1406 int vvMainWindow::GetSlicerIndexFromItem(QTreeWidgetItem* item)
1407 {
1408   QString id = item->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString();
1409   for (int i = 0; i < DataTree->topLevelItemCount(); i++) {
1410     if (DataTree->topLevelItem(i)->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString() == id)
1411       return i;
1412   }
1413   return -1;
1414 }
1415 //------------------------------------------------------------------------------
1416
1417 //------------------------------------------------------------------------------
1418 QTreeWidgetItem* vvMainWindow::GetItemFromSlicerManager(vvSlicerManager* sm)
1419 {
1420   QString id = sm->GetId().c_str();
1421   for (int i = 0; i < DataTree->topLevelItemCount(); i++) {
1422     if (DataTree->topLevelItem(i)->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString() == id)
1423       return DataTree->topLevelItem(i);
1424   }
1425   return NULL;
1426 }
1427 //------------------------------------------------------------------------------
1428
1429 //------------------------------------------------------------------------------
1430 void vvMainWindow::DisplayChanged(QTreeWidgetItem *clickedItem, int column)
1431 {
1432   if ( column >= COLUMN_CLOSE_IMAGE || column <= 0)
1433     return;
1434
1435   // Get parent information (might be the same item)
1436   int slicerManagerIndex = GetSlicerIndexFromItem(clickedItem);
1437   QTreeWidgetItem* clickedParentItem = DataTree->topLevelItem(slicerManagerIndex);
1438   vvSlicer* clickedSlicer = mSlicerManagers[slicerManagerIndex]->GetSlicer(column-1);
1439
1440   // Go over the complete item tree (only 2 levels, parents and children)
1441   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
1442     // Trick to avoid redoing twice the job for a key (sr)
1443     mSlicerManagers[i]->GetSlicer(column-1)->GetRenderWindow()->GetInteractor()->SetKeySym("Crap");
1444
1445     QTreeWidgetItem* currentParentItem = DataTree->topLevelItem(i);
1446     if(currentParentItem != clickedParentItem) {
1447       // Not the branch of the clicked item, uncheck all
1448
1449       // Parent
1450       currentParentItem->setData(column,Qt::CheckStateRole, 0);
1451       mSlicerManagers[i]->UpdateSlicer(column-1, false);
1452
1453       // Children
1454       for (int iChild = 0; iChild < currentParentItem->childCount(); iChild++) {
1455         currentParentItem->child(iChild)->setData(column,Qt::CheckStateRole, 0);
1456       }
1457     }
1458     else {
1459       // Branch of the clicked one: get check status from actor visibility in slicer
1460       // and toggle the clicked one
1461
1462       // Parent
1463       bool vis = clickedSlicer->GetActorVisibility("image", 0);
1464       bool draw = clickedSlicer->GetRenderer()->GetDraw();
1465
1466       // Update slicer (after getting visibility)
1467       mSlicerManagers[slicerManagerIndex]->UpdateSlicer(column-1, true);
1468       mSlicerManagers[slicerManagerIndex]->UpdateInfoOnCursorPosition(column-1);
1469       DisplaySliders(slicerManagerIndex, column-1);
1470       if(clickedParentItem == clickedItem) {
1471         // Toggle
1472         vis = !draw || !vis;
1473       }
1474       clickedSlicer->SetActorVisibility("image", 0, vis);
1475       clickedParentItem->setData(column, Qt::CheckStateRole, vis?2:0);
1476
1477       // Children
1478       std::map<std::string, int> actorTypeCounts;
1479       for (int iChild = 0; iChild < clickedParentItem->childCount(); iChild++) {
1480         QTreeWidgetItem* currentChildItem = clickedParentItem->child(iChild);
1481         std::string actorType = currentChildItem->data(1,Qt::UserRole).toString().toStdString();
1482         vis = clickedSlicer->GetActorVisibility(actorType, actorTypeCounts[actorType]);
1483         if(currentChildItem == clickedItem) {
1484           // Toggle or force visibility if it was not on this branch so far
1485           vis = !draw || !vis;
1486           clickedSlicer->SetActorVisibility(actorType, actorTypeCounts[actorType], vis);
1487         }
1488         currentChildItem->setData(column, Qt::CheckStateRole, vis?2:0);
1489         actorTypeCounts[actorType]++;
1490       }
1491     }
1492   }
1493
1494   clickedSlicer->Render();
1495 }
1496 //------------------------------------------------------------------------------
1497
1498 void vvMainWindow::InitSlicers()
1499 {
1500   if (mSlicerManagers.size()) {
1501     mSlicerManagers.back()->GenerateDefaultLookupTable();
1502
1503     mSlicerManagers.back()->SetSlicerWindow(0,NOViewWidget->GetRenderWindow());
1504     mSlicerManagers.back()->SetSlicerWindow(1,NEViewWidget->GetRenderWindow());
1505     mSlicerManagers.back()->SetSlicerWindow(2,SOViewWidget->GetRenderWindow());
1506     mSlicerManagers.back()->SetSlicerWindow(3,SEViewWidget->GetRenderWindow());
1507   }
1508 }
1509
1510 //------------------------------------------------------------------------------
1511 void vvMainWindow::InitDisplay()
1512 {
1513   if (mSlicerManagers.size()) {
1514     //BE CAREFUL : this is absolutely necessary to set the interactor style
1515     //in order to have the same style instanciation for all SlicerManagers in
1516     // a same window
1517     for (int j = 0; j < 4; j++) {
1518       vvInteractorStyleNavigator* style = vvInteractorStyleNavigator::New();
1519       style->SetAutoAdjustCameraClippingRange(1);
1520       bool AlreadySelected = false;
1521       for (int i = 0; i < DataTree->topLevelItemCount(); i++) {
1522         mSlicerManagers[i]->SetInteractorStyleNavigator(j,style);
1523
1524         //select the image only if previous are not selected
1525         if (DataTree->topLevelItem(i)->data(j+1,Qt::CheckStateRole).toInt() > 1) {
1526           mSlicerManagers[i]->UpdateSlicer(j,1);
1527           AlreadySelected = true;
1528         } else if (i == DataTree->topLevelItemCount()-1 && !AlreadySelected) {
1529           if (DataTree->selectedItems().size() == 0)
1530             DataTree->topLevelItem(i)->setSelected(1);
1531           DataTree->topLevelItem(i)->setData(j+1,Qt::CheckStateRole,2);
1532           mSlicerManagers[i]->UpdateSlicer(j,1);
1533           DisplaySliders(i,j);
1534         } else {
1535           DataTree->topLevelItem(i)->setData(j+1,Qt::CheckStateRole,0);
1536           mSlicerManagers[i]->UpdateSlicer(j,0);
1537         }
1538       }
1539       style->Delete();
1540     }
1541   }
1542 }
1543 //------------------------------------------------------------------------------
1544
1545 //------------------------------------------------------------------------------
1546 void vvMainWindow::DisplaySliders(int slicer, int window)
1547 {
1548   if(!mSlicerManagers[slicer]->GetSlicer(window)->GetRenderer()->GetDraw())
1549     return;
1550
1551   int range[2];
1552   mSlicerManagers[slicer]->GetSlicer(window)->GetSliceRange(range);
1553   int position = mSlicerManagers[slicer]->GetSlicer(window)->GetSlice();
1554   if (range[1]>0)
1555     verticalSliders[window]->show();
1556   else
1557     verticalSliders[window]->hide();
1558   verticalSliders[window]->setRange(range[0],range[1]);
1559   verticalSliders[window]->setValue(position);
1560
1561   int tRange[2];
1562   tRange[0] = 0;
1563   tRange[1] = mSlicerManagers[slicer]->GetSlicer(window)->GetTMax();
1564   if (tRange[1]>0)
1565     horizontalSliders[window]->show();
1566   else
1567     horizontalSliders[window]->hide();
1568   horizontalSliders[window]->setRange(tRange[0],tRange[1]);
1569   int tPosition = mSlicerManagers[slicer]->GetSlicer(window)->GetMaxCurrentTSlice();
1570   horizontalSliders[window]->setValue(tPosition);
1571 }
1572 //------------------------------------------------------------------------------
1573
1574 //------------------------------------------------------------------------------
1575 void vvMainWindow::CloseImage(QTreeWidgetItem* item, int column)
1576 {
1577   int index = GetSlicerIndexFromItem(item);
1578
1579   if (DataTree->topLevelItem(index) != item) {
1580     QString warning = "Do you really want to close the overlay : ";
1581     warning += item->data(COLUMN_IMAGE_NAME,Qt::DisplayRole).toString();
1582     QMessageBox msgBox(QMessageBox::Warning, tr("Close Overlay"),
1583       warning, 0, this);
1584     msgBox.addButton(tr("Close"), QMessageBox::AcceptRole);
1585     msgBox.addButton(tr("Cancel"), QMessageBox::RejectRole);
1586     if (msgBox.exec() == QMessageBox::AcceptRole) {
1587       std::string overlay_type=item->data(1,Qt::UserRole).toString().toStdString();
1588       int overlay_index=0;
1589       for (int child = 0; child < DataTree->topLevelItem(index)->childCount(); child++) {
1590         if (DataTree->topLevelItem(index)->\
1591           child(child)->data(1,Qt::UserRole).toString().toStdString() == overlay_type)
1592           overlay_index++;
1593         if (DataTree->topLevelItem(index)->child(child) == item) break;
1594       }
1595       if (overlay_type=="fusionSequence") {
1596         //removing the overlay sequence in a fusion sequence visualization mode
1597         //reset the transforms
1598         overlayPanel->getFusionSequenceProperty(-1, false, 0, false);
1599
1600         //unlink and untie the slicer managers
1601         RemoveLink(mSlicerManagers[index]->GetId().c_str(), mSlicerManagers[mSlicerManagers[index]->GetFusionSequenceIndexOfLinkedManager()]->GetId().c_str());
1602         mSlicerManagers[index]->SetFusionSequenceInvolvmentCode(-1);
1603         mSlicerManagers[mSlicerManagers[index]->GetFusionSequenceIndexOfLinkedManager()]->SetFusionSequenceInvolvmentCode(-1);
1604         for (unsigned i=0 ; i<4 ; i++) {
1605             mSlicerManagers[index]->GetSlicer(i)->SetFusionSequenceCode(-1);
1606             mSlicerManagers[mSlicerManagers[index]->GetFusionSequenceIndexOfLinkedManager()]->GetSlicer(i)->SetFusionSequenceCode(-1);
1607         }
1608
1609       }
1610       mSlicerManagers[index]->RemoveActor(overlay_type, overlay_index-1);
1611       mSlicerManagers[index]->SetColorMap(0);
1612       DataTree->topLevelItem(index)->takeChild(DataTree->topLevelItem(index)->indexOfChild(item));
1613       mSlicerManagers[index]->Render();
1614     }
1615   } else if (DataTree->topLevelItemCount() <= 1) {
1616     QString warning = "Do you really want to close the image : ";
1617     warning += item->data(COLUMN_IMAGE_NAME,Qt::DisplayRole).toString();
1618     warning += "\nThis is the last image, you're about to close vv !!!";
1619     QMessageBox msgBox(QMessageBox::Warning, tr("Close Image"),
1620       warning, 0, this);
1621     msgBox.addButton(tr("Close vv"), QMessageBox::AcceptRole);
1622     msgBox.addButton(tr("Cancel"), QMessageBox::RejectRole);
1623     if (msgBox.exec() == QMessageBox::AcceptRole) {
1624       this->close();
1625     }
1626   } else {
1627     QString warning = "Do you really want to close the image : ";
1628     warning += item->data(COLUMN_IMAGE_NAME,Qt::DisplayRole).toString();
1629     QMessageBox msgBox(QMessageBox::Warning, tr("Close Image"),
1630       warning, 0, this);
1631     msgBox.addButton(tr("Close"), QMessageBox::AcceptRole);
1632     msgBox.addButton(tr("Cancel"), QMessageBox::RejectRole);
1633     if (msgBox.exec() == QMessageBox::AcceptRole) {
1634
1635       // Tell tools that we close an image
1636       emit AnImageIsBeingClosed(mSlicerManagers[index]);
1637
1638       std::vector<vvSlicerManager*>::iterator Manageriter = mSlicerManagers.begin();
1639       DataTree->takeTopLevelItem(index);
1640       for (int i = 0; i < index; i++) {
1641         Manageriter++;
1642       }
1643       //if the slicer manager was involved in a fusion sequence visualization...
1644       if ( mSlicerManagers[index]->IsInvolvedInFusionSequence() ) {
1645         //reset the transforms
1646         overlayPanel->getFusionSequenceProperty(-1, false, 0, false);
1647
1648         //unlink and untie the slicer managers
1649         RemoveLink(mSlicerManagers[index]->GetId().c_str(), mSlicerManagers[mSlicerManagers[index]->GetFusionSequenceIndexOfLinkedManager()]->GetId().c_str());
1650         mSlicerManagers[index]->SetFusionSequenceInvolvmentCode(-1);
1651         mSlicerManagers[mSlicerManagers[index]->GetFusionSequenceIndexOfLinkedManager()]->SetFusionSequenceInvolvmentCode(-1);
1652         for (unsigned i=0 ; i<4 ; i++) {
1653             mSlicerManagers[index]->GetSlicer(i)->SetFusionSequenceCode(-1);
1654             mSlicerManagers[mSlicerManagers[index]->GetFusionSequenceIndexOfLinkedManager()]->GetSlicer(i)->SetFusionSequenceCode(-1);
1655         }
1656
1657         //TODO: also remove the image overlaid with the main sequence, as it is becoming invalid...
