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 #include "clitkMatrix.h"
  52
  53 // ITK include
  54 #include <itkImage.h>
  55 #include <itkImageFileReader.h>
  56 #include <itkByteSwapper.h>
  57 #include <itkCommand.h>
  58 #include <itkNumericSeriesFileNames.h>
  59
  60 // VTK include
  61 #include <vtkImageData.h>
  62 #include <vtkImageActor.h>
  63 #include <vtkCornerAnnotation.h>
  64 #include <vtkRenderWindow.h>
  65 #include <vtkRenderWindowInteractor.h>
  66 #include <vtkRenderer.h>
  67 #include <vtkRendererCollection.h>
  68 #include <vtkWindowToImageFilter.h>
  69 #include <vtkBMPWriter.h>
  70 #include <vtkTIFFWriter.h>
  71 #include <vtkPNMWriter.h>
  72 #include <vtkPNGWriter.h>
  73 #include <vtkJPEGWriter.h>
  74 #include <vtkGenericMovieWriter.h>
  75 #ifdef CLITK_EXPERIMENTAL
  76 #  include <vvAnimatedGIFWriter.h>
  77 #endif
  78 #ifdef VTK_USE_VIDEO_FOR_WINDOWS
  79 #  include <vtkAVIWriter.h>
  80 #endif
  81 #ifdef VTK_USE_FFMPEG_ENCODER
  82 #  include <vtkFFMPEGWriter.h>
  83 #endif
  84 #ifdef VTK_USE_MPEG2_ENCODER
  85 #  include <vtkMPEG2Writer.h>
  86 #endif
  87 #include <vtkMatrix4x4.h>
  88 #include <vtkTransform.h>
  89
  90 // Standard includes
  91 #include <iostream>
  92 #include <fstream>
  93 #include <sstream>
  94 #include <iomanip>
  95
  96 #define COLUMN_TREE 0
  97 #define COLUMN_UL_VIEW 1
  98 #define COLUMN_UR_VIEW 2
  99 #define COLUMN_DL_VIEW 3
 100 #define COLUMN_DR_VIEW 4
 101 #define COLUMN_CLOSE_IMAGE 5
 102 #define COLUMN_RELOAD_IMAGE 6
 103 #define COLUMN_IMAGE_NAME 7
 104
 105 #ifdef CLITK_PRIVATE_FEATURES
 106 #define EXTENSIONS "Images ( *.bmp *.dcm *.png *.jpeg *.jpg *.tif *.mhd *.mha *.hdr *.vox *.his *.xdr *.SCAN *.nii *.nrrd *.nhdr *.refscan *.nii.gz *.usf *.svl)"
 107 #else
 108 #define EXTENSIONS "Images ( *.bmp *.dcm *.png *.jpeg *.jpg *.tif *.mhd *.mha *.hdr *.vox *.his *.xdr *.SCAN *.nii *.nrrd *.nhdr *.refscan *.nii.gz)"
 109 #endif
 110
 111
 112 /*Data Tree values
 113 0,Qt::UserRole full filename
 114 1,Qt::CheckStateRole checkbutton UL View
 115 1,Qt::UserRole overlay, fusion or vector
 116 2,Qt::CheckStateRole checkbutton UR View
 117 3,Qt::CheckStateRole checkbutton DL View
 118 4,Qt::CheckStateRole checkbutton DR View
 119 5,0  short filename
 120 5,Qt::UserRole mSlicerManager id*/
 121
 122 //------------------------------------------------------------------------------
 123 vvMainWindow::vvMainWindow():vvMainWindowBase()
 124 {
 125   setupUi(this); // this sets up the GUI
 126
 127   mInputPathName = "";
 128   mMenuTools = menuTools;
 129   //  mMenuSegmentation = menuSegmentation;
 130   mContextMenu = &contextMenu;
 131   mMenuExperimentalTools = menuExperimental;
 132   mMainWidget = this;
 133   mCurrentTime = -1;
 134   mCurrentSelectedImageId = "";
 135   mCurrentPickedImageId = "";
 136   mCurrentPickedImageIndex = 0;
 137
 138   //Init the contextMenu
 139   this->setContextMenuPolicy(Qt::CustomContextMenu);
 140   contextActions.resize(0);
 141   QAction* actionOpen_new_image = contextMenu.addAction(QIcon(QString::fromUtf8(":/common/icons/fileopen.png")),
 142     tr("O&pen new Image"));
 143   actionOpen_new_image->setShortcut(QKeySequence(tr("Ctrl+O")));
 144   connect(actionOpen_new_image,SIGNAL(triggered()),this,SLOT(OpenImages()));
 145   contextActions.push_back(actionOpen_new_image);
 146   contextMenu.addSeparator();
 147
 148   QAction* actionClose_Image = contextMenu.addAction(QIcon(QString::fromUtf8(":/common/icons/exit.png")),
 149     tr("Close Current Image"));
 150   connect(actionClose_Image,SIGNAL(triggered()),this,SLOT(CloseImage()));
 151   contextActions.push_back(actionClose_Image);
 152
 153   QAction* actionReload_image = contextMenu.addAction(QIcon(QString::fromUtf8(":/common/icons/rotateright.png")),
 154     tr("Reload Current Image"));
 155   connect(actionReload_image,SIGNAL(triggered()),this,SLOT(ReloadImage()));
 156   contextActions.push_back(actionReload_image);
 157
 158   QAction* actionSave_image = contextMenu.addAction(QIcon(QString::fromUtf8(":/common/icons/filesave.png")),
 159     tr("Save Current Image"));
 160   connect(actionSave_image,SIGNAL(triggered()),this,SLOT(SaveAs()));
 161   contextActions.push_back(actionSave_image);
 162
 163   QAction* actionSave_state = contextMenu.addAction(QIcon(QString::fromUtf8(":/common/icons/filesave.png")),
 164     tr("Save Current State"));
 165   connect(actionSave_state,SIGNAL(triggered()),this,SLOT(SaveCurrentState()));
 166   contextActions.push_back(actionSave_state);
 167
 168   QAction* actionRead_state = contextMenu.addAction(QIcon(QString::fromUtf8(":/common/icons/filesave.png")),
 169     tr("Read Saved State"));
 170   connect(actionRead_state,SIGNAL(triggered()),this,SLOT(ReadSavedState()));
 171   contextActions.push_back(actionRead_state);
 172
 173   contextMenu.addSeparator();
 174
 175   contextMenu.addAction(actionAdd_VF_to_current_Image);
 176   contextActions.push_back(actionAdd_VF_to_current_Image);
 177
 178   //QAction* actionAdd_Overlay_to_current_Image = menuOverlay->addAction(QIcon(QString::fromUtf8(":/common/icons/GPSup.png")),
 179   //    tr("Add overlay image to current image"));
 180   contextMenu.addAction(actionAdd_overlay_image_to_current_image);
 181   contextActions.push_back(actionAdd_overlay_image_to_current_image);
 182
 183   contextMenu.addAction(actionAdd_fusion_image);
 184   contextActions.push_back(actionAdd_fusion_image);
 185
 186 #ifdef CLITK_EXPERIMENTAL
 187   contextMenu.addAction(actionAdd_USSequence_toCT);
 188   contextActions.push_back(actionAdd_USSequence_toCT);
 189 #endif
 190
 191
 192   contextMenu.addSeparator();
 193   QAction* actionResetMatrix = contextMenu.addAction(QIcon(QString::fromUtf8(":/common/icons/identity.png")),
 194     tr("Reset transformation to identity"));
 195   connect(actionResetMatrix, SIGNAL(triggered()), this,SLOT(ResetTransformationToIdentity()));
 196
 197   // TRIAL DS
 198   /*
 199   QMenu * m = new QMenu(menubar);
 200   m->setTitle("TOTO");
 201   //  m->setObjectName(QString::fromUtf8("TOTOTO"));
 202   contextMenu.addMenu(m);
 203   QAction * a = m->addAction(QIcon(QString::fromUtf8(":/common/icons/GPSup.png")),
 204   tr("BIDON"));
 205   QAction * b = m->addAction(QIcon(QString::fromUtf8(":/common/icons/GPSup.png")),
 206   tr("BIDON2"));
 207   m->addAction(a);
 208   m->addAction(b);
 209   connect(a,SIGNAL(triggered()),this,SLOT(AddFusionImage()));
 210   */
 211
 212   //init the DataTree
 213   mSlicerManagers.resize(0);
 214
 215   QStringList header;
 216   header.append("");
 217   header.append("TL");
 218   header.append("TR");
 219   header.append("BL");
 220   header.append("BR");
 221   header.append("");
 222   header.append("");
 223   header.append("Name");
 224
 225   DataTree->setHeaderLabels(header);
 226   DataTree->resizeColumnToContents(COLUMN_TREE);
 227   DataTree->resizeColumnToContents(COLUMN_UL_VIEW);
 228   DataTree->resizeColumnToContents(COLUMN_UR_VIEW);
 229   DataTree->resizeColumnToContents(COLUMN_DL_VIEW);
 230   DataTree->resizeColumnToContents(COLUMN_DR_VIEW);
 231   DataTree->resizeColumnToContents(COLUMN_CLOSE_IMAGE);
 232   DataTree->resizeColumnToContents(COLUMN_RELOAD_IMAGE);
 233   DataTree->resizeColumnToContents(COLUMN_IMAGE_NAME);
 234
 235   viewMode = 1;
 236   documentation = new vvDocumentation();
 237   help_dialog = new vvHelpDialog();
 238   dicomSeriesSelector = new vvDicomSeriesSelector();
 239
 240   inverseButton->setEnabled(0);
 241   actionAdd_overlay_image_to_current_image->setEnabled(0);
 242   actionSave_As->setEnabled(0);
 243   actionAdd_VF_to_current_Image->setEnabled(0);
 244   actionAdd_fusion_image->setEnabled(0);
 245   actionAdd_USSequence_toCT->setEnabled(0);
 246
 247   //init the sliders
 248   verticalSliders.push_back(NOVerticalSlider);
 249   verticalSliders.push_back(NEVerticalSlider);
 250   verticalSliders.push_back(SOVerticalSlider);
 251   verticalSliders.push_back(SEVerticalSlider);
 252
 253   for (int i =0; i < 4; i++)
 254     verticalSliders[i]->hide();
 255
 256   horizontalSliders.push_back(NOHorizontalSlider);
 257   horizontalSliders.push_back(NEHorizontalSlider);
 258   horizontalSliders.push_back(SOHorizontalSlider);
 259   horizontalSliders.push_back(SEHorizontalSlider);
 260
 261   for (int i =0; i < 4; i++)
 262     horizontalSliders[i]->hide();
 263
 264
 265   connect(NOVerticalSlider,SIGNAL(valueChanged(int)),this,SLOT(NOVerticalSliderChanged()));
 266   connect(NEVerticalSlider,SIGNAL(valueChanged(int)),this,SLOT(NEVerticalSliderChanged()));
 267   connect(SOVerticalSlider,SIGNAL(valueChanged(int)),this,SLOT(SOVerticalSliderChanged()));
 268   connect(SEVerticalSlider,SIGNAL(valueChanged(int)),this,SLOT(SEVerticalSliderChanged()));
 269
 270   connect(NOHorizontalSlider,SIGNAL(valueChanged(int)),this,SLOT(NOHorizontalSliderMoved()));
 271   connect(NEHorizontalSlider,SIGNAL(valueChanged(int)),this,SLOT(NEHorizontalSliderMoved()));
 272   connect(SOHorizontalSlider,SIGNAL(valueChanged(int)),this,SLOT(SOHorizontalSliderMoved()));
 273   connect(SEHorizontalSlider,SIGNAL(valueChanged(int)),this,SLOT(SEHorizontalSliderMoved()));
 274
 275   //connect everything
 276   connect(actionCompute_mid_position_image,SIGNAL(triggered()),this,SLOT(ComputeMidPosition()));
 277   connect(actionDeformable_Registration,SIGNAL(triggered()),this,SLOT(ComputeDeformableRegistration()));
 278   connect(actionWarp_image_with_vector_field,SIGNAL(triggered()),this,SLOT(WarpImage()));
 279   connect(actionLoad_images,SIGNAL(triggered()),this,SLOT(OpenImages()));
 280   connect(actionOpen_Dicom,SIGNAL(triggered()),this,SLOT(OpenDicom()));
 281   //  connect(actionOpen_Dicom_Struct,SIGNAL(triggered()),this,SLOT(OpenDCStructContour()));
 282   connect(actionOpen_VTK_contour,SIGNAL(triggered()),this,SLOT(OpenVTKContour()));
 283   connect(actionOpen_Multiple_Images_As_One,SIGNAL(triggered()),this,SLOT(MergeImages()));
 284   connect(actionSlice_Image_As_Multiple_Images,SIGNAL(triggered()),this,SLOT(SliceImages()));
 285   connect(actionOpen_Image_With_Time,SIGNAL(triggered()),this,SLOT(OpenImageWithTime()));
 286   connect(actionMerge_images_as_n_dim_t, SIGNAL(triggered()), this, SLOT(MergeImagesWithTime()));
 287   connect(actionSave_As,SIGNAL(triggered()),this,SLOT(SaveAs()));
 288   connect(actionSave_current_state,SIGNAL(triggered()),this,SLOT(SaveCurrentState()));
 289   connect(actionRead_saved_state,SIGNAL(triggered()),this,SLOT(ReadSavedState()));
 290   connect(actionExit,SIGNAL(triggered()),this,SLOT(close()));
 291   connect(actionAdd_VF_to_current_Image,SIGNAL(triggered()),this,SLOT(OpenField()));
 292   connect(actionAdd_fusion_image,SIGNAL(triggered()),this,SLOT(SelectFusionImage()));
 293   connect(actionAdd_overlay_image_to_current_image,SIGNAL(triggered()), this,SLOT(SelectOverlayImage()));
 294   connect(actionAdd_USSequence_toCT,SIGNAL(triggered()), this,SLOT(SelectFusionSequence()));
 295   connect(actionNavigation_Help,SIGNAL(triggered()),this,SLOT(ShowHelpDialog()));
 296   connect(actionDocumentation,SIGNAL(triggered()),this,SLOT(ShowDocumentation()));
 297   connect(actionRegister_vv,SIGNAL(triggered()),this,SLOT(PopupRegisterForm()));
 298
 299   connect(overlayPanel, SIGNAL(FusionSequenceCorrespondancesButtonPressed()), this, SLOT(SelectFusionSequenceCorrespondances()));
 300
 301
 302   ///////////////////////////////////////////////
 303   connect(actionSegmentation,SIGNAL(triggered()),this,SLOT(SegmentationOnCurrentImage()));
 304   connect(actionSurface_Viewer,SIGNAL(triggered()),this,SLOT(SurfaceViewerLaunch()));
 305   ///////////////////////////////////////////////
 306
 307   actionNorth_East_Window->setEnabled(0);
 308   actionNorth_West_Window->setEnabled(0);
 309   actionSouth_East_Window->setEnabled(0);
 310   actionSouth_West_Window->setEnabled(0);
 311
 312   connect(actionNorth_East_Window,SIGNAL(triggered()),this,SLOT(SaveNEScreenshot()));
 313   connect(actionNorth_West_Window,SIGNAL(triggered()),this,SLOT(SaveNOScreenshot()));
 314   connect(actionSouth_East_Window,SIGNAL(triggered()),this,SLOT(SaveSEScreenshot()));
 315   connect(actionSouth_West_Window,SIGNAL(triggered()),this,SLOT(SaveSOScreenshot()));
 316   connect(actionSave_all_slices,SIGNAL(triggered()),this,SLOT(SaveScreenshotAllSlices()));
 317
 318   connect(DataTree,SIGNAL(itemSelectionChanged()),this,SLOT(ImageInfoChanged()));
 319   connect(DataTree,SIGNAL(itemClicked(QTreeWidgetItem*, int)),this,
 320     SLOT(DisplayChanged(QTreeWidgetItem*, int)));
 321
 322   connect(viewButton,SIGNAL(clicked()),this, SLOT(ChangeViewMode()) );
 323   connect(windowSpinBox,SIGNAL(editingFinished()),this,SLOT(WindowLevelEdited()));
 324   connect(levelSpinBox,SIGNAL(editingFinished()),this,SLOT(WindowLevelEdited()));
 325   connect(colorMapComboBox,SIGNAL(currentIndexChanged(int)),this,SLOT(UpdateColorMap()));
 326   connect(presetComboBox,SIGNAL(currentIndexChanged(int)),this,SLOT(UpdateWindowLevel()));
 327   connect(slicingPresetComboBox, SIGNAL(currentIndexChanged(int)),this,SLOT(UpdateSlicingPreset()));
 328   connect(inverseButton,SIGNAL(clicked()),this,SLOT(SwitchWindowLevel()));
 329   connect(applyWindowLevelToAllButton,SIGNAL(clicked()),this,SLOT(ApplyWindowLevelToAllImages()));
 330
 331   connect(this,SIGNAL(customContextMenuRequested(QPoint)),this,SLOT(ShowContextMenu(QPoint)));
 332
 333   connect(linkPanel,SIGNAL(addLink(QString,QString,bool)),this,SLOT(AddLink(QString,QString,bool)));
 334   connect(linkPanel,SIGNAL(removeLink(QString,QString)),this,SLOT(RemoveLink(QString,QString)));
 335   connect(overlayPanel,SIGNAL(VFPropertyUpdated(int,int,int,int,double,double,double)),this,SLOT(SetVFProperty(int,int,int,int,double,double,double)));
 336   connect(overlayPanel,SIGNAL(OverlayPropertyUpdated(int,int,double,double)),
 337     this,SLOT(SetOverlayProperty(int,int,double,double)));
 338   connect(overlayPanel,SIGNAL(FusionPropertyUpdated(int,int,int,double,double, bool)),
 339     this,SLOT(SetFusionProperty(int,int,int,double,double, bool)));
 340   connect(landmarksPanel,SIGNAL(UpdateRenderWindows()),this,SLOT(UpdateRenderWindows()));
 341   connect(landmarksPanel,SIGNAL(SelectedPointChanged()),this,SLOT(GoToLandmark()));
 342
 343   connect(overlayPanel,SIGNAL(FusionSequencePropertyUpdated(int, bool, unsigned int, bool)),
 344     this,SLOT(SetFusionSequenceProperty(int, bool,unsigned int, bool)));
 345
 346
 347   playMode = 0;//pause
 348   mFrameRate = 10;
 349   playButton->setEnabled(0);
 350   frameRateLabel->setEnabled(0);
 351   frameRateSpinBox->setEnabled(0);
 352   connect(playButton, SIGNAL(clicked()),this,SLOT(PlayPause()));
 353   connect(frameRateSpinBox, SIGNAL(valueChanged(int)),this,SLOT(ChangeFrameRate(int)));
 354
 355   goToCursorPushButton->setEnabled(0);
 356   connect(goToCursorPushButton, SIGNAL(clicked()),this,SLOT(GoToCursor()));
 357
 358   NOViewWidget->hide();
 359   NEViewWidget->hide();
 360   SOViewWidget->hide();
 361   SEViewWidget->hide();
 362
 363   //Recently opened files
 364   std::list<std::string> recent_files = GetRecentlyOpenedImages();
 365   recentlyOpenedFilesMenu=NULL;
 366   if ( !recent_files.empty() ) {
 367     createRecentlyOpenedFilesMenu();
 368     updateRecentlyOpenedFilesMenu(recent_files);
 369   }
 370
 371   // Adding all new tools (insertion in the menu)
 372   vvToolManager::GetInstance()->InsertToolsInMenu(this);
 373   vvToolManager::GetInstance()->EnableToolsInMenu(this, false);
 374
 375   if (!CLITK_EXPERIMENTAL)
 376     menuExperimental->menuAction()->setVisible(false);
 377
 378
 379   QTimer * timerMemory = new QTimer(this);
 380   //timerMemory->setInterval(5);
 381   connect(timerMemory, SIGNAL(timeout()), this, SLOT(UpdateMemoryUsage()));
 382   timerMemory->start(2000);
 383
 384 }
 385 //------------------------------------------------------------------------------
 386 void vvMainWindow::show()
 387 {
 388   vvMainWindowBase::show();
 389   PopupRegisterForm(true);
 390 }
 391 //------------------------------------------------------------------------------
 392 void vvMainWindow::UpdateMemoryUsage()
 393 {
 394   //  clitk::PrintMemory(true);
 395   if (clitk::GetMemoryUsageInMb() == 0) infoPanel->setMemoryInMb("NA");
 396   else infoPanel->setMemoryInMb(QString::number(clitk::GetMemoryUsageInMb())+" MiB");
 397 }
 398 //------------------------------------------------------------------------------
 399
 400
 401 //------------------------------------------------------------------------------
 402 void vvMainWindow::createRecentlyOpenedFilesMenu()
 403 {
 404   recentlyOpenedFilesMenu = new QMenu("Recently opened files...");
 405   recentlyOpenedFilesMenu->setIcon(QIcon(QString::fromUtf8(":/common/icons/open.png")));
 406   menuFile->insertMenu(actionOpen_Image_With_Time,recentlyOpenedFilesMenu);
 407   menuFile->insertSeparator(actionOpen_Image_With_Time);
 408 }
 409 //------------------------------------------------------------------------------
 410
 411
 412 //------------------------------------------------------------------------------
 413
 414 void vvMainWindow::updateRecentlyOpenedFilesMenu(const std::list<std::string> &recent_files)
 415 {
 416   if(recentlyOpenedFilesMenu==NULL) {
 417     createRecentlyOpenedFilesMenu();
 418   } else {
 419     recentlyOpenedFilesMenu->clear();
 420   }
 421   for (std::list<std::string>::const_iterator i = recent_files.begin(); i!=recent_files.end(); i++) {
 422     QAction* current=new QAction(QIcon(QString::fromUtf8(":/common/icons/open.png")), i->c_str(),this);
 423     recentlyOpenedFilesMenu->addAction(current);
 424     connect(current,SIGNAL(triggered()),this,SLOT(OpenRecentImage()));
 425   }
 426 }
 427 //------------------------------------------------------------------------------
 428
 429
 430 //------------------------------------------------------------------------------
 431 void vvMainWindow::ComputeMidPosition()
 432 {
 433   bool ok;
 434   int index=GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
 435   int ref = QInputDialog::getInteger(this,"Chose reference phase","Reference phase",0,0,\
 436     mSlicerManagers[index]->GetImage()->GetVTKImages().size()-1,1,&ok);
 437   if (ok) {
 438     vvMidPosition midp;
 439     midp.slicer_manager = mSlicerManagers[index];
 440     midp.reference_image_index = ref;
 441     QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
 442     midp.Update();
 443     if (midp.error)
 444       QMessageBox::warning(this, "Error computing midposition image",midp.error_message.c_str());
 445     else {
 446       QFileInfo info(midp.slicer_manager->GetFileName().c_str());
