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 <sstream>
  92 #include <iomanip>
  93
  94 #define COLUMN_TREE 0
  95 #define COLUMN_UL_VIEW 1
  96 #define COLUMN_UR_VIEW 2
  97 #define COLUMN_DL_VIEW 3
  98 #define COLUMN_DR_VIEW 4
  99 #define COLUMN_CLOSE_IMAGE 5
 100 #define COLUMN_RELOAD_IMAGE 6
 101 #define COLUMN_IMAGE_NAME 7
 102
 103 #ifdef CLITK_PRIVATE_FEATURES
 104 #define EXTENSIONS "Images ( *.bmp *.png *.jpeg *.jpg *.tif *.mhd *.mha *.hdr *.vox *.his *.xdr *.SCAN *.nii *.nrrd *.nhdr *.refscan *.nii.gz *.usf)"
 105 #else
 106 #define EXTENSIONS "Images ( *.bmp *.png *.jpeg *.jpg *.tif *.mhd *.mha *.hdr *.vox *.his *.xdr *.SCAN *.nii *.nrrd *.nhdr *.refscan *.nii.gz)"
 107 #endif
 108
 109
 110 /*Data Tree values
 111   0,Qt::UserRole full filename
 112   1,Qt::CheckStateRole checkbutton UL View
 113   1,Qt::UserRole overlay, fusion or vector
 114   2,Qt::CheckStateRole checkbutton UR View
 115   3,Qt::CheckStateRole checkbutton DL View
 116   4,Qt::CheckStateRole checkbutton DR View
 117   5,0  short filename
 118   5,Qt::UserRole mSlicerManager id*/
 119
 120 //------------------------------------------------------------------------------
 121 vvMainWindow::vvMainWindow():vvMainWindowBase()
 122 {
 123   setupUi(this); // this sets up the GUI
 124
 125   mInputPathName = "";
 126   mMenuTools = menuTools;
 127   //  mMenuSegmentation = menuSegmentation;
 128   mContextMenu = &contextMenu;
 129   mMenuExperimentalTools = menuExperimental;
 130   mMainWidget = this;
 131   mCurrentTime = -1;
 132   mCurrentSelectedImageId = "";
 133   mCurrentPickedImageId = "";
 134   mCurrentPickedImageIndex = 0;
 135
 136   //Init the contextMenu
 137   this->setContextMenuPolicy(Qt::CustomContextMenu);
 138   contextActions.resize(0);
 139   QAction* actionOpen_new_image = contextMenu.addAction(QIcon(QString::fromUtf8(":/common/icons/fileopen.png")),
 140                                   tr("O&pen new Image"));
 141   actionOpen_new_image->setShortcut(QKeySequence(tr("Ctrl+O")));
 142   connect(actionOpen_new_image,SIGNAL(triggered()),this,SLOT(OpenImages()));
 143   contextActions.push_back(actionOpen_new_image);
 144   contextMenu.addSeparator();
 145
 146   QAction* actionClose_Image = contextMenu.addAction(QIcon(QString::fromUtf8(":/common/icons/exit.png")),
 147                                tr("Close Current Image"));
 148   connect(actionClose_Image,SIGNAL(triggered()),this,SLOT(CloseImage()));
 149   contextActions.push_back(actionClose_Image);
 150
 151   QAction* actionReload_image = contextMenu.addAction(QIcon(QString::fromUtf8(":/common/icons/rotateright.png")),
 152                                 tr("Reload Current Image"));
 153   connect(actionReload_image,SIGNAL(triggered()),this,SLOT(ReloadImage()));
 154   contextActions.push_back(actionReload_image);
 155
 156   QAction* actionSave_image = contextMenu.addAction(QIcon(QString::fromUtf8(":/common/icons/filesave.png")),
 157                               tr("Save Current Image"));
 158   connect(actionSave_image,SIGNAL(triggered()),this,SLOT(SaveAs()));
 159   contextActions.push_back(actionSave_image);
 160
 161   QAction* actionSave_state = contextMenu.addAction(QIcon(QString::fromUtf8(":/common/icons/filesave.png")),
 162                               tr("Save Current State"));
 163   connect(actionSave_state,SIGNAL(triggered()),this,SLOT(SaveCurrentState()));
 164   contextActions.push_back(actionSave_state);
 165
 166   QAction* actionRead_state = contextMenu.addAction(QIcon(QString::fromUtf8(":/common/icons/filesave.png")),
 167                               tr("Read Saved State"));
 168   connect(actionRead_state,SIGNAL(triggered()),this,SLOT(ReadSavedState()));
 169   contextActions.push_back(actionRead_state);
 170
 171   contextMenu.addSeparator();
 172
 173   contextMenu.addAction(actionAdd_VF_to_current_Image);
 174   contextActions.push_back(actionAdd_VF_to_current_Image);
 175
 176   //QAction* actionAdd_Overlay_to_current_Image = menuOverlay->addAction(QIcon(QString::fromUtf8(":/common/icons/GPSup.png")),
 177   //    tr("Add overlay image to current image"));
 178   contextMenu.addAction(actionAdd_overlay_image_to_current_image);
 179   contextActions.push_back(actionAdd_overlay_image_to_current_image);
 180
 181   contextMenu.addAction(actionAdd_fusion_image);
 182   contextActions.push_back(actionAdd_fusion_image);
 183
 184   contextMenu.addSeparator();
 185   QAction* actionResetMatrix = contextMenu.addAction(QIcon(QString::fromUtf8(":/common/icons/identity.png")),
 186                                                       tr("Reset transformation to identity"));
 187   connect(actionResetMatrix, SIGNAL(triggered()), this,SLOT(ResetTransformationToIdentity()));
 188
 189   // TRIAL DS
 190   /*
 191   QMenu * m = new QMenu(menubar);
 192   m->setTitle("TOTO");
 193   //  m->setObjectName(QString::fromUtf8("TOTOTO"));
 194   contextMenu.addMenu(m);
 195   QAction * a = m->addAction(QIcon(QString::fromUtf8(":/common/icons/GPSup.png")),
 196                      tr("BIDON"));
 197   QAction * b = m->addAction(QIcon(QString::fromUtf8(":/common/icons/GPSup.png")),
 198                      tr("BIDON2"));
 199   m->addAction(a);
 200   m->addAction(b);
 201   connect(a,SIGNAL(triggered()),this,SLOT(AddFusionImage()));
 202   */
 203
 204   //init the DataTree
 205   mSlicerManagers.resize(0);
 206
 207   QStringList header;
 208   header.append("");
 209   header.append("TL");
 210   header.append("TR");
 211   header.append("BL");
 212   header.append("BR");
 213   header.append("");
 214   header.append("");
 215   header.append("Name");
 216
 217   DataTree->setHeaderLabels(header);
 218   DataTree->resizeColumnToContents(COLUMN_TREE);
 219   DataTree->resizeColumnToContents(COLUMN_UL_VIEW);
 220   DataTree->resizeColumnToContents(COLUMN_UR_VIEW);
 221   DataTree->resizeColumnToContents(COLUMN_DL_VIEW);
 222   DataTree->resizeColumnToContents(COLUMN_DR_VIEW);
 223   DataTree->resizeColumnToContents(COLUMN_CLOSE_IMAGE);
 224   DataTree->resizeColumnToContents(COLUMN_RELOAD_IMAGE);
 225   DataTree->resizeColumnToContents(COLUMN_IMAGE_NAME);
 226
 227   viewMode = 1;
 228   documentation = new vvDocumentation();
 229   help_dialog = new vvHelpDialog();
 230   dicomSeriesSelector = new vvDicomSeriesSelector();
 231
 232   inverseButton->setEnabled(0);
 233   actionAdd_overlay_image_to_current_image->setEnabled(0);
 234   actionSave_As->setEnabled(0);
 235   actionAdd_VF_to_current_Image->setEnabled(0);
 236   actionAdd_fusion_image->setEnabled(0);
 237
 238   //init the sliders
 239   verticalSliders.push_back(NOVerticalSlider);
 240   verticalSliders.push_back(NEVerticalSlider);
 241   verticalSliders.push_back(SOVerticalSlider);
 242   verticalSliders.push_back(SEVerticalSlider);
 243
 244   for (int i =0; i < 4; i++)
 245     verticalSliders[i]->hide();
 246
 247   horizontalSliders.push_back(NOHorizontalSlider);
 248   horizontalSliders.push_back(NEHorizontalSlider);
 249   horizontalSliders.push_back(SOHorizontalSlider);
 250   horizontalSliders.push_back(SEHorizontalSlider);
 251
 252   for (int i =0; i < 4; i++)
 253     horizontalSliders[i]->hide();
 254
 255
 256   connect(NOVerticalSlider,SIGNAL(valueChanged(int)),this,SLOT(NOVerticalSliderChanged()));
 257   connect(NEVerticalSlider,SIGNAL(valueChanged(int)),this,SLOT(NEVerticalSliderChanged()));
 258   connect(SOVerticalSlider,SIGNAL(valueChanged(int)),this,SLOT(SOVerticalSliderChanged()));
 259   connect(SEVerticalSlider,SIGNAL(valueChanged(int)),this,SLOT(SEVerticalSliderChanged()));
 260
 261   connect(NOHorizontalSlider,SIGNAL(valueChanged(int)),this,SLOT(NOHorizontalSliderMoved()));
 262   connect(NEHorizontalSlider,SIGNAL(valueChanged(int)),this,SLOT(NEHorizontalSliderMoved()));
 263   connect(SOHorizontalSlider,SIGNAL(valueChanged(int)),this,SLOT(SOHorizontalSliderMoved()));
 264   connect(SEHorizontalSlider,SIGNAL(valueChanged(int)),this,SLOT(SEHorizontalSliderMoved()));
 265
 266   //connect everything
 267   connect(actionCompute_mid_position_image,SIGNAL(triggered()),this,SLOT(ComputeMidPosition()));
 268   connect(actionDeformable_Registration,SIGNAL(triggered()),this,SLOT(ComputeDeformableRegistration()));
 269   connect(actionWarp_image_with_vector_field,SIGNAL(triggered()),this,SLOT(WarpImage()));
 270   connect(actionLoad_images,SIGNAL(triggered()),this,SLOT(OpenImages()));
 271   connect(actionOpen_Dicom,SIGNAL(triggered()),this,SLOT(OpenDicom()));
 272   connect(actionOpen_Dicom_Struct,SIGNAL(triggered()),this,SLOT(OpenDCStructContour()));
 273   connect(actionOpen_VTK_contour,SIGNAL(triggered()),this,SLOT(OpenVTKContour()));
 274   connect(actionOpen_Multiple_Images_As_One,SIGNAL(triggered()),this,SLOT(MergeImages()));
 275   connect(actionSlice_Image_As_Multiple_Images,SIGNAL(triggered()),this,SLOT(SliceImages()));
 276   connect(actionOpen_Image_With_Time,SIGNAL(triggered()),this,SLOT(OpenImageWithTime()));
 277   connect(actionMerge_images_as_n_dim_t, SIGNAL(triggered()), this, SLOT(MergeImagesWithTime()));
 278   connect(actionSave_As,SIGNAL(triggered()),this,SLOT(SaveAs()));
 279   connect(actionSave_current_state,SIGNAL(triggered()),this,SLOT(SaveCurrentState()));
 280   connect(actionRead_saved_state,SIGNAL(triggered()),this,SLOT(ReadSavedState()));
 281   connect(actionExit,SIGNAL(triggered()),this,SLOT(close()));
 282   connect(actionAdd_VF_to_current_Image,SIGNAL(triggered()),this,SLOT(OpenField()));
 283   connect(actionAdd_fusion_image,SIGNAL(triggered()),this,SLOT(SelectFusionImage()));
 284   connect(actionAdd_overlay_image_to_current_image,SIGNAL(triggered()), this,SLOT(SelectOverlayImage()));  connect(actionNavigation_Help,SIGNAL(triggered()),this,SLOT(ShowHelpDialog()));
 285   connect(actionDocumentation,SIGNAL(triggered()),this,SLOT(ShowDocumentation()));
 286   connect(actionRegister_vv,SIGNAL(triggered()),this,SLOT(PopupRegisterForm()));
 287
 288   ///////////////////////////////////////////////
 289   connect(actionSegmentation,SIGNAL(triggered()),this,SLOT(SegmentationOnCurrentImage()));
 290   connect(actionSurface_Viewer,SIGNAL(triggered()),this,SLOT(SurfaceViewerLaunch()));
 291   ///////////////////////////////////////////////
 292
 293   actionNorth_East_Window->setEnabled(0);
 294   actionNorth_West_Window->setEnabled(0);
 295   actionSouth_East_Window->setEnabled(0);
 296   actionSouth_West_Window->setEnabled(0);
 297
 298   connect(actionNorth_East_Window,SIGNAL(triggered()),this,SLOT(SaveNEScreenshot()));
 299   connect(actionNorth_West_Window,SIGNAL(triggered()),this,SLOT(SaveNOScreenshot()));
 300   connect(actionSouth_East_Window,SIGNAL(triggered()),this,SLOT(SaveSEScreenshot()));
 301   connect(actionSouth_West_Window,SIGNAL(triggered()),this,SLOT(SaveSOScreenshot()));
 302   connect(actionSave_all_slices,SIGNAL(triggered()),this,SLOT(SaveScreenshotAllSlices()));
 303
 304   connect(DataTree,SIGNAL(itemSelectionChanged()),this,SLOT(ImageInfoChanged()));
 305   connect(DataTree,SIGNAL(itemClicked(QTreeWidgetItem*, int)),this,
 306           SLOT(DisplayChanged(QTreeWidgetItem*, int)));
 307
 308   connect(viewButton,SIGNAL(clicked()),this, SLOT(ChangeViewMode()) );
 309   connect(windowSpinBox,SIGNAL(editingFinished()),this,SLOT(WindowLevelEdited()));
 310   connect(levelSpinBox,SIGNAL(editingFinished()),this,SLOT(WindowLevelEdited()));
 311   connect(colorMapComboBox,SIGNAL(currentIndexChanged(int)),this,SLOT(UpdateColorMap()));
 312   connect(presetComboBox,SIGNAL(currentIndexChanged(int)),this,SLOT(UpdateWindowLevel()));
 313   connect(slicingPresetComboBox, SIGNAL(currentIndexChanged(int)),this,SLOT(UpdateSlicingPreset()));
 314   connect(inverseButton,SIGNAL(clicked()),this,SLOT(SwitchWindowLevel()));
 315   connect(applyWindowLevelToAllButton,SIGNAL(clicked()),this,SLOT(ApplyWindowLevelToAllImages()));
 316
 317   connect(this,SIGNAL(customContextMenuRequested(QPoint)),this,SLOT(ShowContextMenu(QPoint)));
 318
 319   connect(linkPanel,SIGNAL(addLink(QString,QString,bool)),this,SLOT(AddLink(QString,QString,bool)));
 320   connect(linkPanel,SIGNAL(removeLink(QString,QString)),this,SLOT(RemoveLink(QString,QString)));
 321   connect(overlayPanel,SIGNAL(VFPropertyUpdated(int,int,int,int,double,double,double)),this,SLOT(SetVFProperty(int,int,int,int,double,double,double)));
 322   connect(overlayPanel,SIGNAL(OverlayPropertyUpdated(int,int,double,double)),
 323           this,SLOT(SetOverlayProperty(int,int,double,double)));
 324   connect(overlayPanel,SIGNAL(FusionPropertyUpdated(int,int,int,double,double, bool)),
 325           this,SLOT(SetFusionProperty(int,int,int,double,double, bool)));
 326   connect(landmarksPanel,SIGNAL(UpdateRenderWindows()),this,SLOT(UpdateRenderWindows()));
 327
 328   playMode = 0;//pause
 329   mFrameRate = 10;
 330   playButton->setEnabled(0);
 331   frameRateLabel->setEnabled(0);
 332   frameRateSpinBox->setEnabled(0);
 333   connect(playButton, SIGNAL(clicked()),this,SLOT(PlayPause()));
 334   connect(frameRateSpinBox, SIGNAL(valueChanged(int)),this,SLOT(ChangeFrameRate(int)));
 335
 336   goToCursorPushButton->setEnabled(0);
 337   connect(goToCursorPushButton, SIGNAL(clicked()),this,SLOT(GoToCursor()));
 338
 339   NOViewWidget->hide();
 340   NEViewWidget->hide();
 341   SOViewWidget->hide();
 342   SEViewWidget->hide();
 343
 344   //Recently opened files
 345   std::list<std::string> recent_files = GetRecentlyOpenedImages();
 346   recentlyOpenedFilesMenu=NULL;
 347   if ( !recent_files.empty() ) {
 348     createRecentlyOpenedFilesMenu();
 349     updateRecentlyOpenedFilesMenu(recent_files);
 350   }
 351
 352   // Adding all new tools (insertion in the menu)
 353   vvToolManager::GetInstance()->InsertToolsInMenu(this);
 354   vvToolManager::GetInstance()->EnableToolsInMenu(this, false);
 355
 356   if (!CLITK_EXPERIMENTAL)
 357     menuExperimental->menuAction()->setVisible(false);
 358
 359
 360   QTimer * timerMemory = new QTimer(this);
 361   //timerMemory->setInterval(5);
 362   connect(timerMemory, SIGNAL(timeout()), this, SLOT(UpdateMemoryUsage()));
 363   timerMemory->start(2000);
 364 }
 365 //------------------------------------------------------------------------------
 366 void vvMainWindow::show()
 367 {
 368   vvMainWindowBase::show();
 369   PopupRegisterForm(true);
 370 }
 371 //------------------------------------------------------------------------------
 372 void vvMainWindow::UpdateMemoryUsage()
 373 {
 374   //  clitk::PrintMemory(true);
 375   if (clitk::GetMemoryUsageInMb() == 0) infoPanel->setMemoryInMb("NA");
 376   else infoPanel->setMemoryInMb(QString::number(clitk::GetMemoryUsageInMb())+" MiB");
 377 }
 378 //------------------------------------------------------------------------------
 379
 380
 381 //------------------------------------------------------------------------------
 382 void vvMainWindow::createRecentlyOpenedFilesMenu()
 383 {
 384   recentlyOpenedFilesMenu = new QMenu("Recently opened files...");
 385   recentlyOpenedFilesMenu->setIcon(QIcon(QString::fromUtf8(":/common/icons/open.png")));
 386   menuFile->insertMenu(actionOpen_Image_With_Time,recentlyOpenedFilesMenu);
 387   menuFile->insertSeparator(actionOpen_Image_With_Time);
 388 }
 389 //------------------------------------------------------------------------------
 390
 391
 392 //------------------------------------------------------------------------------
 393
 394 void vvMainWindow::updateRecentlyOpenedFilesMenu(const std::list<std::string> &recent_files)
 395 {
 396   if(recentlyOpenedFilesMenu==NULL) {
 397     createRecentlyOpenedFilesMenu();
 398   } else {
 399     recentlyOpenedFilesMenu->clear();
 400   }
 401   for (std::list<std::string>::const_iterator i = recent_files.begin(); i!=recent_files.end(); i++) {
 402     QAction* current=new QAction(QIcon(QString::fromUtf8(":/common/icons/open.png")), i->c_str(),this);
 403     recentlyOpenedFilesMenu->addAction(current);
 404     connect(current,SIGNAL(triggered()),this,SLOT(OpenRecentImage()));
 405   }
 406 }
 407 //------------------------------------------------------------------------------
 408
 409
 410 //------------------------------------------------------------------------------
 411 void vvMainWindow::ComputeMidPosition()
 412 {
 413   bool ok;
 414   int index=GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
 415   int ref = QInputDialog::getInteger(this,"Chose reference phase","Reference phase",0,0,\
 416                                      mSlicerManagers[index]->GetImage()->GetVTKImages().size()-1,1,&ok);
 417   if (ok) {
 418     vvMidPosition midp;
 419     midp.slicer_manager = mSlicerManagers[index];
 420     midp.reference_image_index = ref;
 421     QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
 422     midp.Update();
 423     if (midp.error)
 424       QMessageBox::warning(this, "Error computing midposition image",midp.error_message.c_str());
 425     else {
 426       QFileInfo info(midp.slicer_manager->GetFileName().c_str());
 427       AddImage(midp.output,info.path().toStdString()+"/"+info.completeBaseName().toStdString()+"_midposition.mhd");
 428     }
 429     QApplication::restoreOverrideCursor();
 430   }
 431 }
 432 //------------------------------------------------------------------------------
 433
 434
 435 //------------------------------------------------------------------------------
 436 void vvMainWindow::AddContour(int image_index, vvMesh::Pointer contour, bool propagation)
 437 {
 438   QTreeWidgetItem *item = new QTreeWidgetItem();
 439   item->setData(0,Qt::UserRole,"filename.vtk");
 440   item->setData(1,Qt::UserRole,tr("contour"));
 441   QBrush brush;
 442   brush.setColor(QColor(contour->r*255,contour->g*255,contour->b*255));
 443   brush.setStyle(Qt::SolidPattern);
 444   item->setData(COLUMN_IMAGE_NAME,Qt::BackgroundRole,brush);
 445   item->setData(COLUMN_IMAGE_NAME,Qt::DisplayRole,contour->structure_name.c_str());
 446
 447   for (int j = 1; j <= 4; j++)