1658         //this shall be done by calling this->CloseImage() with the correct index;...
1659       }
1660
1661       linkPanel->removeImage(index);
1662       mSlicerManagers[index]->RemoveActors();
1663
1664       //remove the slicer manager
1665       delete mSlicerManagers[index];
1666       mSlicerManagers.erase(Manageriter);
1667
1668       //
1669       InitDisplay();
1670     }
1671   }
1672   ImageInfoChanged();
1673 }
1674 //------------------------------------------------------------------------------
1675
1676 //------------------------------------------------------------------------------
1677 void vvMainWindow::ReloadImage(QTreeWidgetItem* item, int column)
1678 {
1679   // int index = GetSlicerIndexFromItem(item);
1680   //   QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
1681   //   if (item->data(1,Qt::UserRole).toString() == "vector")
1682   //     mSlicerManagers[index]->ReloadVF();
1683   //   else
1684   //     mSlicerManagers[index]->Reload();
1685
1686   //   QApplication::restoreOverrideCursor();
1687   int index = GetSlicerIndexFromItem(item);
1688   QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
1689   QString role=item->data(1,Qt::UserRole).toString();
1690   if ( role == "vector") {
1691     mSlicerManagers[index]->ReloadVF();
1692   }
1693   else if (role == "overlay") {
1694     mSlicerManagers[index]->ReloadOverlay();
1695   }
1696   else if (role == "fusion") {
1697     mSlicerManagers[index]->ReloadFusion();
1698   }
1699   else if (role == "fusionSequence") {
1700     //both versions of the secondary sequence must be updated.
1701     mSlicerManagers[index]->ReloadFusionSequence();
1702     mSlicerManagers[mSlicerManagers[index]->GetFusionSequenceIndexOfLinkedManager()]->Reload();
1703   }
1704   else {
1705     mSlicerManagers[index]->Reload();
1706     //if we update the secondary sequence, then the overlay of the main sequence should also be updated
1707     if (mSlicerManagers[index]->IsSecondarySequenceOfFusionSequence()) mSlicerManagers[mSlicerManagers[index]->GetFusionSequenceIndexOfLinkedManager()]->ReloadFusionSequence();
1708   }
1709   // Update view and info
1710   ImageInfoChanged();
1711   mSlicerManagers[index]->Render();
1712   QApplication::restoreOverrideCursor();
1713 }
1714 //------------------------------------------------------------------------------
1715
1716 //------------------------------------------------------------------------------
1717 void vvMainWindow::MousePositionChanged(int visibility,double x, double y, double z, double X, double Y, double Z , double value)
1718 {
1719   infoPanel->setCurrentInfo(visibility,x,y,z,X,Y,Z,value);
1720 }
1721 //------------------------------------------------------------------------------
1722
1723 //------------------------------------------------------------------------------
1724 void vvMainWindow::VectorChanged(int visibility,double x, double y, double z, double value)
1725 {
1726   overlayPanel->getCurrentVectorInfo(visibility,x,y,z,value);
1727 }
1728 //------------------------------------------------------------------------------
1729
1730 //------------------------------------------------------------------------------
1731 void vvMainWindow::OverlayChanged(int visibility, double valueOver, double valueRef)
1732 {
1733   overlayPanel->getCurrentOverlayInfo(visibility,valueOver, valueRef);
1734 }
1735 //------------------------------------------------------------------------------
1736
1737 //------------------------------------------------------------------------------
1738 void vvMainWindow::FusionChanged(int visibility, double value)
1739 {
1740   overlayPanel->getCurrentFusionInfo(visibility,value);
1741 }
1742 //------------------------------------------------------------------------------
1743
1744 //------------------------------------------------------------------------------
1745 //called when AddOverlayImage, AddFusionSequence
1746 //or when UpdateWindowLevel() is called ; when slicerManager emits WindowLevelChanged
1747 //when ImageInfoChanged() is called
1748 void vvMainWindow::WindowLevelChanged()
1749 {
1750   // Base image
1751   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1752   if(index==-1) return;
1753   windowSpinBox->setValue(mSlicerManagers[index]->GetColorWindow());
1754   levelSpinBox->setValue(mSlicerManagers[index]->GetColorLevel());
1755   colorMapComboBox->setCurrentIndex(mSlicerManagers[index]->GetColorMap());
1756   presetComboBox->setCurrentIndex(mSlicerManagers[index]->GetPreset());
1757
1758   // Overlay image
1759   if (mSlicerManagers[index]->GetSlicer(0)->GetOverlay())
1760     overlayPanel->getOverlayProperty(mSlicerManagers[index]->GetOverlayColor(),
1761     mSlicerManagers[index]->GetLinkOverlayWindowLevel(),
1762     mSlicerManagers[index]->GetOverlayColorWindow(),
1763     mSlicerManagers[index]->GetOverlayColorLevel());
1764   else
1765     overlayPanel->getOverlayProperty(-1,0,0.,0.);
1766
1767   // Fusion & SequenceFusion image
1768   if (mSlicerManagers[index]->GetSlicer(0)->GetFusion()) {
1769     overlayPanel->getFusionProperty(mSlicerManagers[index]->GetFusionOpacity(),
1770       mSlicerManagers[index]->GetFusionThresholdOpacity(),
1771       mSlicerManagers[index]->GetFusionColorMap(),
1772       mSlicerManagers[index]->GetFusionWindow(),
1773       mSlicerManagers[index]->GetFusionLevel());
1774     if (mSlicerManagers[index]->IsMainSequenceOfFusionSequence()) {
1775       overlayPanel->getFusionSequenceProperty(mSlicerManagers[index]->GetFusionSequenceFrameIndex(),
1776         mSlicerManagers[index]->GetFusionSequenceSpatialSyncFlag(),
1777         mSlicerManagers[index]->GetFusionSequenceNbFrames(),
1778         mSlicerManagers[index]->GetFusionSequenceTemporalSyncFlag());
1779     }
1780   }
1781   else if ( mSlicerManagers[index]->IsSecondarySequenceOfFusionSequence() ) {
1782     //if the image is involved in a fusion sequence, preserve the overlay panel!
1783     int ind = mSlicerManagers[index]->GetFusionSequenceIndexOfLinkedManager();
1784     overlayPanel->getFusionProperty(mSlicerManagers[ind]->GetFusionOpacity(),
1785       mSlicerManagers[ind]->GetFusionThresholdOpacity(),
1786       mSlicerManagers[ind]->GetFusionColorMap(),
1787       mSlicerManagers[ind]->GetFusionWindow(),
1788       mSlicerManagers[ind]->GetFusionLevel());
1789     overlayPanel->getFusionSequenceProperty(mSlicerManagers[ind]->GetFusionSequenceFrameIndex(),
1790       mSlicerManagers[ind]->GetFusionSequenceSpatialSyncFlag(),
1791       mSlicerManagers[ind]->GetFusionSequenceNbFrames(),
1792       mSlicerManagers[ind]->GetFusionSequenceTemporalSyncFlag());
1793   }
1794   else
1795   {
1796     overlayPanel->getFusionProperty(-1, -1, -1, -1, -1);
1797     overlayPanel->getFusionSequenceProperty(-1, false, 0, false);
1798   }
1799 }
1800 //------------------------------------------------------------------------------
1801
1802 //------------------------------------------------------------------------------
1803 void vvMainWindow::WindowLevelEdited()
1804 {
1805   presetComboBox->setCurrentIndex(WL_USER);
1806   UpdateWindowLevel();
1807 }
1808 //------------------------------------------------------------------------------
1809
1810 //------------------------------------------------------------------------------
1811 void vvMainWindow::SetWindowLevel(double w, double l)
1812 {
1813   windowSpinBox->setValue(w);
1814   levelSpinBox->setValue(l);
1815   presetComboBox->setCurrentIndex(WL_USER);
1816   colorMapComboBox->setCurrentIndex(0);
1817   UpdateWindowLevel();
1818 }
1819 //------------------------------------------------------------------------------
1820
1821 //------------------------------------------------------------------------------
1822 void vvMainWindow::UpdateWindowLevel()
1823 {
1824   if (DataTree->selectedItems().size()) {
1825     if (presetComboBox->currentIndex() == WL_VENTILATION) //For ventilation
1826       colorMapComboBox->setCurrentIndex(5);
1827     int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1828     mSlicerManagers[index]->SetColorWindow(windowSpinBox->value());
1829     mSlicerManagers[index]->SetColorLevel(levelSpinBox->value());
1830     mSlicerManagers[index]->SetPreset(presetComboBox->currentIndex());
1831     mSlicerManagers[index]->Render();
1832     WindowLevelChanged();
1833   }
1834 }
1835 //------------------------------------------------------------------------------
1836
1837 //------------------------------------------------------------------------------
1838 void vvMainWindow::UpdateSlicingPreset()
1839 {
1840   if (DataTree->selectedItems().size()) {
1841     int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1842     mSlicerManagers[index]->SetSlicingPreset(vvSlicerManager::SlicingPresetType(slicingPresetComboBox->currentIndex()));
1843   }
1844 }
1845 //------------------------------------------------------------------------------
1846
1847 //------------------------------------------------------------------------------
1848 void vvMainWindow::UpdateColorMap()
1849 {
1850   if (DataTree->selectedItems().size()) {
1851     int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1852     mSlicerManagers[index]->SetColorMap(colorMapComboBox->currentIndex());
1853     mSlicerManagers[index]->Render();
1854   }
1855 }
1856 //------------------------------------------------------------------------------
1857 void vvMainWindow::SwitchWindowLevel()
1858 {
1859   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1860   int window = mSlicerManagers[index]->GetColorWindow();
1861   presetComboBox->setCurrentIndex(WL_USER);
1862   windowSpinBox->setValue(-window);
1863   UpdateWindowLevel();
1864 }
1865 //------------------------------------------------------------------------------
1866
1867 //------------------------------------------------------------------------------
1868 void vvMainWindow::ApplyWindowLevelToAllImages()
1869 {
1870   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1871   if(index==-1) return;
1872   double window = mSlicerManagers[index]->GetColorWindow();
1873   double level = mSlicerManagers[index]->GetColorLevel();
1874
1875   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
1876     if (mSlicerManagers[i] == NULL)
1877       continue;
1878     mSlicerManagers[i]->SetColorWindow(window);
1879     mSlicerManagers[i]->SetColorLevel(level);
1880     mSlicerManagers[i]->SetPreset(WL_USER);
1881     mSlicerManagers[i]->Render();
1882   }
1883 }
1884 //------------------------------------------------------------------------------
1885
1886 //------------------------------------------------------------------------------
1887 void vvMainWindow::ApplyWindowToSetOfImages(double window, unsigned int indexMin, unsigned int indexMax)
1888 {
1889   for (unsigned int i = indexMin; i <= indexMax && i < mSlicerManagers.size(); i++) {
1890     if (mSlicerManagers[i] == NULL)
1891       continue;
1892     mSlicerManagers[i]->SetColorWindow(window);
1893     mSlicerManagers[i]->SetPreset(WL_USER);
1894     mSlicerManagers[i]->Render();
1895   }
1896 }
1897 //------------------------------------------------------------------------------
1898
1899 //------------------------------------------------------------------------------
1900 void vvMainWindow::ApplyLevelToSetOfImages(double level, unsigned int indexMin, unsigned int indexMax)
1901 {
1902   for (unsigned int i = indexMin; i <= indexMax && i < mSlicerManagers.size(); i++) {
1903     if (mSlicerManagers[i] == NULL)
1904       continue;
1905     mSlicerManagers[i]->SetColorLevel(level);
1906     mSlicerManagers[i]->SetPreset(WL_USER);
1907     mSlicerManagers[i]->Render();
1908   }
1909 }
1910 //------------------------------------------------------------------------------
1911
1912 //------------------------------------------------------------------------------
1913 void vvMainWindow::UpdateLinkManager(std::string id, int slicer, double x, double y, double z, int temps)
1914 {
1915   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
1916     if (mSlicerManagers[i]->GetId() == id) {
1917       mSlicerManagers[i]->GetSlicer(slicer)->SetCurrentPosition(x,y,z,temps);
1918       mSlicerManagers[i]->UpdateViews(0,slicer);
1919       break;
1920     }
1921   }
1922 }
1923 //------------------------------------------------------------------------------
1924
1925 //------------------------------------------------------------------------------
1926 void vvMainWindow::UpdateLinkedNavigation(std::string id, vvSlicerManager * sm, vvSlicer* refSlicer)
1927 {
1928   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
1929     if (id == mSlicerManagers[i]->GetId()) {
1930       mSlicerManagers[i]->UpdateLinkedNavigation(refSlicer);
1931     }
1932   }
1933 }
1934 //------------------------------------------------------------------------------
1935
1936 //------------------------------------------------------------------------------
1937 void vvMainWindow::ShowContextMenu(QPoint point)
1938 {
1939   if (!DataTree->selectedItems().size()) {
1940     contextActions[1]->setEnabled(0);
1941     contextActions[2]->setEnabled(0);
1942     contextActions[3]->setEnabled(0);
1943     contextActions[4]->setEnabled(0);
1944     contextActions[5]->setEnabled(0);
1945     contextActions[6]->setEnabled(0);
1946   } else {
1947     int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1948     contextActions[1]->setEnabled(1);
1949     contextActions[2]->setEnabled(
1950       DataTree->itemWidget(DataTree->selectedItems()[0],
1951       COLUMN_RELOAD_IMAGE)->isEnabled());
1952     contextActions[3]->setEnabled(1);
1953     contextActions[5]->setEnabled(1);
1954     contextActions[6]->setEnabled(1);
1955
1956     if (mSlicerManagers[index]->GetDimension() < 3)
1957       contextActions[4]->setEnabled(0);
1958     else
1959       contextActions[4]->setEnabled(1);
1960   }
1961   contextMenu.exec(QCursor::pos());
1962 }
1963 //------------------------------------------------------------------------------