 447       AddImage(midp.output,info.path().toStdString()+"/"+info.completeBaseName().toStdString()+"_midposition.mhd");
 448     }
 449     QApplication::restoreOverrideCursor();
 450   }
 451 }
 452 //------------------------------------------------------------------------------
 453
 454
 455 //------------------------------------------------------------------------------
 456 void vvMainWindow::AddContour(int image_index, vvMesh::Pointer contour, bool propagation)
 457 {
 458   QTreeWidgetItem *item = new QTreeWidgetItem();
 459   item->setData(0,Qt::UserRole,"filename.vtk");
 460   item->setData(1,Qt::UserRole,tr("contour"));
 461   QBrush brush;
 462   brush.setColor(QColor(contour->r*255,contour->g*255,contour->b*255));
 463   brush.setStyle(Qt::SolidPattern);
 464   item->setData(COLUMN_IMAGE_NAME,Qt::BackgroundRole,brush);
 465   //  item->setData(COLUMN_IMAGE_NAME,Qt::DisplayRole,contour->structure_name.c_str());
 466
 467   for (int j = 1; j <= 4; j++)
 468     item->setData(j,Qt::CheckStateRole,DataTree->topLevelItem(image_index)->data(j,Qt::CheckStateRole));
 469
 470   QTreePushButton* cButton = new QTreePushButton;
 471   cButton->setItem(item);
 472   cButton->setColumn(COLUMN_CLOSE_IMAGE);
 473   cButton->setToolTip(tr("close image"));
 474   cButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/exit.png")));
 475   connect(cButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
 476     this,SLOT(CloseImage(QTreeWidgetItem*, int)));
 477
 478   QTreePushButton* rButton = new QTreePushButton;
 479   rButton->setItem(item);
 480   rButton->setColumn(COLUMN_RELOAD_IMAGE);
 481   rButton->setToolTip(tr("reload image"));
 482   rButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/rotateright.png")));
 483   rButton->setEnabled(false);
 484   //Not implemented
 485   //connect(rButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
 486   //this,SLOT(ReloadImage(QTreeWidgetItem*, int)));
 487
 488   DataTree->topLevelItem(image_index)->setExpanded(1);
 489   DataTree->topLevelItem(image_index)->addChild(item);
 490   DataTree->setItemWidget(item, COLUMN_CLOSE_IMAGE, cButton);
 491   DataTree->setItemWidget(item, COLUMN_RELOAD_IMAGE, rButton);
 492   QString id = DataTree->topLevelItem(image_index)->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString();
 493   item->setData(COLUMN_IMAGE_NAME,Qt::UserRole,id.toStdString().c_str());
 494
 495   UpdateTree();
 496   mSlicerManagers[image_index]->AddContour(contour,propagation);
 497   mSlicerManagers[image_index]->Render();
 498 }
 499 //------------------------------------------------------------------------------
 500
 501
 502 //------------------------------------------------------------------------------
 503 void vvMainWindow::OpenVTKContour()
 504 {
 505   if (mSlicerManagers.size() > 0) {
 506     QString Extensions = "Images ( *.vtk *.obj)";
 507     Extensions += ";;All Files (*)";
 508     QString file = QFileDialog::getOpenFileName(this,tr("Open vtkPolyData"),mInputPathName,Extensions);
 509     if (file.isNull())
 510       return;
 511     QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
 512     int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
 513     vvMeshReader reader;
 514     reader.SetImage(mSlicerManagers[index]->GetImage());
 515     reader.SetModeToVTK();
 516     reader.SetFilename(file.toStdString());
 517     reader.Update();
 518     AddContour(index,reader.GetOutput()[0],false);
 519     QApplication::restoreOverrideCursor();
 520   }
 521 }
 522 //------------------------------------------------------------------------------
 523
 524
 525 //------------------------------------------------------------------------------
 526 void vvMainWindow::AddDCStructContour(int index, QString file)
 527 {
 528   vvMeshReader reader;
 529   reader.SetFilename(file.toStdString());
 530   vvStructSelector selector;
 531   selector.SetStructures(reader.GetROINames());
 532   if (!mSlicerManagers[index]->GetVF().IsNull())
 533     selector.EnablePropagationCheckBox();
 534   if (selector.exec()) {
 535     QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
 536     reader.SetSelectedItems(selector.getSelectedItems());
 537     reader.SetImage(mSlicerManagers[index]->GetImage());
 538     if (selector.PropagationEnabled())
 539       reader.SetPropagationVF(mSlicerManagers[index]->GetVF());
 540     reader.Update();
 541     std::vector<vvMesh::Pointer> contours=reader.GetOutput();
 542     for (std::vector<vvMesh::Pointer>::iterator i=contours.begin();
 543       i!=contours.end(); i++)
 544       AddContour(index,*i,selector.PropagationEnabled());
 545     QApplication::restoreOverrideCursor();
 546   }
 547 }
 548
 549 //------------------------------------------------------------------------------
 550 void vvMainWindow::OpenDCStructContour()
 551 {
 552   if (mSlicerManagers.size() > 0) {
 553     QString Extensions = "Dicom Files ( *.dcm RS*)";
 554     Extensions += ";;All Files (*)";
 555     QString file = QFileDialog::getOpenFileName(this,tr("Merge Images"),mInputPathName,Extensions);
 556     if (file.isNull())
 557       return;
 558     int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
 559     AddDCStructContour(index, file);
 560   }
 561 }
 562 //------------------------------------------------------------------------------
 563
 564
 565 //------------------------------------------------------------------------------
 566 void vvMainWindow::ComputeDeformableRegistration()
 567 {
 568   if (mSlicerManagers.size() > 0) {
 569     int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
 570     vvDeformationDialog dialog(index,mSlicerManagers);
 571     if (dialog.exec()) {
 572       std::string base_name=itksys::SystemTools::GetFilenameWithoutExtension(mSlicerManagers[dialog.GetInputFileIndex()]->GetFileName());
 573       AddField(dialog.GetOutput(),dialog.getFieldFile(),dialog.GetInputFileIndex());
 574       WarpImage(dialog.GetSelectedSlicer(),dialog.GetReferenceFrameIndex());
 575     } else
 576       std::cout << "Error or user cancellation while computing deformation field..." << std::endl;
 577   } else QMessageBox::information(this, "Need to open image","You must open an image first.");
 578 }
 579 //------------------------------------------------------------------------------
 580
 581
 582 //------------------------------------------------------------------------------
 583 void vvMainWindow::WarpImage()
 584 {
 585   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
 586   if (!mSlicerManagers[index]->GetVF().IsNull()) {
 587     bool ok;
 588     int ref = QInputDialog::getInteger(this,"Chose reference phase","Reference phase",0,0,\
 589       mSlicerManagers[index]->GetImage()->GetVTKImages().size()-1,1,&ok);
 590     if (ok) {
 591       WarpImage(mSlicerManagers[index],ref);
 592     }
 593   } else
 594     QMessageBox::warning(this,tr("No vector field"),tr("Sorry, can't warp without a vector field"));
 595 }
 596 //------------------------------------------------------------------------------
 597
 598
 599 //------------------------------------------------------------------------------
 600 void vvMainWindow::WarpImage(vvSlicerManager* selected_slicer,int reference_phase)
 601 {
 602   if (!selected_slicer->GetVF().IsNull()) {
 603     QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
 604     QFileInfo info(selected_slicer->GetFileName().c_str());
 605     vvImageWarp warp(selected_slicer->GetImage(),selected_slicer->GetVF(),
 606       reference_phase,this);
 607     if (warp.ComputeWarpedImage()) {
 608       AddImage(warp.GetWarpedImage(),info.path().toStdString()+"/"+info.completeBaseName().toStdString()+"_warped.mhd");
 609       AddImage(warp.GetDiffImage()  ,info.path().toStdString()+"/"+info.completeBaseName().toStdString()+"_diff.mhd");
 610       AddImage(warp.GetJacobianImage()  ,info.path().toStdString()+"/"+info.completeBaseName().toStdString()+"_jacobian.mhd");
 611       QApplication::restoreOverrideCursor();
 612     } else {
 613       QApplication::restoreOverrideCursor();
 614       QMessageBox::warning(this,tr("Different spacings"),tr("The vector field and image spacings must be the same in order to warp."));
 615     }
 616   } else
 617     QMessageBox::warning(this,tr("No vector field"),tr("Sorry, can't warp without a vector field."));
 618 }
 619 //------------------------------------------------------------------------------
 620
 621
 622 //------------------------------------------------------------------------------
 623 vvMainWindow::~vvMainWindow()
 624 {
 625   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
 626     if (mSlicerManagers[i] != NULL)
 627       delete mSlicerManagers[i];
 628   }
 629 }
 630 //------------------------------------------------------------------------------
 631
 632 //------------------------------------------------------------------------------
 633 QTabWidget * vvMainWindow::GetTab()
 634 {
 635   return tabWidget;
 636 }
 637 //------------------------------------------------------------------------------
 638
 639
 640 //------------------------------------------------------------------------------
 641 void vvMainWindow::MergeImages()
 642 {
 643   QString Extensions = EXTENSIONS;
 644   Extensions += ";;All Files (*)";
 645   QStringList files = QFileDialog::getOpenFileNames(this,tr("Merge Images"),mInputPathName,Extensions);
 646   if (files.isEmpty())
 647     return;
 648   mInputPathName = itksys::SystemTools::GetFilenamePath(files[0].toStdString()).c_str();
 649   std::vector<std::string> vector;
 650
 651   unsigned int currentDim = 0;
 652   std::vector<double> currentSpacing;
 653   std::vector<int> currentSize;
 654   std::vector<double> currentOrigin;
 655
 656   for (int i = 0; i < files.size(); i++) {
 657     itk::ImageIOBase::Pointer reader = itk::ImageIOFactory::CreateImageIO(
 658       files[i].toStdString().c_str(), itk::ImageIOFactory::ReadMode);
 659     reader->SetFileName(files[i].toStdString().c_str());
 660     reader->ReadImageInformation();
 661     if (reader)        {
 662       //NOViewWidget->hide();
 663       //NEViewWidget->hide();
 664       //SOViewWidget->hide();
 665       //SEViewWidget->hide();
 666       if (i == 0)
 667         currentDim = reader->GetNumberOfDimensions();
 668       bool IsOk = true;
 669       for (unsigned int j = 0; j < currentDim; j++) {
 670         if (i == 0) {
 671           if (j == 0) {
 672             currentSpacing.resize(currentDim);
 673             currentSize.resize(currentDim);
 674             currentOrigin.resize(currentDim);
 675           }
 676           currentOrigin[j] = reader->GetOrigin(j);
 677           currentSpacing[j] = reader->GetSpacing(j);
 678           currentSize[j] = reader->GetDimensions(j);
 679         } else if (currentDim != reader->GetNumberOfDimensions()
 680           || currentSpacing[j] != reader->GetSpacing(j)
 681           || currentSize[j] != (int)reader->GetDimensions(j)
 682           || currentOrigin[j] != reader->GetOrigin(j)) {
 683             QString error = "Cannot read file (too different from others ";
 684             error += files[i].toStdString().c_str();
 685             QMessageBox::information(this,tr("Reading problem"),error);
 686             IsOk = false;
 687             break;
 688         }
 689       }
 690       if (IsOk)
 691         vector.push_back(files[i].toStdString());
 692     }
 693   }
 694   if (vector.size() > 0)
 695     LoadImages(vector, vvImageReader::MERGED);
 696 }
 697 //------------------------------------------------------------------------------
 698
 699 //------------------------------------------------------------------------------
 700 void vvMainWindow::SliceImages()
 701 {
 702   QString Extensions = EXTENSIONS;
 703   Extensions += ";;All Files (*)";
 704
 705   QStringList files = QFileDialog::getOpenFileNames(this,tr("Slice Images"),mInputPathName,Extensions);
 706   if (files.isEmpty())
 707     return;
 708   mInputPathName = itksys::SystemTools::GetFilenamePath(files[0].toStdString()).c_str();
 709   std::vector<std::string> vector;
 710   for (int i = 0; i < files.size(); i++)
 711     vector.push_back(files[i].toStdString());
 712   LoadImages(vector, vvImageReader::SLICED);
 713 }
 714 //------------------------------------------------------------------------------
 715
 716 //------------------------------------------------------------------------------
 717 void vvMainWindow::MergeImagesWithTime()
 718 {
 719   QString Extensions = EXTENSIONS;
 720   Extensions += ";;All Files (*)";
 721   QStringList files = QFileDialog::getOpenFileNames(this,tr("Merge Images With Time"),mInputPathName,Extensions);
 722   if (files.isEmpty())
 723     return;
 724   mInputPathName = itksys::SystemTools::GetFilenamePath(files[0].toStdString()).c_str();
 725   std::vector<std::string> vector;
 726
 727   for (int i = 0; i < files.size(); i++)
 728     vector.push_back(files[i].toStdString());
 729   sort(vector.begin(),vector.end());
 730   if (vector.size() > 1)
 731     LoadImages(vector, vvImageReader::MERGEDWITHTIME);
 732   else
 733     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.");
 734 }
 735 //------------------------------------------------------------------------------
 736
 737
 738 //------------------------------------------------------------------------------
 739 void vvMainWindow::OpenDicom()
 740 {
 741   std::vector<std::string> files;
 742
 743   //std::cout << "dicomSeriesSelector " << std::endl;
 744   if (dicomSeriesSelector->exec() == QDialog::Accepted) {
 745     files = *(dicomSeriesSelector->GetFilenames());
 746     LoadImages(files, vvImageReader::DICOM);
 747   }
 748 }
 749 //------------------------------------------------------------------------------
 750
 751 //------------------------------------------------------------------------------
 752 void vvMainWindow::OpenImages()
 753 {
 754   QString Extensions = EXTENSIONS;
 755   Extensions += ";;All Files (*)";
 756
 757   QStringList files = QFileDialog::getOpenFileNames(this,tr("Load Images"),mInputPathName,Extensions);
 758   if (files.isEmpty())
 759     return;
 760   mInputPathName = itksys::SystemTools::GetFilenamePath(files[0].toStdString()).c_str();
 761   std::vector<std::string> vector;
 762   for (int i = 0; i < files.size(); i++)
 763     vector.push_back(files[i].toStdString());
 764   LoadImages(vector, vvImageReader::IMAGE);
 765 }
 766 //------------------------------------------------------------------------------
 767 void vvMainWindow::OpenRecentImage()
 768 {
 769   QAction * caller = qobject_cast<QAction*>(sender());
 770   std::vector<std::string> images;
 771   images.push_back(caller->text().toStdString());
 772   mInputPathName = itksys::SystemTools::GetFilenamePath(images[0]).c_str();
 773   LoadImages(images, vvImageReader::IMAGE);
 774 }
 775 //------------------------------------------------------------------------------
 776
 777
 778 //------------------------------------------------------------------------------
 779 void vvMainWindow::OpenImageWithTime()
 780 {
 781   QString Extensions = EXTENSIONS;
 782   Extensions += ";;All Files (*)";
 783
 784   QStringList files = QFileDialog::getOpenFileNames(this,tr("Load Images With Time"),mInputPathName,Extensions);
 785   if (files.isEmpty())
 786     return;
 787   mInputPathName = itksys::SystemTools::GetFilenamePath(files[0].toStdString()).c_str();
 788   std::vector<std::string> vector;
 789   for (int i = 0; i < files.size(); i++) {
 790     vector.push_back(files[i].toStdString());
 791   }
 792   LoadImages(vector, vvImageReader::IMAGEWITHTIME);
 793 }
 794 //------------------------------------------------------------------------------
 795
 796
 797 //------------------------------------------------------------------------------
 798 void vvMainWindow::LoadImages(std::vector<std::string> files, vvImageReader::LoadedImageType filetype)
 799 {
 800   //Separate the way to open images and dicoms
 801   int fileSize;
 802   if (filetype == vvImageReader::IMAGE || filetype == vvImageReader::IMAGEWITHTIME)
 803     fileSize = files.size();
 804   else
 805     fileSize = 1;
 806
 807   // For SLICED, we need the number of slices (ndim and #slices)
 808   std::vector<unsigned int> nSlices;
 809   nSlices.resize(files.size());
 810   std::fill(nSlices.begin(), nSlices.end(), 1);
 811   if (filetype == vvImageReader::SLICED) {
 812     for (int i = 0; i < fileSize; i++) {
 813       itk::ImageIOBase::Pointer header = clitk::readImageHeader(files[i]);
 814       QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
 815       if (!header) {
 816         nSlices[i] = 0;
 817         QString error = "Cannot open file \n";
 818         error += files[i].c_str();
 819         QMessageBox::information(this,tr("Reading problem"),error);
 820         return;
 821       }
 822       if (header->GetNumberOfDimensions() < 3) {
 823         nSlices[i] = 0;
 824         QString error = "Dimension problem. Cannot slice \n";
 825         error += files[i].c_str();
 826         QMessageBox::information(this,tr("Reading problem"),error);
 827         return;
 828       }
 829       nSlices[i] = header->GetDimensions( header->GetNumberOfDimensions()-1 );
 830     }
 831   }
 832
 833   //Only add to the list of recently opened files when a single file is opened,
 834   //to avoid polluting the list of recently opened files
 835   if (files.size() == 1) {
 836     QFileInfo finfo=tr(files[0].c_str());
 837     AddToRecentlyOpenedImages(finfo.absoluteFilePath().toStdString());
 838     updateRecentlyOpenedFilesMenu(GetRecentlyOpenedImages());
 839   }
 840   //init the progress events
 841   QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
 842   vvProgressDialog progress("Opening " + files[0],fileSize>1);
 843   qApp->processEvents();
 844
 845   int numberofsuccesulreads=0;
 846   //open images as 1 or multiples
 847   for (int i = 0; i < fileSize; i++) {
 848     progress.SetText("Opening " + files[i]);
 849     progress.SetProgress(i,fileSize);
 850     qApp->processEvents();
 851
 852     for (unsigned int j = 0; j < nSlices[i]; j++) {
 853       //read the image and put it in mSlicerManagers
 854       vvSlicerManager* imageManager = new vvSlicerManager(4);
 855       qApp->processEvents();
 856
 857       bool SetImageSucceed=false;
 858
 859       // Change filename if an image with the same already exist
 860       int number = GetImageDuplicateFilenameNumber(files[i] + std::string("_slice"));
 861
 862       if (filetype == vvImageReader::IMAGE || filetype == vvImageReader::IMAGEWITHTIME || filetype == vvImageReader::SLICED)