 448     item->setData(j,Qt::CheckStateRole,DataTree->topLevelItem(image_index)->data(j,Qt::CheckStateRole));
 449
 450   QTreePushButton* cButton = new QTreePushButton;
 451   cButton->setItem(item);
 452   cButton->setColumn(COLUMN_CLOSE_IMAGE);
 453   cButton->setToolTip(tr("close image"));
 454   cButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/exit.png")));
 455   connect(cButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
 456           this,SLOT(CloseImage(QTreeWidgetItem*, int)));
 457
 458   QTreePushButton* rButton = new QTreePushButton;
 459   rButton->setItem(item);
 460   rButton->setColumn(COLUMN_RELOAD_IMAGE);
 461   rButton->setToolTip(tr("reload image"));
 462   rButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/rotateright.png")));
 463   rButton->setEnabled(false);
 464   //Not implemented
 465   //connect(rButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
 466   //this,SLOT(ReloadImage(QTreeWidgetItem*, int)));
 467
 468   DataTree->topLevelItem(image_index)->setExpanded(1);
 469   DataTree->topLevelItem(image_index)->addChild(item);
 470   DataTree->setItemWidget(item, COLUMN_CLOSE_IMAGE, cButton);
 471   DataTree->setItemWidget(item, COLUMN_RELOAD_IMAGE, rButton);
 472   QString id = DataTree->topLevelItem(image_index)->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString();
 473   item->setData(COLUMN_IMAGE_NAME,Qt::UserRole,id.toStdString().c_str());
 474
 475   UpdateTree();
 476   mSlicerManagers[image_index]->AddContour(contour,propagation);
 477   mSlicerManagers[image_index]->Render();
 478 }
 479 //------------------------------------------------------------------------------
 480
 481
 482 //------------------------------------------------------------------------------
 483 void vvMainWindow::OpenVTKContour()
 484 {
 485   if (mSlicerManagers.size() > 0) {
 486     QString Extensions = "Images ( *.vtk *.obj)";
 487     Extensions += ";;All Files (*)";
 488     QString file = QFileDialog::getOpenFileName(this,tr("Open vtkPolyData"),mInputPathName,Extensions);
 489     if (file.isNull())
 490       return;
 491     QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
 492     int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
 493     vvMeshReader reader;
 494     reader.SetImage(mSlicerManagers[index]->GetImage());
 495     reader.SetModeToVTK();
 496     reader.SetFilename(file.toStdString());
 497     reader.Update();
 498     AddContour(index,reader.GetOutput()[0],false);
 499     QApplication::restoreOverrideCursor();
 500   }
 501 }
 502 //------------------------------------------------------------------------------
 503
 504
 505 //------------------------------------------------------------------------------
 506 void vvMainWindow::AddDCStructContour(int index, QString file)
 507 {
 508     vvMeshReader reader;
 509     reader.SetFilename(file.toStdString());
 510     vvStructSelector selector;
 511     selector.SetStructures(reader.GetROINames());
 512     if (!mSlicerManagers[index]->GetVF().IsNull())
 513       selector.EnablePropagationCheckBox();
 514     if (selector.exec()) {
 515       QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
 516       reader.SetSelectedItems(selector.getSelectedItems());
 517       reader.SetImage(mSlicerManagers[index]->GetImage());
 518       if (selector.PropagationEnabled())
 519         reader.SetPropagationVF(mSlicerManagers[index]->GetVF());
 520       reader.Update();
 521       std::vector<vvMesh::Pointer> contours=reader.GetOutput();
 522       for (std::vector<vvMesh::Pointer>::iterator i=contours.begin();
 523            i!=contours.end(); i++)
 524         AddContour(index,*i,selector.PropagationEnabled());
 525       QApplication::restoreOverrideCursor();
 526     }
 527 }
 528
 529 //------------------------------------------------------------------------------
 530 void vvMainWindow::OpenDCStructContour()
 531 {
 532   if (mSlicerManagers.size() > 0) {
 533     QString Extensions = "Dicom Files ( *.dcm RS*)";
 534     Extensions += ";;All Files (*)";
 535     QString file = QFileDialog::getOpenFileName(this,tr("Merge Images"),mInputPathName,Extensions);
 536     if (file.isNull())
 537       return;
 538     int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
 539     AddDCStructContour(index, file);
 540   }
 541 }
 542 //------------------------------------------------------------------------------
 543
 544
 545 //------------------------------------------------------------------------------
 546 void vvMainWindow::ComputeDeformableRegistration()
 547 {
 548   if (mSlicerManagers.size() > 0) {
 549     int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
 550     vvDeformationDialog dialog(index,mSlicerManagers);
 551     if (dialog.exec()) {
 552       std::string base_name=itksys::SystemTools::GetFilenameWithoutExtension(mSlicerManagers[dialog.GetInputFileIndex()]->GetFileName());
 553       AddField(dialog.GetOutput(),dialog.getFieldFile(),dialog.GetInputFileIndex());
 554       WarpImage(dialog.GetSelectedSlicer(),dialog.GetReferenceFrameIndex());
 555     } else
 556       std::cout << "Error or user cancellation while computing deformation field..." << std::endl;
 557   } else QMessageBox::information(this, "Need to open image","You must open an image first.");
 558 }
 559 //------------------------------------------------------------------------------
 560
 561
 562 //------------------------------------------------------------------------------
 563 void vvMainWindow::WarpImage()
 564 {
 565   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
 566   if (!mSlicerManagers[index]->GetVF().IsNull()) {
 567     bool ok;
 568     int ref = QInputDialog::getInteger(this,"Chose reference phase","Reference phase",0,0,\
 569                                        mSlicerManagers[index]->GetImage()->GetVTKImages().size()-1,1,&ok);
 570     if (ok) {
 571       WarpImage(mSlicerManagers[index],ref);
 572     }
 573   } else
 574     QMessageBox::warning(this,tr("No vector field"),tr("Sorry, can't warp without a vector field"));
 575 }
 576 //------------------------------------------------------------------------------
 577
 578
 579 //------------------------------------------------------------------------------
 580 void vvMainWindow::WarpImage(vvSlicerManager* selected_slicer,int reference_phase)
 581 {
 582   if (!selected_slicer->GetVF().IsNull()) {
 583     QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
 584     QFileInfo info(selected_slicer->GetFileName().c_str());
 585     vvImageWarp warp(selected_slicer->GetImage(),selected_slicer->GetVF(),
 586                      reference_phase,this);
 587     if (warp.ComputeWarpedImage()) {
 588       AddImage(warp.GetWarpedImage(),info.path().toStdString()+"/"+info.completeBaseName().toStdString()+"_warped.mhd");
 589       AddImage(warp.GetDiffImage()  ,info.path().toStdString()+"/"+info.completeBaseName().toStdString()+"_diff.mhd");
 590       AddImage(warp.GetJacobianImage()  ,info.path().toStdString()+"/"+info.completeBaseName().toStdString()+"_jacobian.mhd");
 591       QApplication::restoreOverrideCursor();
 592     } else {
 593       QApplication::restoreOverrideCursor();
 594       QMessageBox::warning(this,tr("Different spacings"),tr("The vector field and image spacings must be the same in order to warp."));
 595     }
 596   } else
 597     QMessageBox::warning(this,tr("No vector field"),tr("Sorry, can't warp without a vector field."));
 598 }
 599 //------------------------------------------------------------------------------
 600
 601
 602 //------------------------------------------------------------------------------
 603 vvMainWindow::~vvMainWindow()
 604 {
 605   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
 606     if (mSlicerManagers[i] != NULL)
 607       delete mSlicerManagers[i];
 608   }
 609 }
 610 //------------------------------------------------------------------------------
 611
 612 //------------------------------------------------------------------------------
 613 QTabWidget * vvMainWindow::GetTab()
 614 {
 615   return tabWidget;
 616 }
 617 //------------------------------------------------------------------------------
 618
 619
 620 //------------------------------------------------------------------------------
 621 void vvMainWindow::MergeImages()
 622 {
 623   QString Extensions = EXTENSIONS;
 624   Extensions += ";;All Files (*)";
 625   QStringList files = QFileDialog::getOpenFileNames(this,tr("Merge Images"),mInputPathName,Extensions);
 626   if (files.isEmpty())
 627     return;
 628   mInputPathName = itksys::SystemTools::GetFilenamePath(files[0].toStdString()).c_str();
 629   std::vector<std::string> vector;
 630
 631   unsigned int currentDim = 0;
 632   std::vector<double> currentSpacing;
 633   std::vector<int> currentSize;
 634   std::vector<double> currentOrigin;
 635
 636   for (int i = 0; i < files.size(); i++) {
 637     itk::ImageIOBase::Pointer reader = itk::ImageIOFactory::CreateImageIO(
 638                                          files[i].toStdString().c_str(), itk::ImageIOFactory::ReadMode);
 639     reader->SetFileName(files[i].toStdString().c_str());
 640     reader->ReadImageInformation();
 641     if (reader)        {
 642       //NOViewWidget->hide();
 643       //NEViewWidget->hide();
 644       //SOViewWidget->hide();
 645       //SEViewWidget->hide();
 646       if (i == 0)
 647         currentDim = reader->GetNumberOfDimensions();
 648       bool IsOk = true;
 649       for (unsigned int j = 0; j < currentDim; j++) {
 650         if (i == 0) {
 651           if (j == 0) {
 652             currentSpacing.resize(currentDim);
 653             currentSize.resize(currentDim);
 654             currentOrigin.resize(currentDim);
 655           }
 656           currentOrigin[j] = reader->GetOrigin(j);
 657           currentSpacing[j] = reader->GetSpacing(j);
 658           currentSize[j] = reader->GetDimensions(j);
 659         } else if (currentDim != reader->GetNumberOfDimensions()
 660                    || currentSpacing[j] != reader->GetSpacing(j)
 661                    || currentSize[j] != (int)reader->GetDimensions(j)
 662                    || currentOrigin[j] != reader->GetOrigin(j)) {
 663           QString error = "Cannot read file (too different from others ";
 664           error += files[i].toStdString().c_str();
 665           QMessageBox::information(this,tr("Reading problem"),error);
 666           IsOk = false;
 667           break;
 668         }
 669       }
 670       if (IsOk)
 671         vector.push_back(files[i].toStdString());
 672     }
 673   }
 674   if (vector.size() > 0)
 675     LoadImages(vector, vvImageReader::MERGED);
 676 }
 677 //------------------------------------------------------------------------------
 678
 679 //------------------------------------------------------------------------------
 680 void vvMainWindow::SliceImages()
 681 {
 682   QString Extensions = EXTENSIONS;
 683   Extensions += ";;All Files (*)";
 684
 685   QStringList files = QFileDialog::getOpenFileNames(this,tr("Slice Images"),mInputPathName,Extensions);
 686   if (files.isEmpty())
 687     return;
 688   mInputPathName = itksys::SystemTools::GetFilenamePath(files[0].toStdString()).c_str();
 689   std::vector<std::string> vector;
 690   for (int i = 0; i < files.size(); i++)
 691     vector.push_back(files[i].toStdString());
 692   LoadImages(vector, vvImageReader::SLICED);
 693 }
 694 //------------------------------------------------------------------------------
 695
 696 //------------------------------------------------------------------------------
 697 void vvMainWindow::MergeImagesWithTime()
 698 {
 699   QString Extensions = EXTENSIONS;
 700   Extensions += ";;All Files (*)";
 701   QStringList files = QFileDialog::getOpenFileNames(this,tr("Merge Images With Time"),mInputPathName,Extensions);
 702   if (files.isEmpty())
 703     return;
 704   mInputPathName = itksys::SystemTools::GetFilenamePath(files[0].toStdString()).c_str();
 705   std::vector<std::string> vector;
 706
 707   for (int i = 0; i < files.size(); i++)
 708     vector.push_back(files[i].toStdString());
 709   sort(vector.begin(),vector.end());
 710   if (vector.size() > 1)
 711     LoadImages(vector, vvImageReader::MERGEDWITHTIME);
 712   else
 713     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.");
 714 }
 715 //------------------------------------------------------------------------------
 716
 717
 718 //------------------------------------------------------------------------------
 719 void vvMainWindow::OpenDicom()
 720 {
 721   std::vector<std::string> files;
 722
 723   std::cout << "dicomSeriesSelector " << std::endl;
 724   if (dicomSeriesSelector->exec() == QDialog::Accepted) {
 725     files = *(dicomSeriesSelector->GetFilenames());
 726     LoadImages(files, vvImageReader::DICOM);
 727   }
 728 }
 729 //------------------------------------------------------------------------------
 730
 731 //------------------------------------------------------------------------------
 732 void vvMainWindow::OpenImages()
 733 {
 734   QString Extensions = EXTENSIONS;
 735   Extensions += ";;All Files (*)";
 736
 737   QStringList files = QFileDialog::getOpenFileNames(this,tr("Load Images"),mInputPathName,Extensions);
 738   if (files.isEmpty())
 739     return;
 740   mInputPathName = itksys::SystemTools::GetFilenamePath(files[0].toStdString()).c_str();
 741   std::vector<std::string> vector;
 742   for (int i = 0; i < files.size(); i++)
 743     vector.push_back(files[i].toStdString());
 744   LoadImages(vector, vvImageReader::IMAGE);
 745 }
 746 //------------------------------------------------------------------------------
 747 void vvMainWindow::OpenRecentImage()
 748 {
 749   QAction * caller = qobject_cast<QAction*>(sender());
 750   std::vector<std::string> images;
 751   images.push_back(caller->text().toStdString());
 752   mInputPathName = itksys::SystemTools::GetFilenamePath(images[0]).c_str();
 753   LoadImages(images, vvImageReader::IMAGE);
 754 }
 755 //------------------------------------------------------------------------------
 756
 757
 758 //------------------------------------------------------------------------------
 759 void vvMainWindow::OpenImageWithTime()
 760 {
 761   QString Extensions = EXTENSIONS;
 762   Extensions += ";;All Files (*)";
 763
 764   QStringList files = QFileDialog::getOpenFileNames(this,tr("Load Images With Time"),mInputPathName,Extensions);
 765   if (files.isEmpty())
 766     return;
 767   mInputPathName = itksys::SystemTools::GetFilenamePath(files[0].toStdString()).c_str();
 768   std::vector<std::string> vector;
 769   for (int i = 0; i < files.size(); i++) {
 770     vector.push_back(files[i].toStdString());
 771   }
 772   LoadImages(vector, vvImageReader::IMAGEWITHTIME);
 773 }
 774 //------------------------------------------------------------------------------
 775
 776
 777 //------------------------------------------------------------------------------
 778 void vvMainWindow::LoadImages(std::vector<std::string> files, vvImageReader::LoadedImageType filetype)
 779 {
 780   //Separate the way to open images and dicoms
 781   int fileSize;
 782   if (filetype == vvImageReader::IMAGE || filetype == vvImageReader::IMAGEWITHTIME)
 783     fileSize = files.size();
 784   else
 785     fileSize = 1;
 786
 787   // For SLICED, we need the number of slices (ndim and #slices)
 788   std::vector<unsigned int> nSlices;
 789   nSlices.resize(files.size());
 790   std::fill(nSlices.begin(), nSlices.end(), 1);
 791   if (filetype == vvImageReader::SLICED) {
 792     for (int i = 0; i < fileSize; i++) {
 793       itk::ImageIOBase::Pointer header = clitk::readImageHeader(files[i]);
 794       QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
 795       if (!header) {
 796         nSlices[i] = 0;
 797         QString error = "Cannot open file \n";
 798         error += files[i].c_str();
 799         QMessageBox::information(this,tr("Reading problem"),error);
 800         return;
 801       }
 802       if (header->GetNumberOfDimensions() < 3) {
 803         nSlices[i] = 0;
 804         QString error = "Dimension problem. Cannot slice \n";
 805         error += files[i].c_str();
 806         QMessageBox::information(this,tr("Reading problem"),error);
 807         return;
 808       }
 809       nSlices[i] = header->GetDimensions( header->GetNumberOfDimensions()-1 );
 810     }
 811   }
 812
 813   //Only add to the list of recently opened files when a single file is opened,
 814   //to avoid polluting the list of recently opened files
 815   if (files.size() == 1) {
 816     QFileInfo finfo=tr(files[0].c_str());
 817     AddToRecentlyOpenedImages(finfo.absoluteFilePath().toStdString());
 818     updateRecentlyOpenedFilesMenu(GetRecentlyOpenedImages());
 819   }
 820   //init the progress events
 821   QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
 822   vvProgressDialog progress("Opening " + files[0],fileSize>1);
 823   qApp->processEvents();
 824
 825   int numberofsuccesulreads=0;
 826   //open images as 1 or multiples
 827   for (int i = 0; i < fileSize; i++) {
 828
 829     progress.SetText("Opening " + files[i]);
 830     progress.SetProgress(i,fileSize);
 831     qApp->processEvents();
 832
 833     for (unsigned int j = 0; j < nSlices[i]; j++) {
 834       //read the image and put it in mSlicerManagers
 835       vvSlicerManager* imageManager = new vvSlicerManager(4);
 836       qApp->processEvents();
 837
 838       bool SetImageSucceed=false;
 839
 840       // Change filename if an image with the same already exist
 841       int number = GetImageDuplicateFilenameNumber(files[i] + std::string("_slice"));
 842
 843       if (filetype == vvImageReader::IMAGE || filetype == vvImageReader::IMAGEWITHTIME || filetype == vvImageReader::SLICED)
 844         SetImageSucceed = imageManager->SetImage(files[i],filetype, number, j);