1964
1965 //------------------------------------------------------------------------------
1966 void vvMainWindow::CloseImage()
1967 {
1968   CloseImage(DataTree->selectedItems()[0],0);
1969 }
1970 //------------------------------------------------------------------------------
1971
1972 //------------------------------------------------------------------------------
1973 void vvMainWindow::ReloadImage()
1974 {
1975   ReloadImage(DataTree->selectedItems()[0],0);
1976 }
1977 //------------------------------------------------------------------------------
1978
1979 //------------------------------------------------------------------------------
1980 void vvMainWindow::SelectOverlayImage()
1981 {
1982   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1983
1984   //check if one overlay image is added
1985   for (int child = 0; child < DataTree->topLevelItem(index)->childCount(); child++)
1986     if (DataTree->topLevelItem(index)->child(child)->data(1,Qt::UserRole).toString() == "overlay") {
1987       QString error = "Cannot add more than one compared image\n";
1988       error += "Please remove first ";
1989       error += DataTree->topLevelItem(index)->child(child)->data(COLUMN_IMAGE_NAME,Qt::DisplayRole).toString();
1990       QMessageBox::information(this,tr("Problem adding compared image !"),error);
1991       return;
1992     }
1993
1994     QString Extensions = EXTENSIONS;
1995     Extensions += ";;All Files (*)";
1996     QStringList files = QFileDialog::getOpenFileNames(this,tr("Load Overlay image"),mInputPathName,Extensions);
1997     if (files.isEmpty())
1998       return;
1999
2000     std::vector<std::string> vecFileNames;
2001     for (int i = 0; i < files.size(); i++) {
2002       vecFileNames.push_back(files[i].toStdString());
2003     }
2004     AddOverlayImage(index,vecFileNames,vvImageReader::IMAGE);
2005 }
2006 //------------------------------------------------------------------------------
2007
2008 //------------------------------------------------------------------------------
2009 void vvMainWindow::AddOverlayImage(int index, std::vector<std::string> fileNames, vvImageReader::LoadedImageType type)
2010 {
2011   QString file(fileNames[0].c_str());
2012   if (QFile::exists(file))
2013   {
2014     mInputPathName = itksys::SystemTools::GetFilenamePath(file.toStdString()).c_str();
2015     itk::ImageIOBase::Pointer reader = itk::ImageIOFactory::CreateImageIO(
2016       file.toStdString().c_str(), itk::ImageIOFactory::ReadMode);
2017     reader->SetFileName(fileNames[0].c_str());
2018     reader->ReadImageInformation();
2019     std::string component = reader->GetComponentTypeAsString(reader->GetComponentType());
2020     int dimension = reader->GetNumberOfDimensions();
2021     QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
2022     vvProgressDialog progress("Opening " + file.toStdString());
2023     qApp->processEvents();
2024
2025     std::string filename = itksys::SystemTools::GetFilenameWithoutExtension(file.toStdString()).c_str();
2026     if (mSlicerManagers[index]->SetOverlay(fileNames,dimension, component,type)) {
2027       //create an item in the tree with good settings
2028       QTreeWidgetItem *item = new QTreeWidgetItem();
2029       item->setData(0,Qt::UserRole,file.toStdString().c_str());
2030       item->setData(1,Qt::UserRole,tr("overlay"));
2031       QFileInfo fileinfo(file); //Do not show the path
2032       item->setData(COLUMN_IMAGE_NAME,Qt::DisplayRole,fileinfo.fileName());
2033       item->setToolTip(COLUMN_IMAGE_NAME, mSlicerManagers[index]->GetListOfAbsoluteFilePathInOneString("overlay").c_str());
2034       qApp->processEvents();
2035
2036       for (int j = 1; j <= 4; j++) {
2037         item->setData(j,Qt::CheckStateRole,DataTree->topLevelItem(index)->data(j,Qt::CheckStateRole));
2038       }
2039
2040       //Create the buttons for reload and close
2041       qApp->processEvents();
2042       QTreePushButton* cButton = new QTreePushButton;
2043       cButton->setItem(item);
2044       cButton->setColumn(COLUMN_CLOSE_IMAGE);
2045       cButton->setToolTip(tr("close image"));
2046       cButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/exit.png")));
2047       connect(cButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
2048         this,SLOT(CloseImage(QTreeWidgetItem*, int)));
2049
2050       QTreePushButton* rButton = new QTreePushButton;
2051       rButton->setItem(item);
2052       rButton->setColumn(COLUMN_RELOAD_IMAGE);
2053       rButton->setToolTip(tr("reload image"));
2054       rButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/rotateright.png")));
2055       connect(rButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
2056         this,SLOT(ReloadImage(QTreeWidgetItem*, int)));
2057
2058       DataTree->topLevelItem(index)->setExpanded(1);
2059       DataTree->topLevelItem(index)->addChild(item);
2060       DataTree->setItemWidget(item, COLUMN_CLOSE_IMAGE, cButton);
2061       DataTree->setItemWidget(item, COLUMN_RELOAD_IMAGE, rButton);
2062
2063       //set the id of the image
2064       QString id = DataTree->topLevelItem(index)->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString();
2065       item->setData(COLUMN_IMAGE_NAME,Qt::UserRole,id.toStdString().c_str());
2066       UpdateTree();
2067       qApp->processEvents();
2068       ImageInfoChanged();
2069       QApplication::restoreOverrideCursor();
2070
2071       // Update the display to update, e.g., the sliders
2072       for(int i=0; i<4; i++)
2073         DisplaySliders(index, i);
2074     } else {
2075       QApplication::restoreOverrideCursor();
2076       QString error = "Cannot import the new image.\n";
2077       error += mSlicerManagers[index]->GetLastError().c_str();
2078       QMessageBox::information(this,tr("Problem reading image !"),error);
2079     }
2080     WindowLevelChanged();
2081   }
2082   else
2083     QMessageBox::information(this,tr("Problem reading Overlay !"),"File doesn't exist!");
2084 }
2085 //------------------------------------------------------------------------------
2086
2087
2088 //------------------------------------------------------------------------------
2089 void vvMainWindow::AddROI(int index, QString file)
2090 {
2091   /*
2092   // Get slice manager
2093
2094   // Load image
2095
2096   vvImageReader * mReader = new vvImageReader;
2097   mReader->SetInputFilename(filename.toStdString());
2098   mReader->Update(IMAGE);
2099   if (mReader->GetLastError().size() != 0) {
2100   std::cerr << "Error while reading " << filename.toStdString() << std::endl;
2101   QString error = "Cannot open file \n";
2102   error += mReader->GetLastError().c_str();
2103   QMessageBox::information(this,tr("Reading problem"),error);
2104   delete mReader;
2105   return;
2106   }
2107   vvImage::Pointer roi = mReader->GetOutput();
2108
2109   // Create roi in new tool
2110   vvToolStructureSetManager::AddImage(mCurrentSlicerManager, roi);
2111   */
2112 }
2113 //------------------------------------------------------------------------------
2114
2115 //------------------------------------------------------------------------------
2116 void vvMainWindow::SelectFusionImage()
2117 {
2118   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2119
2120   //check if one fusion image is added
2121   for (int child = 0; child < DataTree->topLevelItem(index)->childCount(); child++)
2122     if ( (DataTree->topLevelItem(index)->child(child)->data(1,Qt::UserRole).toString() == "fusion") ||
2123       (DataTree->topLevelItem(index)->child(child)->data(1,Qt::UserRole).toString() == "fusionSequence") ) {
2124         QString error = "Cannot add more than one fusion image\n";
2125         error += "Please remove first ";
2126         error += DataTree->topLevelItem(index)->child(child)->data(COLUMN_IMAGE_NAME,Qt::DisplayRole).toString();
2127         QMessageBox::information(this,tr("Problem adding fusion image !"),error);
2128         return;
2129     }
2130
2131     QString Extensions = EXTENSIONS;
2132     Extensions += ";;All Files (*)";
2133     QString file = QFileDialog::getOpenFileName(this,tr("Load Fusion image"),mInputPathName,Extensions);
2134     if (!file.isEmpty())
2135       AddFusionImage(index,file);
2136 }
2137 //------------------------------------------------------------------------------
2138
2139 //------------------------------------------------------------------------------
2140 void vvMainWindow::ResetTransformationToIdentity()
2141 {
2142   std::string actorType = DataTree->selectedItems()[0]->data(1,Qt::UserRole).toString().toStdString();
2143   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2144   mSlicerManagers[index]->ResetTransformationToIdentity(actorType);
2145   ImageInfoChanged();
2146 }
2147 //------------------------------------------------------------------------------
2148
2149 //------------------------------------------------------------------------------
2150 void vvMainWindow::AddFusionImage(int index, QString file)
2151 {
2152   if (QFile::exists(file))
2153   {
2154     mInputPathName = itksys::SystemTools::GetFilenamePath(file.toStdString()).c_str();
2155     itk::ImageIOBase::Pointer reader = itk::ImageIOFactory::CreateImageIO(
2156       file.toStdString().c_str(), itk::ImageIOFactory::ReadMode);
2157     reader->SetFileName(file.toStdString().c_str());
2158     reader->ReadImageInformation();
2159     std::string component = reader->GetComponentTypeAsString(reader->GetComponentType());
2160     if (reader) {
2161       QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
2162       vvProgressDialog progress("Opening fusion");
2163       qApp->processEvents();
2164
2165       std::string filename = itksys::SystemTools::GetFilenameWithoutExtension(file.toStdString()).c_str();
2166       if (mSlicerManagers[index]->SetFusion(file.toStdString(),
2167         reader->GetNumberOfDimensions(), component)) {
2168           //create an item in the tree with good settings
2169           QTreeWidgetItem *item = new QTreeWidgetItem();
2170           item->setData(0,Qt::UserRole,file.toStdString().c_str());
2171           item->setData(1,Qt::UserRole,tr("fusion"));
2172           QFileInfo fileinfo(filename.c_str()); //Do not show the path
2173           item->setData(COLUMN_IMAGE_NAME,Qt::DisplayRole,fileinfo.fileName());
2174           item->setToolTip(COLUMN_IMAGE_NAME, mSlicerManagers[index]->GetListOfAbsoluteFilePathInOneString("fusion").c_str());
2175           qApp->processEvents();
2176
2177           for (int j = 1; j <= 4; j++) {
2178             item->setData(j,Qt::CheckStateRole,DataTree->topLevelItem(index)->data(j,Qt::CheckStateRole));
2179           }
2180
2181           //Create the buttons for reload and close
2182           qApp->processEvents();
2183           QTreePushButton* cButton = new QTreePushButton;
2184           cButton->setItem(item);
2185           cButton->setColumn(COLUMN_CLOSE_IMAGE);
2186           cButton->setToolTip(tr("close image"));
2187           cButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/exit.png")));
2188           connect(cButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
2189             this,SLOT(CloseImage(QTreeWidgetItem*, int)));
2190
2191           QTreePushButton* rButton = new QTreePushButton;
2192           rButton->setItem(item);
2193           rButton->setColumn(COLUMN_RELOAD_IMAGE);
2194           rButton->setToolTip(tr("reload image"));
2195           rButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/rotateright.png")));
2196           connect(rButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
2197             this,SLOT(ReloadImage(QTreeWidgetItem*, int)));
2198
2199           DataTree->topLevelItem(index)->setExpanded(1);
2200           DataTree->topLevelItem(index)->addChild(item);
2201           DataTree->setItemWidget(item, COLUMN_CLOSE_IMAGE, cButton);
2202           DataTree->setItemWidget(item, COLUMN_RELOAD_IMAGE, rButton);
2203
2204           //set the id of the image
2205           QString id = DataTree->topLevelItem(index)->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString();
2206           item->setData(COLUMN_IMAGE_NAME,Qt::UserRole,id.toStdString().c_str());
2207           UpdateTree();
2208           qApp->processEvents();
2209           ImageInfoChanged();
2210           QApplication::restoreOverrideCursor();
2211       } else {
2212         QApplication::restoreOverrideCursor();
2213         QString error = "Cannot import the new image.\n";
2214         error += mSlicerManagers[index]->GetLastError().c_str();
2215         QMessageBox::information(this,tr("Problem reading image !"),error);
2216       }
2217     } else {
2218       QString error = "Cannot import the new image.\n";
2219       QMessageBox::information(this,tr("Problem reading image !"),error);
2220     }
2221   }
2222   else
2223     QMessageBox::information(this,tr("Problem reading Fusion !"),"File doesn't exist!");
2224 }
2225 //------------------------------------------------------------------------------
2226 //------------------------------------------------------------------------------
2227 void vvMainWindow::AddLandmarks(int index, std::vector<std::string> files)
2228 {
2229     if (!landmarksPanel->LoadFromFile(files))
2230       QMessageBox::information(this,tr("Problem reading Landmarks !"),"File doesn't exist!");
2231
2232     landmarksPanel->SetCurrentPath(mInputPathName.toStdString());
2233     landmarksPanel->SetCurrentImage(mSlicerManagers[index]->GetFileName().c_str());
2234 }
2235
2236 //------------------------------------------------------------------------------
2237 void vvMainWindow::OpenField()
2238 {
2239   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2240   //check if a vector field has already been added
2241   for (int child = 0; child < DataTree->topLevelItem(index)->childCount(); child++)
2242     if (DataTree->topLevelItem(index)->child(child)->data(1,Qt::UserRole).toString() == "vector") {