 863         SetImageSucceed = imageManager->SetImage(files[i],filetype, number, j);
 864       else {
 865         SetImageSucceed = imageManager->SetImages(files,filetype, number);
 866       }
 867
 868       if (!SetImageSucceed) {
 869         QApplication::restoreOverrideCursor();
 870         QString error = "Cannot open file \n";
 871         error += imageManager->GetLastError().c_str();
 872         QMessageBox::information(this,tr("Reading problem"),error);
 873         delete imageManager;
 874       } else {
 875         mSlicerManagers.push_back(imageManager);
 876
 877         //create an item in the tree with good settings
 878         QTreeWidgetItem *item = new QTreeWidgetItem();
 879         item->setData(0,Qt::UserRole,files[i].c_str());
 880         QFileInfo fileinfo(imageManager->GetFileName().c_str()); //Do not show the path
 881         item->setData(COLUMN_IMAGE_NAME,Qt::DisplayRole,fileinfo.fileName());
 882         item->setData(1,Qt::UserRole,tr("image"));
 883         item->setToolTip(COLUMN_IMAGE_NAME, imageManager->GetListOfAbsoluteFilePathInOneString("image").c_str());
 884         qApp->processEvents();
 885
 886         //Create the buttons for reload and close
 887         qApp->processEvents();
 888         QTreePushButton* cButton = new QTreePushButton;
 889         cButton->setItem(item);
 890         cButton->setColumn(COLUMN_CLOSE_IMAGE);
 891         cButton->setToolTip(tr("close image"));
 892         cButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/exit.png")));
 893         connect(cButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
 894           this,SLOT(CloseImage(QTreeWidgetItem*, int)));
 895
 896         QTreePushButton* rButton = new QTreePushButton;
 897         rButton->setItem(item);
 898         rButton->setColumn(COLUMN_RELOAD_IMAGE);
 899         rButton->setToolTip(tr("reload image"));
 900         rButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/rotateright.png")));
 901         connect(rButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
 902           this,SLOT(ReloadImage(QTreeWidgetItem*, int)));
 903
 904         DataTree->addTopLevelItem(item);
 905         DataTree->setItemWidget(item, COLUMN_CLOSE_IMAGE, cButton);
 906         DataTree->setItemWidget(item, COLUMN_RELOAD_IMAGE, rButton);
 907
 908         //set the id of the image
 909         QString id = QDir::current().absoluteFilePath(files[i].c_str()) + QString::number(mSlicerManagers.size()-1);
 910         item->setData(COLUMN_IMAGE_NAME,Qt::UserRole,id.toStdString().c_str());
 911         mSlicerManagers.back()->SetId(id.toStdString());
 912
 913         linkPanel->addImage(imageManager->GetFileName(), id.toStdString());
 914
 915         connect(mSlicerManagers.back(), SIGNAL(currentImageChanged(std::string)),
 916           this,SLOT(CurrentImageChanged(std::string)));
 917         connect(mSlicerManagers.back(), SIGNAL(currentPickedImageChanged(std::string)),
 918           this, SLOT(CurrentPickedImageChanged(std::string)));
 919         connect(mSlicerManagers.back(), SIGNAL(UpdatePosition(int, double, double, double, double, double, double, double)),
 920           this,SLOT(MousePositionChanged(int,double, double, double, double, double, double, double)));
 921         connect(mSlicerManagers.back(), SIGNAL(UpdateVector(int, double, double, double, double)),
 922           this, SLOT(VectorChanged(int,double,double,double, double)));
 923         connect(mSlicerManagers.back(), SIGNAL(UpdateOverlay(int, double, double)),
 924           this, SLOT(OverlayChanged(int,double,double)));
 925         connect(mSlicerManagers.back(), SIGNAL(UpdateFusion(int, double)),
 926           this, SLOT(FusionChanged(int,double)));
 927         connect(mSlicerManagers.back(), SIGNAL(WindowLevelChanged()),
 928           this,SLOT(WindowLevelChanged()));
 929         connect(mSlicerManagers.back(), SIGNAL(UpdateSlice(int,int)),
 930           this,SLOT(UpdateSlice(int,int)));
 931         connect(mSlicerManagers.back(), SIGNAL(UpdateTSlice(int, int, int)),
 932           this,SLOT(UpdateTSlice(int, int, int)));
 933         connect(mSlicerManagers.back(), SIGNAL(UpdateTSlice(int, int, int)),
 934           this,SLOT(ImageInfoChanged()));
 935         connect(mSlicerManagers.back(), SIGNAL(UpdateSliceRange(int,int,int,int,int)),
 936           this,SLOT(UpdateSliceRange(int,int,int,int,int)));
 937         connect(mSlicerManagers.back(), SIGNAL(UpdateLinkManager(std::string,int,double,double,double,int)),
 938           this,SLOT(UpdateLinkManager(std::string,int,double,double,double,int)));
 939         connect(mSlicerManagers.back(), SIGNAL(UpdateLinkedNavigation(std::string,vvSlicerManager*,vvSlicer*)),
 940           this,SLOT(UpdateLinkedNavigation(std::string,vvSlicerManager*,vvSlicer*)));
 941         connect(mSlicerManagers.back(), SIGNAL(ChangeImageWithIndexOffset(vvSlicerManager*,int,int)),
 942           this,SLOT(ChangeImageWithIndexOffset(vvSlicerManager*,int,int)));
 943         connect(mSlicerManagers.back(),SIGNAL(LandmarkAdded()),landmarksPanel,SLOT(AddPoint()));
 944
 945         InitSlicers();
 946         numberofsuccesulreads++;
 947       }
 948     }
 949   }
 950   if (numberofsuccesulreads) {
 951     NOViewWidget->show();
 952     NEViewWidget->show();
 953     SOViewWidget->show();
 954     SEViewWidget->show();
 955     UpdateTree();
 956     InitDisplay();
 957     ShowLastImage();
 958
 959     // Try to guess default WindowLevel
 960     double range[2];
 961     mSlicerManagers.back()->GetImage()->GetFirstVTKImageData()->GetScalarRange(range);
 962     if ((range[0] == 0) && (range[1] == 1)) {
 963       presetComboBox->setCurrentIndex(WL_BINARY);// binary
 964     } else {
 965       // TODO
 966     }
 967   }
 968   QApplication::restoreOverrideCursor();
 969 }
 970 //------------------------------------------------------------------------------
 971
 972 //------------------------------------------------------------------------------
 973 void vvMainWindow::UpdateTree()
 974 {
 975   DataTree->resizeColumnToContents(COLUMN_TREE);
 976   DataTree->resizeColumnToContents(COLUMN_UL_VIEW);
 977   DataTree->resizeColumnToContents(COLUMN_UR_VIEW);
 978   DataTree->resizeColumnToContents(COLUMN_DL_VIEW);
 979   DataTree->resizeColumnToContents(COLUMN_DR_VIEW);
 980   DataTree->resizeColumnToContents(COLUMN_IMAGE_NAME);
 981   DataTree->resizeColumnToContents(COLUMN_CLOSE_IMAGE);
 982   DataTree->resizeColumnToContents(COLUMN_RELOAD_IMAGE);
 983 }
 984 //------------------------------------------------------------------------------
 985
 986 //------------------------------------------------------------------------------
 987 void vvMainWindow::CurrentImageChanged(std::string id)
 988 {
 989   if (id == mCurrentSelectedImageId) return; // Do nothing
 990   int selected = 0;
 991   for (int i = 0; i < DataTree->topLevelItemCount(); i++) {
 992     if (DataTree->topLevelItem(i)->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString().toStdString() == id) {
 993       selected = i;
 994     } else {
 995       DataTree->topLevelItem(i)->setSelected(0);
 996     }
 997     for (int child = 0; child < DataTree->topLevelItem(i)->childCount(); child++)
 998       DataTree->topLevelItem(i)->child(child)->setSelected(0);
 999
1000   }
1001   DataTree->topLevelItem(selected)->setSelected(1);
1002   mCurrentSelectedImageId = id;
1003
1004   landmarksPanel->SetCurrentLandmarks(mSlicerManagers[selected]->GetLandmarks(),
1005                                       mSlicerManagers[selected]->GetTSlice());
1006   landmarksPanel->SetCurrentPath(mInputPathName.toStdString());
1007   landmarksPanel->SetCurrentImage(mSlicerManagers[selected]->GetFileName().c_str());
1008
1009   emit SelectedImageHasChanged(mSlicerManagers[selected]);
1010 }
1011 //------------------------------------------------------------------------------
1012
1013 //------------------------------------------------------------------------------
1014 void vvMainWindow::CurrentPickedImageChanged(std::string id)
1015 {
1016   if (id == mCurrentPickedImageId) return; // Do nothing
1017   int selected = 0;
1018   for (int i = 0; i < DataTree->topLevelItemCount(); i++) {
1019     if (DataTree->topLevelItem(i)->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString().toStdString() == id) {
1020       selected = i;
1021     } else {
1022       DataTree->topLevelItem(i)->setSelected(0);
1023     }
1024     for (int child = 0; child < DataTree->topLevelItem(i)->childCount(); child++)
1025       DataTree->topLevelItem(i)->child(child)->setSelected(0);
1026
1027   }
1028   DataTree->topLevelItem(selected)->setSelected(1);
1029   mCurrentPickedImageId = id;
1030   mCurrentPickedImageIndex = selected;
1031 }
1032 //------------------------------------------------------------------------------
1033
1034 //------------------------------------------------------------------------------
1035 void vvMainWindow::ImageInfoChanged()
1036 {
1037   contextActions[6]->setEnabled(1);
1038   contextActions[5]->setEnabled(1);
1039   actionSave_As->setEnabled(1);
1040   actionAdd_VF_to_current_Image->setEnabled(1);
1041   actionAdd_fusion_image->setEnabled(1);
1042   actionAdd_overlay_image_to_current_image->setEnabled(1);
1043   actionAdd_USSequence_toCT->setEnabled(1);
1044   actionNorth_East_Window->setEnabled(1);
1045   actionNorth_West_Window->setEnabled(1);
1046   actionSouth_East_Window->setEnabled(1);
1047   actionSouth_West_Window->setEnabled(1);
1048   vvToolManager::GetInstance()->EnableToolsInMenu(this, true);
1049   inverseButton->setEnabled(1);
1050
1051   goToCursorPushButton->setEnabled(1);
1052
1053   if (DataTree->selectedItems().size()) {
1054     int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1055
1056     colorMapComboBox->setEnabled(1);
1057     for (int i = 0; i < DataTree->topLevelItem(index)->childCount(); i++) {
1058       if (DataTree->topLevelItem(index)->child(i)->data(1,Qt::UserRole).toString() == "overlay" ||
1059         DataTree->topLevelItem(index)->child(i)->data(1,Qt::UserRole).toString() == "fusion" ||
1060         DataTree->topLevelItem(index)->child(i)->data(1,Qt::UserRole).toString() == "fusionSequence") {
1061           colorMapComboBox->setEnabled(0);
1062           break;
1063       }
1064     }
1065
1066     std::vector<double> origin;
1067     std::vector<double> inputSpacing;
1068     std::vector<int> inputSize;
1069     std::vector<double> sizeMM;
1070     vtkSmartPointer<vtkMatrix4x4> transformation;
1071     int dimension=0;
1072     QString pixelType;
1073     QString inputSizeInBytes;
1074     QString image = DataTree->selectedItems()[0]->data(COLUMN_IMAGE_NAME,Qt::DisplayRole).toString();
1075
1076     int nframes = mSlicerManagers[index]->GetSlicer(0)->GetTMax();
1077
1078     if (nframes > 1 || playMode == 1) {
1079       playButton->setEnabled(1);
1080       frameRateLabel->setEnabled(1);
1081       frameRateSpinBox->setEnabled(1);
1082     } else {
1083       playButton->setEnabled(0);
1084       frameRateLabel->setEnabled(0);
1085       frameRateSpinBox->setEnabled(0);
1086     }
1087
1088     //read image header
1089     int NPixel = 1;
1090
1091     int tSlice = 0;
1092     vvImage::Pointer imageSelected;
1093     if (DataTree->topLevelItem(index) == DataTree->selectedItems()[0]) {
1094       imageSelected = mSlicerManagers[index]->GetSlicer(0)->GetImage();
1095       tSlice = mSlicerManagers[index]->GetSlicer(0)->GetTSlice();
1096     } else if (DataTree->selectedItems()[0]->data(1,Qt::UserRole).toString() == "vector") {
1097       imageSelected = mSlicerManagers[index]->GetSlicer(0)->GetVF();
1098       tSlice = mSlicerManagers[index]->GetSlicer(0)->GetOverlayTSlice();
1099     } else if (DataTree->selectedItems()[0]->data(1,Qt::UserRole).toString() == "overlay") {
1100       imageSelected = mSlicerManagers[index]->GetSlicer(0)->GetOverlay();
1101       tSlice = mSlicerManagers[index]->GetSlicer(0)->GetOverlayTSlice();
1102     } else if (DataTree->selectedItems()[0]->data(1,Qt::UserRole).toString() == "fusion") {
1103       imageSelected = mSlicerManagers[index]->GetSlicer(0)->GetFusion();
1104       tSlice = mSlicerManagers[index]->GetSlicer(0)->GetFusionTSlice();
1105     }
1106     else if (DataTree->selectedItems()[0]->data(1,Qt::UserRole).toString() == "fusionSequence") {
1107       imageSelected = mSlicerManagers[index]->GetSlicer(0)->GetFusion();
1108       tSlice = mSlicerManagers[index]->GetSlicer(0)->GetFusionTSlice();
1109     }
1110     else if (DataTree->selectedItems()[0]->data(1,Qt::UserRole).toString() == "contour") {
1111       imageSelected = mSlicerManagers[index]->GetSlicer(0)->GetImage();
1112       tSlice = mSlicerManagers[index]->GetSlicer(0)->GetTSlice();
1113     }
1114     else {
1115       imageSelected = mSlicerManagers[index]->GetSlicer(0)->GetImage();
1116       tSlice = mSlicerManagers[index]->GetSlicer(0)->GetTSlice();
1117     }
1118
1119     dimension = imageSelected->GetNumberOfDimensions();
1120     origin.resize(dimension);
1121     inputSpacing.resize(dimension);
1122     inputSize.resize(dimension);
1123     sizeMM.resize(dimension);
1124     pixelType = mSlicerManagers[index]->GetImage()->GetScalarTypeAsITKString().c_str();
1125     for (int i = 0; i < dimension; i++) {
1126       origin[i] = imageSelected->GetOrigin()[i];
1127       inputSpacing[i] = imageSelected->GetSpacing()[i];
1128       inputSize[i] = imageSelected->GetSize()[i];
1129       sizeMM[i] = inputSize[i]*inputSpacing[i];
1130       NPixel *= inputSize[i];
1131     }
1132     inputSizeInBytes = GetSizeInBytes(imageSelected->GetActualMemorySize()*1000);
1133
1134     QString dim = QString::number(dimension) + " (";
1135     dim += pixelType + ")";
1136
1137     infoPanel->setFileName(image);
1138     std::string creationImageTimeValue("No creation time");
1139     itk::ExposeMetaData< std::string > (*imageSelected->GetFirstMetaDataDictionary(), "creationImageTime", creationImageTimeValue);
1140     infoPanel->setImageCreationTime(QString(creationImageTimeValue.c_str()));
1141     infoPanel->setDimension(dim);
1142     infoPanel->setSizePixel(GetVectorIntAsString(inputSize));
1143     infoPanel->setSizeMM(GetVectorDoubleAsString(sizeMM));
1144     infoPanel->setOrigin(GetVectorDoubleAsString(origin));
1145     infoPanel->setSpacing(GetVectorDoubleAsString(inputSpacing));
1146     infoPanel->setNPixel(QString::number(NPixel)+" ("+inputSizeInBytes+")");
1147
1148     transformation = imageSelected->GetTransform()[tSlice]->GetMatrix();
1149     infoPanel->setTransformation(clitk::Get4x4MatrixDoubleAsString(transformation).c_str());
1150
1151     landmarksPanel->SetCurrentLandmarks(mSlicerManagers[index]->GetLandmarks(),
1152                                         mSlicerManagers[index]->GetTSlice());
1153     landmarksPanel->SetCurrentPath(mInputPathName.toStdString());
1154     landmarksPanel->SetCurrentImage(mSlicerManagers[index]->GetFileName().c_str());
1155
1156     overlayPanel->getCurrentImageName(mSlicerManagers[index]->GetFileName().c_str());
1157     for (int i = 0; i < 4; i++) {
1158       if (DataTree->selectedItems()[0]->data(i+1,Qt::CheckStateRole).toInt() > 0 || i == 3) {
1159         mSlicerManagers[index]->UpdateInfoOnCursorPosition(i);
1160         break;
1161       }
1162     }
1163
1164 //     infoPanel->setFileName(image);
1165 //     infoPanel->setDimension(dim);
1166 //     infoPanel->setSizePixel(GetVectorIntAsString(inputSize));
1167 //     infoPanel->setSizeMM(GetVectorDoubleAsString(sizeMM));
1168 //     infoPanel->setOrigin(GetVectorDoubleAsString(origin));
1169 //     infoPanel->setSpacing(GetVectorDoubleAsString(inputSpacing));
1170 //     infoPanel->setNPixel(QString::number(NPixel)+" ("+inputSizeInBytes+")");
1171 //
1172 //     landmarksPanel->SetCurrentLandmarks(mSlicerManagers[index]->GetLandmarks(),
1173 //                                         mSlicerManagers[index]->GetTSlice());
1174 //     landmarksPanel->SetCurrentPath(mInputPathName.toStdString());
1175 //     landmarksPanel->SetCurrentImage(mSlicerManagers[index]->GetFileName().c_str());
1176 //
1177 //     overlayPanel->getCurrentImageName(mSlicerManagers[index]->GetFileName().c_str());
1178 //     for (int i = 0; i < 4; i++) {
1179 //       if (DataTree->selectedItems()[0]->data(i+1,Qt::CheckStateRole).toInt() > 0 || i == 3) {
1180 //         mSlicerManagers[index]->UpdateInfoOnCursorPosition(i);
1181 //         break;
1182 //       }
1183 //     }
1184     WindowLevelChanged();
1185
1186     slicingPresetComboBox->setCurrentIndex(mSlicerManagers[index]->GetSlicingPreset());
1187
1188     if (mSlicerManagers[index]->GetSlicer(0)->GetVF()) {
1189       overlayPanel->getVFName(mSlicerManagers[index]->GetVFName().c_str());
1190       overlayPanel->getVFProperty(mSlicerManagers[index]->GetSlicer(0)->GetVFSubSampling(),
1191         mSlicerManagers[index]->GetSlicer(0)->GetVFScale(),
1192         mSlicerManagers[index]->GetSlicer(0)->GetVFLog());
1193     } else {
1194       overlayPanel->getVFName(mSlicerManagers[index]->GetVFName().c_str());
1195       overlayPanel->getVFProperty(-1,-1,-1);
1196     }
1197     if (mSlicerManagers[index]->GetSlicer(0)->GetOverlay()) {
1198       overlayPanel->getOverlayName(mSlicerManagers[index]->GetOverlayName().c_str());
1199     } else {
1200       overlayPanel->getOverlayName(mSlicerManagers[index]->GetOverlayName().c_str());
1201     }
1202
1203     if (mSlicerManagers[index]->GetSlicer(0)->GetFusion()) {
1204       overlayPanel->getFusionName(mSlicerManagers[index]->GetFusionName().c_str());
1205     } else {
1206       overlayPanel->getFusionName(mSlicerManagers[index]->GetFusionName().c_str());
1207     }
1208   }
1209 }
1210 //------------------------------------------------------------------------------
1211
1212 //------------------------------------------------------------------------------
1213 void vvMainWindow::ShowDocumentation()
1214 {
1215   documentation->show();
1216 }
1217 //------------------------------------------------------------------------------
1218
1219 //------------------------------------------------------------------------------
1220 void vvMainWindow::PopupRegisterForm(bool checkCanPush)
1221 {
1222   vvRegisterForm* registerForm = new vvRegisterForm(QUrl("http://www.creatis.insa-lyon.fr/~dsarrut/vvregister/write.php"), getVVSettingsPath(), getSettingsOptionFormat());
1223   if(!checkCanPush) {
1224     registerForm->show();
1225   } else {
1226     if(registerForm->canPush()) {
1227       registerForm->show();
1228       registerForm->acquitPushed();//too bad if there is not internet connection anymore.