 845       else {
 846         SetImageSucceed = imageManager->SetImages(files,filetype, number);
 847       }
 848       if (!SetImageSucceed) {
 849         QApplication::restoreOverrideCursor();
 850         QString error = "Cannot open file \n";
 851         error += imageManager->GetLastError().c_str();
 852         QMessageBox::information(this,tr("Reading problem"),error);
 853         delete imageManager;
 854       } else {
 855         mSlicerManagers.push_back(imageManager);
 856
 857         //create an item in the tree with good settings
 858         QTreeWidgetItem *item = new QTreeWidgetItem();
 859         item->setData(0,Qt::UserRole,files[i].c_str());
 860         QFileInfo fileinfo(imageManager->GetFileName().c_str()); //Do not show the path
 861         item->setData(COLUMN_IMAGE_NAME,Qt::DisplayRole,fileinfo.fileName());
 862         item->setData(1,Qt::UserRole,tr("image"));
 863         item->setToolTip(COLUMN_IMAGE_NAME, imageManager->GetListOfAbsoluteFilePathInOneString("image").c_str());
 864         qApp->processEvents();
 865
 866         //Create the buttons for reload and close
 867         qApp->processEvents();
 868         QTreePushButton* cButton = new QTreePushButton;
 869         cButton->setItem(item);
 870         cButton->setColumn(COLUMN_CLOSE_IMAGE);
 871         cButton->setToolTip(tr("close image"));
 872         cButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/exit.png")));
 873         connect(cButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
 874                 this,SLOT(CloseImage(QTreeWidgetItem*, int)));
 875
 876         QTreePushButton* rButton = new QTreePushButton;
 877         rButton->setItem(item);
 878         rButton->setColumn(COLUMN_RELOAD_IMAGE);
 879         rButton->setToolTip(tr("reload image"));
 880         rButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/rotateright.png")));
 881         connect(rButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
 882                 this,SLOT(ReloadImage(QTreeWidgetItem*, int)));
 883
 884         DataTree->addTopLevelItem(item);
 885         DataTree->setItemWidget(item, COLUMN_CLOSE_IMAGE, cButton);
 886         DataTree->setItemWidget(item, COLUMN_RELOAD_IMAGE, rButton);
 887
 888         //set the id of the image
 889         QString id = QDir::current().absoluteFilePath(files[i].c_str()) + QString::number(mSlicerManagers.size()-1);
 890         item->setData(COLUMN_IMAGE_NAME,Qt::UserRole,id.toStdString().c_str());
 891         mSlicerManagers.back()->SetId(id.toStdString());
 892
 893         linkPanel->addImage(imageManager->GetFileName(), id.toStdString());
 894
 895         connect(mSlicerManagers.back(), SIGNAL(currentImageChanged(std::string)),
 896                 this,SLOT(CurrentImageChanged(std::string)));
 897         connect(mSlicerManagers.back(), SIGNAL(currentPickedImageChanged(std::string)),
 898                 this, SLOT(CurrentPickedImageChanged(std::string)));
 899         connect(mSlicerManagers.back(), SIGNAL(UpdatePosition(int, double, double, double, double, double, double, double)),
 900                 this,SLOT(MousePositionChanged(int,double, double, double, double, double, double, double)));
 901         connect(mSlicerManagers.back(), SIGNAL(UpdateVector(int, double, double, double, double)),
 902                 this, SLOT(VectorChanged(int,double,double,double, double)));
 903         connect(mSlicerManagers.back(), SIGNAL(UpdateOverlay(int, double, double)),
 904                 this, SLOT(OverlayChanged(int,double,double)));
 905         connect(mSlicerManagers.back(), SIGNAL(UpdateFusion(int, double)),
 906                 this, SLOT(FusionChanged(int,double)));
 907         connect(mSlicerManagers.back(), SIGNAL(WindowLevelChanged()),
 908                 this,SLOT(WindowLevelChanged()));
 909         connect(mSlicerManagers.back(), SIGNAL(UpdateSlice(int,int)),
 910                 this,SLOT(UpdateSlice(int,int)));
 911         connect(mSlicerManagers.back(), SIGNAL(UpdateTSlice(int, int)),
 912                 this,SLOT(UpdateTSlice(int, int)));
 913         connect(mSlicerManagers.back(), SIGNAL(UpdateTSlice(int, int)),
 914                 this,SLOT(ImageInfoChanged()));
 915         connect(mSlicerManagers.back(), SIGNAL(UpdateSliceRange(int,int,int,int,int)),
 916                 this,SLOT(UpdateSliceRange(int,int,int,int,int)));
 917         connect(mSlicerManagers.back(), SIGNAL(UpdateLinkManager(std::string,int,double,double,double,int)),
 918                 this,SLOT(UpdateLinkManager(std::string,int,double,double,double,int)));
 919         connect(mSlicerManagers.back(), SIGNAL(UpdateLinkedNavigation(std::string,vvSlicerManager*,vvSlicer*)),
 920                 this,SLOT(UpdateLinkedNavigation(std::string,vvSlicerManager*,vvSlicer*)));
 921         connect(mSlicerManagers.back(), SIGNAL(ChangeImageWithIndexOffset(vvSlicerManager*,int,int)),
 922                 this,SLOT(ChangeImageWithIndexOffset(vvSlicerManager*,int,int)));
 923         connect(mSlicerManagers.back(),SIGNAL(LandmarkAdded()),landmarksPanel,SLOT(AddPoint()));
 924         InitSlicers();
 925         numberofsuccesulreads++;
 926       }
 927     }
 928   }
 929   if (numberofsuccesulreads) {
 930     NOViewWidget->show();
 931     NEViewWidget->show();
 932     SOViewWidget->show();
 933     SEViewWidget->show();
 934     UpdateTree();
 935     InitDisplay();
 936     ShowLastImage();
 937
 938     // Try to guess default WindowLevel
 939     double range[2];
 940     mSlicerManagers.back()->GetImage()->GetFirstVTKImageData()->GetScalarRange(range);
 941     if ((range[0] == 0) && (range[1] == 1)) {
 942       presetComboBox->setCurrentIndex(5);// binary
 943     } else {
 944       // TODO
 945     }
 946   }
 947   QApplication::restoreOverrideCursor();
 948 }
 949 //------------------------------------------------------------------------------
 950
 951 //------------------------------------------------------------------------------
 952 void vvMainWindow::UpdateTree()
 953 {
 954   DataTree->resizeColumnToContents(COLUMN_TREE);
 955   DataTree->resizeColumnToContents(COLUMN_UL_VIEW);
 956   DataTree->resizeColumnToContents(COLUMN_UR_VIEW);
 957   DataTree->resizeColumnToContents(COLUMN_DL_VIEW);
 958   DataTree->resizeColumnToContents(COLUMN_DR_VIEW);
 959   DataTree->resizeColumnToContents(COLUMN_IMAGE_NAME);
 960   DataTree->resizeColumnToContents(COLUMN_CLOSE_IMAGE);
 961   DataTree->resizeColumnToContents(COLUMN_RELOAD_IMAGE);
 962 }
 963 //------------------------------------------------------------------------------
 964
 965 //------------------------------------------------------------------------------
 966 void vvMainWindow::CurrentImageChanged(std::string id)
 967 {
 968   if (id == mCurrentSelectedImageId) return; // Do nothing
 969   int selected = 0;
 970   for (int i = 0; i < DataTree->topLevelItemCount(); i++) {
 971     if (DataTree->topLevelItem(i)->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString().toStdString() == id) {
 972       selected = i;
 973     } else {
 974       DataTree->topLevelItem(i)->setSelected(0);
 975     }
 976     for (int child = 0; child < DataTree->topLevelItem(i)->childCount(); child++)
 977       DataTree->topLevelItem(i)->child(child)->setSelected(0);
 978
 979   }
 980   DataTree->topLevelItem(selected)->setSelected(1);
 981   mCurrentSelectedImageId = id;
 982
 983   landmarksPanel->SetCurrentLandmarks(mSlicerManagers[selected]->GetLandmarks(),
 984                                       mSlicerManagers[selected]->GetTSlice());
 985   landmarksPanel->SetCurrentPath(mInputPathName.toStdString());
 986   landmarksPanel->SetCurrentImage(mSlicerManagers[selected]->GetFileName().c_str());
 987
 988   emit SelectedImageHasChanged(mSlicerManagers[selected]);
 989 }
 990 //------------------------------------------------------------------------------
 991
 992 //------------------------------------------------------------------------------
 993 void vvMainWindow::CurrentPickedImageChanged(std::string id)
 994 {
 995   if (id == mCurrentPickedImageId) return; // Do nothing
 996   int selected = 0;
 997   for (int i = 0; i < DataTree->topLevelItemCount(); i++) {
 998     if (DataTree->topLevelItem(i)->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString().toStdString() == id) {
 999       selected = i;
1000     } else {
1001       DataTree->topLevelItem(i)->setSelected(0);
1002     }
1003     for (int child = 0; child < DataTree->topLevelItem(i)->childCount(); child++)
1004       DataTree->topLevelItem(i)->child(child)->setSelected(0);
1005
1006   }
1007   DataTree->topLevelItem(selected)->setSelected(1);
1008   mCurrentPickedImageId = id;
1009   mCurrentPickedImageIndex = selected;
1010 }
1011 //------------------------------------------------------------------------------
1012
1013 //------------------------------------------------------------------------------
1014 void vvMainWindow::ImageInfoChanged()
1015 {
1016   contextActions[6]->setEnabled(1);
1017   contextActions[5]->setEnabled(1);
1018   actionSave_As->setEnabled(1);
1019   actionAdd_VF_to_current_Image->setEnabled(1);
1020   actionAdd_fusion_image->setEnabled(1);
1021   actionAdd_overlay_image_to_current_image->setEnabled(1);
1022   actionNorth_East_Window->setEnabled(1);
1023   actionNorth_West_Window->setEnabled(1);
1024   actionSouth_East_Window->setEnabled(1);
1025   actionSouth_West_Window->setEnabled(1);
1026   vvToolManager::GetInstance()->EnableToolsInMenu(this, true);
1027   inverseButton->setEnabled(1);
1028
1029   goToCursorPushButton->setEnabled(1);
1030
1031   if (DataTree->selectedItems().size()) {
1032     int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1033
1034     colorMapComboBox->setEnabled(1);
1035     for (int i = 0; i < DataTree->topLevelItem(index)->childCount(); i++) {
1036       if (DataTree->topLevelItem(index)->child(i)->data(1,Qt::UserRole).toString() == "overlay" ||
1037           DataTree->topLevelItem(index)->child(i)->data(1,Qt::UserRole).toString() == "fusion") {
1038         colorMapComboBox->setEnabled(0);
1039         break;
1040       }
1041     }
1042
1043     std::vector<double> origin;
1044     std::vector<double> inputSpacing;
1045     std::vector<int> inputSize;
1046     std::vector<double> sizeMM;
1047     vtkSmartPointer<vtkMatrix4x4> transformation;
1048     int dimension=0;
1049     QString pixelType;
1050     QString inputSizeInBytes;
1051     QString image = DataTree->selectedItems()[0]->data(COLUMN_IMAGE_NAME,Qt::DisplayRole).toString();
1052
1053     int nframes = mSlicerManagers[index]->GetSlicer(0)->GetTMax();
1054     if (nframes > 1 || playMode == 1) {
1055       playButton->setEnabled(1);
1056       frameRateLabel->setEnabled(1);
1057       frameRateSpinBox->setEnabled(1);
1058     } else {
1059       playButton->setEnabled(0);
1060       frameRateLabel->setEnabled(0);
1061       frameRateSpinBox->setEnabled(0);
1062     }
1063
1064     //read image header
1065     int NPixel = 1;
1066
1067     int tSlice = 0;
1068     vvImage::Pointer imageSelected;
1069     if (DataTree->topLevelItem(index) == DataTree->selectedItems()[0]) {
1070       imageSelected = mSlicerManagers[index]->GetSlicer(0)->GetImage();
1071       tSlice = mSlicerManagers[index]->GetSlicer(0)->GetTSlice();
1072     } else if (DataTree->selectedItems()[0]->data(1,Qt::UserRole).toString() == "vector") {
1073       imageSelected = mSlicerManagers[index]->GetSlicer(0)->GetVF();
1074       tSlice = mSlicerManagers[index]->GetSlicer(0)->GetOverlayTSlice();
1075     } else if (DataTree->selectedItems()[0]->data(1,Qt::UserRole).toString() == "overlay") {
1076       imageSelected = mSlicerManagers[index]->GetSlicer(0)->GetOverlay();
1077       tSlice = mSlicerManagers[index]->GetSlicer(0)->GetOverlayTSlice();
1078     } else if (DataTree->selectedItems()[0]->data(1,Qt::UserRole).toString() == "fusion") {
1079       imageSelected = mSlicerManagers[index]->GetSlicer(0)->GetFusion();
1080       tSlice = mSlicerManagers[index]->GetSlicer(0)->GetFusionTSlice();
1081     }
1082     else if (DataTree->selectedItems()[0]->data(1,Qt::UserRole).toString() == "contour") {
1083       imageSelected = mSlicerManagers[index]->GetSlicer(0)->GetImage();
1084       tSlice = mSlicerManagers[index]->GetSlicer(0)->GetTSlice();
1085     }
1086     else {
1087       imageSelected = mSlicerManagers[index]->GetSlicer(0)->GetImage();
1088       tSlice = mSlicerManagers[index]->GetSlicer(0)->GetTSlice();
1089     }
1090
1091     dimension = imageSelected->GetNumberOfDimensions();
1092     origin.resize(dimension);
1093     inputSpacing.resize(dimension);
1094     inputSize.resize(dimension);
1095     sizeMM.resize(dimension);
1096     pixelType = mSlicerManagers[index]->GetImage()->GetScalarTypeAsITKString().c_str();
1097     for (int i = 0; i < dimension; i++) {
1098       origin[i] = imageSelected->GetOrigin()[i];
1099       inputSpacing[i] = imageSelected->GetSpacing()[i];
1100       inputSize[i] = imageSelected->GetSize()[i];
1101       sizeMM[i] = inputSize[i]*inputSpacing[i];
1102       NPixel *= inputSize[i];
1103     }
1104     inputSizeInBytes = GetSizeInBytes(imageSelected->GetActualMemorySize()*1000);
1105
1106     QString dim = QString::number(dimension) + " (";
1107     dim += pixelType + ")";
1108
1109     infoPanel->setFileName(image);
1110     infoPanel->setDimension(dim);
1111     infoPanel->setSizePixel(GetVectorIntAsString(inputSize));
1112     infoPanel->setSizeMM(GetVectorDoubleAsString(sizeMM));
1113     infoPanel->setOrigin(GetVectorDoubleAsString(origin));
1114     infoPanel->setSpacing(GetVectorDoubleAsString(inputSpacing));
1115     infoPanel->setNPixel(QString::number(NPixel)+" ("+inputSizeInBytes+")");
1116     transformation = imageSelected->GetTransform()[tSlice]->GetMatrix();
1117     infoPanel->setTransformation(Get4x4MatrixDoubleAsString(transformation));
1118
1119     landmarksPanel->SetCurrentLandmarks(mSlicerManagers[index]->GetLandmarks(),
1120                                         mSlicerManagers[index]->GetTSlice());
1121     landmarksPanel->SetCurrentPath(mInputPathName.toStdString());
1122     landmarksPanel->SetCurrentImage(mSlicerManagers[index]->GetFileName().c_str());
1123
1124     overlayPanel->getCurrentImageName(mSlicerManagers[index]->GetFileName().c_str());
1125     for (int i = 0; i < 4; i++) {
1126       if (DataTree->selectedItems()[0]->data(i+1,Qt::CheckStateRole).toInt() > 0 || i == 3) {
1127         mSlicerManagers[index]->UpdateInfoOnCursorPosition(i);
1128         break;
1129       }
1130     }
1131
1132 //     infoPanel->setFileName(image);
1133 //     infoPanel->setDimension(dim);
1134 //     infoPanel->setSizePixel(GetVectorIntAsString(inputSize));
1135 //     infoPanel->setSizeMM(GetVectorDoubleAsString(sizeMM));
1136 //     infoPanel->setOrigin(GetVectorDoubleAsString(origin));
1137 //     infoPanel->setSpacing(GetVectorDoubleAsString(inputSpacing));
1138 //     infoPanel->setNPixel(QString::number(NPixel)+" ("+inputSizeInBytes+")");
1139 //
1140 //     landmarksPanel->SetCurrentLandmarks(mSlicerManagers[index]->GetLandmarks(),
1141 //                                         mSlicerManagers[index]->GetTSlice());
1142 //     landmarksPanel->SetCurrentPath(mInputPathName.toStdString());
1143 //     landmarksPanel->SetCurrentImage(mSlicerManagers[index]->GetFileName().c_str());
1144 //
1145 //     overlayPanel->getCurrentImageName(mSlicerManagers[index]->GetFileName().c_str());
1146 //     for (int i = 0; i < 4; i++) {
1147 //       if (DataTree->selectedItems()[0]->data(i+1,Qt::CheckStateRole).toInt() > 0 || i == 3) {
1148 //         mSlicerManagers[index]->UpdateInfoOnCursorPosition(i);
1149 //         break;
1150 //       }
1151 //     }
1152     WindowLevelChanged();
1153     slicingPresetComboBox->setCurrentIndex(mSlicerManagers[index]->GetSlicingPreset());
1154
1155     if (mSlicerManagers[index]->GetSlicer(0)->GetVF()) {
1156       overlayPanel->getVFName(mSlicerManagers[index]->GetVFName().c_str());
1157       overlayPanel->getVFProperty(mSlicerManagers[index]->GetSlicer(0)->GetVFSubSampling(),
1158                                   mSlicerManagers[index]->GetSlicer(0)->GetVFScale(),
1159                                   mSlicerManagers[index]->GetSlicer(0)->GetVFLog());
1160     } else {
1161       overlayPanel->getVFName(mSlicerManagers[index]->GetVFName().c_str());
1162       overlayPanel->getVFProperty(-1,-1,-1);
1163     }
1164     if (mSlicerManagers[index]->GetSlicer(0)->GetOverlay()) {
1165       overlayPanel->getOverlayName(mSlicerManagers[index]->GetOverlayName().c_str());
1166     } else {
1167       overlayPanel->getOverlayName(mSlicerManagers[index]->GetOverlayName().c_str());
1168     }
1169
1170     if (mSlicerManagers[index]->GetSlicer(0)->GetFusion()) {
1171       overlayPanel->getFusionName(mSlicerManagers[index]->GetFusionName().c_str());
1172     } else {
1173       overlayPanel->getFusionName(mSlicerManagers[index]->GetFusionName().c_str());
1174     }
1175   }
1176 }
1177 //------------------------------------------------------------------------------
1178
1179 //------------------------------------------------------------------------------
1180 void vvMainWindow::ShowDocumentation()
1181 {
1182   documentation->show();
1183 }
1184 //------------------------------------------------------------------------------
1185
1186 //------------------------------------------------------------------------------
1187 void vvMainWindow::PopupRegisterForm(bool checkCanPush)
1188 {
1189   vvRegisterForm* registerForm = new vvRegisterForm(QUrl("http://www.creatis.insa-lyon.fr/~dsarrut/vvregister/write.php"), getVVSettingsPath(), getSettingsOptionFormat());
1190   if(!checkCanPush) {
1191     registerForm->show();
1192   } else {
1193     if(registerForm->canPush()) {
1194       registerForm->show();
1195       registerForm->acquitPushed();//too bad if there is not internet connection anymore.