2243       QString error = "Cannot add more than one vector field\n";
2244       error += "Please remove first ";
2245       error += DataTree->topLevelItem(index)->child(child)->data(COLUMN_IMAGE_NAME,Qt::DisplayRole).toString();
2246       QMessageBox::information(this,tr("Problem adding vector field!"),error);
2247       return;
2248     }
2249
2250     QString Extensions = "Images ( *.mhd)";
2251     Extensions += ";;Images ( *.mha)";
2252     Extensions += ";;VF Images ( *.vf)";
2253     Extensions += ";;nii Images ( *.nii)";
2254     Extensions += ";;nrrd Images ( *.nrrd)";
2255     Extensions += ";;nhdr Images ( *.nhdr)";
2256     Extensions += ";;All Files (*)";
2257     QString file = QFileDialog::getOpenFileName(this,tr("Load deformation field"),mInputPathName,Extensions);
2258     if (!file.isEmpty())
2259       AddField(file,index);
2260 }
2261 //------------------------------------------------------------------------------
2262
2263
2264 //------------------------------------------------------------------------------
2265 void vvMainWindow::AddFieldEntry(QString filename,int index,bool from_disk)
2266 {
2267   //create an item in the tree with good settings
2268   QTreeWidgetItem *item = new QTreeWidgetItem();
2269   item->setData(0,Qt::UserRole,filename.toStdString().c_str());
2270   item->setData(1,Qt::UserRole,tr("vector"));
2271   QFileInfo fileinfo(filename); //Do not show the path
2272   item->setData(COLUMN_IMAGE_NAME,Qt::DisplayRole,fileinfo.fileName());
2273   item->setToolTip(COLUMN_IMAGE_NAME, mSlicerManagers[index]->GetListOfAbsoluteFilePathInOneString("vector").c_str());
2274   qApp->processEvents();
2275
2276   for (int j = 1; j <= 4; j++) {
2277     item->setData(j,Qt::CheckStateRole,DataTree->topLevelItem(index)->data(j,Qt::CheckStateRole));
2278   }
2279
2280   //Create the buttons for reload and close
2281   qApp->processEvents();
2282   QTreePushButton* cButton = new QTreePushButton;
2283   cButton->setItem(item);
2284   cButton->setColumn(COLUMN_CLOSE_IMAGE);
2285   cButton->setToolTip(tr("close vector field"));
2286   cButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/exit.png")));
2287   connect(cButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
2288     this,SLOT(CloseImage(QTreeWidgetItem*, int)));
2289
2290   QTreePushButton* rButton = new QTreePushButton;
2291   rButton->setItem(item);
2292   rButton->setColumn(COLUMN_RELOAD_IMAGE);
2293   rButton->setToolTip(tr("reload vector field"));
2294   rButton->setEnabled(from_disk);
2295   rButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/rotateright.png")));
2296   connect(rButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
2297     this,SLOT(ReloadImage(QTreeWidgetItem*, int)));
2298
2299   DataTree->topLevelItem(index)->setExpanded(1);
2300   DataTree->topLevelItem(index)->addChild(item);
2301   DataTree->setItemWidget(item, COLUMN_RELOAD_IMAGE, rButton);
2302   DataTree->setItemWidget(item, COLUMN_CLOSE_IMAGE, cButton);
2303
2304   //set the id of the image
2305   QString id = DataTree->topLevelItem(index)->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString();
2306   item->setData(COLUMN_IMAGE_NAME,Qt::UserRole,id.toStdString().c_str());
2307   UpdateTree();
2308   qApp->processEvents();
2309   ImageInfoChanged();
2310   QApplication::restoreOverrideCursor();
2311 }
2312 //------------------------------------------------------------------------------
2313
2314
2315 //------------------------------------------------------------------------------
2316 void vvMainWindow::AddField(vvImage::Pointer vf,QString file,int index)
2317 {
2318   QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
2319   vvSlicerManager* imageManager = mSlicerManagers[index];
2320   if (imageManager->SetVF(vf,file.toStdString())) {
2321     AddFieldEntry(file,index,false);
2322   } else {
2323     QString error = "Cannot import the vector field for this image.\n";
2324     error += imageManager->GetLastError().c_str();
2325     QMessageBox::information(this,tr("Problem reading VF !"),error);
2326   }
2327   QApplication::restoreOverrideCursor();
2328 }
2329 //------------------------------------------------------------------------------
2330
2331
2332 //------------------------------------------------------------------------------
2333 void vvMainWindow::AddField(QString file,int index)
2334 {
2335   if (QFile::exists(file)) {
2336     mInputPathName = itksys::SystemTools::GetFilenamePath(file.toStdString()).c_str();
2337
2338     //init the progress events
2339     QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
2340     vvProgressDialog progress("Opening " + file.toStdString());
2341     qApp->processEvents();
2342
2343     //read the vector and put it in the current mSlicerManager
2344     vvSlicerManager* imageManager = mSlicerManagers[index];
2345     qApp->processEvents();
2346
2347     std::string filename = itksys::SystemTools::GetFilenameWithoutExtension(file.toStdString()).c_str();
2348     if (imageManager->SetVF(file.toStdString())) {
2349       imageManager->Render();
2350       AddFieldEntry(file,index,true);
2351     } else {
2352       QApplication::restoreOverrideCursor();
2353       QString error = "Cannot import the vector field for this image.\n";
2354       error += imageManager->GetLastError().c_str();
2355       QMessageBox::information(this,tr("Problem reading VF !"),error);
2356     }
2357   } else
2358     QMessageBox::information(this,tr("Problem reading VF !"),"File doesn't exist!");
2359
2360 }
2361 //------------------------------------------------------------------------------
2362
2363
2364 //------------------------------------------------------------------------------
2365 void vvMainWindow::SetVFProperty(int subsampling, int scale, int log, int width, double r, double g, double b)
2366 {
2367   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2368   if (mSlicerManagers[index]->GetSlicer(0)->GetVF()) {
2369     for (int i = 0; i < 4; i++) {
2370       mSlicerManagers[index]->GetSlicer(i)->SetVFSubSampling(subsampling);
2371       mSlicerManagers[index]->GetSlicer(i)->SetVFScale(scale);
2372       mSlicerManagers[index]->GetSlicer(i)->SetVFWidth(width);
2373       mSlicerManagers[index]->GetSlicer(i)->SetVFColor(r,g,b);
2374       if (log > 0)
2375         mSlicerManagers[index]->GetSlicer(i)->SetVFLog(1);
2376       else
2377         mSlicerManagers[index]->GetSlicer(i)->SetVFLog(0);
2378     }
2379   }
2380 }
2381 //------------------------------------------------------------------------------
2382
2383
2384 //------------------------------------------------------------------------------
2385 void vvMainWindow::SetOverlayProperty(int color, int linked, double window, double level)
2386 {
2387   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2388   if (mSlicerManagers[index]->GetSlicer(0)->GetOverlay()) {
2389     mSlicerManagers[index]->SetOverlayColor(color);
2390     mSlicerManagers[index]->SetColorMap(0);
2391     mSlicerManagers[index]->SetLinkOverlayWindowLevel(linked);
2392     mSlicerManagers[index]->SetOverlayColorWindow(window);
2393     mSlicerManagers[index]->SetOverlayColorLevel(level);
2394     mSlicerManagers[index]->Render();
2395   }
2396 }
2397 //------------------------------------------------------------------------------
2398
2399 //------------------------------------------------------------------------------
2400 void vvMainWindow::SetFusionProperty(int opacity, int thresOpacity, int colormap,double window, double level, bool showLegend)
2401 {
2402   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2403   if (mSlicerManagers[index]->GetSlicer(0)->GetFusion()) {
2404     mSlicerManagers[index]->SetFusionColorMap(colormap);
2405     mSlicerManagers[index]->SetFusionOpacity(opacity);
2406     mSlicerManagers[index]->SetFusionThresholdOpacity(thresOpacity);
2407     mSlicerManagers[index]->SetFusionWindow(window);
2408     mSlicerManagers[index]->SetFusionLevel(level);
2409     mSlicerManagers[index]->SetFusionShowLegend(showLegend);
2410     mSlicerManagers[index]->SetColorMap(0);
2411     mSlicerManagers[index]->Render();
2412   }
2413 }
2414 //------------------------------------------------------------------------------
2415
2416
2417 //------------------------------------------------------------------------------
2418 void vvMainWindow::SelectFusionSequence()
2419 {
2420   //get the index of the slicer manager of the main sequence (CT)
2421   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2422   //check if one overlay image is already associated
2423   for (int child = 0; child < DataTree->topLevelItem(index)->childCount(); child++)
2424     if ( (DataTree->topLevelItem(index)->child(child)->data(1,Qt::UserRole).toString() == "fusion") ||
2425       (DataTree->topLevelItem(index)->child(child)->data(1,Qt::UserRole).toString() == "fusionSequence") ) {
2426         QString error = "Cannot add more than one compared image\n";
2427         error += "Please remove first ";
2428         error += DataTree->topLevelItem(index)->child(child)->data(COLUMN_IMAGE_NAME,Qt::DisplayRole).toString();
2429         QMessageBox::information(this,tr("Problem adding compared image !"),error);
2430         return;
2431     }
2432
2433     QString Extensions = EXTENSIONS;
2434     Extensions += ";;All Files (*)";
2435     QStringList files = QFileDialog::getOpenFileNames(this,tr("Load Overlay image sequence"),mInputPathName,Extensions);
2436     if (files.isEmpty())
2437       return;
2438
2439     std::vector<std::string> vecFileNames;
2440     for (int i = 0; i < files.size(); i++) {
2441       vecFileNames.push_back(files[i].toStdString());
2442     }
2443
2444     //associate the secondary sequence (US) to the main one
2445     AddFusionSequence(index,vecFileNames,vvImageReader::MERGEDWITHTIME);
2446 }
2447 //------------------------------------------------------------------------------
2448
2449
2450 //------------------------------------------------------------------------------
2451 void vvMainWindow::SelectFusionSequenceCorrespondances() {
2452
2453   //make sure the index is right?
2454   //in the end, I should attach the temporal data to the right sequence!
2455   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2456   //in case the other sequence got selected, make sure we select the primary sequence
2457   if ( (!mSlicerManagers[index]->GetSlicer(0)->GetFusion()) && mSlicerManagers[index]->GetFusionSequenceIndexOfLinkedManager()>=0 ) {
2458     index = mSlicerManagers[index]->GetFusionSequenceIndexOfLinkedManager();
2459   }
2460
2461   //open a dialog box to find a file
2462   //QString Extensions = EXTENSIONS;
2463   QString Extensions = ";;All Files (*)";
2464   QString fileName = QFileDialog::getOpenFileName(this,tr("Load respiratory signal for fused sequence"),mInputPathName,Extensions);
2465   if (fileName.isNull())
2466     return;
2467
2468   //read it as a vector of values
2469   vnl_vector<double> tmpVect;
2470
2471   std::ifstream file;
2472   file.open(fileName.toStdString().c_str());
2473   tmpVect.read_ascii(file);
2474   file.close();
2475
2476   //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
2477   bool signalOK = true;
2478   unsigned nbFrameMain = mSlicerManagers[index]->GetImage()->GetTransform().size();
2479   unsigned nbFrameSecondary = mSlicerManagers[index]->GetFusionSequenceNbFrames();
2480 std::cout<<"nbFrameMain = "<<nbFrameMain<<", nbFrameSecondary= "<<nbFrameSecondary<<", signal size: "<<tmpVect.size()<<std::endl;
2481   std::vector<unsigned> temporalCorrespondances;
2482   if ( tmpVect.size() == nbFrameMain + nbFrameSecondary ) {
2483     for (unsigned i=0 ; i<tmpVect.size() ; i++) {
2484       if (i<nbFrameMain) { //first part of the file: i -> index in secondary seq.
2485         if ( tmpVect(i)<nbFrameSecondary ) temporalCorrespondances.push_back(tmpVect(i));
2486         else { signalOK=false; break; } //pointing outside the secondary sequence...
2487       }
2488       else { //first part of the file -> index in secondary seq.
2489         if ( tmpVect(i)<nbFrameMain ) temporalCorrespondances.push_back(tmpVect(i));
2490         else { signalOK=false; break; } //pointing outside the secondary sequence...
2491       }
2492     }
2493   }
2494   else {signalOK=false;}
2495   if (!signalOK) {//else, send a message to signal the failure...
2496     QString error = "The provided temporal correspondances is invalid - check tooltip.\n";
2497     error += "Ignoring file: " + fileName;
2498     QMessageBox::information(this,tr("Problem adding temporal correspondances!"),error);
2499     return;
2500   }
2501   else {
2502     //for convenience, associate this sequence to both the current slicer manager, and to the linked one
2503     mSlicerManagers[index]->SetFusionSequenceCorrespondances(temporalCorrespondances);
2504     mSlicerManagers[ mSlicerManagers[index]->GetFusionSequenceIndexOfLinkedManager() ]->SetFusionSequenceCorrespondances(temporalCorrespondances);
2505     overlayPanel->enableFusionSequenceTemporalSync();
2506   }
2507
2508 }
2509 //------------------------------------------------------------------------------
2510
2511
2512 //------------------------------------------------------------------------------
2513 //when this function is called index is the slicer manager index corresponding to the main sequence (CT)
2514 //the files behind fileNames points to the data for the secondary sequence
2515 void vvMainWindow::AddFusionSequence(int index, std::vector<std::string> fileNames, vvImageReader::LoadedImageType type)
2516 {
2517   QString file(fileNames[0].c_str());
2518   if (QFile::exists(file))
2519   {
2520     mInputPathName = itksys::SystemTools::GetFilenamePath(file.toStdString()).c_str();
2521     itk::ImageIOBase::Pointer reader = itk::ImageIOFactory::CreateImageIO(
2522       file.toStdString().c_str(), itk::ImageIOFactory::ReadMode);
2523     std::sort (fileNames.begin(), fileNames.end());//make sure the files are sorted.