1229     }
1230   }
1231 }
1232 //------------------------------------------------------------------------------
1233
1234 //------------------------------------------------------------------------------
1235 void vvMainWindow::ShowHelpDialog()
1236 {
1237   help_dialog->show();
1238 }
1239 //------------------------------------------------------------------------------
1240
1241 //------------------------------------------------------------------------------
1242 void vvMainWindow::ChangeViewMode()
1243 {
1244   typedef struct _SIZE{
1245     QSplitter* splitter;
1246     QList<int> size1, size2;
1247     int cols[3];
1248   }SplitterSize;
1249   SplitterSize sizes[4];
1250   sizes[0].splitter = OSplitter;
1251   sizes[0].size1.push_back(1);
1252   sizes[0].size1.push_back(0);
1253   sizes[0].size2.push_back(1);
1254   sizes[0].size2.push_back(0);
1255   sizes[0].cols[0] = 2;
1256   sizes[0].cols[1] = 3;
1257   sizes[0].cols[2] = 4;
1258
1259   sizes[1].splitter = ESplitter;
1260   sizes[1].size1.push_back(0);
1261   sizes[1].size1.push_back(1);
1262   sizes[1].size2.push_back(1);
1263   sizes[1].size2.push_back(0);
1264   sizes[1].cols[0] = 1;
1265   sizes[1].cols[1] = 3;
1266   sizes[1].cols[2] = 4;
1267
1268   sizes[2].splitter = OSplitter;
1269   sizes[2].size1.push_back(1);
1270   sizes[2].size1.push_back(0);
1271   sizes[2].size2.push_back(0);
1272   sizes[2].size2.push_back(1);
1273   sizes[2].cols[0] = 1;
1274   sizes[2].cols[1] = 2;
1275   sizes[2].cols[2] = 4;
1276
1277   sizes[3].splitter = ESplitter;
1278   sizes[3].size1.push_back(0);
1279   sizes[3].size1.push_back(1);
1280   sizes[3].size2.push_back(0);
1281   sizes[3].size2.push_back(1);
1282   sizes[3].cols[0] = 1;
1283   sizes[3].cols[1] = 2;
1284   sizes[3].cols[2] = 3;
1285
1286   int slicer = mSlicerManagers[mCurrentPickedImageIndex]->GetSelectedSlicer();
1287   if (viewMode == 1) {
1288     if (slicer >= 0) {
1289       viewMode = 0;
1290       splitter_3->setSizes(sizes[slicer].size1);
1291       sizes[slicer].splitter->setSizes(sizes[slicer].size2);
1292       DataTree->setColumnHidden(sizes[slicer].cols[0],1);
1293       DataTree->setColumnHidden(sizes[slicer].cols[1],1);
1294       DataTree->setColumnHidden(sizes[slicer].cols[2],1);
1295     }
1296   } else {
1297     QList<int> size;
1298     if (slicer >= 0) {
1299       viewMode = 1;
1300       size.push_back(1);
1301       size.push_back(1);
1302       splitter_3->setSizes(size);
1303       sizes[slicer].splitter->setSizes(size);
1304       DataTree->setColumnHidden(sizes[slicer].cols[0],0);
1305       DataTree->setColumnHidden(sizes[slicer].cols[1],0);
1306       DataTree->setColumnHidden(sizes[slicer].cols[2],0);
1307     }
1308   }
1309   UpdateRenderWindows();
1310   /*
1311   ** I don't know why but for both resized QVTKWidget we also need to render
1312   ** the associated Slicer to redraw crosses.
1313   */
1314   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
1315     //     if (DataTree->topLevelItem(i)->data(COLUMN_UL_VIEW,Qt::CheckStateRole).toInt() > 1)
1316     mSlicerManagers[i]->GetSlicer(0)->Render();
1317     mSlicerManagers[i]->GetSlicer(1)->Render();
1318     //     if (DataTree->topLevelItem(i)->data(COLUMN_DL_VIEW,Qt::CheckStateRole).toInt() > 1)
1319     mSlicerManagers[i]->GetSlicer(2)->Render();
1320     mSlicerManagers[i]->GetSlicer(3)->Render();
1321   }
1322 }
1323 //------------------------------------------------------------------------------
1324
1325 //------------------------------------------------------------------------------
1326 QString vvMainWindow::GetSizeInBytes(unsigned long size)
1327 {
1328   QString result = "";// QString::number(size);
1329   //result += " bytes (";
1330   if (size > 1000000000) {
1331     size /= 1000000000;
1332     result += QString::number(size);
1333     result += "Gb";//)";
1334   } else if (size > 1000000) {
1335     size /= 1000000;
1336     result += QString::number(size);
1337     result += "Mb";//)";
1338   } else if (size > 1000) {
1339     size /= 1000;
1340     result += QString::number(size);
1341     result += "kb";//)";
1342   }
1343   return result;
1344 }
1345 //------------------------------------------------------------------------------
1346
1347 //------------------------------------------------------------------------------
1348 QString vvMainWindow::GetVectorDoubleAsString(std::vector<double> vectorDouble)
1349 {
1350   QString result;
1351   for (unsigned int i= 0; i < vectorDouble.size(); i++) {
1352     if (i != 0)
1353       result += " ";
1354     result += QString::number(vectorDouble[i]);
1355   }
1356   return result;
1357 }
1358 //------------------------------------------------------------------------------
1359
1360 //------------------------------------------------------------------------------
1361 QString vvMainWindow::GetVectorIntAsString(std::vector<int> vectorInt)
1362 {
1363   QString result;
1364   for (unsigned int i= 0; i < vectorInt.size(); i++) {
1365     if (i != 0)
1366       result += " ";
1367     result += QString::number(vectorInt[i]);
1368   }
1369   return result;
1370 }
1371 //------------------------------------------------------------------------------
1372
1373 //------------------------------------------------------------------------------
1374 //this actually returns the SlicerManager index!
1375 int vvMainWindow::GetSlicerIndexFromItem(QTreeWidgetItem* item)
1376 {
1377   QString id = item->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString();
1378   for (int i = 0; i < DataTree->topLevelItemCount(); i++) {
1379     if (DataTree->topLevelItem(i)->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString() == id)
1380       return i;
1381   }
1382   return -1;
1383 }
1384 //------------------------------------------------------------------------------
1385
1386 //------------------------------------------------------------------------------
1387 QTreeWidgetItem* vvMainWindow::GetItemFromSlicerManager(vvSlicerManager* sm)
1388 {
1389   QString id = sm->GetId().c_str();
1390   for (int i = 0; i < DataTree->topLevelItemCount(); i++) {
1391     if (DataTree->topLevelItem(i)->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString() == id)
1392       return DataTree->topLevelItem(i);
1393   }
1394   return NULL;
1395 }
1396 //------------------------------------------------------------------------------
1397
1398 //------------------------------------------------------------------------------
1399 void vvMainWindow::DisplayChanged(QTreeWidgetItem *clickedItem, int column)
1400 {
1401   if ( column >= COLUMN_CLOSE_IMAGE || column <= 0)
1402     return;
1403
1404   // Get parent information (might be the same item)
1405   int slicerManagerIndex = GetSlicerIndexFromItem(clickedItem);
1406   QTreeWidgetItem* clickedParentItem = DataTree->topLevelItem(slicerManagerIndex);
1407   vvSlicer* clickedSlicer = mSlicerManagers[slicerManagerIndex]->GetSlicer(column-1);
1408
1409   // Go over the complete item tree (only 2 levels, parents and children)
1410   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
1411     // Trick to avoid redoing twice the job for a key (sr)
1412     mSlicerManagers[i]->GetSlicer(column-1)->GetRenderWindow()->GetInteractor()->SetKeySym("Crap");
1413
1414     QTreeWidgetItem* currentParentItem = DataTree->topLevelItem(i);
1415     if(currentParentItem != clickedParentItem) {
1416       // Not the branch of the clicked item, uncheck all
1417
1418       // Parent
1419       currentParentItem->setData(column,Qt::CheckStateRole, 0);
1420       mSlicerManagers[i]->UpdateSlicer(column-1, false);
1421
1422       // Children
1423       for (int iChild = 0; iChild < currentParentItem->childCount(); iChild++) {
1424         currentParentItem->child(iChild)->setData(column,Qt::CheckStateRole, 0);
1425       }
1426     }
1427     else {
1428       // Branch of the clicked one: get check status from actor visibility in slicer
1429       // and toggle the clicked one
1430
1431       // Parent
1432       bool vis = clickedSlicer->GetActorVisibility("image", 0);
1433       bool draw = clickedSlicer->GetRenderer()->GetDraw();
1434
1435       // Update slicer (after getting visibility)
1436       mSlicerManagers[slicerManagerIndex]->UpdateSlicer(column-1, true);
1437       mSlicerManagers[slicerManagerIndex]->UpdateInfoOnCursorPosition(column-1);
1438       DisplaySliders(slicerManagerIndex, column-1);
1439       if(clickedParentItem == clickedItem) {
1440         // Toggle
1441         vis = !draw || !vis;
1442       }
1443       clickedSlicer->SetActorVisibility("image", 0, vis);
1444       clickedParentItem->setData(column, Qt::CheckStateRole, vis?2:0);
1445
1446       // Children
1447       std::map<std::string, int> actorTypeCounts;
1448       for (int iChild = 0; iChild < clickedParentItem->childCount(); iChild++) {
1449         QTreeWidgetItem* currentChildItem = clickedParentItem->child(iChild);
1450         std::string actorType = currentChildItem->data(1,Qt::UserRole).toString().toStdString();
1451         vis = clickedSlicer->GetActorVisibility(actorType, actorTypeCounts[actorType]);
1452         if(currentChildItem == clickedItem) {
1453           // Toggle or force visibility if it was not on this branch so far
1454           vis = !draw || !vis;
1455           clickedSlicer->SetActorVisibility(actorType, actorTypeCounts[actorType], vis);
1456         }
1457         currentChildItem->setData(column, Qt::CheckStateRole, vis?2:0);
1458         actorTypeCounts[actorType]++;
1459       }
1460     }
1461   }
1462
1463   clickedSlicer->Render();
1464 }
1465 //------------------------------------------------------------------------------
1466
1467 void vvMainWindow::InitSlicers()
1468 {
1469   if (mSlicerManagers.size()) {
1470     mSlicerManagers.back()->GenerateDefaultLookupTable();
1471
1472     mSlicerManagers.back()->SetSlicerWindow(0,NOViewWidget->GetRenderWindow());
1473     mSlicerManagers.back()->SetSlicerWindow(1,NEViewWidget->GetRenderWindow());
1474     mSlicerManagers.back()->SetSlicerWindow(2,SOViewWidget->GetRenderWindow());
1475     mSlicerManagers.back()->SetSlicerWindow(3,SEViewWidget->GetRenderWindow());
1476   }
1477 }
1478
1479 //------------------------------------------------------------------------------
1480 void vvMainWindow::InitDisplay()
1481 {
1482   if (mSlicerManagers.size()) {
1483     //BE CAREFUL : this is absolutely necessary to set the interactor style
1484     //in order to have the same style instanciation for all SlicerManagers in
1485     // a same window
1486     for (int j = 0; j < 4; j++) {
1487       vvInteractorStyleNavigator* style = vvInteractorStyleNavigator::New();
1488       style->SetAutoAdjustCameraClippingRange(1);
1489       bool AlreadySelected = false;
1490       for (int i = 0; i < DataTree->topLevelItemCount(); i++) {
1491         mSlicerManagers[i]->SetInteractorStyleNavigator(j,style);
1492
1493         //select the image only if previous are not selected
1494         if (DataTree->topLevelItem(i)->data(j+1,Qt::CheckStateRole).toInt() > 1) {
1495           mSlicerManagers[i]->UpdateSlicer(j,1);
1496           AlreadySelected = true;
1497         } else if (i == DataTree->topLevelItemCount()-1 && !AlreadySelected) {
1498           if (DataTree->selectedItems().size() == 0)
1499             DataTree->topLevelItem(i)->setSelected(1);
1500           DataTree->topLevelItem(i)->setData(j+1,Qt::CheckStateRole,2);
1501           mSlicerManagers[i]->UpdateSlicer(j,1);
1502           DisplaySliders(i,j);
1503         } else {
1504           DataTree->topLevelItem(i)->setData(j+1,Qt::CheckStateRole,0);
1505           mSlicerManagers[i]->UpdateSlicer(j,0);
1506         }
1507       }
1508       style->Delete();
1509     }
1510   }
1511 }
1512 //------------------------------------------------------------------------------
1513
1514 //------------------------------------------------------------------------------
1515 void vvMainWindow::DisplaySliders(int slicer, int window)
1516 {
1517   if(!mSlicerManagers[slicer]->GetSlicer(window)->GetRenderer()->GetDraw())
1518     return;
1519
1520   int range[2];
1521   mSlicerManagers[slicer]->GetSlicer(window)->GetSliceRange(range);
1522   int position = mSlicerManagers[slicer]->GetSlicer(window)->GetSlice();
1523   if (range[1]>0)
1524     verticalSliders[window]->show();
1525   else
1526     verticalSliders[window]->hide();
1527   verticalSliders[window]->setRange(range[0],range[1]);
1528   verticalSliders[window]->setValue(position);
1529
1530   int tRange[2];
1531   tRange[0] = 0;
1532   tRange[1] = mSlicerManagers[slicer]->GetSlicer(window)->GetTMax();
1533   if (tRange[1]>0)
1534     horizontalSliders[window]->show();
1535   else
1536     horizontalSliders[window]->hide();
1537   horizontalSliders[window]->setRange(tRange[0],tRange[1]);
1538   int tPosition = mSlicerManagers[slicer]->GetSlicer(window)->GetMaxCurrentTSlice();
1539   horizontalSliders[window]->setValue(tPosition);
1540 }
1541 //------------------------------------------------------------------------------
1542
1543 //------------------------------------------------------------------------------
1544 void vvMainWindow::CloseImage(QTreeWidgetItem* item, int column)
1545 {
1546   int index = GetSlicerIndexFromItem(item);
1547
1548   if (DataTree->topLevelItem(index) != item) {
1549     QString warning = "Do you really want to close the overlay : ";
1550     warning += item->data(COLUMN_IMAGE_NAME,Qt::DisplayRole).toString();
1551     QMessageBox msgBox(QMessageBox::Warning, tr("Close Overlay"),
1552       warning, 0, this);
1553     msgBox.addButton(tr("Close"), QMessageBox::AcceptRole);
1554     msgBox.addButton(tr("Cancel"), QMessageBox::RejectRole);
1555     if (msgBox.exec() == QMessageBox::AcceptRole) {
1556       std::string overlay_type=item->data(1,Qt::UserRole).toString().toStdString();
1557       int overlay_index=0;
1558       for (int child = 0; child < DataTree->topLevelItem(index)->childCount(); child++) {
1559         if (DataTree->topLevelItem(index)->\
1560           child(child)->data(1,Qt::UserRole).toString().toStdString() == overlay_type)
1561           overlay_index++;
1562         if (DataTree->topLevelItem(index)->child(child) == item) break;
1563       }
1564       if (overlay_type=="fusionSequence") {
1565         //removing the overlay sequence in a fusion sequence visualization mode
1566         //reset the transforms
1567         overlayPanel->getFusionSequenceProperty(-1, false, 0, false);
1568
1569         //unlink and untie the slicer managers
1570         RemoveLink(mSlicerManagers[index]->GetId().c_str(), mSlicerManagers[mSlicerManagers[index]->GetFusionSequenceIndexOfLinkedManager()]->GetId().c_str());
1571         mSlicerManagers[index]->SetFusionSequenceInvolvmentCode(-1);
1572         mSlicerManagers[mSlicerManagers[index]->GetFusionSequenceIndexOfLinkedManager()]->SetFusionSequenceInvolvmentCode(-1);
1573         for (unsigned i=0 ; i<4 ; i++) {
1574             mSlicerManagers[index]->GetSlicer(i)->SetFusionSequenceCode(-1);
1575             mSlicerManagers[mSlicerManagers[index]->GetFusionSequenceIndexOfLinkedManager()]->GetSlicer(i)->SetFusionSequenceCode(-1);
1576         }
1577
1578       }
1579       mSlicerManagers[index]->RemoveActor(overlay_type, overlay_index-1);
1580       mSlicerManagers[index]->SetColorMap(0);
1581       DataTree->topLevelItem(index)->takeChild(DataTree->topLevelItem(index)->indexOfChild(item));
1582       mSlicerManagers[index]->Render();
1583     }
1584   } else if (DataTree->topLevelItemCount() <= 1) {
1585     QString warning = "Do you really want to close the image : ";
1586     warning += item->data(COLUMN_IMAGE_NAME,Qt::DisplayRole).toString();
1587     warning += "\nThis is the last image, you're about to close vv !!!";
1588     QMessageBox msgBox(QMessageBox::Warning, tr("Close Image"),
1589       warning, 0, this);
1590     msgBox.addButton(tr("Close vv"), QMessageBox::AcceptRole);
1591     msgBox.addButton(tr("Cancel"), QMessageBox::RejectRole);
1592     if (msgBox.exec() == QMessageBox::AcceptRole) {
1593       this->close();
1594     }
1595   } else {
1596     QString warning = "Do you really want to close the image : ";
1597     warning += item->data(COLUMN_IMAGE_NAME,Qt::DisplayRole).toString();
1598     QMessageBox msgBox(QMessageBox::Warning, tr("Close Image"),
1599       warning, 0, this);
1600     msgBox.addButton(tr("Close"), QMessageBox::AcceptRole);
1601     msgBox.addButton(tr("Cancel"), QMessageBox::RejectRole);
1602     if (msgBox.exec() == QMessageBox::AcceptRole) {
1603
1604       // Tell tools that we close an image
1605       emit AnImageIsBeingClosed(mSlicerManagers[index]);
1606
1607       std::vector<vvSlicerManager*>::iterator Manageriter = mSlicerManagers.begin();
1608       DataTree->takeTopLevelItem(index);
1609       for (int i = 0; i < index; i++) {
1610         Manageriter++;
1611       }
1612       //if the slicer manager was involved in a fusion sequence visualization...
1613       if ( mSlicerManagers[index]->IsInvolvedInFusionSequence() ) {
1614         //in both cases, close the overlay: find it... and close it
1615         //ideally, I should duplicate the code, and avoid calling CloseImage, since this pops up another interactive box
1616         QTreeWidgetItem* overlayItem;
1617         if (mSlicerManagers[index]->IsMainSequenceOfFusionSequence()) {
1618           for (unsigned i=0 ; i<item->childCount() ; i++) {
1619             overlayItem = item->child(i);
1620             this->CloseImage( overlayItem, 0 );
1621           }
1622         }
1623         else {
1624           QTreeWidgetItem* linkedItem = this->GetItemFromSlicerManager( mSlicerManagers[mSlicerManagers[index]->GetFusionSequenceIndexOfLinkedManager()] );
1625           for (unsigned i=0 ; i<linkedItem->childCount() ; i++) {
1626             overlayItem = linkedItem->child(i);
1627             this->CloseImage( overlayItem, 0 );
1628           }
1629         }
1630
1631         /* -- this is normally already done when closing the overlay.
1632         //reset the transforms
1633         overlayPanel->getFusionSequenceProperty(-1, false, 0, false);
1634
1635         //unlink and untie the slicer managers
1636         RemoveLink(mSlicerManagers[index]->GetId().c_str(), mSlicerManagers[mSlicerManagers[index]->GetFusionSequenceIndexOfLinkedManager()]->GetId().c_str());
1637         mSlicerManagers[index]->SetFusionSequenceInvolvmentCode(-1);
1638         mSlicerManagers[mSlicerManagers[index]->GetFusionSequenceIndexOfLinkedManager()]->SetFusionSequenceInvolvmentCode(-1);
1639         for (unsigned i=0 ; i<4 ; i++) {
1640             mSlicerManagers[index]->GetSlicer(i)->SetFusionSequenceCode(-1);
1641             mSlicerManagers[mSlicerManagers[index]->GetFusionSequenceIndexOfLinkedManager()]->GetSlicer(i)->SetFusionSequenceCode(-1);
1642         }
1643         */
1644       }
1645
1646       linkPanel->removeImage(index);
1647       mSlicerManagers[index]->RemoveActors();
1648
1649       //remove the slicer manager
1650       delete mSlicerManagers[index];
1651       mSlicerManagers.erase(Manageriter);
1652
1653       //
1654       InitDisplay();
1655     }
1656   }
1657   ImageInfoChanged();
1658 }
1659 //------------------------------------------------------------------------------
1660
1661 //------------------------------------------------------------------------------
1662 void vvMainWindow::ReloadImage(QTreeWidgetItem* item, int column)
1663 {
1664   // int index = GetSlicerIndexFromItem(item);
1665   //   QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
1666   //   if (item->data(1,Qt::UserRole).toString() == "vector")
1667   //     mSlicerManagers[index]->ReloadVF();
1668   //   else
1669   //     mSlicerManagers[index]->Reload();
1670
1671   //   QApplication::restoreOverrideCursor();
1672   int index = GetSlicerIndexFromItem(item);
1673   QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
1674   QString role=item->data(1,Qt::UserRole).toString();
1675   if ( role == "vector") {
1676     mSlicerManagers[index]->ReloadVF();
1677   }
1678   else if (role == "overlay") {
1679     mSlicerManagers[index]->ReloadOverlay();
1680   }
1681   else if (role == "fusion") {
1682     mSlicerManagers[index]->ReloadFusion();
1683   }
1684   else if (role == "fusionSequence") {
1685     //both versions of the secondary sequence must be updated.