1196     }
1197   }
1198 }
1199 //------------------------------------------------------------------------------
1200
1201 //------------------------------------------------------------------------------
1202 void vvMainWindow::ShowHelpDialog()
1203 {
1204   help_dialog->show();
1205 }
1206 //------------------------------------------------------------------------------
1207
1208 //------------------------------------------------------------------------------
1209 void vvMainWindow::ChangeViewMode()
1210 {
1211   typedef struct _SIZE{
1212     QSplitter* splitter;
1213     QList<int> size1, size2;
1214     int cols[3];
1215   }SplitterSize;
1216   SplitterSize sizes[4];
1217   sizes[0].splitter = OSplitter;
1218   sizes[0].size1.push_back(1);
1219   sizes[0].size1.push_back(0);
1220   sizes[0].size2.push_back(1);
1221   sizes[0].size2.push_back(0);
1222   sizes[0].cols[0] = 2;
1223   sizes[0].cols[1] = 3;
1224   sizes[0].cols[2] = 4;
1225
1226   sizes[1].splitter = ESplitter;
1227   sizes[1].size1.push_back(0);
1228   sizes[1].size1.push_back(1);
1229   sizes[1].size2.push_back(1);
1230   sizes[1].size2.push_back(0);
1231   sizes[1].cols[0] = 1;
1232   sizes[1].cols[1] = 3;
1233   sizes[1].cols[2] = 4;
1234
1235   sizes[2].splitter = OSplitter;
1236   sizes[2].size1.push_back(1);
1237   sizes[2].size1.push_back(0);
1238   sizes[2].size2.push_back(0);
1239   sizes[2].size2.push_back(1);
1240   sizes[2].cols[0] = 1;
1241   sizes[2].cols[1] = 2;
1242   sizes[2].cols[2] = 4;
1243
1244   sizes[3].splitter = ESplitter;
1245   sizes[3].size1.push_back(0);
1246   sizes[3].size1.push_back(1);
1247   sizes[3].size2.push_back(0);
1248   sizes[3].size2.push_back(1);
1249   sizes[3].cols[0] = 1;
1250   sizes[3].cols[1] = 2;
1251   sizes[3].cols[2] = 3;
1252
1253   int slicer = mSlicerManagers[mCurrentPickedImageIndex]->GetSelectedSlicer();
1254   if (viewMode == 1) {
1255     if (slicer >= 0) {
1256       viewMode = 0;
1257       splitter_3->setSizes(sizes[slicer].size1);
1258       sizes[slicer].splitter->setSizes(sizes[slicer].size2);
1259       DataTree->setColumnHidden(sizes[slicer].cols[0],1);
1260       DataTree->setColumnHidden(sizes[slicer].cols[1],1);
1261       DataTree->setColumnHidden(sizes[slicer].cols[2],1);
1262     }
1263   } else {
1264     QList<int> size;
1265     if (slicer >= 0) {
1266       viewMode = 1;
1267       size.push_back(1);
1268       size.push_back(1);
1269       splitter_3->setSizes(size);
1270       sizes[slicer].splitter->setSizes(size);
1271       DataTree->setColumnHidden(sizes[slicer].cols[0],0);
1272       DataTree->setColumnHidden(sizes[slicer].cols[1],0);
1273       DataTree->setColumnHidden(sizes[slicer].cols[2],0);
1274     }
1275   }
1276   UpdateRenderWindows();
1277   /*
1278   ** I don't know why but for both resized QVTKWidget we also need to render
1279   ** the associated Slicer to redraw crosses.
1280   */
1281   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
1282 //     if (DataTree->topLevelItem(i)->data(COLUMN_UL_VIEW,Qt::CheckStateRole).toInt() > 1)
1283       mSlicerManagers[i]->GetSlicer(0)->Render();
1284       mSlicerManagers[i]->GetSlicer(1)->Render();
1285 //     if (DataTree->topLevelItem(i)->data(COLUMN_DL_VIEW,Qt::CheckStateRole).toInt() > 1)
1286       mSlicerManagers[i]->GetSlicer(2)->Render();
1287       mSlicerManagers[i]->GetSlicer(3)->Render();
1288   }
1289 }
1290 //------------------------------------------------------------------------------
1291
1292 //------------------------------------------------------------------------------
1293 QString vvMainWindow::GetSizeInBytes(unsigned long size)
1294 {
1295   QString result = "";// QString::number(size);
1296   //result += " bytes (";
1297   if (size > 1000000000) {
1298     size /= 1000000000;
1299     result += QString::number(size);
1300     result += "Gb";//)";
1301   } else if (size > 1000000) {
1302     size /= 1000000;
1303     result += QString::number(size);
1304     result += "Mb";//)";
1305   } else if (size > 1000) {
1306     size /= 1000;
1307     result += QString::number(size);
1308     result += "kb";//)";
1309   }
1310   return result;
1311 }
1312 //------------------------------------------------------------------------------
1313
1314 //------------------------------------------------------------------------------
1315 QString vvMainWindow::Get4x4MatrixDoubleAsString(vtkSmartPointer<vtkMatrix4x4> matrix, const int precision)
1316 {
1317   std::ostringstream strmatrix;
1318
1319   // Figure out the number of digits of the integer part of the largest absolute value
1320   // for each column
1321   unsigned width[4];
1322   for (unsigned int j = 0; j < 4; j++){
1323     double absmax = 0.;
1324     for (unsigned int i = 0; i < 4; i++)
1325       absmax = std::max(absmax, vnl_math_abs(matrix->GetElement(i, j)));
1326     unsigned ndigits = (unsigned)std::max(0.,std::log10(absmax))+1;
1327     width[j] = precision+ndigits+3;
1328   }
1329
1330   // Output with correct width, aligned to the right
1331   for (unsigned int i = 0; i < 4; i++) {
1332     for (unsigned int j = 0; j < 4; j++) {
1333       strmatrix.setf(ios::fixed,ios::floatfield);
1334       strmatrix.precision(precision);
1335       strmatrix.fill(' ');
1336       strmatrix.width(width[j]);
1337       strmatrix << std::right << matrix->GetElement(i, j);
1338     }
1339     strmatrix << std::endl;
1340   }
1341   QString result = strmatrix.str().c_str();
1342   return result;
1343 }
1344 //------------------------------------------------------------------------------
1345
1346 //------------------------------------------------------------------------------
1347 QString vvMainWindow::GetVectorDoubleAsString(std::vector<double> vectorDouble)
1348 {
1349   QString result;
1350   for (unsigned int i= 0; i < vectorDouble.size(); i++) {
1351     if (i != 0)
1352       result += " ";
1353     result += QString::number(vectorDouble[i]);
1354   }
1355   return result;
1356 }
1357 //------------------------------------------------------------------------------
1358
1359 //------------------------------------------------------------------------------
1360 QString vvMainWindow::GetVectorIntAsString(std::vector<int> vectorInt)
1361 {
1362   QString result;
1363   for (unsigned int i= 0; i < vectorInt.size(); i++) {
1364     if (i != 0)
1365       result += " ";
1366     result += QString::number(vectorInt[i]);
1367   }
1368   return result;
1369 }
1370 //------------------------------------------------------------------------------
1371
1372 //------------------------------------------------------------------------------
1373 int vvMainWindow::GetSlicerIndexFromItem(QTreeWidgetItem* item)
1374 {
1375   QString id = item->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString();
1376   for (int i = 0; i < DataTree->topLevelItemCount(); i++) {
1377     if (DataTree->topLevelItem(i)->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString() == id)
1378       return i;
1379   }
1380   return -1;
1381 }
1382 //------------------------------------------------------------------------------
1383
1384 //------------------------------------------------------------------------------
1385 QTreeWidgetItem* vvMainWindow::GetItemFromSlicerManager(vvSlicerManager* sm)
1386 {
1387   QString id = sm->GetId().c_str();
1388   for (int i = 0; i < DataTree->topLevelItemCount(); i++) {
1389     if (DataTree->topLevelItem(i)->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString() == id)
1390       return DataTree->topLevelItem(i);
1391   }
1392   return NULL;
1393 }
1394 //------------------------------------------------------------------------------
1395
1396 //------------------------------------------------------------------------------
1397 void vvMainWindow::DisplayChanged(QTreeWidgetItem *clickedItem, int column)
1398 {
1399   if ( column >= COLUMN_CLOSE_IMAGE || column <= 0)
1400     return;
1401
1402   // Get parent information (might be the same item)
1403   int slicerManagerIndex = GetSlicerIndexFromItem(clickedItem);
1404   QTreeWidgetItem* clickedParentItem = DataTree->topLevelItem(slicerManagerIndex);
1405   vvSlicer* clickedSlicer = mSlicerManagers[slicerManagerIndex]->GetSlicer(column-1);
1406
1407   // Go over the complete item tree (only 2 levels, parents and children)
1408   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
1409     // Trick to avoid redoing twice the job for a key (sr)
1410     mSlicerManagers[i]->GetSlicer(column-1)->GetRenderWindow()->GetInteractor()->SetKeySym("Crap");
1411
1412     QTreeWidgetItem* currentParentItem = DataTree->topLevelItem(i);
1413     if(currentParentItem != clickedParentItem) {
1414       // Not the branch of the clicked item, uncheck all
1415
1416       // Parent
1417       currentParentItem->setData(column,Qt::CheckStateRole, 0);
1418       mSlicerManagers[i]->UpdateSlicer(column-1, false);
1419
1420       // Children
1421       for (int iChild = 0; iChild < currentParentItem->childCount(); iChild++) {
1422         currentParentItem->child(iChild)->setData(column,Qt::CheckStateRole, 0);
1423       }
1424     }
1425     else {
1426       // Branch of the clicked one: get check status from actor visibility in slicer
1427       // and toggle the clicked one
1428
1429       // Parent
1430       bool vis = clickedSlicer->GetActorVisibility("image", 0);
1431       bool draw = clickedSlicer->GetRenderer()->GetDraw();
1432
1433       // Update slicer (after getting visibility)
1434       mSlicerManagers[slicerManagerIndex]->UpdateSlicer(column-1, true);
1435       mSlicerManagers[slicerManagerIndex]->UpdateInfoOnCursorPosition(column-1);
1436       DisplaySliders(slicerManagerIndex, column-1);
1437       if(clickedParentItem == clickedItem) {
1438         // Toggle
1439         vis = !draw || !vis;
1440       }
1441       clickedSlicer->SetActorVisibility("image", 0, vis);
1442       clickedParentItem->setData(column, Qt::CheckStateRole, vis?2:0);
1443
1444       // Children
1445       std::map<std::string, int> actorTypeCounts;
1446       for (int iChild = 0; iChild < clickedParentItem->childCount(); iChild++) {
1447         QTreeWidgetItem* currentChildItem = clickedParentItem->child(iChild);
1448         std::string actorType = currentChildItem->data(1,Qt::UserRole).toString().toStdString();
1449         vis = clickedSlicer->GetActorVisibility(actorType, actorTypeCounts[actorType]);
1450         if(currentChildItem == clickedItem) {
1451           // Toggle or force visibility if it was not on this branch so far
1452           vis = !draw || !vis;
1453           clickedSlicer->SetActorVisibility(actorType, actorTypeCounts[actorType], vis);
1454         }
1455         currentChildItem->setData(column, Qt::CheckStateRole, vis?2:0);
1456         actorTypeCounts[actorType]++;
1457       }
1458     }
1459   }
1460
1461   clickedSlicer->Render();
1462 }
1463 //------------------------------------------------------------------------------
1464
1465 void vvMainWindow::InitSlicers()
1466 {
1467   if (mSlicerManagers.size()) {
1468     mSlicerManagers.back()->GenerateDefaultLookupTable();
1469
1470     mSlicerManagers.back()->SetSlicerWindow(0,NOViewWidget->GetRenderWindow());
1471     mSlicerManagers.back()->SetSlicerWindow(1,NEViewWidget->GetRenderWindow());
1472     mSlicerManagers.back()->SetSlicerWindow(2,SOViewWidget->GetRenderWindow());
1473     mSlicerManagers.back()->SetSlicerWindow(3,SEViewWidget->GetRenderWindow());
1474   }
1475 }
1476
1477 //------------------------------------------------------------------------------
1478 void vvMainWindow::InitDisplay()
1479 {
1480   if (mSlicerManagers.size()) {
1481     //BE CAREFUL : this is absolutely necessary to set the interactor style
1482     //in order to have the same style instanciation for all SlicerManagers in
1483     // a same window
1484     for (int j = 0; j < 4; j++) {
1485       vvInteractorStyleNavigator* style = vvInteractorStyleNavigator::New();
1486       style->SetAutoAdjustCameraClippingRange(1);
1487       bool AlreadySelected = false;
1488       for (int i = 0; i < DataTree->topLevelItemCount(); i++) {
1489         mSlicerManagers[i]->SetInteractorStyleNavigator(j,style);
1490
1491         //select the image only if previous are not selected
1492         if (DataTree->topLevelItem(i)->data(j+1,Qt::CheckStateRole).toInt() > 1) {
1493           mSlicerManagers[i]->UpdateSlicer(j,1);
1494           AlreadySelected = true;
1495         } else if (i == DataTree->topLevelItemCount()-1 && !AlreadySelected) {
1496           if (DataTree->selectedItems().size() == 0)
1497             DataTree->topLevelItem(i)->setSelected(1);
1498           DataTree->topLevelItem(i)->setData(j+1,Qt::CheckStateRole,2);
1499           mSlicerManagers[i]->UpdateSlicer(j,1);
1500           DisplaySliders(i,j);
1501         } else {
1502           DataTree->topLevelItem(i)->setData(j+1,Qt::CheckStateRole,0);
1503           mSlicerManagers[i]->UpdateSlicer(j,0);
1504         }
1505       }
1506       style->Delete();
1507     }
1508   }
1509 }
1510 //------------------------------------------------------------------------------
1511
1512 //------------------------------------------------------------------------------
1513 void vvMainWindow::DisplaySliders(int slicer, int window)
1514 {
1515   if(!mSlicerManagers[slicer]->GetSlicer(window)->GetRenderer()->GetDraw())
1516     return;
1517
1518   int range[2];
1519   mSlicerManagers[slicer]->GetSlicer(window)->GetSliceRange(range);
1520   int position = mSlicerManagers[slicer]->GetSlicer(window)->GetSlice();
1521   if (range[1]>0)
1522     verticalSliders[window]->show();
1523   else
1524     verticalSliders[window]->hide();
1525   verticalSliders[window]->setRange(range[0],range[1]);
1526   verticalSliders[window]->setValue(position);
1527
1528   int tRange[2];
1529   tRange[0] = 0;
1530   tRange[1] = mSlicerManagers[slicer]->GetSlicer(window)->GetTMax();
1531   if (tRange[1]>0)
1532     horizontalSliders[window]->show();
1533   else
1534     horizontalSliders[window]->hide();
1535   horizontalSliders[window]->setRange(tRange[0],tRange[1]);
1536   int tPosition = mSlicerManagers[slicer]->GetSlicer(window)->GetMaxCurrentTSlice();
1537   horizontalSliders[window]->setValue(tPosition);
1538 }
1539 //------------------------------------------------------------------------------
1540
1541 //------------------------------------------------------------------------------
1542 void vvMainWindow::CloseImage(QTreeWidgetItem* item, int column)
1543 {
1544   int index = GetSlicerIndexFromItem(item);
1545
1546   if (DataTree->topLevelItem(index) != item) {
1547     QString warning = "Do you really want to close the overlay : ";
1548     warning += item->data(COLUMN_IMAGE_NAME,Qt::DisplayRole).toString();
1549     QMessageBox msgBox(QMessageBox::Warning, tr("Close Overlay"),
1550                        warning, 0, this);
1551     msgBox.addButton(tr("Close"), QMessageBox::AcceptRole);
1552     msgBox.addButton(tr("Cancel"), QMessageBox::RejectRole);
1553     if (msgBox.exec() == QMessageBox::AcceptRole) {
1554       std::string overlay_type=item->data(1,Qt::UserRole).toString().toStdString();
1555       int overlay_index=0;
1556       for (int child = 0; child < DataTree->topLevelItem(index)->childCount(); child++) {
1557         if (DataTree->topLevelItem(index)->\
1558             child(child)->data(1,Qt::UserRole).toString().toStdString() == overlay_type)
1559           overlay_index++;
1560         if (DataTree->topLevelItem(index)->child(child) == item) break;
1561       }
1562       mSlicerManagers[index]->RemoveActor(overlay_type, overlay_index-1);
1563       mSlicerManagers[index]->SetColorMap(0);
1564       DataTree->topLevelItem(index)->takeChild(DataTree->topLevelItem(index)->indexOfChild(item));
1565       mSlicerManagers[index]->Render();
1566     }
1567   } else if (DataTree->topLevelItemCount() <= 1) {
1568     QString warning = "Do you really want to close the image : ";
1569     warning += item->data(COLUMN_IMAGE_NAME,Qt::DisplayRole).toString();
1570     warning += "\nThis is the last image, you're about to close vv !!!";
1571     QMessageBox msgBox(QMessageBox::Warning, tr("Close Image"),
1572                        warning, 0, this);
1573     msgBox.addButton(tr("Close vv"), QMessageBox::AcceptRole);
1574     msgBox.addButton(tr("Cancel"), QMessageBox::RejectRole);
1575     if (msgBox.exec() == QMessageBox::AcceptRole) {
1576       this->close();
1577     }
1578   } else {
1579     QString warning = "Do you really want to close the image : ";
1580     warning += item->data(COLUMN_IMAGE_NAME,Qt::DisplayRole).toString();
1581     QMessageBox msgBox(QMessageBox::Warning, tr("Close Image"),
1582                        warning, 0, this);
1583     msgBox.addButton(tr("Close"), QMessageBox::AcceptRole);
1584     msgBox.addButton(tr("Cancel"), QMessageBox::RejectRole);
1585     if (msgBox.exec() == QMessageBox::AcceptRole) {
1586
1587       // Tell tools that we close an image
1588       emit AnImageIsBeingClosed(mSlicerManagers[index]);
1589
1590       std::vector<vvSlicerManager*>::iterator Manageriter = mSlicerManagers.begin();
1591       DataTree->takeTopLevelItem(index);
1592       for (int i = 0; i < index; i++) {
1593         Manageriter++;
1594       }
1595       linkPanel->removeImage(index);
1596       mSlicerManagers[index]->RemoveActors();
1597       delete mSlicerManagers[index];
1598       mSlicerManagers.erase(Manageriter);
1599
1600       //
1601       InitDisplay();
1602     }
1603   }
1604   ImageInfoChanged();
1605 }
1606 //------------------------------------------------------------------------------
1607
1608 //------------------------------------------------------------------------------
1609 void vvMainWindow::ReloadImage(QTreeWidgetItem* item, int column)
1610 {
1611   // int index = GetSlicerIndexFromItem(item);
1612   //   QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
1613   //   if (item->data(1,Qt::UserRole).toString() == "vector")
1614   //     mSlicerManagers[index]->ReloadVF();
1615   //   else
1616   //     mSlicerManagers[index]->Reload();
1617
1618   //   QApplication::restoreOverrideCursor();