2524     reader->SetFileName(fileNames[0].c_str());
2525     reader->ReadImageInformation();
2526     std::string component = reader->GetComponentTypeAsString(reader->GetComponentType());
2527     int dimension = reader->GetNumberOfDimensions();
2528     QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
2529     vvProgressDialog progress("Opening " + file.toStdString());
2530     qApp->processEvents();
2531
2532     std::string filename = itksys::SystemTools::GetFilenameWithoutExtension(file.toStdString()).c_str();
2533
2534     if (mSlicerManagers[index]->SetFusionSequence(fileNames,dimension, component,type)) {
2535       //create an item in the tree with good settings
2536       QTreeWidgetItem *item = new QTreeWidgetItem();
2537       item->setData(0,Qt::UserRole,file.toStdString().c_str());
2538       item->setData(1,Qt::UserRole,tr("fusionSequence"));
2539
2540       QFileInfo fileinfo(file); //Do not show the path
2541       item->setData(COLUMN_IMAGE_NAME,Qt::DisplayRole,fileinfo.fileName());
2542       item->setToolTip(COLUMN_IMAGE_NAME, mSlicerManagers[index]->GetListOfAbsoluteFilePathInOneString("fusionSequence").c_str());
2543       qApp->processEvents();
2544       for (int j = 1; j <= 4; j++) {
2545         item->setData(j,Qt::CheckStateRole,DataTree->topLevelItem(index)->data(j,Qt::CheckStateRole));
2546       }
2547
2548       //Create the buttons for reload and close
2549       qApp->processEvents();
2550       QTreePushButton* cButton = new QTreePushButton;
2551       cButton->setItem(item);
2552       cButton->setColumn(COLUMN_CLOSE_IMAGE);
2553       cButton->setToolTip(tr("close image"));
2554       cButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/exit.png")));
2555       connect(cButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
2556         this,SLOT(CloseImage(QTreeWidgetItem*, int)));
2557
2558       QTreePushButton* rButton = new QTreePushButton;
2559       rButton->setItem(item);
2560       rButton->setColumn(COLUMN_RELOAD_IMAGE);
2561       rButton->setToolTip(tr("reload image"));
2562       rButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/rotateright.png")));
2563       connect(rButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
2564         this,SLOT(ReloadImage(QTreeWidgetItem*, int)));
2565
2566       DataTree->topLevelItem(index)->setExpanded(1);
2567       DataTree->topLevelItem(index)->addChild(item);
2568       DataTree->setItemWidget(item, COLUMN_CLOSE_IMAGE, cButton);
2569       DataTree->setItemWidget(item, COLUMN_RELOAD_IMAGE, rButton);
2570
2571       //store the original transform matrix
2572       int indexParent = GetSlicerIndexFromItem( DataTree->topLevelItem(index) );
2573       mSlicerManagers[indexParent]->SetFusionSequenceMainTransformMatrix( mSlicerManagers[indexParent]->GetSlicer(0)->GetImage()->GetTransform()[0]->GetMatrix() );
2574
2575       //set the id of the image
2576       QString id = DataTree->topLevelItem(index)->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString();
2577       item->setData(COLUMN_IMAGE_NAME,Qt::UserRole,id.toStdString().c_str());
2578       UpdateTree();
2579       qApp->processEvents();
2580
2581       //ImageInfoChanged();
2582
2583       QApplication::restoreOverrideCursor();
2584       // Update the display to update, e.g., the sliders
2585       for(int i=0; i<4; i++)
2586         DisplaySliders(index, i);
2587
2588
2589       //This loads the secondary sequence (US) as an independent sequence
2590       LoadImages(fileNames, type);
2591       //reset the transforms to identiy
2592       for (unsigned i=0 ; i<mSlicerManagers.back()->GetImage()->GetTransform().size() ; i++) {
2593         mSlicerManagers.back()->GetImage()->GetTransform()[i]->Identity();
2594         mSlicerManagers.back()->GetImage()->GetTransform()[i]->Update();
2595       }
2596
2597       //automatically link both images...
2598       AddLink(mSlicerManagers[indexParent]->GetId().c_str(), mSlicerManagers.back()->GetId().c_str(), false);
2599
2600       //tie the main and secondary sequences by raising flags and informing each another of their respective SlicerManager indices
2601       mSlicerManagers[indexParent]->SetFusionSequenceIndexOfLinkedManager(mSlicerManagers.size()-1);
2602       mSlicerManagers[indexParent]->SetFusionSequenceInvolvmentCode(0); //main sequence
2603       mSlicerManagers.back()->SetFusionSequenceIndexOfLinkedManager(indexParent);
2604       mSlicerManagers.back()->SetFusionSequenceInvolvmentCode(1); //secondary sequence
2605       for (unsigned i=0 ; i<4 ; i++) {
2606         mSlicerManagers.back()->GetSlicer(i)->SetFusionSequenceCode(1); //flag the slicers of the secondary sequence
2607       }
2608
2609     } else {
2610       QApplication::restoreOverrideCursor();
2611       QString error = "Cannot import the new image.\n";
2612       error += mSlicerManagers[index]->GetLastError().c_str();
2613       QMessageBox::information(this,tr("Problem reading image !"),error);
2614     }
2615     //WindowLevelChanged();
2616     ImageInfoChanged(); //this internally calls WindowLevelChanged...
2617   }
2618   else {
2619     QMessageBox::information(this,tr("Problem reading fusion sequence !"),"File doesn't exist!");
2620     return;
2621   }
2622
2623 }
2624 //------------------------------------------------------------------------------
2625
2626
2627 //------------------------------------------------------------------------------
2628 //fusionSequenceFrameIndex and fusionSequenceNbFrames are relative to the secondary sequence (US)
2629 void vvMainWindow::SetFusionSequenceProperty(int fusionSequenceFrameIndex, bool spatialSyncFlag, unsigned int fusionSequenceNbFrames, bool temporalSyncFlag)
2630 {
2631   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2632
2633   if (!mSlicerManagers[index]->IsInvolvedInFusionSequence()) return;
2634
2635   //check if the focus moved to the linked sequence, and in this case, select the master sequence instead
2636   if (!mSlicerManagers[index]->IsMainSequenceOfFusionSequence()) {
2637     index = mSlicerManagers[index]->GetFusionSequenceIndexOfLinkedManager();
2638   }
2639   int secondaryIndex = mSlicerManagers[index]->GetFusionSequenceIndexOfLinkedManager();
2640   if (secondaryIndex==-1) return; //this should never happen
2641   if ( (!mSlicerManagers[index]->IsMainSequenceOfFusionSequence()) ||
2642     (!mSlicerManagers[secondaryIndex]->IsSecondarySequenceOfFusionSequence()) )
2643   {return;} //this should never happen, raise an exception?
2644
2645   if (mSlicerManagers[index]->GetSlicer(0)->GetFusion()) {
2646
2647     //First, if the spatialSync button is unchecked, then reposition the parent sequence (CT) in its original coordinate frame
2648     if ( (!spatialSyncFlag) && (mSlicerManagers[index]->GetFusionSequenceSpatialSyncFlag()) ) {
2649       for ( unsigned i=0 ; i<mSlicerManagers[index]->GetSlicer(0)->GetImage()->GetTransform().size() ; i++ ) {
2650         mSlicerManagers[index]->GetSlicer(0)->GetImage()->GetTransform()[i]->SetMatrix( mSlicerManagers[index]->GetFusionSequenceMainTransformMatrix() );
2651         mSlicerManagers[index]->GetSlicer(0)->GetImage()->GetTransform()[i]->Update();
2652       }
2653
2654       for (int i=0; i<mSlicerManagers[index]->GetNumberOfSlicers(); i++) {
2655         mSlicerManagers[index]->GetSlicer(i)->ForceUpdateDisplayExtent();
2656         mSlicerManagers[index]->GetSlicer(i)->Render();
2657       }
2658     }
2659
2660     //then, update the property values in the slicer manager
2661     mSlicerManagers[index]->SetFusionSequenceLength(fusionSequenceNbFrames);
2662     mSlicerManagers[index]->SetFusionSequenceSpatialSyncFlag(spatialSyncFlag);
2663     mSlicerManagers[index]->SetFusionSequenceTemporalSyncFlag(temporalSyncFlag);
2664     mSlicerManagers[index]->SetFusionSequenceFrameIndex(fusionSequenceFrameIndex);
2665
2666     //select the right frame of the US sequence
2667     mSlicerManagers[index]->SetFusionSequenceTSlice(fusionSequenceFrameIndex); //here, I should only update the overlayed sequence
2668     mSlicerManagers[secondaryIndex]->SetTSlice(fusionSequenceFrameIndex, false); //this should update the secondary sequence (individual version)
2669
2670     //update the horizontal sliders of the main window
2671     overlayPanel->updateFusionSequenceSliderValueFromWindow(fusionSequenceFrameIndex, false);
2672
2673     if (spatialSyncFlag) { //reslice the CT
2674
2675       if (temporalSyncFlag) { //do the temporal synchronisation
2676         int mainSequenceFrameIndex=0;
2677         //estimate the TSlice to set to the CT
2678         unsigned nbFramesMain = mSlicerManagers[index]->GetImage()->GetTransform().size();
2679         mainSequenceFrameIndex = mSlicerManagers[index]->GetFusionSequenceCorrespondances()[ nbFramesMain + fusionSequenceFrameIndex];
2680         //and set it!
2681         mSlicerManagers[index]->SetTSlice(mainSequenceFrameIndex, false);
2682         //warning, there is a loopback, and modification of the TSlice in main sequence forces an update of the TSlice in secondary, etc...
2683       }
2684
2685
2686       //Set the transform matrix of the parent sequence (typically CT / 4DCT)
2687       vtkSmartPointer<vtkMatrix4x4> tmpMat = vtkSmartPointer<vtkMatrix4x4>::New();
2688       vtkMatrix4x4::Invert( mSlicerManagers[index]->GetFusionSequenceInitialTransformMatrixAtFrame(fusionSequenceFrameIndex), tmpMat );
2689       for ( unsigned i=0 ; i<mSlicerManagers[index]->GetSlicer(0)->GetImage()->GetTransform().size() ; i++ ) {
2690         mSlicerManagers[index]->GetSlicer(0)->GetImage()->GetTransform()[i]->SetMatrix( mSlicerManagers[index]->GetFusionSequenceMainTransformMatrix() );
2691         mSlicerManagers[index]->GetSlicer(0)->GetImage()->GetTransform()[i]->PreMultiply();
2692         mSlicerManagers[index]->GetSlicer(0)->GetImage()->GetTransform()[i]->Concatenate( tmpMat );
2693         mSlicerManagers[index]->GetSlicer(0)->GetImage()->GetTransform()[i]->Update();
2694       }
2695
2696       for (int i=0; i<mSlicerManagers[index]->GetNumberOfSlicers(); i++) {
2697         mSlicerManagers[index]->GetSlicer(i)->ForceUpdateDisplayExtent();
2698         mSlicerManagers[index]->GetSlicer(i)->Render();
2699       }
2700
2701     }
2702
2703   }
2704 }
2705 //------------------------------------------------------------------------------
2706
2707
2708 //------------------------------------------------------------------------------
2709 void vvMainWindow::SaveAs()
2710 {
2711   if (DataTree->selectedItems()[0]->data(1,Qt::UserRole).toString() == "vector") {
2712     QMessageBox::warning(this,tr("Unsupported type"),tr("Sorry, saving a vector field is unsupported for the moment"));
2713     return;
2714   }
2715
2716   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2717   int dimension = mSlicerManagers[index]->GetDimension();
2718   QStringList OutputListeFormat;
2719   OutputListeFormat.clear();
2720   if (dimension == 1) {
2721     OutputListeFormat.push_back(".mhd");
2722     OutputListeFormat.push_back(".mha");
2723   }
2724   if (dimension == 2) {
2725     OutputListeFormat.push_back(".bmp");
2726     OutputListeFormat.push_back(".png");
2727     OutputListeFormat.push_back(".jpeg");
2728     OutputListeFormat.push_back(".tif");
2729     OutputListeFormat.push_back(".mhd");
2730     OutputListeFormat.push_back(".mha");
2731     OutputListeFormat.push_back(".hdr");
2732     OutputListeFormat.push_back(".vox");
2733   } else if (dimension == 3) {
2734     OutputListeFormat.push_back(".mhd");
2735     OutputListeFormat.push_back(".mha");
2736     OutputListeFormat.push_back(".nii");
2737     OutputListeFormat.push_back(".nrrd");
2738     OutputListeFormat.push_back(".nhdr");
2739     OutputListeFormat.push_back(".hdr");
2740     OutputListeFormat.push_back(".vox");
2741   } else if (dimension == 4) {
2742     OutputListeFormat.push_back(".mhd");
2743     OutputListeFormat.push_back(".mha");
2744     OutputListeFormat.push_back(".nii");
2745     OutputListeFormat.push_back(".nrrd");
2746     OutputListeFormat.push_back(".nhdr");
2747   }
2748   QString Extensions = "AllFiles(*.*)";
2749   for (int i = 0; i < OutputListeFormat.count(); i++) {
2750     Extensions += ";;Images ( *";
2751     Extensions += OutputListeFormat[i];
2752     Extensions += ")";
2753   }
2754   QString fileName = QFileDialog::getSaveFileName(this,
2755     tr("Save As"),
2756     mSlicerManagers[index]->GetFileName().c_str(),
2757     Extensions);
2758   if (!fileName.isEmpty()) {
2759     std::string fileformat = itksys::SystemTools::GetFilenameLastExtension(fileName.toStdString());
2760     if (OutputListeFormat.contains(
2761       fileformat.c_str())) {
2762         QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
2763         std::string action = "Saving";
2764         vvProgressDialog progress("Saving "+fileName.toStdString());
2765         qApp->processEvents();
2766         vvImageWriter::Pointer writer = vvImageWriter::New();
2767         writer->SetOutputFileName(fileName.toStdString());
2768         writer->SetInput(mSlicerManagers[index]->GetImage());
2769
2770         // Check on transform and prompt user
2771         writer->SetSaveTransform(false);
2772         bool bId = true;
2773         for(int i=0; i<4; i++)
2774           for(int j=0; j<4; j++) {
2775             // TODO SR and BP: check on the list of transforms and not the first only
2776             double elt = mSlicerManagers[index]->GetImage()->GetTransform()[0]->GetMatrix()->GetElement(i,j);
2777             if(i==j && elt!=1.)