1686     mSlicerManagers[index]->ReloadFusionSequence();
1687     mSlicerManagers[mSlicerManagers[index]->GetFusionSequenceIndexOfLinkedManager()]->Reload();
1688   }
1689   else {
1690     mSlicerManagers[index]->Reload();
1691     //if we update the secondary sequence, then the overlay of the main sequence should also be updated
1692     if (mSlicerManagers[index]->IsSecondarySequenceOfFusionSequence()) mSlicerManagers[mSlicerManagers[index]->GetFusionSequenceIndexOfLinkedManager()]->ReloadFusionSequence();
1693   }
1694   // Update view and info
1695   ImageInfoChanged();
1696   mSlicerManagers[index]->Render();
1697   QApplication::restoreOverrideCursor();
1698 }
1699 //------------------------------------------------------------------------------
1700
1701 //------------------------------------------------------------------------------
1702 void vvMainWindow::MousePositionChanged(int visibility,double x, double y, double z, double X, double Y, double Z , double value)
1703 {
1704   infoPanel->setCurrentInfo(visibility,x,y,z,X,Y,Z,value);
1705 }
1706 //------------------------------------------------------------------------------
1707
1708 //------------------------------------------------------------------------------
1709 void vvMainWindow::VectorChanged(int visibility,double x, double y, double z, double value)
1710 {
1711   overlayPanel->getCurrentVectorInfo(visibility,x,y,z,value);
1712 }
1713 //------------------------------------------------------------------------------
1714
1715 //------------------------------------------------------------------------------
1716 void vvMainWindow::OverlayChanged(int visibility, double valueOver, double valueRef)
1717 {
1718   overlayPanel->getCurrentOverlayInfo(visibility,valueOver, valueRef);
1719 }
1720 //------------------------------------------------------------------------------
1721
1722 //------------------------------------------------------------------------------
1723 void vvMainWindow::FusionChanged(int visibility, double value)
1724 {
1725   overlayPanel->getCurrentFusionInfo(visibility,value);
1726 }
1727 //------------------------------------------------------------------------------
1728
1729 //------------------------------------------------------------------------------
1730 //called when AddOverlayImage, AddFusionSequence
1731 //or when UpdateWindowLevel() is called ; when slicerManager emits WindowLevelChanged
1732 //when ImageInfoChanged() is called
1733 void vvMainWindow::WindowLevelChanged()
1734 {
1735   // Base image
1736   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1737   if(index==-1) return;
1738   windowSpinBox->setValue(mSlicerManagers[index]->GetColorWindow());
1739   levelSpinBox->setValue(mSlicerManagers[index]->GetColorLevel());
1740   colorMapComboBox->setCurrentIndex(mSlicerManagers[index]->GetColorMap());
1741   presetComboBox->setCurrentIndex(mSlicerManagers[index]->GetPreset());
1742
1743   // Overlay image
1744   if (mSlicerManagers[index]->GetSlicer(0)->GetOverlay())
1745     overlayPanel->getOverlayProperty(mSlicerManagers[index]->GetOverlayColor(),
1746     mSlicerManagers[index]->GetLinkOverlayWindowLevel(),
1747     mSlicerManagers[index]->GetOverlayColorWindow(),
1748     mSlicerManagers[index]->GetOverlayColorLevel());
1749   else
1750     overlayPanel->getOverlayProperty(-1,0,0.,0.);
1751
1752   // Fusion & SequenceFusion image
1753   if (mSlicerManagers[index]->GetSlicer(0)->GetFusion()) {
1754     overlayPanel->getFusionProperty(mSlicerManagers[index]->GetFusionOpacity(),
1755       mSlicerManagers[index]->GetFusionThresholdOpacity(),
1756       mSlicerManagers[index]->GetFusionColorMap(),
1757       mSlicerManagers[index]->GetFusionWindow(),
1758       mSlicerManagers[index]->GetFusionLevel());
1759     if (mSlicerManagers[index]->IsMainSequenceOfFusionSequence()) {
1760       overlayPanel->getFusionSequenceProperty(mSlicerManagers[index]->GetFusionSequenceFrameIndex(),
1761         mSlicerManagers[index]->GetFusionSequenceSpatialSyncFlag(),
1762         mSlicerManagers[index]->GetFusionSequenceNbFrames(),
1763         mSlicerManagers[index]->GetFusionSequenceTemporalSyncFlag());
1764     }
1765   }
1766   else if ( mSlicerManagers[index]->IsSecondarySequenceOfFusionSequence() ) {
1767     //if the image is involved in a fusion sequence, preserve the overlay panel!
1768     int ind = mSlicerManagers[index]->GetFusionSequenceIndexOfLinkedManager();
1769     overlayPanel->getFusionProperty(mSlicerManagers[ind]->GetFusionOpacity(),
1770       mSlicerManagers[ind]->GetFusionThresholdOpacity(),
1771       mSlicerManagers[ind]->GetFusionColorMap(),
1772       mSlicerManagers[ind]->GetFusionWindow(),
1773       mSlicerManagers[ind]->GetFusionLevel());
1774     overlayPanel->getFusionSequenceProperty(mSlicerManagers[ind]->GetFusionSequenceFrameIndex(),
1775       mSlicerManagers[ind]->GetFusionSequenceSpatialSyncFlag(),
1776       mSlicerManagers[ind]->GetFusionSequenceNbFrames(),
1777       mSlicerManagers[ind]->GetFusionSequenceTemporalSyncFlag());
1778   }
1779   else
1780   {
1781     overlayPanel->getFusionProperty(-1, -1, -1, -1, -1);
1782     overlayPanel->getFusionSequenceProperty(-1, false, 0, false);
1783   }
1784 }
1785 //------------------------------------------------------------------------------
1786
1787 //------------------------------------------------------------------------------
1788 void vvMainWindow::WindowLevelEdited()
1789 {
1790   presetComboBox->setCurrentIndex(WL_USER);
1791   UpdateWindowLevel();
1792 }
1793 //------------------------------------------------------------------------------
1794
1795 //------------------------------------------------------------------------------
1796 void vvMainWindow::SetWindowLevel(double w, double l)
1797 {
1798   windowSpinBox->setValue(w);
1799   levelSpinBox->setValue(l);
1800   presetComboBox->setCurrentIndex(WL_USER);
1801   colorMapComboBox->setCurrentIndex(0);
1802   UpdateWindowLevel();
1803 }
1804 //------------------------------------------------------------------------------
1805
1806 //------------------------------------------------------------------------------
1807 void vvMainWindow::UpdateWindowLevel()
1808 {
1809   if (DataTree->selectedItems().size()) {
1810     if (presetComboBox->currentIndex() == WL_VENTILATION) //For ventilation
1811       colorMapComboBox->setCurrentIndex(5);
1812     int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1813     mSlicerManagers[index]->SetColorWindow(windowSpinBox->value());
1814     mSlicerManagers[index]->SetColorLevel(levelSpinBox->value());
1815     mSlicerManagers[index]->SetPreset(presetComboBox->currentIndex());
1816     mSlicerManagers[index]->Render();
1817     WindowLevelChanged();
1818   }
1819 }
1820 //------------------------------------------------------------------------------
1821
1822 //------------------------------------------------------------------------------
1823 void vvMainWindow::UpdateSlicingPreset()
1824 {
1825   if (DataTree->selectedItems().size()) {
1826     int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1827     mSlicerManagers[index]->SetSlicingPreset(vvSlicerManager::SlicingPresetType(slicingPresetComboBox->currentIndex()));
1828   }
1829 }
1830 //------------------------------------------------------------------------------
1831
1832 //------------------------------------------------------------------------------
1833 void vvMainWindow::UpdateColorMap()
1834 {
1835   if (DataTree->selectedItems().size()) {
1836     int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1837     mSlicerManagers[index]->SetColorMap(colorMapComboBox->currentIndex());
1838     mSlicerManagers[index]->Render();
1839   }
1840 }
1841 //------------------------------------------------------------------------------
1842 void vvMainWindow::SwitchWindowLevel()
1843 {
1844   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1845   int window = mSlicerManagers[index]->GetColorWindow();
1846   presetComboBox->setCurrentIndex(WL_USER);
1847   windowSpinBox->setValue(-window);
1848   UpdateWindowLevel();
1849 }
1850 //------------------------------------------------------------------------------
1851
1852 //------------------------------------------------------------------------------
1853 void vvMainWindow::ApplyWindowLevelToAllImages()
1854 {
1855   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1856   if(index==-1) return;
1857   double window = mSlicerManagers[index]->GetColorWindow();
1858   double level = mSlicerManagers[index]->GetColorLevel();
1859
1860   double fusWindow = mSlicerManagers[index]->GetFusionWindow();
1861   double fusLevel = mSlicerManagers[index]->GetFusionLevel();
1862
1863   double overWindow = mSlicerManagers[index]->GetOverlayColorWindow();
1864   double overLevel = mSlicerManagers[index]->GetOverlayColorLevel();
1865
1866   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
1867     if (mSlicerManagers[i] == NULL)
1868       continue;
1869     mSlicerManagers[i]->SetColorWindow(window);
1870     mSlicerManagers[i]->SetColorLevel(level);
1871     mSlicerManagers[i]->SetPreset(WL_USER);
1872     mSlicerManagers[i]->SetFusionWindow(fusWindow);
1873     mSlicerManagers[i]->SetFusionLevel(fusLevel);
1874     mSlicerManagers[i]->SetOverlayColorWindow(overWindow);
1875     mSlicerManagers[i]->SetOverlayColorLevel(overLevel);
1876     mSlicerManagers[i]->Render();
1877   }
1878 }
1879 //------------------------------------------------------------------------------
1880
1881 //------------------------------------------------------------------------------
1882 void vvMainWindow::ApplyWindowToSetOfImages(double window, unsigned int indexMin, unsigned int indexMax)
1883 {
1884   for (unsigned int i = indexMin; i <= indexMax && i < mSlicerManagers.size(); i++) {
1885     if (mSlicerManagers[i] == NULL)
1886       continue;
1887     mSlicerManagers[i]->SetColorWindow(window);
1888     mSlicerManagers[i]->SetPreset(WL_USER);
1889     mSlicerManagers[i]->Render();
1890   }
1891 }
1892 //------------------------------------------------------------------------------
1893
1894 //------------------------------------------------------------------------------
1895 void vvMainWindow::ApplyLevelToSetOfImages(double level, unsigned int indexMin, unsigned int indexMax)
1896 {
1897   for (unsigned int i = indexMin; i <= indexMax && i < mSlicerManagers.size(); i++) {
1898     if (mSlicerManagers[i] == NULL)
1899       continue;
1900     mSlicerManagers[i]->SetColorLevel(level);
1901     mSlicerManagers[i]->SetPreset(WL_USER);
1902     mSlicerManagers[i]->Render();
1903   }
1904 }
1905 //------------------------------------------------------------------------------
1906
1907 //------------------------------------------------------------------------------
1908 void vvMainWindow::UpdateLinkManager(std::string id, int slicer, double x, double y, double z, int temps)
1909 {
1910   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
1911     if (mSlicerManagers[i]->GetId() == id) {
1912       mSlicerManagers[i]->GetSlicer(slicer)->SetCurrentPosition(x,y,z,temps);
1913       mSlicerManagers[i]->UpdateViews(0,slicer);
1914       break;
1915     }
1916   }
1917 }
1918 //------------------------------------------------------------------------------
1919
1920 //------------------------------------------------------------------------------
1921 void vvMainWindow::UpdateLinkedNavigation(std::string id, vvSlicerManager * sm, vvSlicer* refSlicer)
1922 {
1923   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
1924     if (id == mSlicerManagers[i]->GetId()) {
1925       mSlicerManagers[i]->UpdateLinkedNavigation(refSlicer);
1926     }
1927   }
1928 }
1929 //------------------------------------------------------------------------------
1930
1931 //------------------------------------------------------------------------------
1932 void vvMainWindow::ShowContextMenu(QPoint point)
1933 {
1934   if (!DataTree->selectedItems().size()) {
1935     contextActions[1]->setEnabled(0);
1936     contextActions[2]->setEnabled(0);
1937     contextActions[3]->setEnabled(0);
1938     contextActions[4]->setEnabled(0);
1939     contextActions[5]->setEnabled(0);
1940     contextActions[6]->setEnabled(0);
1941   } else {
1942     int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1943     contextActions[1]->setEnabled(1);
1944     contextActions[2]->setEnabled(
1945       DataTree->itemWidget(DataTree->selectedItems()[0],
1946       COLUMN_RELOAD_IMAGE)->isEnabled());
1947     contextActions[3]->setEnabled(1);
1948     contextActions[5]->setEnabled(1);
1949     contextActions[6]->setEnabled(1);
1950
1951     if (mSlicerManagers[index]->GetDimension() < 3)
1952       contextActions[4]->setEnabled(0);
1953     else
1954       contextActions[4]->setEnabled(1);
1955   }
1956   contextMenu.exec(QCursor::pos());
1957 }
1958 //------------------------------------------------------------------------------
1959
1960 //------------------------------------------------------------------------------
1961 void vvMainWindow::CloseImage()
1962 {
1963   CloseImage(DataTree->selectedItems()[0],0);
1964 }
1965 //------------------------------------------------------------------------------
1966
1967 //------------------------------------------------------------------------------
1968 void vvMainWindow::ReloadImage()
1969 {
1970   ReloadImage(DataTree->selectedItems()[0],0);
1971 }
1972 //------------------------------------------------------------------------------
1973
1974 //------------------------------------------------------------------------------
1975 void vvMainWindow::SelectOverlayImage()
1976 {
1977   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1978
1979   //check if one overlay image is added
1980   for (int child = 0; child < DataTree->topLevelItem(index)->childCount(); child++)
1981     if (DataTree->topLevelItem(index)->child(child)->data(1,Qt::UserRole).toString() == "overlay") {
1982       QString error = "Cannot add more than one compared image\n";
1983       error += "Please remove first ";
1984       error += DataTree->topLevelItem(index)->child(child)->data(COLUMN_IMAGE_NAME,Qt::DisplayRole).toString();
1985       QMessageBox::information(this,tr("Problem adding compared image !"),error);
1986       return;
1987     }
1988
1989     QString Extensions = EXTENSIONS;
1990     Extensions += ";;All Files (*)";
1991     QStringList files = QFileDialog::getOpenFileNames(this,tr("Load Overlay image"),mInputPathName,Extensions);
1992     if (files.isEmpty())
1993       return;
1994
1995     std::vector<std::string> vecFileNames;
1996     for (int i = 0; i < files.size(); i++) {
1997       vecFileNames.push_back(files[i].toStdString());
1998     }
1999     AddOverlayImage(index,vecFileNames,vvImageReader::IMAGE);
2000 }
2001 //------------------------------------------------------------------------------
2002
2003 //------------------------------------------------------------------------------
2004 void vvMainWindow::AddOverlayImage(int index, std::vector<std::string> fileNames, vvImageReader::LoadedImageType type)
2005 {
2006   QString file(fileNames[0].c_str());
2007   if (QFile::exists(file))
2008   {
2009     mInputPathName = itksys::SystemTools::GetFilenamePath(file.toStdString()).c_str();
2010     itk::ImageIOBase::Pointer reader = itk::ImageIOFactory::CreateImageIO(
2011       file.toStdString().c_str(), itk::ImageIOFactory::ReadMode);
2012     reader->SetFileName(fileNames[0].c_str());
2013     reader->ReadImageInformation();
2014     std::string component = reader->GetComponentTypeAsString(reader->GetComponentType());
2015     int dimension = reader->GetNumberOfDimensions();
2016     QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
2017     vvProgressDialog progress("Opening " + file.toStdString());
2018     qApp->processEvents();
2019
2020     std::string filename = itksys::SystemTools::GetFilenameWithoutExtension(file.toStdString()).c_str();
2021     if (mSlicerManagers[index]->SetOverlay(fileNames,dimension, component,type)) {
2022       //create an item in the tree with good settings
2023       QTreeWidgetItem *item = new QTreeWidgetItem();
2024       item->setData(0,Qt::UserRole,file.toStdString().c_str());
2025       item->setData(1,Qt::UserRole,tr("overlay"));
2026       QFileInfo fileinfo(file); //Do not show the path
2027       item->setData(COLUMN_IMAGE_NAME,Qt::DisplayRole,fileinfo.fileName());
2028       item->setToolTip(COLUMN_IMAGE_NAME, mSlicerManagers[index]->GetListOfAbsoluteFilePathInOneString("overlay").c_str());
2029       qApp->processEvents();
2030
2031       for (int j = 1; j <= 4; j++) {
2032         item->setData(j,Qt::CheckStateRole,DataTree->topLevelItem(index)->data(j,Qt::CheckStateRole));
2033       }
2034
2035       //Create the buttons for reload and close
2036       qApp->processEvents();
2037       QTreePushButton* cButton = new QTreePushButton;
2038       cButton->setItem(item);
2039       cButton->setColumn(COLUMN_CLOSE_IMAGE);
2040       cButton->setToolTip(tr("close image"));
2041       cButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/exit.png")));
2042       connect(cButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
2043         this,SLOT(CloseImage(QTreeWidgetItem*, int)));
2044
2045       QTreePushButton* rButton = new QTreePushButton;
2046       rButton->setItem(item);
2047       rButton->setColumn(COLUMN_RELOAD_IMAGE);
2048       rButton->setToolTip(tr("reload image"));
2049       rButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/rotateright.png")));
2050       connect(rButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
2051         this,SLOT(ReloadImage(QTreeWidgetItem*, int)));
2052
2053       DataTree->topLevelItem(index)->setExpanded(1);
2054       DataTree->topLevelItem(index)->addChild(item);
2055       DataTree->setItemWidget(item, COLUMN_CLOSE_IMAGE, cButton);
2056       DataTree->setItemWidget(item, COLUMN_RELOAD_IMAGE, rButton);
2057
2058       //set the id of the image
2059       QString id = DataTree->topLevelItem(index)->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString();
2060       item->setData(COLUMN_IMAGE_NAME,Qt::UserRole,id.toStdString().c_str());
2061       UpdateTree();
2062       qApp->processEvents();
2063       ImageInfoChanged();
2064       QApplication::restoreOverrideCursor();
2065
2066       // Update the display to update, e.g., the sliders
2067       for(int i=0; i<4; i++)
2068         DisplaySliders(index, i);
2069     } else {
2070       QApplication::restoreOverrideCursor();
2071       QString error = "Cannot import the new image.\n";
2072       error += mSlicerManagers[index]->GetLastError().c_str();
2073       QMessageBox::information(this,tr("Problem reading image !"),error);
2074     }
2075     WindowLevelChanged();
2076   }
2077   else
2078     QMessageBox::information(this,tr("Problem reading Overlay !"),"File doesn't exist!");
2079 }
2080 //------------------------------------------------------------------------------
2081
2082
2083 //------------------------------------------------------------------------------
2084 void vvMainWindow::AddROI(int index, QString file)
2085 {
2086   /*
2087   // Get slice manager
2088
2089   // Load image
2090
2091   vvImageReader * mReader = new vvImageReader;
2092   mReader->SetInputFilename(filename.toStdString());
2093   mReader->Update(IMAGE);
2094   if (mReader->GetLastError().size() != 0) {
2095   std::cerr << "Error while reading " << filename.toStdString() << std::endl;
2096   QString error = "Cannot open file \n";
2097   error += mReader->GetLastError().c_str();
2098   QMessageBox::information(this,tr("Reading problem"),error);
2099   delete mReader;
2100   return;
2101   }
2102   vvImage::Pointer roi = mReader->GetOutput();
2103
2104   // Create roi in new tool
2105   vvToolStructureSetManager::AddImage(mCurrentSlicerManager, roi);
2106   */
2107 }
2108 //------------------------------------------------------------------------------
2109
2110 //------------------------------------------------------------------------------
2111 void vvMainWindow::SelectFusionImage()
2112 {
2113   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2114
2115   //check if one fusion image is added
2116   for (int child = 0; child < DataTree->topLevelItem(index)->childCount(); child++)
2117     if ( (DataTree->topLevelItem(index)->child(child)->data(1,Qt::UserRole).toString() == "fusion") ||
2118       (DataTree->topLevelItem(index)->child(child)->data(1,Qt::UserRole).toString() == "fusionSequence") ) {
2119         QString error = "Cannot add more than one fusion image\n";