1619   int index = GetSlicerIndexFromItem(item);
1620   QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
1621   QString role=item->data(1,Qt::UserRole).toString();
1622   if ( role == "vector"){
1623     mSlicerManagers[index]->ReloadVF();
1624   }
1625   else if (role == "overlay"){
1626     mSlicerManagers[index]->ReloadOverlay();
1627   }
1628   else if (role == "fusion"){
1629     mSlicerManagers[index]->ReloadFusion();
1630   }
1631   else{
1632     mSlicerManagers[index]->Reload();
1633   }
1634   // Update view and info
1635   ImageInfoChanged();
1636   mSlicerManagers[index]->Render();
1637   QApplication::restoreOverrideCursor();
1638 }
1639 //------------------------------------------------------------------------------
1640
1641 //------------------------------------------------------------------------------
1642 void vvMainWindow::MousePositionChanged(int visibility,double x, double y, double z, double X, double Y, double Z , double value)
1643 {
1644   infoPanel->setCurrentInfo(visibility,x,y,z,X,Y,Z,value);
1645 }
1646 //------------------------------------------------------------------------------
1647
1648 //------------------------------------------------------------------------------
1649 void vvMainWindow::VectorChanged(int visibility,double x, double y, double z, double value)
1650 {
1651   overlayPanel->getCurrentVectorInfo(visibility,x,y,z,value);
1652 }
1653 //------------------------------------------------------------------------------
1654
1655 //------------------------------------------------------------------------------
1656 void vvMainWindow::OverlayChanged(int visibility, double valueOver, double valueRef)
1657 {
1658   overlayPanel->getCurrentOverlayInfo(visibility,valueOver, valueRef);
1659 }
1660 //------------------------------------------------------------------------------
1661
1662 //------------------------------------------------------------------------------
1663 void vvMainWindow::FusionChanged(int visibility, double value)
1664 {
1665   overlayPanel->getCurrentFusionInfo(visibility,value);
1666 }
1667 //------------------------------------------------------------------------------
1668
1669 //------------------------------------------------------------------------------
1670 void vvMainWindow::WindowLevelChanged()
1671 {
1672   // Base image
1673   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1674   if(index==-1) return;
1675   windowSpinBox->setValue(mSlicerManagers[index]->GetColorWindow());
1676   levelSpinBox->setValue(mSlicerManagers[index]->GetColorLevel());
1677   colorMapComboBox->setCurrentIndex(mSlicerManagers[index]->GetColorMap());
1678   presetComboBox->setCurrentIndex(mSlicerManagers[index]->GetPreset());
1679
1680   // Overlay image
1681   if (mSlicerManagers[index]->GetSlicer(0)->GetOverlay())
1682     overlayPanel->getOverlayProperty(mSlicerManagers[index]->GetOverlayColor(),
1683                                      mSlicerManagers[index]->GetLinkOverlayWindowLevel(),
1684                                      mSlicerManagers[index]->GetOverlayColorWindow(),
1685                                      mSlicerManagers[index]->GetOverlayColorLevel());
1686   else
1687     overlayPanel->getOverlayProperty(-1,0,0.,0.);
1688
1689   // Fusion image
1690   if (mSlicerManagers[index]->GetSlicer(0)->GetFusion())
1691     overlayPanel->getFusionProperty(mSlicerManagers[index]->GetFusionOpacity(),
1692                                     mSlicerManagers[index]->GetFusionThresholdOpacity(),
1693                                     mSlicerManagers[index]->GetFusionColorMap(),
1694                                     mSlicerManagers[index]->GetFusionWindow(),
1695                                     mSlicerManagers[index]->GetFusionLevel());
1696   else
1697     overlayPanel->getFusionProperty(-1, -1, -1, -1, -1);
1698 }
1699 //------------------------------------------------------------------------------
1700
1701 //------------------------------------------------------------------------------
1702 void vvMainWindow::WindowLevelEdited()
1703 {
1704   presetComboBox->setCurrentIndex(6);
1705   UpdateWindowLevel();
1706 }
1707 //------------------------------------------------------------------------------
1708
1709 //------------------------------------------------------------------------------
1710 void vvMainWindow::SetWindowLevel(double w, double l)
1711 {
1712   windowSpinBox->setValue(w);
1713   levelSpinBox->setValue(l);
1714   presetComboBox->setCurrentIndex(6);
1715   colorMapComboBox->setCurrentIndex(0);
1716   UpdateWindowLevel();
1717 }
1718 //------------------------------------------------------------------------------
1719
1720 //------------------------------------------------------------------------------
1721 void vvMainWindow::UpdateWindowLevel()
1722 {
1723   if (DataTree->selectedItems().size()) {
1724     if (presetComboBox->currentIndex() == 7) //For ventilation
1725       colorMapComboBox->setCurrentIndex(5);
1726     int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1727     mSlicerManagers[index]->SetColorWindow(windowSpinBox->value());
1728     mSlicerManagers[index]->SetColorLevel(levelSpinBox->value());
1729     mSlicerManagers[index]->SetPreset(presetComboBox->currentIndex());
1730     mSlicerManagers[index]->Render();
1731     WindowLevelChanged();
1732   }
1733 }
1734 //------------------------------------------------------------------------------
1735
1736 //------------------------------------------------------------------------------
1737 void vvMainWindow::UpdateSlicingPreset()
1738 {
1739   if (DataTree->selectedItems().size()) {
1740     int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1741     mSlicerManagers[index]->SetSlicingPreset(vvSlicerManager::SlicingPresetType(slicingPresetComboBox->currentIndex()));
1742   }
1743 }
1744 //------------------------------------------------------------------------------
1745
1746 //------------------------------------------------------------------------------
1747 void vvMainWindow::UpdateColorMap()
1748 {
1749   if (DataTree->selectedItems().size()) {
1750     int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1751     mSlicerManagers[index]->SetColorMap(colorMapComboBox->currentIndex());
1752     mSlicerManagers[index]->Render();
1753   }
1754 }
1755 //------------------------------------------------------------------------------
1756 void vvMainWindow::SwitchWindowLevel()
1757 {
1758   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1759   int window = mSlicerManagers[index]->GetColorWindow();
1760   presetComboBox->setCurrentIndex(6);
1761   windowSpinBox->setValue(-window);
1762   UpdateWindowLevel();
1763 }
1764 //------------------------------------------------------------------------------
1765
1766 //------------------------------------------------------------------------------
1767 void vvMainWindow::ApplyWindowLevelToAllImages()
1768 {
1769   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1770   if(index==-1) return;
1771   double window = mSlicerManagers[index]->GetColorWindow();
1772   double level = mSlicerManagers[index]->GetColorLevel();
1773
1774   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
1775     if (mSlicerManagers[i] == NULL)
1776       continue;
1777     mSlicerManagers[i]->SetColorWindow(window);
1778     mSlicerManagers[i]->SetColorLevel(level);
1779     mSlicerManagers[i]->SetPreset(6);
1780     mSlicerManagers[i]->Render();
1781   }
1782 }
1783 //------------------------------------------------------------------------------
1784
1785 //------------------------------------------------------------------------------
1786 void vvMainWindow::ApplyWindowToSetOfImages(double window, unsigned int indexMin, unsigned int indexMax)
1787 {
1788   for (unsigned int i = indexMin; i <= indexMax && i < mSlicerManagers.size(); i++) {
1789     if (mSlicerManagers[i] == NULL)
1790       continue;
1791     mSlicerManagers[i]->SetColorWindow(window);
1792     mSlicerManagers[i]->SetPreset(6);
1793     mSlicerManagers[i]->Render();
1794   }
1795 }
1796 //------------------------------------------------------------------------------
1797
1798 //------------------------------------------------------------------------------
1799 void vvMainWindow::ApplyLevelToSetOfImages(double level, unsigned int indexMin, unsigned int indexMax)
1800 {
1801   for (unsigned int i = indexMin; i <= indexMax && i < mSlicerManagers.size(); i++) {
1802     if (mSlicerManagers[i] == NULL)
1803       continue;
1804     mSlicerManagers[i]->SetColorLevel(level);
1805     mSlicerManagers[i]->SetPreset(6);
1806     mSlicerManagers[i]->Render();
1807   }
1808 }
1809 //------------------------------------------------------------------------------
1810
1811 //------------------------------------------------------------------------------
1812 void vvMainWindow::UpdateLinkManager(std::string id, int slicer, double x, double y, double z, int temps)
1813 {
1814   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
1815     if (mSlicerManagers[i]->GetId() == id) {
1816       //mSlicerManagers[i]->SetTSlice(temps);
1817       mSlicerManagers[i]->GetSlicer(slicer)->SetCurrentPosition(x,y,z,temps);
1818       mSlicerManagers[i]->UpdateViews(0,slicer);
1819       break;
1820     }
1821   }
1822 }
1823 //------------------------------------------------------------------------------
1824
1825 //------------------------------------------------------------------------------
1826 void vvMainWindow::UpdateLinkedNavigation(std::string id, vvSlicerManager * sm, vvSlicer* refSlicer)
1827 {
1828   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
1829     if (id == mSlicerManagers[i]->GetId()) {
1830       mSlicerManagers[i]->UpdateLinkedNavigation(refSlicer);
1831     }
1832   }
1833 }
1834 //------------------------------------------------------------------------------
1835
1836 //------------------------------------------------------------------------------
1837 void vvMainWindow::ShowContextMenu(QPoint point)
1838 {
1839   if (!DataTree->selectedItems().size()) {
1840     contextActions[1]->setEnabled(0);
1841     contextActions[2]->setEnabled(0);
1842     contextActions[3]->setEnabled(0);
1843     contextActions[4]->setEnabled(0);
1844     contextActions[5]->setEnabled(0);
1845     contextActions[6]->setEnabled(0);
1846   } else {
1847     int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1848     contextActions[1]->setEnabled(1);
1849     contextActions[2]->setEnabled(
1850       DataTree->itemWidget(DataTree->selectedItems()[0],
1851                            COLUMN_RELOAD_IMAGE)->isEnabled());
1852     contextActions[3]->setEnabled(1);
1853     contextActions[5]->setEnabled(1);
1854     contextActions[6]->setEnabled(1);
1855
1856     if (mSlicerManagers[index]->GetDimension() < 3)
1857       contextActions[4]->setEnabled(0);
1858     else
1859       contextActions[4]->setEnabled(1);
1860   }
1861   contextMenu.exec(QCursor::pos());
1862 }
1863 //------------------------------------------------------------------------------
1864
1865 //------------------------------------------------------------------------------
1866 void vvMainWindow::CloseImage()
1867 {
1868   CloseImage(DataTree->selectedItems()[0],0);
1869 }
1870 //------------------------------------------------------------------------------
1871
1872 //------------------------------------------------------------------------------
1873 void vvMainWindow::ReloadImage()
1874 {
1875   ReloadImage(DataTree->selectedItems()[0],0);
1876 }
1877 //------------------------------------------------------------------------------
1878
1879 //------------------------------------------------------------------------------
1880 void vvMainWindow::SelectOverlayImage()
1881 {
1882   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1883
1884   //check if one overlay image is added
1885   for (int child = 0; child < DataTree->topLevelItem(index)->childCount(); child++)
1886     if (DataTree->topLevelItem(index)->child(child)->data(1,Qt::UserRole).toString() == "overlay") {
1887       QString error = "Cannot add more than one compared image\n";
1888       error += "Please remove first ";
1889       error += DataTree->topLevelItem(index)->child(child)->data(COLUMN_IMAGE_NAME,Qt::DisplayRole).toString();
1890       QMessageBox::information(this,tr("Problem adding compared image !"),error);
1891       return;
1892     }
1893
1894   QString Extensions = EXTENSIONS;
1895   Extensions += ";;All Files (*)";
1896   QStringList files = QFileDialog::getOpenFileNames(this,tr("Load Overlay image"),mInputPathName,Extensions);
1897   if (files.isEmpty())
1898     return;
1899
1900   std::vector<std::string> vecFileNames;
1901   for (int i = 0; i < files.size(); i++) {
1902     vecFileNames.push_back(files[i].toStdString());
1903   }
1904   AddOverlayImage(index,vecFileNames,vvImageReader::IMAGE);
1905 }
1906 //------------------------------------------------------------------------------
1907
1908 //------------------------------------------------------------------------------
1909 void vvMainWindow::AddOverlayImage(int index, std::vector<std::string> fileNames, vvImageReader::LoadedImageType type)
1910 {
1911   QString file(fileNames[0].c_str());
1912   if (QFile::exists(file))
1913   {
1914     mInputPathName = itksys::SystemTools::GetFilenamePath(file.toStdString()).c_str();
1915     itk::ImageIOBase::Pointer reader = itk::ImageIOFactory::CreateImageIO(
1916         file.toStdString().c_str(), itk::ImageIOFactory::ReadMode);
1917     reader->SetFileName(fileNames[0].c_str());
1918     reader->ReadImageInformation();
1919     std::string component = reader->GetComponentTypeAsString(reader->GetComponentType());
1920     int dimension = reader->GetNumberOfDimensions();
1921     QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
1922     vvProgressDialog progress("Opening " + file.toStdString());
1923     qApp->processEvents();
1924
1925     std::string filename = itksys::SystemTools::GetFilenameWithoutExtension(file.toStdString()).c_str();
1926     if (mSlicerManagers[index]->SetOverlay(fileNames,dimension, component,type)) {
1927       //create an item in the tree with good settings
1928       QTreeWidgetItem *item = new QTreeWidgetItem();
1929       item->setData(0,Qt::UserRole,file.toStdString().c_str());
1930       item->setData(1,Qt::UserRole,tr("overlay"));
1931       QFileInfo fileinfo(file); //Do not show the path
1932       item->setData(COLUMN_IMAGE_NAME,Qt::DisplayRole,fileinfo.fileName());
1933       item->setToolTip(COLUMN_IMAGE_NAME, mSlicerManagers[index]->GetListOfAbsoluteFilePathInOneString("overlay").c_str());
1934       qApp->processEvents();
1935
1936       for (int j = 1; j <= 4; j++) {
1937         item->setData(j,Qt::CheckStateRole,DataTree->topLevelItem(index)->data(j,Qt::CheckStateRole));
1938       }
1939
1940       //Create the buttons for reload and close
1941       qApp->processEvents();
1942       QTreePushButton* cButton = new QTreePushButton;
1943       cButton->setItem(item);
1944       cButton->setColumn(COLUMN_CLOSE_IMAGE);
1945       cButton->setToolTip(tr("close image"));
1946       cButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/exit.png")));
1947       connect(cButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
1948           this,SLOT(CloseImage(QTreeWidgetItem*, int)));
1949
1950       QTreePushButton* rButton = new QTreePushButton;
1951       rButton->setItem(item);
1952       rButton->setColumn(COLUMN_RELOAD_IMAGE);
1953       rButton->setToolTip(tr("reload image"));
1954       rButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/rotateright.png")));
1955       connect(rButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
1956           this,SLOT(ReloadImage(QTreeWidgetItem*, int)));
1957
1958       DataTree->topLevelItem(index)->setExpanded(1);
1959       DataTree->topLevelItem(index)->addChild(item);
1960       DataTree->setItemWidget(item, COLUMN_CLOSE_IMAGE, cButton);
1961       DataTree->setItemWidget(item, COLUMN_RELOAD_IMAGE, rButton);
1962
1963       //set the id of the image
1964       QString id = DataTree->topLevelItem(index)->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString();
1965       item->setData(COLUMN_IMAGE_NAME,Qt::UserRole,id.toStdString().c_str());
1966       UpdateTree();
1967       qApp->processEvents();
1968       ImageInfoChanged();
1969       QApplication::restoreOverrideCursor();
1970
1971       // Update the display to update, e.g., the sliders
1972       for(int i=0; i<4; i++)
1973         DisplaySliders(index, i);
1974     } else {
1975       QApplication::restoreOverrideCursor();
1976       QString error = "Cannot import the new image.\n";
1977       error += mSlicerManagers[index]->GetLastError().c_str();
1978       QMessageBox::information(this,tr("Problem reading image !"),error);
1979     }
1980     WindowLevelChanged();
1981   }
1982   else
1983     QMessageBox::information(this,tr("Problem reading Overlay !"),"File doesn't exist!");
1984 }
1985 //------------------------------------------------------------------------------
1986
1987
1988 //------------------------------------------------------------------------------
1989 void vvMainWindow::AddROI(int index, QString file)
1990 {
1991   /*
1992   // Get slice manager
1993
1994   // Load image
1995
1996   vvImageReader * mReader = new vvImageReader;
1997   mReader->SetInputFilename(filename.toStdString());
1998   mReader->Update(IMAGE);
1999   if (mReader->GetLastError().size() != 0) {
2000     std::cerr << "Error while reading " << filename.toStdString() << std::endl;
2001     QString error = "Cannot open file \n";
2002     error += mReader->GetLastError().c_str();
2003     QMessageBox::information(this,tr("Reading problem"),error);
2004     delete mReader;
2005     return;
2006   }
2007   vvImage::Pointer roi = mReader->GetOutput();
2008
2009   // Create roi in new tool
2010   vvToolStructureSetManager::AddImage(mCurrentSlicerManager, roi);
2011   */
2012 }
2013 //------------------------------------------------------------------------------
2014