2778               bId = false;
2779             if(i!=j && elt!=0.)
2780               bId = false;
2781           }
2782           if( !bId ) {
2783             QString warning = "The image has an associated linear transform. Do you want to save it along?";
2784             QMessageBox msgBox(QMessageBox::Warning, tr("Save transform"), warning, 0, this);
2785             msgBox.addButton(tr("Yes"), QMessageBox::AcceptRole);
2786             msgBox.addButton(tr("No"), QMessageBox::RejectRole);
2787             if (msgBox.exec() == QMessageBox::AcceptRole)
2788               writer->SetSaveTransform(true);
2789           }
2790
2791           writer->Update();
2792           QApplication::restoreOverrideCursor();
2793           if (writer->GetLastError().size()) {
2794             QString error = "Saving did not succeed\n";
2795             error += writer->GetLastError().c_str();
2796             QMessageBox::information(this,tr("Saving Problem"),error);
2797             SaveAs();
2798           }
2799     } else {
2800       QString error = fileformat.c_str();
2801       if (error.isEmpty())
2802         error += "no file format specified !";
2803       else
2804         error += " format unknown !!!\n";
2805       QMessageBox::information(this,tr("Saving Problem"),error);
2806       SaveAs();
2807     }
2808   }
2809 }
2810 //------------------------------------------------------------------------------
2811
2812 //------------------------------------------------------------------------------
2813 void vvMainWindow::SaveCurrentState()
2814 {
2815   QString Extensions = "XML Files(*.xml)";
2816   QString fileName = QFileDialog::getSaveFileName(this,
2817     tr("Save Current Window State"),
2818     "",
2819     Extensions);
2820
2821   SaveCurrentStateAs(fileName.toStdString());
2822 }
2823 //------------------------------------------------------------------------------
2824
2825 //------------------------------------------------------------------------------
2826 void vvMainWindow::SaveCurrentStateAs(const std::string& stateFile)
2827 {
2828   vvSaveState save_state;
2829   save_state.Run(this, stateFile);
2830 }
2831
2832 //------------------------------------------------------------------------------
2833 void vvMainWindow::ReadSavedState()
2834 {
2835   QString Extensions = "XML Files(*.xml)";
2836   QString fileName = QFileDialog::getOpenFileName(this,
2837     tr("Load Window State"),
2838     "",
2839     Extensions);
2840
2841   ReadSavedStateFile(fileName.toStdString());
2842 }
2843 //------------------------------------------------------------------------------
2844
2845 //------------------------------------------------------------------------------
2846 void vvMainWindow::ReadSavedStateFile(const std::string& stateFile)
2847 {
2848   vvReadState read_state;
2849   read_state.Run(this, stateFile);
2850 }
2851 //------------------------------------------------------------------------------
2852
2853 //------------------------------------------------------------------------------
2854 void vvMainWindow::LinkAllImages()
2855 {
2856   linkPanel->linkAll();
2857 }
2858
2859 //------------------------------------------------------------------------------
2860 void vvMainWindow::AddLink(QString image1,QString image2,bool fromPanel)
2861 {
2862   if (!fromPanel) {
2863     // delegate to linkPanel if call came from elsewhere...
2864     linkPanel->addLinkFromIds(image1, image2);
2865     return;
2866   }
2867
2868   unsigned int sm1 = 0;
2869   unsigned int sm2 = 0;
2870
2871   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
2872     if (image1.toStdString() == mSlicerManagers[i]->GetId()) {
2873       mSlicerManagers[i]->AddLink(image2.toStdString());
2874       sm1 = i;
2875     }
2876     if (image2.toStdString() == mSlicerManagers[i]->GetId()) {
2877       mSlicerManagers[i]->AddLink(image1.toStdString());
2878       sm2 = i;
2879     }
2880   }
2881
2882   if (linkPanel->isLinkAll())   {
2883     emit UpdateLinkedNavigation(mSlicerManagers[sm1]->GetId(), mSlicerManagers[mCurrentPickedImageIndex], mSlicerManagers[mCurrentPickedImageIndex]->GetSlicer(0));
2884     emit UpdateLinkedNavigation(mSlicerManagers[sm2]->GetId(), mSlicerManagers[mCurrentPickedImageIndex], mSlicerManagers[mCurrentPickedImageIndex]->GetSlicer(0));
2885   } else {
2886     emit UpdateLinkedNavigation(mSlicerManagers[sm2]->GetId(), mSlicerManagers[sm1], mSlicerManagers[sm1]->GetSlicer(0));
2887   }
2888 }
2889
2890 //------------------------------------------------------------------------------
2891
2892
2893 //------------------------------------------------------------------------------
2894 void vvMainWindow::RemoveLink(QString image1,QString image2)
2895 {
2896   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
2897     if (image1.toStdString() == mSlicerManagers[i]->GetId()) {
2898       mSlicerManagers[i]->RemoveLink(image2.toStdString());
2899     }
2900     if (image2.toStdString() == mSlicerManagers[i]->GetId()) {
2901       mSlicerManagers[i]->RemoveLink(image1.toStdString());
2902     }
2903   }
2904 }
2905 //------------------------------------------------------------------------------
2906
2907 //------------------------------------------------------------------------------
2908 void vvMainWindow::ChangeImageWithIndexOffset(vvSlicerManager *sm, int slicer, int offset)
2909 {
2910   if(mSlicerManagers.size()==1)
2911     return;
2912
2913   int index = 0;
2914   while(sm != mSlicerManagers[index])
2915     index++;
2916   index = (index+offset+mSlicerManagers.size()) % mSlicerManagers.size();
2917
2918   QTreeWidgetItem* item = GetItemFromSlicerManager(mSlicerManagers[index]);
2919   item->setData(slicer+1,Qt::CheckStateRole,2);         //change checkbox
2920   CurrentImageChanged(mSlicerManagers[index]->GetId()); //select new image
2921   DisplayChanged(item,slicer+1);
2922 }
2923 //------------------------------------------------------------------------------
2924 void vvMainWindow::HorizontalSliderMoved(int value,int column, int slicer_index)
2925 {
2926   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
2927     if (DataTree->topLevelItem(i)->data(column,Qt::CheckStateRole).toInt() > 1) {
2928       //i is the SlicerManager that is in charge of this slicer.
2929       if (mSlicerManagers[i]->IsInvolvedInFusionSequence()) {
2930         //if the slicerManager is involved in a fusionSequence as the secondary sequence, then update the slider position in the overlay panel and everything accordingly
2931         if (mSlicerManagers[i]->IsSecondarySequenceOfFusionSequence()) {
2932           overlayPanel->updateFusionSequenceSliderValueFromWindow(value, true);
2933         }
2934         else { //if this is the primary sequence that has been modified
2935           if (mSlicerManagers[i]->GetFusionSequenceTemporalSyncFlag()) {
2936             //WARNING: for some obscure reason, there are problems when accessing mSlicerManagers[mSlicerManagers[i]->GetFusionSequenceIndexOfLinkedManager()]->GetFusionSequenceFrameIndex();
2937
2938             int estimatedValue=0;
2939             //estimate a corresponding time index for the secondary (US) sequence, and update it accordingly.
2940             estimatedValue = mSlicerManagers[i]->GetFusionSequenceCorrespondances()[ value ];
2941             //TODO: at the moment, there is a loop in TSlice modifications
2942             //modifying sequence 1 causes seq 2 to update, which in turns update seq1...
2943             //I disable control on seq1 at the moment.
2944             //overlayPanel->updateFusionSequenceSliderValueFromWindow(estimatedValue, true);
2945           }
2946         }
2947       }
2948
2949       for (int j = 0; j < 4; j++) {
2950         mSlicerManagers[i]->SetTSliceInSlicer(value,j);
2951       }
2952       mSlicerManagers[i]->GetSlicer(slicer_index)->Render();
2953       break;
2954     }
2955   }
2956 }
2957 //------------------------------------------------------------------------------
2958
2959
2960 //------------------------------------------------------------------------------
2961 void vvMainWindow::NOHorizontalSliderMoved()
2962 {
2963   // if (mCurrentTime == NOHorizontalSlider->value()) return;
2964   HorizontalSliderMoved(NOHorizontalSlider->value(),COLUMN_UL_VIEW,0);
2965   //  mCurrentTime = NOHorizontalSlider->value();
2966 }
2967 //------------------------------------------------------------------------------
2968
2969
2970 //------------------------------------------------------------------------------
2971 void vvMainWindow::NEHorizontalSliderMoved()
2972 {
2973   // if (mCurrentTime == NEHorizontalSlider->value()) return;
2974   HorizontalSliderMoved(NEHorizontalSlider->value(),COLUMN_UR_VIEW,1);
2975   //  mCurrentTime = NEHorizontalSlider->value();
2976 }
2977 //------------------------------------------------------------------------------
2978
2979
2980 //------------------------------------------------------------------------------
2981 void vvMainWindow::SOHorizontalSliderMoved()
2982 {
2983   // if (mCurrentTime == SOHorizontalSlider->value()) return;
2984   HorizontalSliderMoved(SOHorizontalSlider->value(),COLUMN_DL_VIEW,2);
2985   // mCurrentTime = SOHorizontalSlider->value();
2986 }
2987 //------------------------------------------------------------------------------
2988
2989
2990 //------------------------------------------------------------------------------
2991 void vvMainWindow::SEHorizontalSliderMoved()
2992 {
2993   // if (mCurrentTime == SEHorizontalSlider->value()) return;
2994   HorizontalSliderMoved(SEHorizontalSlider->value(),COLUMN_DR_VIEW,3);
2995   // mCurrentTime = SEHorizontalSlider->value();
2996 }
2997 //------------------------------------------------------------------------------
2998
2999 //------------------------------------------------------------------------------
3000 void vvMainWindow::NOVerticalSliderChanged()
3001 {
3002   static int value=-1;
3003   if (value == NOVerticalSlider->value()) return;
3004   else value = NOVerticalSlider->value();
3005   //  int value = NOVerticalSlider->value();
3006   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
3007     if (DataTree->topLevelItem(i)->data(COLUMN_UL_VIEW,Qt::CheckStateRole).toInt() > 1) {
3008       if (mSlicerManagers[i]->GetSlicer(0)->GetSlice() != value) {
3009         mSlicerManagers[i]->GetSlicer(0)->SetSlice(value);
3010         mSlicerManagers[i]->VerticalSliderHasChanged(0, value);
3011
3012         // If nor Update/Render -> slider not work
3013         // only render = ok navigation, but for contour Update needed but slower ?
3014
3015         mSlicerManagers[i]->UpdateSlice(0);  // <-- DS add this. Not too much update ? YES. but needed for ImageContour ...
3016         //mSlicerManagers[i]->GetSlicer(0)->Render(); // <-- DS add this, needed for contour, seems ok ? not too slow ?
3017       }
3018       break;
3019     }
3020   }
3021 }
3022 //------------------------------------------------------------------------------
3023
3024
3025 //------------------------------------------------------------------------------
3026 void vvMainWindow::NEVerticalSliderChanged()
3027 {
3028   static int value=-1;
3029   if (value == NEVerticalSlider->value()) return;
3030   else value = NEVerticalSlider->value();
3031   //  int value = NEVerticalSlider->value();
3032   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
3033     if (DataTree->topLevelItem(i)->data(COLUMN_UR_VIEW,Qt::CheckStateRole).toInt() > 1) {
3034       if (mSlicerManagers[i]->GetSlicer(1)->GetSlice() != value) {
3035         mSlicerManagers[i]->GetSlicer(1)->SetSlice(value);
3036         mSlicerManagers[i]->VerticalSliderHasChanged(1, value);
3037         mSlicerManagers[i]->UpdateSlice(1);
3038         //mSlicerManagers[i]->GetSlicer(1)->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::SOVerticalSliderChanged()
3049 {
3050   static int value=-1;
3051   if (value == SOVerticalSlider->value()) return;
3052   else value = SOVerticalSlider->value();
3053   //int value = SOVerticalSlider->value();
3054   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
3055     if (DataTree->topLevelItem(i)->data(COLUMN_DL_VIEW,Qt::CheckStateRole).toInt() > 1) {
3056       if (mSlicerManagers[i]->GetSlicer(2)->GetSlice() != value) {
3057         mSlicerManagers[i]->GetSlicer(2)->SetSlice(value);
3058         mSlicerManagers[i]->VerticalSliderHasChanged(2, value);
3059         mSlicerManagers[i]->UpdateSlice(2);
3060         //mSlicerManagers[i]->GetSlicer(2)->Render(); // <-- DS add this, needed for contour, seems ok ? not too slow ?