2120         error += "Please remove first ";
2121         error += DataTree->topLevelItem(index)->child(child)->data(COLUMN_IMAGE_NAME,Qt::DisplayRole).toString();
2122         QMessageBox::information(this,tr("Problem adding fusion image !"),error);
2123         return;
2124     }
2125
2126     QString Extensions = EXTENSIONS;
2127     Extensions += ";;All Files (*)";
2128     QStringList files = QFileDialog::getOpenFileNames(this,tr("Load Fusion image"),mInputPathName,Extensions);
2129     if (files.isEmpty())
2130       return;
2131
2132     std::vector<std::string> vecFileNames;
2133     for (int i = 0; i < files.size(); i++) {
2134       vecFileNames.push_back(files[i].toStdString());
2135     }
2136     AddFusionImage(index,vecFileNames,vvImageReader::IMAGE);
2137 }
2138 //------------------------------------------------------------------------------
2139
2140 //------------------------------------------------------------------------------
2141 void vvMainWindow::ResetTransformationToIdentity()
2142 {
2143   std::string actorType = DataTree->selectedItems()[0]->data(1,Qt::UserRole).toString().toStdString();
2144   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2145   mSlicerManagers[index]->ResetTransformationToIdentity(actorType);
2146   ImageInfoChanged();
2147 }
2148 //------------------------------------------------------------------------------
2149
2150 //------------------------------------------------------------------------------
2151 void vvMainWindow::AddFusionImage(int index, std::vector<std::string> fileNames, vvImageReader::LoadedImageType type)
2152 {
2153   QString file(fileNames[0].c_str());
2154   if (QFile::exists(file))
2155   {
2156     mInputPathName = itksys::SystemTools::GetFilenamePath(file.toStdString()).c_str();
2157     itk::ImageIOBase::Pointer reader = itk::ImageIOFactory::CreateImageIO(
2158       file.toStdString().c_str(), itk::ImageIOFactory::ReadMode);
2159     reader->SetFileName(fileNames[0].c_str());
2160     reader->ReadImageInformation();
2161     std::string component = reader->GetComponentTypeAsString(reader->GetComponentType());
2162     int dimension = reader->GetNumberOfDimensions();
2163     QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
2164     vvProgressDialog progress("Opening fusion");
2165     qApp->processEvents();
2166
2167     std::string filename = itksys::SystemTools::GetFilenameWithoutExtension(file.toStdString()).c_str();
2168     if (mSlicerManagers[index]->SetFusion(fileNames,dimension, component,type)) {
2169       //create an item in the tree with good settings
2170       QTreeWidgetItem *item = new QTreeWidgetItem();
2171       item->setData(0,Qt::UserRole,file.toStdString().c_str());
2172       item->setData(1,Qt::UserRole,tr("fusion"));
2173       QFileInfo fileinfo(file); //Do not show the path
2174           item->setData(COLUMN_IMAGE_NAME,Qt::DisplayRole,fileinfo.fileName());
2175           item->setToolTip(COLUMN_IMAGE_NAME, mSlicerManagers[index]->GetListOfAbsoluteFilePathInOneString("fusion").c_str());
2176           qApp->processEvents();
2177
2178       for (int j = 1; j <= 4; j++) {
2179         item->setData(j,Qt::CheckStateRole,DataTree->topLevelItem(index)->data(j,Qt::CheckStateRole));
2180       }
2181
2182       //Create the buttons for reload and close
2183       qApp->processEvents();
2184       QTreePushButton* cButton = new QTreePushButton;
2185       cButton->setItem(item);
2186       cButton->setColumn(COLUMN_CLOSE_IMAGE);
2187       cButton->setToolTip(tr("close image"));
2188       cButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/exit.png")));
2189       connect(cButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
2190         this,SLOT(CloseImage(QTreeWidgetItem*, int)));
2191
2192       QTreePushButton* rButton = new QTreePushButton;
2193       rButton->setItem(item);
2194       rButton->setColumn(COLUMN_RELOAD_IMAGE);
2195       rButton->setToolTip(tr("reload image"));
2196       rButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/rotateright.png")));
2197       connect(rButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
2198         this,SLOT(ReloadImage(QTreeWidgetItem*, int)));
2199
2200       DataTree->topLevelItem(index)->setExpanded(1);
2201       DataTree->topLevelItem(index)->addChild(item);
2202       DataTree->setItemWidget(item, COLUMN_CLOSE_IMAGE, cButton);
2203       DataTree->setItemWidget(item, COLUMN_RELOAD_IMAGE, rButton);
2204
2205       //set the id of the image
2206       QString id = DataTree->topLevelItem(index)->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString();
2207       item->setData(COLUMN_IMAGE_NAME,Qt::UserRole,id.toStdString().c_str());
2208       UpdateTree();
2209       qApp->processEvents();
2210       ImageInfoChanged();
2211       QApplication::restoreOverrideCursor();
2212
2213       // Update the display to update, e.g., the sliders
2214       for(int i=0; i<4; i++)
2215         DisplaySliders(index, i);
2216     } else {
2217       QApplication::restoreOverrideCursor();
2218       QString error = "Cannot import the new image.\n";
2219       error += mSlicerManagers[index]->GetLastError().c_str();
2220       QMessageBox::information(this,tr("Problem reading image !"),error);
2221     }
2222     WindowLevelChanged();
2223   }
2224   else
2225     QMessageBox::information(this,tr("Problem reading Fusion !"),"File doesn't exist!");
2226 }
2227 //------------------------------------------------------------------------------
2228 //------------------------------------------------------------------------------
2229 void vvMainWindow::AddLandmarks(int index, std::vector<std::string> files)
2230 {
2231     if (!landmarksPanel->LoadFromFile(files))
2232       QMessageBox::information(this,tr("Problem reading Landmarks !"),"File doesn't exist!");
2233
2234     landmarksPanel->SetCurrentPath(mInputPathName.toStdString());
2235     landmarksPanel->SetCurrentImage(mSlicerManagers[index]->GetFileName().c_str());
2236 }
2237
2238 //------------------------------------------------------------------------------
2239 void vvMainWindow::OpenField()
2240 {
2241   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2242   //check if a vector field has already been added
2243   for (int child = 0; child < DataTree->topLevelItem(index)->childCount(); child++)
2244     if (DataTree->topLevelItem(index)->child(child)->data(1,Qt::UserRole).toString() == "vector") {
2245       QString error = "Cannot add more than one vector field\n";
2246       error += "Please remove first ";
2247       error += DataTree->topLevelItem(index)->child(child)->data(COLUMN_IMAGE_NAME,Qt::DisplayRole).toString();
2248       QMessageBox::information(this,tr("Problem adding vector field!"),error);
2249       return;
2250     }
2251
2252     QString Extensions = "Images ( *.mhd *.mha *.vf *.nii *.nrrd *.nhdr)";
2253     // Extensions += ";;Images ( *.mha)";
2254     // Extensions += ";;VF Images ( *.vf)";
2255     // Extensions += ";;nii Images ( *.nii)";
2256     // Extensions += ";;nrrd Images ( *.nrrd)";
2257     // Extensions += ";;nhdr Images ( *.nhdr)";
2258     Extensions += ";;All Files (*)";
2259     QString file = QFileDialog::getOpenFileName(this,tr("Load deformation field"),mInputPathName,Extensions);
2260     if (!file.isEmpty())
2261       AddField(file,index);
2262 }
2263 //------------------------------------------------------------------------------
2264
2265
2266 //------------------------------------------------------------------------------
2267 void vvMainWindow::AddFieldEntry(QString filename,int index,bool from_disk)
2268 {
2269   //create an item in the tree with good settings
2270   QTreeWidgetItem *item = new QTreeWidgetItem();
2271   item->setData(0,Qt::UserRole,filename.toStdString().c_str());
2272   item->setData(1,Qt::UserRole,tr("vector"));
2273   QFileInfo fileinfo(filename); //Do not show the path
2274   item->setData(COLUMN_IMAGE_NAME,Qt::DisplayRole,fileinfo.fileName());
2275   item->setToolTip(COLUMN_IMAGE_NAME, mSlicerManagers[index]->GetListOfAbsoluteFilePathInOneString("vector").c_str());
2276   qApp->processEvents();
2277
2278   for (int j = 1; j <= 4; j++) {
2279     item->setData(j,Qt::CheckStateRole,DataTree->topLevelItem(index)->data(j,Qt::CheckStateRole));
2280   }
2281
2282   //Create the buttons for reload and close
2283   qApp->processEvents();
2284   QTreePushButton* cButton = new QTreePushButton;
2285   cButton->setItem(item);
2286   cButton->setColumn(COLUMN_CLOSE_IMAGE);
2287   cButton->setToolTip(tr("close vector field"));
2288   cButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/exit.png")));
2289   connect(cButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
2290     this,SLOT(CloseImage(QTreeWidgetItem*, int)));
2291
2292   QTreePushButton* rButton = new QTreePushButton;
2293   rButton->setItem(item);
2294   rButton->setColumn(COLUMN_RELOAD_IMAGE);
2295   rButton->setToolTip(tr("reload vector field"));
2296   rButton->setEnabled(from_disk);
2297   rButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/rotateright.png")));
2298   connect(rButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
2299     this,SLOT(ReloadImage(QTreeWidgetItem*, int)));
2300
2301   DataTree->topLevelItem(index)->setExpanded(1);
2302   DataTree->topLevelItem(index)->addChild(item);
2303   DataTree->setItemWidget(item, COLUMN_RELOAD_IMAGE, rButton);
2304   DataTree->setItemWidget(item, COLUMN_CLOSE_IMAGE, cButton);
2305
2306   //set the id of the image
2307   QString id = DataTree->topLevelItem(index)->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString();
2308   item->setData(COLUMN_IMAGE_NAME,Qt::UserRole,id.toStdString().c_str());
2309   UpdateTree();
2310   qApp->processEvents();
2311   ImageInfoChanged();
2312   QApplication::restoreOverrideCursor();
2313 }
2314 //------------------------------------------------------------------------------
2315
2316
2317 //------------------------------------------------------------------------------
2318 void vvMainWindow::AddField(vvImage::Pointer vf,QString file,int index)
2319 {
2320   QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
2321   vvSlicerManager* imageManager = mSlicerManagers[index];
2322   if (imageManager->SetVF(vf,file.toStdString())) {
2323     AddFieldEntry(file,index,false);
2324   } else {
2325     QString error = "Cannot import the vector field for this image.\n";
2326     error += imageManager->GetLastError().c_str();
2327     QMessageBox::information(this,tr("Problem reading VF !"),error);
2328   }
2329   QApplication::restoreOverrideCursor();
2330 }
2331 //------------------------------------------------------------------------------
2332
2333
2334 //------------------------------------------------------------------------------
2335 void vvMainWindow::AddField(QString file,int index)
2336 {
2337   if (QFile::exists(file)) {
2338     mInputPathName = itksys::SystemTools::GetFilenamePath(file.toStdString()).c_str();
2339
2340     //init the progress events
2341     QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
2342     vvProgressDialog progress("Opening " + file.toStdString());
2343     qApp->processEvents();
2344
2345     //read the vector and put it in the current mSlicerManager
2346     vvSlicerManager* imageManager = mSlicerManagers[index];
2347     qApp->processEvents();
2348
2349     std::string filename = itksys::SystemTools::GetFilenameWithoutExtension(file.toStdString()).c_str();
2350     if (imageManager->SetVF(file.toStdString())) {
2351       imageManager->Render();
2352       AddFieldEntry(file,index,true);
2353     } else {
2354       QApplication::restoreOverrideCursor();
2355       QString error = "Cannot import the vector field for this image.\n";
2356       error += imageManager->GetLastError().c_str();
2357       QMessageBox::information(this,tr("Problem reading VF !"),error);
2358     }
2359   } else
2360     QMessageBox::information(this,tr("Problem reading VF !"),"File doesn't exist!");
2361
2362 }
2363 //------------------------------------------------------------------------------
2364
2365
2366 //------------------------------------------------------------------------------
2367 void vvMainWindow::SetVFProperty(int subsampling, int scale, int log, int width, double r, double g, double b)
2368 {
2369   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2370   if (mSlicerManagers[index]->GetSlicer(0)->GetVF()) {
2371     for (int i = 0; i < 4; i++) {
2372       mSlicerManagers[index]->GetSlicer(i)->SetVFSubSampling(subsampling);
2373       mSlicerManagers[index]->GetSlicer(i)->SetVFScale(scale);
2374       mSlicerManagers[index]->GetSlicer(i)->SetVFWidth(width);
2375       mSlicerManagers[index]->GetSlicer(i)->SetVFColor(r,g,b);
2376       if (log > 0)
2377         mSlicerManagers[index]->GetSlicer(i)->SetVFLog(1);
2378       else
2379         mSlicerManagers[index]->GetSlicer(i)->SetVFLog(0);
2380     }
2381   }
2382 }
2383 //------------------------------------------------------------------------------
2384
2385
2386 //------------------------------------------------------------------------------
2387 void vvMainWindow::SetOverlayProperty(int color, int linked, double window, double level)
2388 {
2389   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2390   if (mSlicerManagers[index]->GetSlicer(0)->GetOverlay()) {
2391     mSlicerManagers[index]->SetOverlayColor(color);
2392     mSlicerManagers[index]->SetColorMap(0);
2393     mSlicerManagers[index]->SetLinkOverlayWindowLevel(linked);
2394     mSlicerManagers[index]->SetOverlayColorWindow(window);
2395     mSlicerManagers[index]->SetOverlayColorLevel(level);
2396     mSlicerManagers[index]->Render();
2397   }
2398 }
2399 //------------------------------------------------------------------------------
2400
2401 //------------------------------------------------------------------------------
2402 void vvMainWindow::SetFusionProperty(int opacity, int thresOpacity, int colormap,double window, double level, bool showLegend)
2403 {
2404   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2405   if (mSlicerManagers[index]->GetSlicer(0)->GetFusion()) {
2406     mSlicerManagers[index]->SetFusionColorMap(colormap);
2407     mSlicerManagers[index]->SetFusionOpacity(opacity);
2408     mSlicerManagers[index]->SetFusionThresholdOpacity(thresOpacity);
2409     mSlicerManagers[index]->SetFusionWindow(window);
2410     mSlicerManagers[index]->SetFusionLevel(level);
2411     mSlicerManagers[index]->SetFusionShowLegend(showLegend);
2412     mSlicerManagers[index]->SetColorMap(0);
2413     mSlicerManagers[index]->Render();
2414   }
2415 }
2416 //------------------------------------------------------------------------------
2417
2418
2419 //------------------------------------------------------------------------------
2420 void vvMainWindow::SelectFusionSequence()
2421 {
2422   //get the index of the slicer manager of the main sequence (CT)
2423   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2424   //check if one overlay image is already associated
2425   for (int child = 0; child < DataTree->topLevelItem(index)->childCount(); child++)
2426     if ( (DataTree->topLevelItem(index)->child(child)->data(1,Qt::UserRole).toString() == "fusion") ||
2427       (DataTree->topLevelItem(index)->child(child)->data(1,Qt::UserRole).toString() == "fusionSequence") ) {
2428         QString error = "Cannot add more than one compared image\n";
2429         error += "Please remove first ";
2430         error += DataTree->topLevelItem(index)->child(child)->data(COLUMN_IMAGE_NAME,Qt::DisplayRole).toString();
2431         QMessageBox::information(this,tr("Problem adding compared image !"),error);
2432         return;
2433     }
2434
2435     QString Extensions = EXTENSIONS;
2436     Extensions += ";;All Files (*)";
2437     QStringList files = QFileDialog::getOpenFileNames(this,tr("Load Overlay image sequence"),mInputPathName,Extensions);
2438     if (files.isEmpty())
2439       return;
2440
2441     std::vector<std::string> vecFileNames;
2442     for (int i = 0; i < files.size(); i++) {
2443       vecFileNames.push_back(files[i].toStdString());
2444     }
2445
2446     //associate the secondary sequence (US) to the main one
2447     AddFusionSequence(index,vecFileNames,vvImageReader::MERGEDWITHTIME);
2448 }
2449 //------------------------------------------------------------------------------
2450
2451
2452 //------------------------------------------------------------------------------
2453 void vvMainWindow::SelectFusionSequenceCorrespondances() {
2454
2455   //make sure the index is right?
2456   //in the end, I should attach the temporal data to the right sequence!
2457   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2458   //in case the other sequence got selected, make sure we select the primary sequence
2459   if ( (!mSlicerManagers[index]->GetSlicer(0)->GetFusion()) && mSlicerManagers[index]->GetFusionSequenceIndexOfLinkedManager()>=0 ) {
2460     index = mSlicerManagers[index]->GetFusionSequenceIndexOfLinkedManager();
2461   }
2462
2463   //open a dialog box to find a file
2464   //QString Extensions = EXTENSIONS;
2465   QString Extensions = ";;All Files (*)";
2466   QString fileName = QFileDialog::getOpenFileName(this,tr("Load respiratory signal for fused sequence"),mInputPathName,Extensions);
2467   if (fileName.isNull())
2468     return;
2469
2470   //read it as a vector of values
2471   vnl_vector<double> tmpVect;
2472
2473   std::ifstream file;
2474   file.open(fileName.toStdString().c_str());
2475   tmpVect.read_ascii(file);
2476   file.close();
2477
2478   //if compatible with the fused image sequence (number of entries = nb of entries in main sequence + nb of entries in joint sequence), enable the temporalSync
2479   bool signalOK = true;
2480   unsigned nbFrameMain = mSlicerManagers[index]->GetImage()->GetTransform().size();
2481   unsigned nbFrameSecondary = mSlicerManagers[index]->GetFusionSequenceNbFrames();
2482 std::cout<<"nbFrameMain = "<<nbFrameMain<<", nbFrameSecondary= "<<nbFrameSecondary<<", signal size: "<<tmpVect.size()<<std::endl;
2483   std::vector<unsigned> temporalCorrespondances;
2484   if ( tmpVect.size() == nbFrameMain + nbFrameSecondary ) {
2485     for (unsigned i=0 ; i<tmpVect.size() ; i++) {
2486       if (i<nbFrameMain) { //first part of the file: i -> index in secondary seq.
2487         if ( tmpVect(i)<nbFrameSecondary ) temporalCorrespondances.push_back(tmpVect(i));
2488         else { signalOK=false; break; } //pointing outside the secondary sequence...
2489       }
2490       else { //first part of the file -> index in secondary seq.
2491         if ( tmpVect(i)<nbFrameMain ) temporalCorrespondances.push_back(tmpVect(i));
2492         else { signalOK=false; break; } //pointing outside the secondary sequence...
2493       }
2494     }
2495   }
2496   else {signalOK=false;}
2497   if (!signalOK) {//else, send a message to signal the failure...
2498     QString error = "The provided temporal correspondances is invalid - check tooltip.\n";
2499     error += "Ignoring file: " + fileName;
2500     QMessageBox::information(this,tr("Problem adding temporal correspondances!"),error);
2501     return;
2502   }
2503   else {
2504     //for convenience, associate this sequence to both the current slicer manager, and to the linked one
2505     mSlicerManagers[index]->SetFusionSequenceCorrespondances(temporalCorrespondances);
2506     mSlicerManagers[ mSlicerManagers[index]->GetFusionSequenceIndexOfLinkedManager() ]->SetFusionSequenceCorrespondances(temporalCorrespondances);
2507     overlayPanel->enableFusionSequenceTemporalSync();
2508   }
2509
2510 }
2511 //------------------------------------------------------------------------------
2512
2513
2514 //------------------------------------------------------------------------------
2515 //when this function is called index is the slicer manager index corresponding to the main sequence (CT)
2516 //the files behind fileNames points to the data for the secondary sequence
2517 void vvMainWindow::AddFusionSequence(int index, std::vector<std::string> fileNames, vvImageReader::LoadedImageType type)
2518 {
2519   QString file(fileNames[0].c_str());
2520   if (QFile::exists(file))
2521   {
2522     mInputPathName = itksys::SystemTools::GetFilenamePath(file.toStdString()).c_str();
2523     itk::ImageIOBase::Pointer reader = itk::ImageIOFactory::CreateImageIO(
2524       file.toStdString().c_str(), itk::ImageIOFactory::ReadMode);
2525     std::sort (fileNames.begin(), fileNames.end());//make sure the files are sorted.