2015 //------------------------------------------------------------------------------
2016 void vvMainWindow::SelectFusionImage()
2017 {
2018   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2019
2020   //check if one fusion image is added
2021   for (int child = 0; child < DataTree->topLevelItem(index)->childCount(); child++)
2022     if (DataTree->topLevelItem(index)->child(child)->data(1,Qt::UserRole).toString() == "fusion") {
2023       QString error = "Cannot add more than one fusion image\n";
2024       error += "Please remove first ";
2025       error += DataTree->topLevelItem(index)->child(child)->data(COLUMN_IMAGE_NAME,Qt::DisplayRole).toString();
2026       QMessageBox::information(this,tr("Problem adding fusion image !"),error);
2027       return;
2028     }
2029
2030   QString Extensions = EXTENSIONS;
2031   Extensions += ";;All Files (*)";
2032   QString file = QFileDialog::getOpenFileName(this,tr("Load Fusion image"),mInputPathName,Extensions);
2033   if (!file.isEmpty())
2034     AddFusionImage(index,file);
2035 }
2036 //------------------------------------------------------------------------------
2037
2038 //------------------------------------------------------------------------------
2039 void vvMainWindow::ResetTransformationToIdentity()
2040 {
2041   std::string actorType = DataTree->selectedItems()[0]->data(1,Qt::UserRole).toString().toStdString();
2042   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2043   mSlicerManagers[index]->ResetTransformationToIdentity(actorType);
2044   ImageInfoChanged();
2045 }
2046 //------------------------------------------------------------------------------
2047
2048 //------------------------------------------------------------------------------
2049 void vvMainWindow::AddFusionImage(int index, QString file)
2050 {
2051   if (QFile::exists(file))
2052   {
2053     mInputPathName = itksys::SystemTools::GetFilenamePath(file.toStdString()).c_str();
2054     itk::ImageIOBase::Pointer reader = itk::ImageIOFactory::CreateImageIO(
2055         file.toStdString().c_str(), itk::ImageIOFactory::ReadMode);
2056     reader->SetFileName(file.toStdString().c_str());
2057     reader->ReadImageInformation();
2058     std::string component = reader->GetComponentTypeAsString(reader->GetComponentType());
2059     if (reader) {
2060       QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
2061       vvProgressDialog progress("Opening fusion");
2062       qApp->processEvents();
2063
2064       std::string filename = itksys::SystemTools::GetFilenameWithoutExtension(file.toStdString()).c_str();
2065       if (mSlicerManagers[index]->SetFusion(file.toStdString(),
2066             reader->GetNumberOfDimensions(), component)) {
2067         //create an item in the tree with good settings
2068         QTreeWidgetItem *item = new QTreeWidgetItem();
2069         item->setData(0,Qt::UserRole,file.toStdString().c_str());
2070         item->setData(1,Qt::UserRole,tr("fusion"));
2071         QFileInfo fileinfo(filename.c_str()); //Do not show the path
2072         item->setData(COLUMN_IMAGE_NAME,Qt::DisplayRole,fileinfo.fileName());
2073         item->setToolTip(COLUMN_IMAGE_NAME, mSlicerManagers[index]->GetListOfAbsoluteFilePathInOneString("fusion").c_str());
2074         qApp->processEvents();
2075
2076         for (int j = 1; j <= 4; j++) {
2077           item->setData(j,Qt::CheckStateRole,DataTree->topLevelItem(index)->data(j,Qt::CheckStateRole));
2078         }
2079
2080         //Create the buttons for reload and close
2081         qApp->processEvents();
2082         QTreePushButton* cButton = new QTreePushButton;
2083         cButton->setItem(item);
2084         cButton->setColumn(COLUMN_CLOSE_IMAGE);
2085         cButton->setToolTip(tr("close image"));
2086         cButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/exit.png")));
2087         connect(cButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
2088             this,SLOT(CloseImage(QTreeWidgetItem*, int)));
2089
2090         QTreePushButton* rButton = new QTreePushButton;
2091         rButton->setItem(item);
2092         rButton->setColumn(COLUMN_RELOAD_IMAGE);
2093         rButton->setToolTip(tr("reload image"));
2094         rButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/rotateright.png")));
2095         connect(rButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
2096             this,SLOT(ReloadImage(QTreeWidgetItem*, int)));
2097
2098         DataTree->topLevelItem(index)->setExpanded(1);
2099         DataTree->topLevelItem(index)->addChild(item);
2100         DataTree->setItemWidget(item, COLUMN_CLOSE_IMAGE, cButton);
2101         DataTree->setItemWidget(item, COLUMN_RELOAD_IMAGE, rButton);
2102
2103         //set the id of the image
2104         QString id = DataTree->topLevelItem(index)->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString();
2105         item->setData(COLUMN_IMAGE_NAME,Qt::UserRole,id.toStdString().c_str());
2106         UpdateTree();
2107         qApp->processEvents();
2108         ImageInfoChanged();
2109         QApplication::restoreOverrideCursor();
2110       } else {
2111         QApplication::restoreOverrideCursor();
2112         QString error = "Cannot import the new image.\n";
2113         error += mSlicerManagers[index]->GetLastError().c_str();
2114         QMessageBox::information(this,tr("Problem reading image !"),error);
2115       }
2116     } else {
2117       QString error = "Cannot import the new image.\n";
2118       QMessageBox::information(this,tr("Problem reading image !"),error);
2119     }
2120   }
2121   else
2122     QMessageBox::information(this,tr("Problem reading Fusion !"),"File doesn't exist!");
2123 }
2124 //------------------------------------------------------------------------------
2125 //------------------------------------------------------------------------------
2126 void vvMainWindow::AddLandmarks(int index, std::vector<std::string> files)
2127 {
2128     if (!landmarksPanel->LoadFromFile(files))
2129       QMessageBox::information(this,tr("Problem reading Landmarks !"),"File doesn't exist!");
2130
2131     landmarksPanel->SetCurrentPath(mInputPathName.toStdString());
2132     landmarksPanel->SetCurrentImage(mSlicerManagers[index]->GetFileName().c_str());
2133 }
2134
2135 //------------------------------------------------------------------------------
2136 void vvMainWindow::OpenField()
2137 {
2138   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2139   //check if a vector field has already been added
2140   for (int child = 0; child < DataTree->topLevelItem(index)->childCount(); child++)
2141     if (DataTree->topLevelItem(index)->child(child)->data(1,Qt::UserRole).toString() == "vector") {
2142       QString error = "Cannot add more than one vector field\n";
2143       error += "Please remove first ";
2144       error += DataTree->topLevelItem(index)->child(child)->data(COLUMN_IMAGE_NAME,Qt::DisplayRole).toString();
2145       QMessageBox::information(this,tr("Problem adding vector field!"),error);
2146       return;
2147     }
2148
2149   QString Extensions = "Images ( *.mhd)";
2150   Extensions += ";;Images ( *.mha)";
2151   Extensions += ";;VF Images ( *.vf)";
2152   Extensions += ";;nii Images ( *.nii)";
2153   Extensions += ";;nrrd Images ( *.nrrd)";
2154   Extensions += ";;nhdr Images ( *.nhdr)";
2155   Extensions += ";;All Files (*)";
2156   QString file = QFileDialog::getOpenFileName(this,tr("Load deformation field"),mInputPathName,Extensions);
2157   if (!file.isEmpty())
2158     AddField(file,index);
2159 }
2160 //------------------------------------------------------------------------------
2161
2162
2163 //------------------------------------------------------------------------------
2164 void vvMainWindow::AddFieldEntry(QString filename,int index,bool from_disk)
2165 {
2166   //create an item in the tree with good settings
2167   QTreeWidgetItem *item = new QTreeWidgetItem();
2168   item->setData(0,Qt::UserRole,filename.toStdString().c_str());
2169   item->setData(1,Qt::UserRole,tr("vector"));
2170   QFileInfo fileinfo(filename); //Do not show the path
2171   item->setData(COLUMN_IMAGE_NAME,Qt::DisplayRole,fileinfo.fileName());
2172   item->setToolTip(COLUMN_IMAGE_NAME, mSlicerManagers[index]->GetListOfAbsoluteFilePathInOneString("vector").c_str());
2173   qApp->processEvents();
2174
2175   for (int j = 1; j <= 4; j++) {
2176     item->setData(j,Qt::CheckStateRole,DataTree->topLevelItem(index)->data(j,Qt::CheckStateRole));
2177   }
2178
2179   //Create the buttons for reload and close
2180   qApp->processEvents();
2181   QTreePushButton* cButton = new QTreePushButton;
2182   cButton->setItem(item);
2183   cButton->setColumn(COLUMN_CLOSE_IMAGE);
2184   cButton->setToolTip(tr("close vector field"));
2185   cButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/exit.png")));
2186   connect(cButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
2187           this,SLOT(CloseImage(QTreeWidgetItem*, int)));
2188
2189   QTreePushButton* rButton = new QTreePushButton;
2190   rButton->setItem(item);
2191   rButton->setColumn(COLUMN_RELOAD_IMAGE);
2192   rButton->setToolTip(tr("reload vector field"));
2193   rButton->setEnabled(from_disk);
2194   rButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/rotateright.png")));
2195   connect(rButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
2196           this,SLOT(ReloadImage(QTreeWidgetItem*, int)));
2197
2198   DataTree->topLevelItem(index)->setExpanded(1);
2199   DataTree->topLevelItem(index)->addChild(item);
2200   DataTree->setItemWidget(item, COLUMN_RELOAD_IMAGE, rButton);
2201   DataTree->setItemWidget(item, COLUMN_CLOSE_IMAGE, cButton);
2202
2203   //set the id of the image
2204   QString id = DataTree->topLevelItem(index)->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString();
2205   item->setData(COLUMN_IMAGE_NAME,Qt::UserRole,id.toStdString().c_str());
2206   UpdateTree();
2207   qApp->processEvents();
2208   ImageInfoChanged();
2209   QApplication::restoreOverrideCursor();
2210 }
2211 //------------------------------------------------------------------------------
2212
2213
2214 //------------------------------------------------------------------------------
2215 void vvMainWindow::AddField(vvImage::Pointer vf,QString file,int index)
2216 {
2217   QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
2218   vvSlicerManager* imageManager = mSlicerManagers[index];
2219   if (imageManager->SetVF(vf,file.toStdString())) {
2220     AddFieldEntry(file,index,false);
2221   } else {
2222     QString error = "Cannot import the vector field for this image.\n";
2223     error += imageManager->GetLastError().c_str();
2224     QMessageBox::information(this,tr("Problem reading VF !"),error);
2225   }
2226   QApplication::restoreOverrideCursor();
2227 }
2228 //------------------------------------------------------------------------------
2229
2230
2231 //------------------------------------------------------------------------------
2232 void vvMainWindow::AddField(QString file,int index)
2233 {
2234   if (QFile::exists(file)) {
2235     mInputPathName = itksys::SystemTools::GetFilenamePath(file.toStdString()).c_str();
2236
2237     //init the progress events
2238     QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
2239     vvProgressDialog progress("Opening " + file.toStdString());
2240     qApp->processEvents();
2241
2242     //read the vector and put it in the current mSlicerManager
2243     vvSlicerManager* imageManager = mSlicerManagers[index];
2244     qApp->processEvents();
2245
2246     std::string filename = itksys::SystemTools::GetFilenameWithoutExtension(file.toStdString()).c_str();
2247     if (imageManager->SetVF(file.toStdString())) {
2248       imageManager->Render();
2249       AddFieldEntry(file,index,true);
2250     } else {
2251       QApplication::restoreOverrideCursor();
2252       QString error = "Cannot import the vector field for this image.\n";
2253       error += imageManager->GetLastError().c_str();
2254       QMessageBox::information(this,tr("Problem reading VF !"),error);
2255     }
2256   } else
2257     QMessageBox::information(this,tr("Problem reading VF !"),"File doesn't exist!");
2258
2259 }
2260 //------------------------------------------------------------------------------
2261
2262
2263 //------------------------------------------------------------------------------
2264 void vvMainWindow::SetVFProperty(int subsampling, int scale, int log, int width, double r, double g, double b)
2265 {
2266   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2267   if (mSlicerManagers[index]->GetSlicer(0)->GetVF()) {
2268     for (int i = 0; i < 4; i++) {
2269       mSlicerManagers[index]->GetSlicer(i)->SetVFSubSampling(subsampling);
2270       mSlicerManagers[index]->GetSlicer(i)->SetVFScale(scale);
2271       mSlicerManagers[index]->GetSlicer(i)->SetVFWidth(width);
2272       mSlicerManagers[index]->GetSlicer(i)->SetVFColor(r,g,b);
2273       if (log > 0)
2274         mSlicerManagers[index]->GetSlicer(i)->SetVFLog(1);
2275       else
2276         mSlicerManagers[index]->GetSlicer(i)->SetVFLog(0);
2277     }
2278   }
2279 }
2280 //------------------------------------------------------------------------------
2281
2282
2283 //------------------------------------------------------------------------------
2284 void vvMainWindow::SetOverlayProperty(int color, int linked, double window, double level)
2285 {
2286   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2287   if (mSlicerManagers[index]->GetSlicer(0)->GetOverlay()) {
2288     mSlicerManagers[index]->SetOverlayColor(color);
2289     mSlicerManagers[index]->SetColorMap(0);
2290     mSlicerManagers[index]->SetLinkOverlayWindowLevel(linked);
2291     mSlicerManagers[index]->SetOverlayColorWindow(window);
2292     mSlicerManagers[index]->SetOverlayColorLevel(level);
2293     mSlicerManagers[index]->Render();
2294   }
2295 }
2296 //------------------------------------------------------------------------------
2297
2298 //------------------------------------------------------------------------------
2299 void vvMainWindow::SetFusionProperty(int opacity, int thresOpacity, int colormap,double window, double level, bool showLegend)
2300 {
2301   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2302   if (mSlicerManagers[index]->GetSlicer(0)->GetFusion()) {
2303     mSlicerManagers[index]->SetFusionColorMap(colormap);
2304     mSlicerManagers[index]->SetFusionOpacity(opacity);
2305     mSlicerManagers[index]->SetFusionThresholdOpacity(thresOpacity);
2306     mSlicerManagers[index]->SetFusionWindow(window);
2307     mSlicerManagers[index]->SetFusionLevel(level);
2308     mSlicerManagers[index]->SetFusionShowLegend(showLegend);
2309     mSlicerManagers[index]->SetColorMap(0);
2310     mSlicerManagers[index]->Render();
2311   }
2312 }
2313 //------------------------------------------------------------------------------
2314
2315 //------------------------------------------------------------------------------
2316 void vvMainWindow::SaveAs()
2317 {
2318   if (DataTree->selectedItems()[0]->data(1,Qt::UserRole).toString() == "vector") {
2319     QMessageBox::warning(this,tr("Unsupported type"),tr("Sorry, saving a vector field is unsupported for the moment"));
2320     return;
2321   }
2322
2323   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2324   int dimension = mSlicerManagers[index]->GetDimension();
2325   QStringList OutputListeFormat;
2326   OutputListeFormat.clear();
2327   if (dimension == 1) {
2328     OutputListeFormat.push_back(".mhd");
2329     OutputListeFormat.push_back(".mha");
2330   }
2331   if (dimension == 2) {
2332     OutputListeFormat.push_back(".bmp");
2333     OutputListeFormat.push_back(".png");
2334     OutputListeFormat.push_back(".jpeg");
2335     OutputListeFormat.push_back(".tif");
2336     OutputListeFormat.push_back(".mhd");
2337     OutputListeFormat.push_back(".mha");
2338     OutputListeFormat.push_back(".hdr");
2339     OutputListeFormat.push_back(".vox");
2340   } else if (dimension == 3) {
2341     OutputListeFormat.push_back(".mhd");
2342     OutputListeFormat.push_back(".mha");
2343     OutputListeFormat.push_back(".nii");
2344     OutputListeFormat.push_back(".nrrd");
2345     OutputListeFormat.push_back(".nhdr");
2346     OutputListeFormat.push_back(".hdr");
2347     OutputListeFormat.push_back(".vox");
2348   } else if (dimension == 4) {
2349     OutputListeFormat.push_back(".mhd");
2350     OutputListeFormat.push_back(".mha");
2351     OutputListeFormat.push_back(".nii");
2352     OutputListeFormat.push_back(".nrrd");
2353     OutputListeFormat.push_back(".nhdr");
2354   }
2355   QString Extensions = "AllFiles(*.*)";
2356   for (int i = 0; i < OutputListeFormat.count(); i++) {
2357     Extensions += ";;Images ( *";
2358     Extensions += OutputListeFormat[i];
2359     Extensions += ")";
2360   }
2361   QString fileName = QFileDialog::getSaveFileName(this,
2362                      tr("Save As"),
2363                      mSlicerManagers[index]->GetFileName().c_str(),
2364                      Extensions);
2365   if (!fileName.isEmpty()) {
2366     std::string fileformat = itksys::SystemTools::GetFilenameLastExtension(fileName.toStdString());
2367     if (OutputListeFormat.contains(
2368           fileformat.c_str())) {
2369       QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
2370       std::string action = "Saving";
2371       vvProgressDialog progress("Saving "+fileName.toStdString());
2372       qApp->processEvents();
2373       vvImageWriter::Pointer writer = vvImageWriter::New();
2374       writer->SetOutputFileName(fileName.toStdString());
2375       writer->SetInput(mSlicerManagers[index]->GetImage());
2376
2377       // Check on transform and prompt user
2378       writer->SetSaveTransform(false);
2379       bool bId = true;
2380       for(int i=0; i<4; i++)
2381         for(int j=0; j<4; j++) {
2382           // TODO SR and BP: check on the list of transforms and not the first only
2383           double elt = mSlicerManagers[index]->GetImage()->GetTransform()[0]->GetMatrix()->GetElement(i,j);
2384           if(i==j && elt!=1.)