3061       }
3062       // else { DD("avoid SOVerticalSlider slicer update"); }
3063       break;
3064     }
3065   }
3066 }
3067 //------------------------------------------------------------------------------
3068
3069
3070 //------------------------------------------------------------------------------
3071 void vvMainWindow::SEVerticalSliderChanged()
3072 {
3073   static int value=-1;
3074   if (value == SEVerticalSlider->value()) return;
3075   else value = SEVerticalSlider->value();
3076   // int value = SEVerticalSlider->value();
3077   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
3078     if (DataTree->topLevelItem(i)->data(COLUMN_DR_VIEW,Qt::CheckStateRole).toInt() > 1) {
3079       if (mSlicerManagers[i]->GetSlicer(3)->GetSlice() != value) {
3080         mSlicerManagers[i]->GetSlicer(3)->SetSlice(value);
3081         mSlicerManagers[i]->VerticalSliderHasChanged(3, value);
3082         mSlicerManagers[i]->UpdateSlice(3);
3083         //mSlicerManagers[i]->GetSlicer(3)->Render(); // <-- DS add this, needed for contour, seems ok ? not too slow ?
3084       }
3085       break;
3086     }
3087   }
3088 }
3089 //------------------------------------------------------------------------------
3090
3091
3092 //------------------------------------------------------------------------------
3093 void vvMainWindow::UpdateSlice(int slicer, int slice)
3094 {
3095   // DD("vvMainWindow::UpdateSlice");
3096   //   DD(slicer);
3097   //   DD(slice);
3098   if (slicer == 0) {
3099     //    if (slice != NOVerticalSlider->value())
3100     NOVerticalSlider->setValue(slice);
3101   } else {
3102     if (slicer == 1)
3103       NEVerticalSlider->setValue(slice);
3104     else {
3105       if (slicer == 2)
3106         SOVerticalSlider->setValue(slice);
3107       else {
3108         if (slicer == 3)
3109           SEVerticalSlider->setValue(slice);
3110       }
3111     }
3112   }
3113   // DD("vvMainWindow:UpdateSlice END");
3114 }
3115 //------------------------------------------------------------------------------
3116
3117
3118 //------------------------------------------------------------------------------
3119 void vvMainWindow::UpdateTSlice(int slicer, int slice, int code)
3120 {
3121   //FusionSequence: the slider value should be updated for slicers which show the same sequence as requested
3122   bool doUpdate=false;
3123   if (code==-1) doUpdate=true;
3124   else {
3125     for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
3126       if (DataTree->topLevelItem(i)->data(slicer+1,Qt::CheckStateRole).toInt() > 1) {
3127         //i is the active SlicerManager
3128         if (mSlicerManagers[i]->GetFusionSequenceInvolvmentCode()==code) doUpdate=true;
3129         break;
3130       }
3131     }
3132   }
3133   if (!doUpdate) return;
3134
3135   switch (slicer) {
3136   case 0:
3137     if (NOHorizontalSlider->value()==slice) return;
3138     NOHorizontalSlider->setValue(slice);
3139     break;
3140   case 1:
3141     if (NEHorizontalSlider->value()==slice) return;
3142     NEHorizontalSlider->setValue(slice);
3143     break;
3144   case 2:
3145     if (SOHorizontalSlider->value()==slice) return;
3146     SOHorizontalSlider->setValue(slice);
3147     break;
3148   case 3:
3149     if (SEHorizontalSlider->value()==slice) return;
3150     SEHorizontalSlider->setValue(slice);
3151     break;
3152   }
3153 }
3154 //------------------------------------------------------------------------------
3155
3156
3157 //------------------------------------------------------------------------------
3158 void vvMainWindow::UpdateSliceRange(int slicer, int min, int max, int tmin, int tmax)
3159 {
3160   //int position = int((min+max)/2);
3161   int position = mSlicerManagers[mCurrentPickedImageIndex]->GetSlicer(slicer)->GetSlice();
3162   if (slicer == 0) {
3163     NOVerticalSlider->setRange(min,max);
3164     NOHorizontalSlider->setRange(tmin,tmax);
3165     NOVerticalSlider->setValue(position);
3166   } else if (slicer == 1) {
3167     NEVerticalSlider->setRange(min,max);
3168     NEHorizontalSlider->setRange(tmin,tmax);
3169     NEVerticalSlider->setValue(position);
3170   } else if (slicer == 2) {
3171     SOVerticalSlider->setRange(min,max);
3172     SOHorizontalSlider->setRange(tmin,tmax);
3173     SOVerticalSlider->setValue(position);
3174   } else if (slicer == 3) {
3175     SEVerticalSlider->setRange(min,max);
3176     SEHorizontalSlider->setRange(tmin,tmax);
3177     SEVerticalSlider->setValue(position);
3178   }
3179 }
3180 //------------------------------------------------------------------------------
3181
3182
3183 //------------------------------------------------------------------------------
3184 void vvMainWindow::SaveNOScreenshot()
3185 {
3186   SaveScreenshot(NOViewWidget);
3187 }
3188 //------------------------------------------------------------------------------
3189
3190
3191 //------------------------------------------------------------------------------
3192 void vvMainWindow::SaveNEScreenshot()
3193 {
3194   SaveScreenshot(NEViewWidget);
3195 }
3196 //------------------------------------------------------------------------------
3197
3198
3199 //------------------------------------------------------------------------------
3200 void vvMainWindow::SaveSOScreenshot()
3201 {
3202   SaveScreenshot(SOViewWidget);
3203 }
3204 //------------------------------------------------------------------------------
3205
3206
3207 //------------------------------------------------------------------------------
3208 void vvMainWindow::SaveSEScreenshot()
3209 {
3210   SaveScreenshot(SEViewWidget);
3211 }
3212 //------------------------------------------------------------------------------
3213
3214
3215 //------------------------------------------------------------------------------
3216 void vvMainWindow::SaveScreenshotAllSlices()
3217 {
3218   QVTKWidget *widget = NOViewWidget;
3219
3220   int index = 0;// GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
3221   vvSlicerManager * SM = mSlicerManagers[index];
3222   vvImage * image = SM->GetImage();
3223   vvSlicer * slicer = SM->GetSlicer(0);
3224   int orientation = slicer->GetOrientation();
3225   int nbSlices = image->GetSize()[orientation];
3226   vtkSmartPointer<vtkRenderWindow>  renderWindow = widget->GetRenderWindow();
3227
3228   // Select filename base
3229   QString filename = QFileDialog::getSaveFileName(this,
3230     tr("Save As (filename will be completed by slice number)"),
3231     itksys::SystemTools::GetFilenamePath(mSlicerManagers[index]->GetFileName()).c_str(),
3232     "Images( *.png);;Images( *.jpg)");
3233
3234   // Loop on slices
3235   for(int i=0; i<nbSlices; i++) {
3236     // Change the slice
3237     slicer->SetSlice(i); // -> change the slice of the current slicer
3238     SM->UpdateSlice(0); // --> this one emit UpdateSlice
3239     QCoreApplication::flush(); // -> needed to force display of contours
3240
3241     // Screenshot
3242     vtkSmartPointer<vtkWindowToImageFilter> windowToImageFilter = vtkSmartPointer<vtkWindowToImageFilter>::New();
3243     windowToImageFilter->SetInput(renderWindow);
3244     windowToImageFilter->SetMagnification(1);
3245     windowToImageFilter->SetInputBufferTypeToRGBA(); //also record the alpha (transparency) channel
3246     windowToImageFilter->Update();
3247
3248     vtkSmartPointer<vtkPNGWriter> writer = vtkSmartPointer<vtkPNGWriter>::New();
3249     std::string fn = itksys::SystemTools::GetFilenameWithoutLastExtension(filename.toStdString());
3250     std::string num = clitk::toString(i);
3251     if (i<10) num = "0"+num;
3252     if (i<100) num = "0"+num;
3253     if (i<1000) num = "0"+num;
3254
3255     fn = itksys::SystemTools::GetFilenamePath(filename.toStdString()) + "/"+ fn
3256       + "_" + num + itksys::SystemTools::GetFilenameLastExtension(filename.toStdString());
3257     writer->SetFileName(fn.c_str());
3258     writer->SetInput(windowToImageFilter->GetOutput());
3259     writer->Write();
3260   }
3261 }
3262 //------------------------------------------------------------------------------
3263
3264
3265 //------------------------------------------------------------------------------
3266 void vvMainWindow::SaveScreenshot(QVTKWidget *widget)
3267 {
3268   QString Extensions = "Images( *.png);;";
3269   Extensions += "Images( *.jpg);;";
3270   Extensions += "Images( *.bmp);;";
3271   Extensions += "Images( *.tif);;";
3272   Extensions += "Images( *.ppm)";
3273 #if defined(VTK_USE_FFMPEG_ENCODER) || defined(VTK_USE_VIDEO_FOR_WINDOWS)
3274   Extensions += ";;Video( *.avi)";
3275 #endif
3276 #ifdef VTK_USE_MPEG2_ENCODER
3277   Extensions += ";;Video( *.mpg)";
3278 #endif
3279 #ifdef CLITK_EXPERIMENTAL
3280   Extensions += ";;Video( *.gif)";
3281 #endif
3282
3283   int smIndex=GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
3284   QString fileName = QFileDialog::getSaveFileName(this,
3285     tr("Save As"),
3286     itksys::SystemTools::GetFilenamePath(mSlicerManagers[smIndex]->GetFileName()).c_str(),
3287     Extensions);
3288
3289   if (!fileName.isEmpty()) {
3290     vtkSmartPointer<vtkWindowToImageFilter> w2i = vtkSmartPointer<vtkWindowToImageFilter>::New();
3291     w2i->SetInput(widget->GetRenderWindow());
3292     w2i->Update();
3293     vtkImageData *image = w2i->GetOutput();
3294
3295     std::string ext(itksys::SystemTools::GetFilenameLastExtension(fileName.toStdString()));
3296
3297     // Image
3298     vtkImageWriter *imgwriter = NULL;
3299     if (ext==".bmp")
3300       imgwriter = vtkBMPWriter::New();
3301     else if (ext==".tif")
3302       imgwriter = vtkTIFFWriter::New();
3303     else if (ext==".ppm")
3304       imgwriter = vtkPNMWriter::New();
3305     else if (ext==".png")
3306       imgwriter = vtkPNGWriter::New();
3307     else if (ext==".jpg")
3308       imgwriter = vtkJPEGWriter::New();
3309
3310     // Snapshot image if not null
3311     if(imgwriter!=NULL) {
3312       imgwriter->SetInput(image);
3313       imgwriter->SetFileName(fileName.toStdString().c_str());
3314       imgwriter->Write();
3315       return;
3316     }
3317
3318     // Video
3319     vtkGenericMovieWriter *vidwriter = NULL;
3320 #if CLITK_EXPERIMENTAL == 1
3321     if (ext==".gif") {
3322       vvAnimatedGIFWriter *gif = vvAnimatedGIFWriter::New();
3323       vidwriter = gif;
3324
3325       // FPS
3326       bool ok;
3327       int fps = QInputDialog::getInteger(this, tr("Number of frames per second"),
3328         tr("FPS:"), 5, 0, 1000, 1, &ok);
3329       if(ok)
3330         gif->SetRate(fps);
3331
3332       // Loops
3333       int loops = QInputDialog::getInteger(this, tr("Loops"),
3334         tr("Number of loops (0 means infinite):"), 0, 0, 1000000000, 1, &ok);
3335       if(ok)
3336         gif->SetLoops(loops);
3337
3338       // Dithering
3339       QString msg = "Would you like to activate dithering?";
3340       QMessageBox msgBox(QMessageBox::Question, tr("Dithering"),msg, 0, this);
3341       msgBox.addButton(tr("Yes"), QMessageBox::AcceptRole);
3342       msgBox.addButton(tr("No"), QMessageBox::RejectRole);
3343       gif->SetDither(msgBox.exec() == QMessageBox::AcceptRole);
3344     }
3345 #endif
3346 #ifdef VTK_USE_VIDEO_FOR_WINDOWS
3347     if (ext==".avi") {
3348       vtkAVIWriter *mpg = vtkAVIWriter::New();
3349       vidwriter = mpg;
3350       mpg->SetQuality(2);
3351       bool ok;
3352       int fps = QInputDialog::getInteger(this, tr("Number of frames per second"),
3353         tr("FPS:"), 5, 0, 1024, 1, &ok);
3354       if(!ok)
3355         fps = 5;
3356       mpg->SetRate(fps);
3357     }
3358 #endif
3359 #ifdef VTK_USE_FFMPEG_ENCODER
3360     if (ext==".avi") {
3361       vtkFFMPEGWriter *mpg = vtkFFMPEGWriter::New();
3362       vidwriter = mpg;
3363       mpg->SetQuality(2);
3364       bool ok;
3365       int fps = QInputDialog::getInteger(this, tr("Number of frames per second"),
3366         tr("FPS:"), 5, 0, 1024, 1, &ok);
3367       if(!ok)
3368         fps = 5;
3369       mpg->SetRate(fps);
3370       mpg->SetBitRateTolerance(int(ceil(12.0*1024*1024/fps)));
3371     }
3372 #endif
3373 #ifdef VTK_USE_MPEG2_ENCODER
3374     if (ext==".mpg") {
3375       vtkMPEG2Writer *mpg = vtkMPEG2Writer::New();
3376       vidwriter = mpg;
3377     }
3378 #endif
3379
3380     // Take video if not null
3381     if(vidwriter!=NULL){
3382       vidwriter->SetInput(image);
3383       vidwriter->SetFileName(fileName.toStdString().c_str());
3384       vidwriter->Start();
3385       int nSlice = mSlicerManagers[smIndex]->GetSlicer(0)->GetTMax();