2526     reader->SetFileName(fileNames[0].c_str());
2527     reader->ReadImageInformation();
2528     std::string component = reader->GetComponentTypeAsString(reader->GetComponentType());
2529     int dimension = reader->GetNumberOfDimensions();
2530     QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
2531     vvProgressDialog progress("Opening " + file.toStdString());
2532     qApp->processEvents();
2533
2534     std::string filename = itksys::SystemTools::GetFilenameWithoutExtension(file.toStdString()).c_str();
2535
2536     if (mSlicerManagers[index]->SetFusionSequence(fileNames,dimension, component,type)) {
2537       //create an item in the tree with good settings
2538       QTreeWidgetItem *item = new QTreeWidgetItem();
2539       item->setData(0,Qt::UserRole,file.toStdString().c_str());
2540       item->setData(1,Qt::UserRole,tr("fusionSequence"));
2541
2542       QFileInfo fileinfo(file); //Do not show the path
2543       item->setData(COLUMN_IMAGE_NAME,Qt::DisplayRole,fileinfo.fileName());
2544       item->setToolTip(COLUMN_IMAGE_NAME, mSlicerManagers[index]->GetListOfAbsoluteFilePathInOneString("fusionSequence").c_str());
2545       qApp->processEvents();
2546       for (int j = 1; j <= 4; j++) {
2547         item->setData(j,Qt::CheckStateRole,DataTree->topLevelItem(index)->data(j,Qt::CheckStateRole));
2548       }
2549
2550       //Create the buttons for reload and close
2551       qApp->processEvents();
2552       QTreePushButton* cButton = new QTreePushButton;
2553       cButton->setItem(item);
2554       cButton->setColumn(COLUMN_CLOSE_IMAGE);
2555       cButton->setToolTip(tr("close image"));
2556       cButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/exit.png")));
2557       connect(cButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
2558         this,SLOT(CloseImage(QTreeWidgetItem*, int)));
2559
2560       QTreePushButton* rButton = new QTreePushButton;
2561       rButton->setItem(item);
2562       rButton->setColumn(COLUMN_RELOAD_IMAGE);
2563       rButton->setToolTip(tr("reload image"));
2564       rButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/rotateright.png")));
2565       connect(rButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
2566         this,SLOT(ReloadImage(QTreeWidgetItem*, int)));
2567
2568       DataTree->topLevelItem(index)->setExpanded(1);
2569       DataTree->topLevelItem(index)->addChild(item);
2570       DataTree->setItemWidget(item, COLUMN_CLOSE_IMAGE, cButton);
2571       DataTree->setItemWidget(item, COLUMN_RELOAD_IMAGE, rButton);
2572
2573       //store the original transform matrix
2574       int indexParent = GetSlicerIndexFromItem( DataTree->topLevelItem(index) );
2575       mSlicerManagers[indexParent]->SetFusionSequenceMainTransformMatrix( mSlicerManagers[indexParent]->GetSlicer(0)->GetImage()->GetTransform()[0]->GetMatrix() );
2576
2577       //set the id of the image
2578       QString id = DataTree->topLevelItem(index)->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString();
2579       item->setData(COLUMN_IMAGE_NAME,Qt::UserRole,id.toStdString().c_str());
2580       UpdateTree();
2581       qApp->processEvents();
2582
2583       //ImageInfoChanged();
2584
2585       QApplication::restoreOverrideCursor();
2586       // Update the display to update, e.g., the sliders
2587       for(int i=0; i<4; i++)
2588         DisplaySliders(index, i);
2589
2590
2591       //This loads the secondary sequence (US) as an independent sequence
2592       LoadImages(fileNames, type);
2593       //reset the transforms to identity
2594       //FIX -- and set the thickness of the US slices to a large value (necessary for visualization purposes...)
2595       double sp_x, sp_y, sp_z;
2596       mSlicerManagers[indexParent]->GetImage()->GetVTKImages()[0]->GetSpacing(sp_x, sp_y, sp_z);
2597       sp_z = std::max(sp_x, std::max(sp_y, sp_z)) + 0.5; //
2598       for (unsigned i=0 ; i<mSlicerManagers.back()->GetImage()->GetTransform().size() ; i++) {
2599         sp_x = mSlicerManagers.back()->GetImage()->GetVTKImages()[i]->GetSpacing()[0];
2600         sp_y = mSlicerManagers.back()->GetImage()->GetVTKImages()[i]->GetSpacing()[1];
2601         mSlicerManagers.back()->GetImage()->GetVTKImages()[i]->SetSpacing( sp_x, sp_y, sp_z);
2602         mSlicerManagers.back()->GetImage()->GetTransform()[i]->Identity();
2603         mSlicerManagers.back()->GetImage()->GetTransform()[i]->Update();
2604       }
2605
2606       //automatically link both images...
2607       AddLink(mSlicerManagers[indexParent]->GetId().c_str(), mSlicerManagers.back()->GetId().c_str(), false);
2608
2609       //tie the main and secondary sequences by raising flags and informing each another of their respective SlicerManager indices
2610       mSlicerManagers[indexParent]->SetFusionSequenceIndexOfLinkedManager(mSlicerManagers.size()-1);
2611       mSlicerManagers[indexParent]->SetFusionSequenceInvolvmentCode(0); //main sequence
2612       mSlicerManagers.back()->SetFusionSequenceIndexOfLinkedManager(indexParent);
2613       mSlicerManagers.back()->SetFusionSequenceInvolvmentCode(1); //secondary sequence
2614       for (unsigned i=0 ; i<4 ; i++) {
2615         mSlicerManagers.back()->GetSlicer(i)->SetFusionSequenceCode(1); //flag the slicers of the secondary sequence
2616       }
2617
2618     } else {
2619       QApplication::restoreOverrideCursor();
2620       QString error = "Cannot import the new image.\n";
2621       error += mSlicerManagers[index]->GetLastError().c_str();
2622       QMessageBox::information(this,tr("Problem reading image !"),error);
2623     }
2624     WindowLevelChanged();
2625     ImageInfoChanged(); //this internally calls WindowLevelChanged...
2626   }
2627   else {
2628     QMessageBox::information(this,tr("Problem reading fusion sequence !"),"File doesn't exist!");
2629     return;
2630   }
2631
2632 }
2633 //------------------------------------------------------------------------------
2634
2635
2636 //------------------------------------------------------------------------------
2637 //fusionSequenceFrameIndex and fusionSequenceNbFrames are relative to the secondary sequence (US)
2638 void vvMainWindow::SetFusionSequenceProperty(int fusionSequenceFrameIndex, bool spatialSyncFlag, unsigned int fusionSequenceNbFrames, bool temporalSyncFlag)
2639 {
2640   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2641
2642   if (!mSlicerManagers[index]->IsInvolvedInFusionSequence()) return;
2643
2644   //check if the focus moved to the linked sequence, and in this case, select the master sequence instead
2645   if (!mSlicerManagers[index]->IsMainSequenceOfFusionSequence()) {
2646     index = mSlicerManagers[index]->GetFusionSequenceIndexOfLinkedManager();
2647   }
2648   int secondaryIndex = mSlicerManagers[index]->GetFusionSequenceIndexOfLinkedManager();
2649   if (secondaryIndex==-1) return; //this should never happen
2650   if ( (!mSlicerManagers[index]->IsMainSequenceOfFusionSequence()) ||
2651     (!mSlicerManagers[secondaryIndex]->IsSecondarySequenceOfFusionSequence()) )
2652   {return;} //this should never happen, raise an exception?
2653
2654   if (mSlicerManagers[index]->GetSlicer(0)->GetFusion()) {
2655
2656     //First, if the spatialSync button is unchecked, then reposition the parent sequence (CT) in its original coordinate frame
2657     if ( (!spatialSyncFlag) && (mSlicerManagers[index]->GetFusionSequenceSpatialSyncFlag()) ) {
2658       for ( unsigned i=0 ; i<mSlicerManagers[index]->GetSlicer(0)->GetImage()->GetTransform().size() ; i++ ) {
2659         mSlicerManagers[index]->GetSlicer(0)->GetImage()->GetTransform()[i]->SetMatrix( mSlicerManagers[index]->GetFusionSequenceMainTransformMatrix() );
2660         mSlicerManagers[index]->GetSlicer(0)->GetImage()->GetTransform()[i]->Update();
2661       }
2662
2663       for (int i=0; i<mSlicerManagers[index]->GetNumberOfSlicers(); i++) {
2664         mSlicerManagers[index]->GetSlicer(i)->ForceUpdateDisplayExtent();
2665         mSlicerManagers[index]->GetSlicer(i)->Render();
2666       }
2667     }
2668
2669     //then, update the property values in the slicer manager
2670     mSlicerManagers[index]->SetFusionSequenceLength(fusionSequenceNbFrames);
2671     mSlicerManagers[index]->SetFusionSequenceSpatialSyncFlag(spatialSyncFlag);
2672     mSlicerManagers[index]->SetFusionSequenceTemporalSyncFlag(temporalSyncFlag);
2673     mSlicerManagers[index]->SetFusionSequenceFrameIndex(fusionSequenceFrameIndex);
2674
2675     //select the right frame of the US sequence
2676     mSlicerManagers[index]->SetFusionSequenceTSlice(fusionSequenceFrameIndex); //here, I should only update the overlayed sequence
2677     mSlicerManagers[secondaryIndex]->SetTSlice(fusionSequenceFrameIndex, false); //this should update the secondary sequence (individual version)
2678
2679     //update the horizontal sliders of the main window
2680     overlayPanel->updateFusionSequenceSliderValueFromWindow(fusionSequenceFrameIndex, false);
2681
2682     if (spatialSyncFlag) { //reslice the CT
2683
2684       if (temporalSyncFlag) { //do the temporal synchronisation
2685         int mainSequenceFrameIndex=0;
2686         //estimate the TSlice to set to the CT
2687         unsigned nbFramesMain = mSlicerManagers[index]->GetImage()->GetTransform().size();
2688         mainSequenceFrameIndex = mSlicerManagers[index]->GetFusionSequenceCorrespondances()[ nbFramesMain + fusionSequenceFrameIndex];
2689         //and set it!
2690         mSlicerManagers[index]->SetTSlice(mainSequenceFrameIndex, false);
2691         //warning, there is a loopback, and modification of the TSlice in main sequence forces an update of the TSlice in secondary, etc...
2692       }
2693
2694
2695       //Set the transform matrix of the parent sequence (typically CT / 4DCT)
2696       vtkSmartPointer<vtkMatrix4x4> tmpMat = vtkSmartPointer<vtkMatrix4x4>::New();
2697       vtkMatrix4x4::Invert( mSlicerManagers[index]->GetFusionSequenceInitialTransformMatrixAtFrame(fusionSequenceFrameIndex), tmpMat );
2698       for ( unsigned i=0 ; i<mSlicerManagers[index]->GetSlicer(0)->GetImage()->GetTransform().size() ; i++ ) {
2699         mSlicerManagers[index]->GetSlicer(0)->GetImage()->GetTransform()[i]->SetMatrix( mSlicerManagers[index]->GetFusionSequenceMainTransformMatrix() );
2700         mSlicerManagers[index]->GetSlicer(0)->GetImage()->GetTransform()[i]->PreMultiply();
2701         mSlicerManagers[index]->GetSlicer(0)->GetImage()->GetTransform()[i]->Concatenate( tmpMat );
2702         mSlicerManagers[index]->GetSlicer(0)->GetImage()->GetTransform()[i]->Update();
2703       }
2704
2705       for (int i=0; i<mSlicerManagers[index]->GetNumberOfSlicers(); i++) {
2706         mSlicerManagers[index]->GetSlicer(i)->ForceUpdateDisplayExtent();
2707         mSlicerManagers[index]->GetSlicer(i)->Render();
2708       }
2709
2710     }
2711
2712   }
2713 }
2714 //------------------------------------------------------------------------------
2715
2716
2717 //------------------------------------------------------------------------------
2718 void vvMainWindow::SaveAs()
2719 {
2720   if (DataTree->selectedItems()[0]->data(1,Qt::UserRole).toString() == "vector") {
2721     QMessageBox::warning(this,tr("Unsupported type"),tr("Sorry, saving a vector field is unsupported for the moment"));
2722     return;
2723   }
2724
2725   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2726   int dimension = mSlicerManagers[index]->GetDimension();
2727   QStringList OutputListeFormat;
2728   OutputListeFormat.clear();
2729   if (dimension == 1) {
2730     OutputListeFormat.push_back(".mhd");
2731     OutputListeFormat.push_back(".mha");
2732   }
2733   if (dimension == 2) {
2734     OutputListeFormat.push_back(".bmp");
2735     OutputListeFormat.push_back(".png");
2736     OutputListeFormat.push_back(".jpeg");
2737     OutputListeFormat.push_back(".tif");
2738     OutputListeFormat.push_back(".mhd");
2739     OutputListeFormat.push_back(".mha");
2740     OutputListeFormat.push_back(".hdr");
2741     OutputListeFormat.push_back(".vox");
2742   } else if (dimension == 3) {
2743     OutputListeFormat.push_back(".mhd");
2744     OutputListeFormat.push_back(".mha");
2745     OutputListeFormat.push_back(".nii");
2746     OutputListeFormat.push_back(".nrrd");
2747     OutputListeFormat.push_back(".nhdr");
2748     OutputListeFormat.push_back(".hdr");
2749     OutputListeFormat.push_back(".vox");
2750   } else if (dimension == 4) {
2751     OutputListeFormat.push_back(".mhd");
2752     OutputListeFormat.push_back(".mha");
2753     OutputListeFormat.push_back(".nii");
2754     OutputListeFormat.push_back(".nrrd");
2755     OutputListeFormat.push_back(".nhdr");
2756   }
2757   QString Extensions = "AllFiles(*.*)";
2758   for (int i = 0; i < OutputListeFormat.count(); i++) {
2759     Extensions += ";;Images ( *";
2760     Extensions += OutputListeFormat[i];
2761     Extensions += ")";
2762   }
2763   QString fileName = QFileDialog::getSaveFileName(this,
2764     tr("Save As"),
2765     mSlicerManagers[index]->GetFileName().c_str(),
2766     Extensions);
2767   if (!fileName.isEmpty()) {
2768     std::string fileformat = itksys::SystemTools::GetFilenameLastExtension(fileName.toStdString());
2769     if (OutputListeFormat.contains(
2770       fileformat.c_str())) {
2771         QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
2772         std::string action = "Saving";
2773         vvProgressDialog progress("Saving "+fileName.toStdString());
2774         qApp->processEvents();
2775         vvImageWriter::Pointer writer = vvImageWriter::New();
2776         writer->SetOutputFileName(fileName.toStdString());
2777         writer->SetInput(mSlicerManagers[index]->GetImage());
2778
2779         // Check on transform and prompt user
2780         writer->SetSaveTransform(false);
2781         bool bId = true;
2782         for(int i=0; i<4; i++)
2783           for(int j=0; j<4; j++) {
2784             // TODO SR and BP: check on the list of transforms and not the first only
2785             double elt = mSlicerManagers[index]->GetImage()->GetTransform()[0]->GetMatrix()->GetElement(i,j);
2786             if(i==j && elt!=1.)
2787               bId = false;
2788             if(i!=j && elt!=0.)
2789               bId = false;
2790           }
2791           if( !bId ) {
2792             QString warning = "The image has an associated linear transform. Do you want to save it along?";
2793             QMessageBox msgBox(QMessageBox::Warning, tr("Save transform"), warning, 0, this);
2794             msgBox.addButton(tr("Yes"), QMessageBox::AcceptRole);
2795             msgBox.addButton(tr("No"), QMessageBox::RejectRole);
2796             if (msgBox.exec() == QMessageBox::AcceptRole)
2797               writer->SetSaveTransform(true);
2798           }
2799
2800           writer->Update();
2801           QApplication::restoreOverrideCursor();
2802           if (writer->GetLastError().size()) {
2803             QString error = "Saving did not succeed\n";
2804             error += writer->GetLastError().c_str();
2805             QMessageBox::information(this,tr("Saving Problem"),error);
2806             SaveAs();
2807           }
2808     } else {
2809       QString error = fileformat.c_str();
2810       if (error.isEmpty())
2811         error += "no file format specified !";
2812       else
2813         error += " format unknown !!!\n";
2814       QMessageBox::information(this,tr("Saving Problem"),error);
2815       SaveAs();
2816     }
2817   }
2818 }
2819 //------------------------------------------------------------------------------
2820
2821 //------------------------------------------------------------------------------
2822 void vvMainWindow::SaveCurrentState()
2823 {
2824   QString Extensions = "XML Files(*.xml)";
2825   QString fileName = QFileDialog::getSaveFileName(this,
2826     tr("Save Current Window State"),
2827     "",
2828     Extensions);
2829
2830   SaveCurrentStateAs(fileName.toStdString());
2831 }
2832 //------------------------------------------------------------------------------
2833
2834 //------------------------------------------------------------------------------
2835 void vvMainWindow::SaveCurrentStateAs(const std::string& stateFile)
2836 {
2837   vvSaveState save_state;
2838   save_state.Run(this, stateFile);
2839 }
2840
2841 //------------------------------------------------------------------------------
2842 void vvMainWindow::ReadSavedState()
2843 {
2844   QString Extensions = "XML Files(*.xml)";
2845   QString fileName = QFileDialog::getOpenFileName(this,
2846     tr("Load Window State"),
2847     "",
2848     Extensions);
2849
2850   ReadSavedStateFile(fileName.toStdString());
2851 }
2852 //------------------------------------------------------------------------------
2853
2854 //------------------------------------------------------------------------------
2855 void vvMainWindow::ReadSavedStateFile(const std::string& stateFile)
2856 {
2857   vvReadState read_state;
2858   read_state.Run(this, stateFile);
2859 }
2860 //------------------------------------------------------------------------------
2861
2862 //------------------------------------------------------------------------------
2863 void vvMainWindow::LinkAllImages()
2864 {
2865   linkPanel->linkAll();
2866 }
2867
2868 //------------------------------------------------------------------------------
2869 void vvMainWindow::AddLink(QString image1,QString image2,bool fromPanel)
2870 {
2871   if (!fromPanel) {
2872     // delegate to linkPanel if call came from elsewhere...
2873     linkPanel->addLinkFromIds(image1, image2);
2874     return;
2875   }
2876
2877   unsigned int sm1 = 0;
2878   unsigned int sm2 = 0;
2879
2880   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
2881     if (image1.toStdString() == mSlicerManagers[i]->GetId()) {
2882       mSlicerManagers[i]->AddLink(image2.toStdString());
2883       sm1 = i;
2884     }
2885     if (image2.toStdString() == mSlicerManagers[i]->GetId()) {
2886       mSlicerManagers[i]->AddLink(image1.toStdString());
2887       sm2 = i;
2888     }
2889   }
2890
2891   if (linkPanel->isLinkAll())   {
2892     emit UpdateLinkedNavigation(mSlicerManagers[sm1]->GetId(), mSlicerManagers[mCurrentPickedImageIndex], mSlicerManagers[mCurrentPickedImageIndex]->GetSlicer(0));
2893     emit UpdateLinkedNavigation(mSlicerManagers[sm2]->GetId(), mSlicerManagers[mCurrentPickedImageIndex], mSlicerManagers[mCurrentPickedImageIndex]->GetSlicer(0));
2894   } else {
2895     emit UpdateLinkedNavigation(mSlicerManagers[sm2]->GetId(), mSlicerManagers[sm1], mSlicerManagers[sm1]->GetSlicer(0));
2896   }
2897 }
2898
2899 //------------------------------------------------------------------------------
2900
2901
2902 //------------------------------------------------------------------------------
2903 void vvMainWindow::RemoveLink(QString image1,QString image2)
2904 {
2905   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
2906     if (image1.toStdString() == mSlicerManagers[i]->GetId()) {
2907       mSlicerManagers[i]->RemoveLink(image2.toStdString());
2908     }
2909     if (image2.toStdString() == mSlicerManagers[i]->GetId()) {
2910       mSlicerManagers[i]->RemoveLink(image1.toStdString());
2911     }
2912   }
2913 }
2914 //------------------------------------------------------------------------------
2915
2916 //------------------------------------------------------------------------------
2917 void vvMainWindow::ChangeImageWithIndexOffset(vvSlicerManager *sm, int slicer, int offset)
2918 {
2919   if(mSlicerManagers.size()==1)
2920     return;
2921
2922   int index = 0;
2923   while(sm != mSlicerManagers[index])
2924     index++;
2925   index = (index+offset+mSlicerManagers.size()) % mSlicerManagers.size();
2926
2927   QTreeWidgetItem* item = GetItemFromSlicerManager(mSlicerManagers[index]);
2928   item->setData(slicer+1,Qt::CheckStateRole,2);         //change checkbox
2929   CurrentImageChanged(mSlicerManagers[index]->GetId()); //select new image
2930   DisplayChanged(item,slicer+1);
2931 }
2932 //------------------------------------------------------------------------------
2933 void vvMainWindow::HorizontalSliderMoved(int value,int column, int slicer_index)
2934 {
2935   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
2936     if (DataTree->topLevelItem(i)->data(column,Qt::CheckStateRole).toInt() > 1) {
2937       //i is the SlicerManager that is in charge of this slicer.