2385             bId = false;
2386           if(i!=j && elt!=0.)
2387             bId = false;
2388         }
2389       if( !bId ) {
2390         QString warning = "The image has an associated linear transform. Do you want to save it along?";
2391         QMessageBox msgBox(QMessageBox::Warning, tr("Save transform"), warning, 0, this);
2392         msgBox.addButton(tr("Yes"), QMessageBox::AcceptRole);
2393         msgBox.addButton(tr("No"), QMessageBox::RejectRole);
2394         if (msgBox.exec() == QMessageBox::AcceptRole)
2395           writer->SetSaveTransform(true);
2396       }
2397
2398       writer->Update();
2399       QApplication::restoreOverrideCursor();
2400       if (writer->GetLastError().size()) {
2401         QString error = "Saving did not succeed\n";
2402         error += writer->GetLastError().c_str();
2403         QMessageBox::information(this,tr("Saving Problem"),error);
2404         SaveAs();
2405       }
2406     } else {
2407       QString error = fileformat.c_str();
2408       if (error.isEmpty())
2409         error += "no file format specified !";
2410       else
2411         error += " format unknown !!!\n";
2412       QMessageBox::information(this,tr("Saving Problem"),error);
2413       SaveAs();
2414     }
2415   }
2416 }
2417 //------------------------------------------------------------------------------
2418
2419 //------------------------------------------------------------------------------
2420 void vvMainWindow::SaveCurrentState()
2421 {
2422   QString Extensions = "XML Files(*.xml)";
2423   QString fileName = QFileDialog::getSaveFileName(this,
2424                      tr("Save Current Window State"),
2425                      "",
2426                      Extensions);
2427
2428   SaveCurrentStateAs(fileName.toStdString());
2429 }
2430 //------------------------------------------------------------------------------
2431
2432 //------------------------------------------------------------------------------
2433 void vvMainWindow::SaveCurrentStateAs(const std::string& stateFile)
2434 {
2435   vvSaveState save_state;
2436   save_state.Run(this, stateFile);
2437 }
2438
2439 //------------------------------------------------------------------------------
2440 void vvMainWindow::ReadSavedState()
2441 {
2442   QString Extensions = "XML Files(*.xml)";
2443   QString fileName = QFileDialog::getOpenFileName(this,
2444                      tr("Load Window State"),
2445                      "",
2446                      Extensions);
2447
2448   ReadSavedStateFile(fileName.toStdString());
2449 }
2450 //------------------------------------------------------------------------------
2451
2452 //------------------------------------------------------------------------------
2453 void vvMainWindow::ReadSavedStateFile(const std::string& stateFile)
2454 {
2455   vvReadState read_state;
2456   read_state.Run(this, stateFile);
2457 }
2458 //------------------------------------------------------------------------------
2459
2460 //------------------------------------------------------------------------------
2461 void vvMainWindow::LinkAllImages()
2462 {
2463         linkPanel->linkAll();
2464 }
2465
2466 //------------------------------------------------------------------------------
2467 void vvMainWindow::AddLink(QString image1,QString image2,bool fromPanel)
2468 {
2469   if (!fromPanel) {
2470     // delegate to linkPanel if call came from elsewhere...
2471     linkPanel->addLinkFromIds(image1, image2);
2472     return;
2473   }
2474
2475   unsigned int sm1 = 0;
2476   unsigned int sm2 = 0;
2477
2478   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
2479     if (image1.toStdString() == mSlicerManagers[i]->GetId()) {
2480       mSlicerManagers[i]->AddLink(image2.toStdString());
2481       sm1 = i;
2482     }
2483     if (image2.toStdString() == mSlicerManagers[i]->GetId()) {
2484       mSlicerManagers[i]->AddLink(image1.toStdString());
2485       sm2 = i;
2486     }
2487   }
2488
2489   if (linkPanel->isLinkAll())   {
2490     emit UpdateLinkedNavigation(mSlicerManagers[sm1]->GetId(), mSlicerManagers[mCurrentPickedImageIndex], mSlicerManagers[mCurrentPickedImageIndex]->GetSlicer(0));
2491     emit UpdateLinkedNavigation(mSlicerManagers[sm2]->GetId(), mSlicerManagers[mCurrentPickedImageIndex], mSlicerManagers[mCurrentPickedImageIndex]->GetSlicer(0));
2492   } else {
2493     emit UpdateLinkedNavigation(mSlicerManagers[sm2]->GetId(), mSlicerManagers[sm1], mSlicerManagers[sm1]->GetSlicer(0));
2494   }
2495 }
2496
2497 //------------------------------------------------------------------------------
2498
2499
2500 //------------------------------------------------------------------------------
2501 void vvMainWindow::RemoveLink(QString image1,QString image2)
2502 {
2503   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
2504     if (image1.toStdString() == mSlicerManagers[i]->GetId()) {
2505       mSlicerManagers[i]->RemoveLink(image2.toStdString());
2506     }
2507     if (image2.toStdString() == mSlicerManagers[i]->GetId()) {
2508       mSlicerManagers[i]->RemoveLink(image1.toStdString());
2509     }
2510   }
2511 }
2512 //------------------------------------------------------------------------------
2513
2514 //------------------------------------------------------------------------------
2515 void vvMainWindow::ChangeImageWithIndexOffset(vvSlicerManager *sm, int slicer, int offset)
2516 {
2517   if(mSlicerManagers.size()==1)
2518     return;
2519
2520   int index = 0;
2521   while(sm != mSlicerManagers[index])
2522     index++;
2523   index = (index+offset+mSlicerManagers.size()) % mSlicerManagers.size();
2524
2525   QTreeWidgetItem* item = GetItemFromSlicerManager(mSlicerManagers[index]);
2526   item->setData(slicer+1,Qt::CheckStateRole,2);         //change checkbox
2527   CurrentImageChanged(mSlicerManagers[index]->GetId()); //select new image
2528   DisplayChanged(item,slicer+1);
2529 }
2530 //------------------------------------------------------------------------------
2531
2532 void vvMainWindow::HorizontalSliderMoved(int value,int column, int slicer_index)
2533 {
2534   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
2535     if (DataTree->topLevelItem(i)->data(column,Qt::CheckStateRole).toInt() > 1) {
2536       for (int j = 0; j < 4; j++) {
2537         mSlicerManagers[i]->SetTSliceInSlicer(value,j);
2538         //if (mSlicerManagers[i]->GetSlicer(j)->GetImageActor()->GetVisibility())
2539         //UpdateTSlice(j,value);
2540       }
2541       mSlicerManagers[i]->GetSlicer(slicer_index)->Render();
2542       break;
2543     }
2544   }
2545 }
2546 //------------------------------------------------------------------------------
2547
2548
2549 //------------------------------------------------------------------------------
2550 void vvMainWindow::NOHorizontalSliderMoved()
2551 {
2552   // if (mCurrentTime == NOHorizontalSlider->value()) return;
2553   HorizontalSliderMoved(NOHorizontalSlider->value(),COLUMN_UL_VIEW,0);
2554 //  mCurrentTime = NOHorizontalSlider->value();
2555 }
2556 //------------------------------------------------------------------------------
2557
2558
2559 //------------------------------------------------------------------------------
2560 void vvMainWindow::NEHorizontalSliderMoved()
2561 {
2562   // if (mCurrentTime == NEHorizontalSlider->value()) return;
2563   HorizontalSliderMoved(NEHorizontalSlider->value(),COLUMN_UR_VIEW,1);
2564 //  mCurrentTime = NEHorizontalSlider->value();
2565 }
2566 //------------------------------------------------------------------------------
2567
2568
2569 //------------------------------------------------------------------------------
2570 void vvMainWindow::SOHorizontalSliderMoved()
2571 {
2572   // if (mCurrentTime == SOHorizontalSlider->value()) return;
2573   HorizontalSliderMoved(SOHorizontalSlider->value(),COLUMN_DL_VIEW,2);
2574   // mCurrentTime = SOHorizontalSlider->value();
2575 }
2576 //------------------------------------------------------------------------------
2577
2578
2579 //------------------------------------------------------------------------------
2580 void vvMainWindow::SEHorizontalSliderMoved()
2581 {
2582   // if (mCurrentTime == SEHorizontalSlider->value()) return;
2583   HorizontalSliderMoved(SEHorizontalSlider->value(),COLUMN_DR_VIEW,3);
2584   // mCurrentTime = SEHorizontalSlider->value();
2585 }
2586 //------------------------------------------------------------------------------
2587
2588 //------------------------------------------------------------------------------
2589 void vvMainWindow::NOVerticalSliderChanged()
2590 {
2591   static int value=-1;
2592   if (value == NOVerticalSlider->value()) return;
2593   else value = NOVerticalSlider->value();
2594   //  int value = NOVerticalSlider->value();
2595   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
2596     if (DataTree->topLevelItem(i)->data(COLUMN_UL_VIEW,Qt::CheckStateRole).toInt() > 1) {
2597       if (mSlicerManagers[i]->GetSlicer(0)->GetSlice() != value) {
2598         mSlicerManagers[i]->GetSlicer(0)->SetSlice(value);
2599         mSlicerManagers[i]->VerticalSliderHasChanged(0, value);
2600
2601         // If nor Update/Render -> slider not work
2602         // only render = ok navigation, but for contour Update needed but slower ?
2603
2604         mSlicerManagers[i]->UpdateSlice(0);  // <-- DS add this. Not too much update ? YES. but needed for ImageContour ...
2605         //mSlicerManagers[i]->GetSlicer(0)->Render(); // <-- DS add this, needed for contour, seems ok ? not too slow ?
2606       }
2607       break;
2608     }
2609   }
2610 }
2611 //------------------------------------------------------------------------------
2612
2613
2614 //------------------------------------------------------------------------------
2615 void vvMainWindow::NEVerticalSliderChanged()
2616 {
2617   static int value=-1;
2618   if (value == NEVerticalSlider->value()) return;
2619   else value = NEVerticalSlider->value();
2620   //  int value = NEVerticalSlider->value();
2621   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
2622     if (DataTree->topLevelItem(i)->data(COLUMN_UR_VIEW,Qt::CheckStateRole).toInt() > 1) {
2623       if (mSlicerManagers[i]->GetSlicer(1)->GetSlice() != value) {
2624         mSlicerManagers[i]->GetSlicer(1)->SetSlice(value);
2625         mSlicerManagers[i]->VerticalSliderHasChanged(1, value);
2626         mSlicerManagers[i]->UpdateSlice(1);
2627         //mSlicerManagers[i]->GetSlicer(1)->Render(); // <-- DS add this, needed for contour, seems ok ? not too slow ?
2628       }
2629       break;
2630     }
2631   }
2632 }
2633 //------------------------------------------------------------------------------
2634
2635
2636 //------------------------------------------------------------------------------
2637 void vvMainWindow::SOVerticalSliderChanged()
2638 {
2639   static int value=-1;
2640   if (value == SOVerticalSlider->value()) return;
2641   else value = SOVerticalSlider->value();
2642   //int value = SOVerticalSlider->value();
2643   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
2644     if (DataTree->topLevelItem(i)->data(COLUMN_DL_VIEW,Qt::CheckStateRole).toInt() > 1) {
2645       if (mSlicerManagers[i]->GetSlicer(2)->GetSlice() != value) {
2646         mSlicerManagers[i]->GetSlicer(2)->SetSlice(value);
2647         mSlicerManagers[i]->VerticalSliderHasChanged(2, value);
2648         mSlicerManagers[i]->UpdateSlice(2);
2649         //mSlicerManagers[i]->GetSlicer(2)->Render(); // <-- DS add this, needed for contour, seems ok ? not too slow ?
2650       }
2651       // else { DD("avoid SOVerticalSlider slicer update"); }
2652       break;
2653     }
2654   }
2655 }
2656 //------------------------------------------------------------------------------
2657
2658
2659 //------------------------------------------------------------------------------
2660 void vvMainWindow::SEVerticalSliderChanged()
2661 {
2662   static int value=-1;
2663   if (value == SEVerticalSlider->value()) return;
2664   else value = SEVerticalSlider->value();
2665   // int value = SEVerticalSlider->value();
2666   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
2667     if (DataTree->topLevelItem(i)->data(COLUMN_DR_VIEW,Qt::CheckStateRole).toInt() > 1) {
2668       if (mSlicerManagers[i]->GetSlicer(3)->GetSlice() != value) {
2669         mSlicerManagers[i]->GetSlicer(3)->SetSlice(value);
2670         mSlicerManagers[i]->VerticalSliderHasChanged(3, value);
2671         mSlicerManagers[i]->UpdateSlice(3);
2672         //mSlicerManagers[i]->GetSlicer(3)->Render(); // <-- DS add this, needed for contour, seems ok ? not too slow ?