3386       for(int i=0; i<=nSlice; i++) {
3387         mSlicerManagers[smIndex]->SetNextTSlice(0);
3388         vtkSmartPointer<vtkWindowToImageFilter> w2i = vtkSmartPointer<vtkWindowToImageFilter>::New();
3389         w2i->SetInput(widget->GetRenderWindow());
3390         w2i->Update();
3391         vidwriter->SetInput(w2i->GetOutput());
3392         vidwriter->Write();
3393       }
3394       vidwriter->End();
3395       vidwriter->Delete();
3396       return;
3397     }
3398
3399     QMessageBox::information(this,tr("Problem saving screenshot !"),tr("Cannot save image.\nPlease set a file extension !!!"));
3400   }
3401 }
3402 //------------------------------------------------------------------------------
3403
3404
3405 //------------------------------------------------------------------------------
3406 void vvMainWindow::GoToCursor()
3407 {
3408   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
3409   for (int column = 1; column < 5; column++) {
3410     if (DataTree->selectedItems()[0]->data(column,Qt::CheckStateRole).toInt() > 1) {
3411       double* cursorPos = mSlicerManagers[index]->GetSlicer(column-1)->GetCursorPosition();
3412       mSlicerManagers[index]->GetSlicer(column-1)->SetCurrentPosition(
3413         cursorPos[0],cursorPos[1],cursorPos[2],cursorPos[3]);
3414       mSlicerManagers[index]->UpdateViews(1,column-1);
3415       mSlicerManagers[index]->UpdateLinked(column-1);
3416       break;
3417     }
3418   }
3419 }
3420 //------------------------------------------------------------------------------
3421
3422 //------------------------------------------------------------------------------
3423 void vvMainWindow::GoToLandmark()
3424 {
3425   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
3426   for (int column = 1; column < 5; column++) {
3427     if (DataTree->selectedItems()[0]->data(column,Qt::CheckStateRole).toInt() > 1) {
3428       double* cursorPos = landmarksPanel->GetSelectedPoint();
3429       mSlicerManagers[index]->GetSlicer(column-1)->SetCurrentPosition(
3430         cursorPos[0],cursorPos[1],cursorPos[2],cursorPos[3]);
3431       mSlicerManagers[index]->UpdateViews(1,column-1);
3432       mSlicerManagers[index]->UpdateLinked(column-1);
3433       break;
3434     }
3435   }
3436 }
3437 //------------------------------------------------------------------------------
3438
3439 //------------------------------------------------------------------------------
3440 void vvMainWindow::PlayPause()
3441 {
3442   if (playMode) {
3443     playMode = 0;
3444     playButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/player_play.png")));
3445     ImageInfoChanged();
3446     return;
3447   } else {
3448     int image_number=DataTree->topLevelItemCount();
3449     bool has_temporal;
3450     for (int i=0; i<image_number; i++)
3451       if (mSlicerManagers[i]->GetSlicer(0)->GetTMax() > 0) {
3452         has_temporal=true;
3453         break;
3454       }
3455       if (has_temporal) {
3456         playMode = 1;
3457         playButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/player_pause.png")));
3458         QTimer::singleShot(1000/mFrameRate, this, SLOT(PlayNext()));
3459       }
3460   }
3461 }
3462 //------------------------------------------------------------------------------
3463
3464 //------------------------------------------------------------------------------
3465 void vvMainWindow::PlayNext()
3466 {
3467   if (playMode && !this->isHidden()) {
3468     int image_number=DataTree->topLevelItemCount();
3469     ///Only play one slicer per SM, and only if the SM is being displayed
3470     for (int i=0; i<image_number; i++)
3471       for (int j=0; j<4; j++)
3472         if (mSlicerManagers[i]->GetSlicer(0)->GetTMax() > 0 &&
3473           DataTree->topLevelItem(i)->data(j+1,Qt::CheckStateRole).toInt() > 0) {
3474             mSlicerManagers[i]->SetNextTSlice(j);
3475             break;
3476         }
3477         QTimer::singleShot(1000/mFrameRate, this, SLOT(PlayNext()));
3478   }
3479 }
3480 //------------------------------------------------------------------------------
3481
3482 void vvMainWindow::ShowLastImage()
3483 {
3484   if (mSlicerManagers.size() > 1) {
3485     QTreeWidgetItem * item=DataTree->topLevelItem(DataTree->topLevelItemCount()-1);
3486     CurrentImageChanged(mSlicerManagers.back()->GetId()); //select new image
3487     item->setData(1,Qt::CheckStateRole,2); //show the new image in the first panel
3488     DisplayChanged(item,1);
3489   }
3490 }
3491
3492 //------------------------------------------------------------------------------
3493 void vvMainWindow::UpdateRenderWindows()
3494 {
3495   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
3496     mSlicerManagers[i]->GetSlicer(0)->UpdateLandmarks();
3497     mSlicerManagers[i]->GetSlicer(1)->UpdateLandmarks();
3498     mSlicerManagers[i]->GetSlicer(2)->UpdateLandmarks();
3499     mSlicerManagers[i]->GetSlicer(3)->UpdateLandmarks();
3500   }
3501   if (NOViewWidget->GetRenderWindow()) NOViewWidget->GetRenderWindow()->Render();
3502   if (NEViewWidget->GetRenderWindow()) NEViewWidget->GetRenderWindow()->Render();
3503   if (SOViewWidget->GetRenderWindow()) SOViewWidget->GetRenderWindow()->Render();
3504   if (SEViewWidget->GetRenderWindow()) SEViewWidget->GetRenderWindow()->Render();
3505 }
3506 //------------------------------------------------------------------------------
3507
3508 //------------------------------------------------------------------------------
3509 void vvMainWindow::SegmentationOnCurrentImage()
3510 {
3511   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
3512
3513   vvSegmentationDialog segmentation;
3514   segmentation.SetImage(mSlicerManagers[index]->GetSlicer(0)->GetImage());
3515   segmentation.exec();
3516 }
3517 //------------------------------------------------------------------------------
3518
3519 void vvMainWindow::SurfaceViewerLaunch()
3520 {
3521   vvSurfaceViewerDialog surfaceViewer;
3522   surfaceViewer.exec();
3523 }
3524 //------------------------------------------------------------------------------
3525
3526
3527 //------------------------------------------------------------------------------
3528 int vvMainWindow::GetImageDuplicateFilenameNumber(std::string filename)
3529 {
3530   int number=0;
3531   for(unsigned int l=0; l<mSlicerManagers.size(); l++) {
3532     vvSlicerManager * v = mSlicerManagers[l];
3533     if (v->GetBaseFileName() ==
3534       vtksys::SystemTools::GetFilenameName(vtksys::SystemTools::GetFilenameWithoutLastExtension(filename))) {
3535         number = std::max(number, v->GetBaseFileNameNumber()+1);
3536     }
3537   }
3538   return number;
3539 }
3540 //------------------------------------------------------------------------------
3541
3542
3543 //------------------------------------------------------------------------------
3544 vvSlicerManager* vvMainWindow::AddImage(vvImage::Pointer image,std::string filename)
3545 {
3546   // Change filename if another image exist with the same name
3547   int number = GetImageDuplicateFilenameNumber(filename);
3548
3549   // Create new SliceManager
3550   vvSlicerManager* slicer_manager = new vvSlicerManager(4);
3551   slicer_manager->SetImage(image);//, IMAGE, number);
3552   //  filename = filename+"_"+clitk::toString(number);
3553   slicer_manager->SetFilename(filename, number);
3554   mSlicerManagers.push_back(slicer_manager);
3555
3556   //create an item in the tree with good settings
3557   QTreeWidgetItem *item = new QTreeWidgetItem();
3558   item->setData(0,Qt::UserRole,slicer_manager->GetFileName().c_str());//files[i].c_str());
3559   item->setData(1,Qt::UserRole,tr("image"));
3560   item->setData(COLUMN_IMAGE_NAME,Qt::DisplayRole,slicer_manager->GetFileName().c_str());//filename.c_str());
3561   qApp->processEvents();
3562
3563   for (int j = 1; j <= 4; j++) item->setData(j,Qt::CheckStateRole,1);
3564
3565   //Create the buttons for reload and close
3566   qApp->processEvents();
3567   QTreePushButton* cButton = new QTreePushButton;
3568   cButton->setItem(item);
3569   cButton->setColumn(COLUMN_CLOSE_IMAGE);
3570   cButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/exit.png")));
3571   connect(cButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
3572     this,SLOT(CloseImage(QTreeWidgetItem*, int)));
3573
3574   QTreePushButton* rButton = new QTreePushButton;
3575   rButton->setItem(item);
3576   rButton->setColumn(COLUMN_RELOAD_IMAGE);
3577   rButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/rotateright.png")));
3578   rButton->setEnabled(0);
3579   connect(rButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
3580     this,SLOT(ReloadImage(QTreeWidgetItem*, int)));
3581
3582   DataTree->addTopLevelItem(item);
3583   DataTree->setItemWidget(item, COLUMN_CLOSE_IMAGE, cButton);
3584   DataTree->setItemWidget(item, COLUMN_RELOAD_IMAGE, rButton);
3585
3586   //set the id of the image
3587   QString id = QDir::current().absoluteFilePath(slicer_manager->GetFileName().c_str()) + QString::number(mSlicerManagers.size()-1);
3588   item->setData(COLUMN_IMAGE_NAME,Qt::UserRole,id.toStdString().c_str());
3589   mSlicerManagers.back()->SetId(id.toStdString());
3590
3591   linkPanel->addImage(slicer_manager->GetFileName().c_str()// filename
3592     , id.toStdString());
3593
3594   connect(mSlicerManagers.back(), SIGNAL(currentImageChanged(std::string)),
3595     this, SLOT(CurrentImageChanged(std::string)));
3596   connect(mSlicerManagers.back(), SIGNAL(currentPickedImageChanged(std::string)),
3597     this, SLOT(CurrentPickedImageChanged(std::string)));
3598   connect(mSlicerManagers.back(), SIGNAL(UpdatePosition(int, double, double, double, double, double, double, double)),
3599     this, SLOT(MousePositionChanged(int,double, double, double, double, double, double, double)));
3600   connect(mSlicerManagers.back(), SIGNAL(UpdateVector(int, double, double, double, double)),
3601     this, SLOT(VectorChanged(int,double,double,double, double)));
3602   connect(mSlicerManagers.back(), SIGNAL(UpdateOverlay(int, double, double)),
3603     this, SLOT(OverlayChanged(int,double,double)));
3604   connect(mSlicerManagers.back(), SIGNAL(UpdateFusion(int, double)),
3605     this, SLOT(FusionChanged(int,double)));
3606   //connect(mSlicerManagers.back(), SIGNAL(UpdateFusionSequence(int, bool, unsigned int)),
3607   //  this, SLOT(FusionSequenceChanged(int, bool, unsigned int)));
3608   connect(mSlicerManagers.back(), SIGNAL(WindowLevelChanged()),
3609     this,SLOT(WindowLevelChanged()));
3610   connect(mSlicerManagers.back(), SIGNAL(UpdateSlice(int,int)),
3611     this,SLOT(UpdateSlice(int,int)));
3612   connect(mSlicerManagers.back(), SIGNAL(UpdateTSlice(int, int, int)),
3613     this,SLOT(UpdateTSlice(int, int, int)));
3614   connect(mSlicerManagers.back(), SIGNAL(UpdateTSlice(int, int, int)),
3615     this,SLOT(ImageInfoChanged()));
3616   connect(mSlicerManagers.back(), SIGNAL(UpdateSliceRange(int,int,int,int,int)),
3617     this,SLOT(UpdateSliceRange(int,int,int,int,int)));
3618   connect(mSlicerManagers.back(), SIGNAL(UpdateLinkManager(std::string,int,double,double,double,int)),
3619     this,SLOT(UpdateLinkManager(std::string,int,double,double,double,int)));
3620   connect(mSlicerManagers.back(), SIGNAL(UpdateLinkedNavigation(std::string,vvSlicerManager*,vvSlicer*)),
3621     this,SLOT(UpdateLinkedNavigation(std::string,vvSlicerManager*,vvSlicer*)));
3622   connect(mSlicerManagers.back(), SIGNAL(ChangeImageWithIndexOffset(vvSlicerManager*,int,int)),
3623     this,SLOT(ChangeImageWithIndexOffset(vvSlicerManager*,int,int)));
3624   connect(mSlicerManagers.back(), SIGNAL(LandmarkAdded()),landmarksPanel,SLOT(AddPoint()));
3625
3626
3627   UpdateTree();
3628   qApp->processEvents();
3629   InitSlicers();
3630   ShowLastImage();
3631   InitDisplay();
3632   qApp->processEvents();
3633
3634   // End
3635   ImageInfoChanged();
3636   return slicer_manager;
3637 }
3638 //------------------------------------------------------------------------------
3639
3640
3641 //------------------------------------------------------------------------------
3642 void vvMainWindow::UpdateCurrentSlicer()
3643 {
3644   int index = -1;
3645   if (DataTree->selectedItems().size() > 0) {
3646     index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
3647   }
3648   mSlicerManagerCurrentIndex = index;
3649 }
3650 //------------------------------------------------------------------------------
3651