2673       }
2674       break;
2675     }
2676   }
2677 }
2678 //------------------------------------------------------------------------------
2679
2680
2681 //------------------------------------------------------------------------------
2682 void vvMainWindow::UpdateSlice(int slicer, int slice)
2683 {
2684   // DD("vvMainWindow::UpdateSlice");
2685 //   DD(slicer);
2686 //   DD(slice);
2687   if (slicer == 0) {
2688     //    if (slice != NOVerticalSlider->value())
2689     NOVerticalSlider->setValue(slice);
2690   } else {
2691     if (slicer == 1)
2692       NEVerticalSlider->setValue(slice);
2693     else {
2694       if (slicer == 2)
2695         SOVerticalSlider->setValue(slice);
2696       else {
2697         if (slicer == 3)
2698           SEVerticalSlider->setValue(slice);
2699       }
2700     }
2701   }
2702   // DD("vvMainWindow:UpdateSlice END");
2703 }
2704 //------------------------------------------------------------------------------
2705
2706
2707 //------------------------------------------------------------------------------
2708 void vvMainWindow::UpdateTSlice(int slicer, int slice)
2709 {
2710   switch (slicer) {
2711   case 0:
2712     NOHorizontalSlider->setValue(slice);
2713     break;
2714   case 1:
2715     NEHorizontalSlider->setValue(slice);
2716     break;
2717   case 2:
2718     SOHorizontalSlider->setValue(slice);
2719     break;
2720   case 3:
2721     SEHorizontalSlider->setValue(slice);
2722     break;
2723   }
2724 }
2725 //------------------------------------------------------------------------------
2726
2727
2728 //------------------------------------------------------------------------------
2729 void vvMainWindow::UpdateSliceRange(int slicer, int min, int max, int tmin, int tmax)
2730 {
2731   //int position = int((min+max)/2);
2732   int position = mSlicerManagers[mCurrentPickedImageIndex]->GetSlicer(slicer)->GetSlice();
2733   if (slicer == 0) {
2734     NOVerticalSlider->setRange(min,max);
2735     NOHorizontalSlider->setRange(tmin,tmax);
2736     NOVerticalSlider->setValue(position);
2737   } else if (slicer == 1) {
2738     NEVerticalSlider->setRange(min,max);
2739     NEHorizontalSlider->setRange(tmin,tmax);
2740     NEVerticalSlider->setValue(position);
2741   } else if (slicer == 2) {
2742     SOVerticalSlider->setRange(min,max);
2743     SOHorizontalSlider->setRange(tmin,tmax);
2744     SOVerticalSlider->setValue(position);
2745   } else if (slicer == 3) {
2746     SEVerticalSlider->setRange(min,max);
2747     SEHorizontalSlider->setRange(tmin,tmax);
2748     SEVerticalSlider->setValue(position);
2749   }
2750 }
2751 //------------------------------------------------------------------------------
2752
2753
2754 //------------------------------------------------------------------------------
2755 void vvMainWindow::SaveNOScreenshot()
2756 {
2757   SaveScreenshot(NOViewWidget);
2758 }
2759 //------------------------------------------------------------------------------
2760
2761
2762 //------------------------------------------------------------------------------
2763 void vvMainWindow::SaveNEScreenshot()
2764 {
2765   SaveScreenshot(NEViewWidget);
2766 }
2767 //------------------------------------------------------------------------------
2768
2769
2770 //------------------------------------------------------------------------------
2771 void vvMainWindow::SaveSOScreenshot()
2772 {
2773   SaveScreenshot(SOViewWidget);
2774 }
2775 //------------------------------------------------------------------------------
2776
2777
2778 //------------------------------------------------------------------------------
2779 void vvMainWindow::SaveSEScreenshot()
2780 {
2781   SaveScreenshot(SEViewWidget);
2782 }
2783 //------------------------------------------------------------------------------
2784
2785
2786 //------------------------------------------------------------------------------
2787 void vvMainWindow::SaveScreenshotAllSlices()
2788 {
2789   QVTKWidget *widget = NOViewWidget;
2790
2791   int index = 0;// GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2792   vvSlicerManager * SM = mSlicerManagers[index];
2793   vvImage * image = SM->GetImage();
2794   vvSlicer * slicer = SM->GetSlicer(0);
2795   int orientation = slicer->GetOrientation();
2796   int nbSlices = image->GetSize()[orientation];
2797   vtkSmartPointer<vtkRenderWindow>  renderWindow = widget->GetRenderWindow();
2798
2799   // Select filename base
2800   QString filename = QFileDialog::getSaveFileName(this,
2801                                                   tr("Save As (filename will be completed by slice number)"),
2802                                                   itksys::SystemTools::GetFilenamePath(mSlicerManagers[index]->GetFileName()).c_str(),
2803                                                   "Images( *.png);;Images( *.jpg)");
2804
2805   // Loop on slices
2806   for(int i=0; i<nbSlices; i++) {
2807     // Change the slice
2808     slicer->SetSlice(i); // -> change the slice of the current slicer
2809     SM->UpdateSlice(0); // --> this one emit UpdateSlice
2810     QCoreApplication::flush(); // -> needed to force display of contours
2811
2812     // Screenshot
2813     vtkSmartPointer<vtkWindowToImageFilter> windowToImageFilter = vtkSmartPointer<vtkWindowToImageFilter>::New();
2814     windowToImageFilter->SetInput(renderWindow);
2815     windowToImageFilter->SetMagnification(1);
2816     windowToImageFilter->SetInputBufferTypeToRGBA(); //also record the alpha (transparency) channel
2817     windowToImageFilter->Update();
2818
2819     vtkSmartPointer<vtkPNGWriter> writer = vtkSmartPointer<vtkPNGWriter>::New();
2820     std::string fn = itksys::SystemTools::GetFilenameWithoutLastExtension(filename.toStdString());
2821     std::string num = clitk::toString(i);
2822     if (i<10) num = "0"+num;
2823     if (i<100) num = "0"+num;
2824     if (i<1000) num = "0"+num;
2825
2826     fn = itksys::SystemTools::GetFilenamePath(filename.toStdString()) + "/"+ fn
2827       + "_" + num + itksys::SystemTools::GetFilenameLastExtension(filename.toStdString());
2828     writer->SetFileName(fn.c_str());
2829     writer->SetInput(windowToImageFilter->GetOutput());
2830     writer->Write();
2831   }
2832 }
2833 //------------------------------------------------------------------------------
2834
2835
2836 //------------------------------------------------------------------------------
2837 void vvMainWindow::SaveScreenshot(QVTKWidget *widget)
2838 {
2839   QString Extensions = "Images( *.png);;";
2840   Extensions += "Images( *.jpg);;";
2841   Extensions += "Images( *.bmp);;";
2842   Extensions += "Images( *.tif);;";
2843   Extensions += "Images( *.ppm)";
2844 #if defined(VTK_USE_FFMPEG_ENCODER) || defined(VTK_USE_VIDEO_FOR_WINDOWS)
2845   Extensions += ";;Video( *.avi)";
2846 #endif
2847 #ifdef VTK_USE_MPEG2_ENCODER
2848   Extensions += ";;Video( *.mpg)";
2849 #endif
2850 #ifdef CLITK_EXPERIMENTAL
2851   Extensions += ";;Video( *.gif)";
2852 #endif
2853
2854   int smIndex=GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2855   QString fileName = QFileDialog::getSaveFileName(this,
2856                      tr("Save As"),
2857                      itksys::SystemTools::GetFilenamePath(mSlicerManagers[smIndex]->GetFileName()).c_str(),
2858                      Extensions);
2859
2860   if (!fileName.isEmpty()) {
2861     vtkSmartPointer<vtkWindowToImageFilter> w2i = vtkSmartPointer<vtkWindowToImageFilter>::New();
2862     w2i->SetInput(widget->GetRenderWindow());
2863     w2i->Update();
2864     vtkImageData *image = w2i->GetOutput();
2865
2866     std::string ext(itksys::SystemTools::GetFilenameLastExtension(fileName.toStdString()));
2867
2868     // Image
2869     vtkImageWriter *imgwriter = NULL;
2870     if (ext==".bmp")
2871       imgwriter = vtkBMPWriter::New();
2872     else if (ext==".tif")
2873       imgwriter = vtkTIFFWriter::New();
2874     else if (ext==".ppm")
2875       imgwriter = vtkPNMWriter::New();
2876     else if (ext==".png")
2877       imgwriter = vtkPNGWriter::New();
2878     else if (ext==".jpg")
2879       imgwriter = vtkJPEGWriter::New();
2880
2881     // Snapshot image if not null
2882     if(imgwriter!=NULL) {
2883       imgwriter->SetInput(image);
2884       imgwriter->SetFileName(fileName.toStdString().c_str());
2885       imgwriter->Write();
2886       return;
2887     }
2888
2889     // Video
2890     vtkGenericMovieWriter *vidwriter = NULL;
2891 #if CLITK_EXPERIMENTAL == 1
2892     if (ext==".gif") {
2893       vvAnimatedGIFWriter *gif = vvAnimatedGIFWriter::New();
2894       vidwriter = gif;
2895
2896       // FPS
2897       bool ok;
2898       int fps = QInputDialog::getInteger(this, tr("Number of frames per second"),
2899                                      tr("FPS:"), 5, 0, 1000, 1, &ok);
2900       if(ok)
2901         gif->SetRate(fps);
2902
2903       // Loops
2904       int loops = QInputDialog::getInteger(this, tr("Loops"),
2905                                      tr("Number of loops (0 means infinite):"), 0, 0, 1000000000, 1, &ok);
2906       if(ok)
2907         gif->SetLoops(loops);
2908
2909       // Dithering
2910       QString msg = "Would you like to activate dithering?";
2911       QMessageBox msgBox(QMessageBox::Question, tr("Dithering"),msg, 0, this);
2912       msgBox.addButton(tr("Yes"), QMessageBox::AcceptRole);
2913       msgBox.addButton(tr("No"), QMessageBox::RejectRole);
2914       gif->SetDither(msgBox.exec() == QMessageBox::AcceptRole);
2915     }
2916 #endif
2917 #ifdef VTK_USE_VIDEO_FOR_WINDOWS
2918     if (ext==".avi") {
2919       vtkAVIWriter *mpg = vtkAVIWriter::New();
2920       vidwriter = mpg;
2921       mpg->SetQuality(2);
2922       bool ok;
2923       int fps = QInputDialog::getInteger(this, tr("Number of frames per second"),
2924                                      tr("FPS:"), 5, 0, 1024, 1, &ok);
2925       if(!ok)
2926         fps = 5;
2927       mpg->SetRate(fps);
2928     }
2929 #endif
2930 #ifdef VTK_USE_FFMPEG_ENCODER
2931     if (ext==".avi") {
2932       vtkFFMPEGWriter *mpg = vtkFFMPEGWriter::New();
2933       vidwriter = mpg;
2934       mpg->SetQuality(2);
2935       bool ok;
2936       int fps = QInputDialog::getInteger(this, tr("Number of frames per second"),
2937                                      tr("FPS:"), 5, 0, 1024, 1, &ok);
2938       if(!ok)
2939         fps = 5;
2940       mpg->SetRate(fps);
2941       mpg->SetBitRateTolerance(int(ceil(12.0*1024*1024/fps)));
2942     }
2943 #endif
2944 #ifdef VTK_USE_MPEG2_ENCODER
2945     if (ext==".mpg") {
2946       vtkMPEG2Writer *mpg = vtkMPEG2Writer::New();
2947       vidwriter = mpg;
2948     }
2949 #endif
2950
2951     // Take video if not null
2952     if(vidwriter!=NULL){
2953       vidwriter->SetInput(image);
2954       vidwriter->SetFileName(fileName.toStdString().c_str());
2955       vidwriter->Start();
2956       int nSlice = mSlicerManagers[smIndex]->GetSlicer(0)->GetTMax();
2957       for(int i=0; i<=nSlice; i++) {
2958         mSlicerManagers[smIndex]->SetNextTSlice(0);
2959         vtkSmartPointer<vtkWindowToImageFilter> w2i = vtkSmartPointer<vtkWindowToImageFilter>::New();
2960         w2i->SetInput(widget->GetRenderWindow());
2961         w2i->Update();
2962         vidwriter->SetInput(w2i->GetOutput());
2963         vidwriter->Write();
2964       }
2965       vidwriter->End();
2966       vidwriter->Delete();
2967       return;
2968     }
2969
2970     QMessageBox::information(this,tr("Problem saving screenshot !"),tr("Cannot save image.\nPlease set a file extension !!!"));
2971   }
2972 }
2973 //------------------------------------------------------------------------------
2974
2975
2976 //------------------------------------------------------------------------------
2977 void vvMainWindow::GoToCursor()
2978 {
2979   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2980   for (int column = 1; column < 5; column++) {
2981     if (DataTree->selectedItems()[0]->data(column,Qt::CheckStateRole).toInt() > 1) {
2982       double* cursorPos = mSlicerManagers[index]->GetSlicer(column-1)->GetCursorPosition();
2983       mSlicerManagers[index]->GetSlicer(column-1)->SetCurrentPosition(
2984         cursorPos[0],cursorPos[1],cursorPos[2],cursorPos[3]);
2985       mSlicerManagers[index]->UpdateViews(1,column-1);
2986       mSlicerManagers[index]->UpdateLinked(column-1);
2987       break;
2988     }
2989   }
2990 }
2991 //------------------------------------------------------------------------------
2992
2993 //------------------------------------------------------------------------------
2994 void vvMainWindow::PlayPause()
2995 {
2996   if (playMode) {
2997     playMode = 0;
2998     playButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/player_play.png")));
2999     ImageInfoChanged();
3000     return;
3001   } else {
3002     int image_number=DataTree->topLevelItemCount();
3003     bool has_temporal;
3004     for (int i=0; i<image_number; i++)
3005       if (mSlicerManagers[i]->GetSlicer(0)->GetTMax() > 0) {
3006         has_temporal=true;
3007         break;
3008       }
3009     if (has_temporal) {
3010       playMode = 1;
3011       playButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/player_pause.png")));
3012       QTimer::singleShot(1000/mFrameRate, this, SLOT(PlayNext()));
3013     }
3014   }
3015 }
3016 //------------------------------------------------------------------------------
3017
3018 //------------------------------------------------------------------------------
3019 void vvMainWindow::PlayNext()
3020 {
3021   if (playMode && !this->isHidden()) {
3022     int image_number=DataTree->topLevelItemCount();
3023     ///Only play one slicer per SM, and only if the SM is being displayed
3024     for (int i=0; i<image_number; i++)
3025       for (int j=0; j<4; j++)
3026         if (mSlicerManagers[i]->GetSlicer(0)->GetTMax() > 0 &&
3027             DataTree->topLevelItem(i)->data(j+1,Qt::CheckStateRole).toInt() > 0) {
3028           mSlicerManagers[i]->SetNextTSlice(j);
3029           break;
3030         }
3031     QTimer::singleShot(1000/mFrameRate, this, SLOT(PlayNext()));
3032   }
3033 }
3034 //------------------------------------------------------------------------------
3035
3036 void vvMainWindow::ShowLastImage()
3037 {
3038   if (mSlicerManagers.size() > 1) {
3039     QTreeWidgetItem * item=DataTree->topLevelItem(DataTree->topLevelItemCount()-1);
3040     CurrentImageChanged(mSlicerManagers.back()->GetId()); //select new image
3041     item->setData(1,Qt::CheckStateRole,2); //show the new image in the first panel
3042     DisplayChanged(item,1);
3043   }
3044 }
3045
3046 //------------------------------------------------------------------------------
3047 void vvMainWindow::UpdateRenderWindows()
3048 {
3049   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
3050     mSlicerManagers[i]->GetSlicer(0)->UpdateLandmarks();
3051     mSlicerManagers[i]->GetSlicer(1)->UpdateLandmarks();
3052     mSlicerManagers[i]->GetSlicer(2)->UpdateLandmarks();
3053     mSlicerManagers[i]->GetSlicer(3)->UpdateLandmarks();
3054   }
3055   if (NOViewWidget->GetRenderWindow()) NOViewWidget->GetRenderWindow()->Render();
3056   if (NEViewWidget->GetRenderWindow()) NEViewWidget->GetRenderWindow()->Render();
3057   if (SOViewWidget->GetRenderWindow()) SOViewWidget->GetRenderWindow()->Render();
3058   if (SEViewWidget->GetRenderWindow()) SEViewWidget->GetRenderWindow()->Render();
3059 }
3060 //------------------------------------------------------------------------------
3061
3062 //------------------------------------------------------------------------------
3063 void vvMainWindow::SegmentationOnCurrentImage()
3064 {
3065   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
3066
3067   vvSegmentationDialog segmentation;
3068   segmentation.SetImage(mSlicerManagers[index]->GetSlicer(0)->GetImage());
3069   segmentation.exec();
3070 }
3071 //------------------------------------------------------------------------------
3072
3073 void vvMainWindow::SurfaceViewerLaunch()
3074 {
3075   vvSurfaceViewerDialog surfaceViewer;
3076   surfaceViewer.exec();
3077 }
3078 //------------------------------------------------------------------------------
3079
3080
3081 //------------------------------------------------------------------------------
3082 int vvMainWindow::GetImageDuplicateFilenameNumber(std::string filename)
3083 {
3084   int number=0;
3085   for(unsigned int l=0; l<mSlicerManagers.size(); l++) {
3086     vvSlicerManager * v = mSlicerManagers[l];
3087     if (v->GetBaseFileName() ==
3088         vtksys::SystemTools::GetFilenameName(vtksys::SystemTools::GetFilenameWithoutLastExtension(filename))) {
3089       number = std::max(number, v->GetBaseFileNameNumber()+1);
3090     }
3091   }
3092   return number;
3093 }
3094 //------------------------------------------------------------------------------
3095
3096
3097 //------------------------------------------------------------------------------
3098 vvSlicerManager* vvMainWindow::AddImage(vvImage::Pointer image,std::string filename)
3099 {
3100   // Change filename if another image exist with the same name
3101   int number = GetImageDuplicateFilenameNumber(filename);
3102
3103   // Create new SliceManager
3104   vvSlicerManager* slicer_manager = new vvSlicerManager(4);
3105   slicer_manager->SetImage(image);//, IMAGE, number);
3106   //  filename = filename+"_"+clitk::toString(number);
3107   slicer_manager->SetFilename(filename, number);
3108   mSlicerManagers.push_back(slicer_manager);
3109
3110   //create an item in the tree with good settings
3111   QTreeWidgetItem *item = new QTreeWidgetItem();
3112   item->setData(0,Qt::UserRole,slicer_manager->GetFileName().c_str());//files[i].c_str());
3113   item->setData(1,Qt::UserRole,tr("image"));
3114   item->setData(COLUMN_IMAGE_NAME,Qt::DisplayRole,slicer_manager->GetFileName().c_str());//filename.c_str());
3115   qApp->processEvents();
3116
3117   for (int j = 1; j <= 4; j++) item->setData(j,Qt::CheckStateRole,1);
3118
3119   //Create the buttons for reload and close
3120   qApp->processEvents();
3121   QTreePushButton* cButton = new QTreePushButton;
3122   cButton->setItem(item);
3123   cButton->setColumn(COLUMN_CLOSE_IMAGE);
3124   cButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/exit.png")));
3125   connect(cButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
3126           this,SLOT(CloseImage(QTreeWidgetItem*, int)));
3127
3128   QTreePushButton* rButton = new QTreePushButton;
3129   rButton->setItem(item);
3130   rButton->setColumn(COLUMN_RELOAD_IMAGE);
3131   rButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/rotateright.png")));
3132   rButton->setEnabled(0);
3133   connect(rButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
3134           this,SLOT(ReloadImage(QTreeWidgetItem*, int)));
3135
3136   DataTree->addTopLevelItem(item);
3137   DataTree->setItemWidget(item, COLUMN_CLOSE_IMAGE, cButton);
3138   DataTree->setItemWidget(item, COLUMN_RELOAD_IMAGE, rButton);
3139
3140   //set the id of the image
3141   QString id = QDir::current().absoluteFilePath(slicer_manager->GetFileName().c_str()) + QString::number(mSlicerManagers.size()-1);
3142   item->setData(COLUMN_IMAGE_NAME,Qt::UserRole,id.toStdString().c_str());
3143   mSlicerManagers.back()->SetId(id.toStdString());
3144
3145   linkPanel->addImage(slicer_manager->GetFileName().c_str()// filename
3146                       , id.toStdString());
3147
3148   connect(mSlicerManagers.back(), SIGNAL(currentImageChanged(std::string)),
3149           this, SLOT(CurrentImageChanged(std::string)));
3150   connect(mSlicerManagers.back(), SIGNAL(currentPickedImageChanged(std::string)),
3151           this, SLOT(CurrentPickedImageChanged(std::string)));
3152   connect(mSlicerManagers.back(), SIGNAL(UpdatePosition(int, double, double, double, double, double, double, double)),
3153           this, SLOT(MousePositionChanged(int,double, double, double, double, double, double, double)));
3154   connect(mSlicerManagers.back(), SIGNAL(UpdateVector(int, double, double, double, double)),
3155           this, SLOT(VectorChanged(int,double,double,double, double)));
3156   connect(mSlicerManagers.back(), SIGNAL(UpdateOverlay(int, double, double)),
3157           this, SLOT(OverlayChanged(int,double,double)));
3158   connect(mSlicerManagers.back(), SIGNAL(UpdateFusion(int, double)),
3159           this, SLOT(FusionChanged(int,double)));
3160   connect(mSlicerManagers.back(), SIGNAL(WindowLevelChanged()),
3161           this,SLOT(WindowLevelChanged()));
3162   connect(mSlicerManagers.back(), SIGNAL(UpdateSlice(int,int)),
3163           this,SLOT(UpdateSlice(int,int)));
3164   connect(mSlicerManagers.back(), SIGNAL(UpdateTSlice(int, int)),
3165           this,SLOT(UpdateTSlice(int, int)));
3166   connect(mSlicerManagers.back(), SIGNAL(UpdateTSlice(int, int)),
3167           this,SLOT(ImageInfoChanged()));
3168   connect(mSlicerManagers.back(), SIGNAL(UpdateSliceRange(int,int,int,int,int)),
3169           this,SLOT(UpdateSliceRange(int,int,int,int,int)));
3170   connect(mSlicerManagers.back(), SIGNAL(UpdateLinkManager(std::string,int,double,double,double,int)),
3171           this,SLOT(UpdateLinkManager(std::string,int,double,double,double,int)));
3172   connect(mSlicerManagers.back(), SIGNAL(UpdateLinkedNavigation(std::string,vvSlicerManager*,vvSlicer*)),
3173           this,SLOT(UpdateLinkedNavigation(std::string,vvSlicerManager*,vvSlicer*)));
3174   connect(mSlicerManagers.back(), SIGNAL(ChangeImageWithIndexOffset(vvSlicerManager*,int,int)),
3175           this,SLOT(ChangeImageWithIndexOffset(vvSlicerManager*,int,int)));
3176   connect(mSlicerManagers.back(), SIGNAL(LandmarkAdded()),landmarksPanel,SLOT(AddPoint()));
3177   UpdateTree();
3178   qApp->processEvents();
3179   InitSlicers();
3180   ShowLastImage();
3181   InitDisplay();
3182   qApp->processEvents();
3183
3184   // End
3185   ImageInfoChanged();
3186   return slicer_manager;
3187 }
3188 //------------------------------------------------------------------------------
3189
3190
3191 //------------------------------------------------------------------------------
3192 void vvMainWindow::UpdateCurrentSlicer()
3193 {
3194   int index = -1;
3195   if (DataTree->selectedItems().size() > 0) {
3196     index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
3197   }
3198   mSlicerManagerCurrentIndex = index;
3199 }
3200 //------------------------------------------------------------------------------
3201