2938       if (mSlicerManagers[i]->IsInvolvedInFusionSequence()) {
2939         //if the slicerManager is involved in a fusionSequence as the secondary sequence, then update the slider position in the overlay panel and everything accordingly
2940         if (mSlicerManagers[i]->IsSecondarySequenceOfFusionSequence()) {
2941           overlayPanel->updateFusionSequenceSliderValueFromWindow(value, true);
2942         }
2943         else { //if this is the primary sequence that has been modified
2944           if (mSlicerManagers[i]->GetFusionSequenceTemporalSyncFlag()) {
2945             //WARNING: for some obscure reason, there are problems when accessing mSlicerManagers[mSlicerManagers[i]->GetFusionSequenceIndexOfLinkedManager()]->GetFusionSequenceFrameIndex();
2946
2947             int estimatedValue=0;
2948             //estimate a corresponding time index for the secondary (US) sequence, and update it accordingly.
2949             estimatedValue = mSlicerManagers[i]->GetFusionSequenceCorrespondances()[ value ];
2950             //TODO: at the moment, there is a loop in TSlice modifications
2951             //modifying sequence 1 causes seq 2 to update, which in turns update seq1...
2952             //I disable control on seq1 at the moment.
2953             //overlayPanel->updateFusionSequenceSliderValueFromWindow(estimatedValue, true);
2954           }
2955         }
2956       }
2957
2958       for (int j = 0; j < 4; j++) {
2959         mSlicerManagers[i]->SetTSliceInSlicer(value,j);
2960       }
2961       mSlicerManagers[i]->GetSlicer(slicer_index)->Render();
2962       break;
2963     }
2964   }
2965 }
2966 //------------------------------------------------------------------------------
2967
2968
2969 //------------------------------------------------------------------------------
2970 void vvMainWindow::NOHorizontalSliderMoved()
2971 {
2972   // if (mCurrentTime == NOHorizontalSlider->value()) return;
2973   HorizontalSliderMoved(NOHorizontalSlider->value(),COLUMN_UL_VIEW,0);
2974   //  mCurrentTime = NOHorizontalSlider->value();
2975 }
2976 //------------------------------------------------------------------------------
2977
2978
2979 //------------------------------------------------------------------------------
2980 void vvMainWindow::NEHorizontalSliderMoved()
2981 {
2982   // if (mCurrentTime == NEHorizontalSlider->value()) return;
2983   HorizontalSliderMoved(NEHorizontalSlider->value(),COLUMN_UR_VIEW,1);
2984   //  mCurrentTime = NEHorizontalSlider->value();
2985 }
2986 //------------------------------------------------------------------------------
2987
2988
2989 //------------------------------------------------------------------------------
2990 void vvMainWindow::SOHorizontalSliderMoved()
2991 {
2992   // if (mCurrentTime == SOHorizontalSlider->value()) return;
2993   HorizontalSliderMoved(SOHorizontalSlider->value(),COLUMN_DL_VIEW,2);
2994   // mCurrentTime = SOHorizontalSlider->value();
2995 }
2996 //------------------------------------------------------------------------------
2997
2998
2999 //------------------------------------------------------------------------------
3000 void vvMainWindow::SEHorizontalSliderMoved()
3001 {
3002   // if (mCurrentTime == SEHorizontalSlider->value()) return;
3003   HorizontalSliderMoved(SEHorizontalSlider->value(),COLUMN_DR_VIEW,3);
3004   // mCurrentTime = SEHorizontalSlider->value();
3005 }
3006 //------------------------------------------------------------------------------
3007
3008 //------------------------------------------------------------------------------
3009 void vvMainWindow::NOVerticalSliderChanged()
3010 {
3011   static int value=-1;
3012   if (value == NOVerticalSlider->value()) return;
3013   else value = NOVerticalSlider->value();
3014   //  int value = NOVerticalSlider->value();
3015   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
3016     if (DataTree->topLevelItem(i)->data(COLUMN_UL_VIEW,Qt::CheckStateRole).toInt() > 1) {
3017       if (mSlicerManagers[i]->GetSlicer(0)->GetSlice() != value) {
3018         mSlicerManagers[i]->GetSlicer(0)->SetSlice(value);
3019         mSlicerManagers[i]->VerticalSliderHasChanged(0, value);
3020
3021         // If nor Update/Render -> slider not work
3022         // only render = ok navigation, but for contour Update needed but slower ?
3023
3024         mSlicerManagers[i]->UpdateSlice(0);  // <-- DS add this. Not too much update ? YES. but needed for ImageContour ...
3025         //mSlicerManagers[i]->GetSlicer(0)->Render(); // <-- DS add this, needed for contour, seems ok ? not too slow ?
3026       }
3027       break;
3028     }
3029   }
3030 }
3031 //------------------------------------------------------------------------------
3032
3033
3034 //------------------------------------------------------------------------------
3035 void vvMainWindow::NEVerticalSliderChanged()
3036 {
3037   static int value=-1;
3038   if (value == NEVerticalSlider->value()) return;
3039   else value = NEVerticalSlider->value();
3040   //  int value = NEVerticalSlider->value();
3041   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
3042     if (DataTree->topLevelItem(i)->data(COLUMN_UR_VIEW,Qt::CheckStateRole).toInt() > 1) {
3043       if (mSlicerManagers[i]->GetSlicer(1)->GetSlice() != value) {
3044         mSlicerManagers[i]->GetSlicer(1)->SetSlice(value);
3045         mSlicerManagers[i]->VerticalSliderHasChanged(1, value);
3046         mSlicerManagers[i]->UpdateSlice(1);
3047         //mSlicerManagers[i]->GetSlicer(1)->Render(); // <-- DS add this, needed for contour, seems ok ? not too slow ?
3048       }
3049       break;
3050     }
3051   }
3052 }
3053 //------------------------------------------------------------------------------
3054
3055
3056 //------------------------------------------------------------------------------
3057 void vvMainWindow::SOVerticalSliderChanged()
3058 {
3059   static int value=-1;
3060   if (value == SOVerticalSlider->value()) return;
3061   else value = SOVerticalSlider->value();
3062   //int value = SOVerticalSlider->value();
3063   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
3064     if (DataTree->topLevelItem(i)->data(COLUMN_DL_VIEW,Qt::CheckStateRole).toInt() > 1) {
3065       if (mSlicerManagers[i]->GetSlicer(2)->GetSlice() != value) {
3066         mSlicerManagers[i]->GetSlicer(2)->SetSlice(value);
3067         mSlicerManagers[i]->VerticalSliderHasChanged(2, value);
3068         mSlicerManagers[i]->UpdateSlice(2);
3069         //mSlicerManagers[i]->GetSlicer(2)->Render(); // <-- DS add this, needed for contour, seems ok ? not too slow ?
3070       }
3071       // else { DD("avoid SOVerticalSlider slicer update"); }
3072       break;
3073     }
3074   }
3075 }
3076 //------------------------------------------------------------------------------
3077
3078
3079 //------------------------------------------------------------------------------
3080 void vvMainWindow::SEVerticalSliderChanged()
3081 {
3082   static int value=-1;
3083   if (value == SEVerticalSlider->value()) return;
3084   else value = SEVerticalSlider->value();
3085   // int value = SEVerticalSlider->value();
3086   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
3087     if (DataTree->topLevelItem(i)->data(COLUMN_DR_VIEW,Qt::CheckStateRole).toInt() > 1) {
3088       if (mSlicerManagers[i]->GetSlicer(3)->GetSlice() != value) {
3089         mSlicerManagers[i]->GetSlicer(3)->SetSlice(value);
3090         mSlicerManagers[i]->VerticalSliderHasChanged(3, value);
3091         mSlicerManagers[i]->UpdateSlice(3);
3092         //mSlicerManagers[i]->GetSlicer(3)->Render(); // <-- DS add this, needed for contour, seems ok ? not too slow ?
3093       }
3094       break;
3095     }
3096   }
3097 }
3098 //------------------------------------------------------------------------------
3099
3100
3101 //------------------------------------------------------------------------------
3102 void vvMainWindow::UpdateSlice(int slicer, int slice)
3103 {
3104   // DD("vvMainWindow::UpdateSlice");
3105   //   DD(slicer);
3106   //   DD(slice);
3107   if (slicer == 0) {
3108     //    if (slice != NOVerticalSlider->value())
3109     NOVerticalSlider->setValue(slice);
3110   } else {
3111     if (slicer == 1)
3112       NEVerticalSlider->setValue(slice);
3113     else {
3114       if (slicer == 2)
3115         SOVerticalSlider->setValue(slice);
3116       else {
3117         if (slicer == 3)
3118           SEVerticalSlider->setValue(slice);
3119       }
3120     }
3121   }
3122   // DD("vvMainWindow:UpdateSlice END");
3123 }
3124 //------------------------------------------------------------------------------
3125
3126
3127 //------------------------------------------------------------------------------
3128 void vvMainWindow::UpdateTSlice(int slicer, int slice, int code)
3129 {
3130   //FusionSequence: the slider value should be updated for slicers which show the same sequence as requested
3131   bool doUpdate=false;
3132   if (code==-1) doUpdate=true;
3133   else {
3134     for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
3135       if (DataTree->topLevelItem(i)->data(slicer+1,Qt::CheckStateRole).toInt() > 1) {
3136         //i is the active SlicerManager
3137         if (mSlicerManagers[i]->GetFusionSequenceInvolvmentCode()==code) doUpdate=true;
3138         break;
3139       }
3140     }
3141   }
3142   if (!doUpdate) return;
3143
3144   switch (slicer) {
3145   case 0:
3146     if (NOHorizontalSlider->value()==slice) return;
3147     NOHorizontalSlider->setValue(slice);
3148     break;
3149   case 1:
3150     if (NEHorizontalSlider->value()==slice) return;
3151     NEHorizontalSlider->setValue(slice);
3152     break;
3153   case 2:
3154     if (SOHorizontalSlider->value()==slice) return;
3155     SOHorizontalSlider->setValue(slice);
3156     break;
3157   case 3:
3158     if (SEHorizontalSlider->value()==slice) return;
3159     SEHorizontalSlider->setValue(slice);
3160     break;
3161   }
3162 }
3163 //------------------------------------------------------------------------------
3164
3165
3166 //------------------------------------------------------------------------------
3167 void vvMainWindow::UpdateSliceRange(int slicer, int min, int max, int tmin, int tmax)
3168 {
3169   //int position = int((min+max)/2);
3170   int position = mSlicerManagers[mCurrentPickedImageIndex]->GetSlicer(slicer)->GetSlice();
3171   if (slicer == 0) {
3172     NOVerticalSlider->setRange(min,max);
3173     NOHorizontalSlider->setRange(tmin,tmax);
3174     NOVerticalSlider->setValue(position);
3175   } else if (slicer == 1) {
3176     NEVerticalSlider->setRange(min,max);
3177     NEHorizontalSlider->setRange(tmin,tmax);
3178     NEVerticalSlider->setValue(position);
3179   } else if (slicer == 2) {
3180     SOVerticalSlider->setRange(min,max);
3181     SOHorizontalSlider->setRange(tmin,tmax);
3182     SOVerticalSlider->setValue(position);
3183   } else if (slicer == 3) {
3184     SEVerticalSlider->setRange(min,max);
3185     SEHorizontalSlider->setRange(tmin,tmax);
3186     SEVerticalSlider->setValue(position);
3187   }
3188 }
3189 //------------------------------------------------------------------------------
3190
3191
3192 //------------------------------------------------------------------------------
3193 void vvMainWindow::SaveNOScreenshot()
3194 {
3195   SaveScreenshot(NOViewWidget);
3196 }
3197 //------------------------------------------------------------------------------
3198
3199
3200 //------------------------------------------------------------------------------
3201 void vvMainWindow::SaveNEScreenshot()
3202 {
3203   SaveScreenshot(NEViewWidget);
3204 }
3205 //------------------------------------------------------------------------------
3206
3207
3208 //------------------------------------------------------------------------------
3209 void vvMainWindow::SaveSOScreenshot()
3210 {
3211   SaveScreenshot(SOViewWidget);
3212 }
3213 //------------------------------------------------------------------------------
3214
3215
3216 //------------------------------------------------------------------------------
3217 void vvMainWindow::SaveSEScreenshot()
3218 {
3219   SaveScreenshot(SEViewWidget);
3220 }
3221 //------------------------------------------------------------------------------
3222
3223
3224 //------------------------------------------------------------------------------
3225 void vvMainWindow::SaveScreenshotAllSlices()
3226 {
3227   QVTKWidget *widget = NOViewWidget;
3228
3229   int index = 0;// GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
3230   vvSlicerManager * SM = mSlicerManagers[index];
3231   vvImage * image = SM->GetImage();
3232   vvSlicer * slicer = SM->GetSlicer(0);
3233   int orientation = slicer->GetOrientation();
3234   int nbSlices = image->GetSize()[orientation];
3235   vtkSmartPointer<vtkRenderWindow>  renderWindow = widget->GetRenderWindow();
3236
3237   // Select filename base
3238   QString filename = QFileDialog::getSaveFileName(this,
3239     tr("Save As (filename will be completed by slice number)"),
3240     itksys::SystemTools::GetFilenamePath(mSlicerManagers[index]->GetFileName()).c_str(),
3241     "Images( *.png);;Images( *.jpg)");
3242
3243   // Loop on slices
3244   for(int i=0; i<nbSlices; i++) {
3245     // Change the slice
3246     slicer->SetSlice(i); // -> change the slice of the current slicer
3247     SM->UpdateSlice(0); // --> this one emit UpdateSlice
3248     QCoreApplication::flush(); // -> needed to force display of contours
3249
3250     // Screenshot
3251     vtkSmartPointer<vtkWindowToImageFilter> windowToImageFilter = vtkSmartPointer<vtkWindowToImageFilter>::New();
3252     windowToImageFilter->SetInput(renderWindow);
3253     windowToImageFilter->SetMagnification(1);
3254     windowToImageFilter->SetInputBufferTypeToRGBA(); //also record the alpha (transparency) channel
3255     windowToImageFilter->Update();
3256
3257     vtkSmartPointer<vtkPNGWriter> writer = vtkSmartPointer<vtkPNGWriter>::New();
3258     std::string fn = itksys::SystemTools::GetFilenameWithoutLastExtension(filename.toStdString());
3259     std::string num = clitk::toString(i);
3260     if (i<10) num = "0"+num;
3261     if (i<100) num = "0"+num;
3262     if (i<1000) num = "0"+num;
3263
3264     fn = itksys::SystemTools::GetFilenamePath(filename.toStdString()) + "/"+ fn
3265       + "_" + num + itksys::SystemTools::GetFilenameLastExtension(filename.toStdString());
3266     writer->SetFileName(fn.c_str());
3267     writer->SetInput(windowToImageFilter->GetOutput());
3268     writer->Write();
3269   }
3270 }
3271 //------------------------------------------------------------------------------
3272
3273
3274 //------------------------------------------------------------------------------
3275 void vvMainWindow::SaveScreenshot(QVTKWidget *widget)
3276 {
3277   QString Extensions = "Images( *.png);;";
3278   Extensions += "Images( *.jpg);;";
3279   Extensions += "Images( *.bmp);;";
3280   Extensions += "Images( *.tif);;";
3281   Extensions += "Images( *.ppm)";
3282 #if defined(VTK_USE_FFMPEG_ENCODER) || defined(VTK_USE_VIDEO_FOR_WINDOWS)
3283   Extensions += ";;Video( *.avi)";
3284 #endif
3285 #ifdef VTK_USE_MPEG2_ENCODER
3286   Extensions += ";;Video( *.mpg)";
3287 #endif
3288 #ifdef CLITK_EXPERIMENTAL
3289   Extensions += ";;Video( *.gif)";
3290 #endif
3291
3292   int smIndex=GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
3293   QString fileName = QFileDialog::getSaveFileName(this,
3294     tr("Save As"),
3295     itksys::SystemTools::GetFilenamePath(mSlicerManagers[smIndex]->GetFileName()).c_str(),
3296     Extensions);
3297
3298   if (!fileName.isEmpty()) {
3299     vtkSmartPointer<vtkWindowToImageFilter> w2i = vtkSmartPointer<vtkWindowToImageFilter>::New();
3300     w2i->SetInput(widget->GetRenderWindow());
3301     w2i->Update();
3302     vtkImageData *image = w2i->GetOutput();
3303
3304     std::string ext(itksys::SystemTools::GetFilenameLastExtension(fileName.toStdString()));
3305
3306     // Image
3307     vtkImageWriter *imgwriter = NULL;
3308     if (ext==".bmp")
3309       imgwriter = vtkBMPWriter::New();
3310     else if (ext==".tif")
3311       imgwriter = vtkTIFFWriter::New();
3312     else if (ext==".ppm")
3313       imgwriter = vtkPNMWriter::New();
3314     else if (ext==".png")
3315       imgwriter = vtkPNGWriter::New();
3316     else if (ext==".jpg")
3317       imgwriter = vtkJPEGWriter::New();
3318
3319     // Snapshot image if not null
3320     if(imgwriter!=NULL) {
3321       imgwriter->SetInput(image);
3322       imgwriter->SetFileName(fileName.toStdString().c_str());
3323       imgwriter->Write();
3324       return;
3325     }
3326
3327     // Video
3328     vtkGenericMovieWriter *vidwriter = NULL;
3329 #if CLITK_EXPERIMENTAL == 1
3330     if (ext==".gif") {
3331       vvAnimatedGIFWriter *gif = vvAnimatedGIFWriter::New();
3332       vidwriter = gif;
3333
3334       // FPS
3335       bool ok;
3336       int fps = QInputDialog::getInteger(this, tr("Number of frames per second"),
3337         tr("FPS:"), 5, 0, 1000, 1, &ok);
3338       if(ok)
3339         gif->SetRate(fps);
3340
3341       // Loops
3342       int loops = QInputDialog::getInteger(this, tr("Loops"),
3343         tr("Number of loops (0 means infinite):"), 0, 0, 1000000000, 1, &ok);
3344       if(ok)
3345         gif->SetLoops(loops);
3346
3347       // Dithering
3348       QString msg = "Would you like to activate dithering?";
3349       QMessageBox msgBox(QMessageBox::Question, tr("Dithering"),msg, 0, this);
3350       msgBox.addButton(tr("Yes"), QMessageBox::AcceptRole);
3351       msgBox.addButton(tr("No"), QMessageBox::RejectRole);
3352       gif->SetDither(msgBox.exec() == QMessageBox::AcceptRole);
3353     }
3354 #endif
3355 #ifdef VTK_USE_VIDEO_FOR_WINDOWS
3356     if (ext==".avi") {
3357       vtkAVIWriter *mpg = vtkAVIWriter::New();
3358       vidwriter = mpg;
3359       mpg->SetQuality(2);
3360       bool ok;
3361       int fps = QInputDialog::getInteger(this, tr("Number of frames per second"),
3362         tr("FPS:"), 5, 0, 1024, 1, &ok);
3363       if(!ok)
3364         fps = 5;
3365       mpg->SetRate(fps);
3366     }
3367 #endif
3368 #ifdef VTK_USE_FFMPEG_ENCODER
3369     if (ext==".avi") {
3370       vtkFFMPEGWriter *mpg = vtkFFMPEGWriter::New();
3371       vidwriter = mpg;
3372       mpg->SetQuality(2);
3373       bool ok;
3374       int fps = QInputDialog::getInteger(this, tr("Number of frames per second"),
3375         tr("FPS:"), 5, 0, 1024, 1, &ok);
3376       if(!ok)
3377         fps = 5;
3378       mpg->SetRate(fps);
3379       mpg->SetBitRateTolerance(int(ceil(12.0*1024*1024/fps)));
3380     }
3381 #endif
3382 #ifdef VTK_USE_MPEG2_ENCODER
3383     if (ext==".mpg") {
3384       vtkMPEG2Writer *mpg = vtkMPEG2Writer::New();
3385       vidwriter = mpg;
3386     }
3387 #endif
3388
3389     // Take video if not null
3390     if(vidwriter!=NULL){
3391       vidwriter->SetInput(image);
3392       vidwriter->SetFileName(fileName.toStdString().c_str());
3393       vidwriter->Start();
3394       int nSlice = mSlicerManagers[smIndex]->GetSlicer(0)->GetTMax();
3395       for(int i=0; i<=nSlice; i++) {
3396         mSlicerManagers[smIndex]->SetNextTSlice(0);
3397         vtkSmartPointer<vtkWindowToImageFilter> w2i = vtkSmartPointer<vtkWindowToImageFilter>::New();
3398         w2i->SetInput(widget->GetRenderWindow());
3399         w2i->Update();
3400         vidwriter->SetInput(w2i->GetOutput());
3401         vidwriter->Write();
3402       }
3403       vidwriter->End();
3404       vidwriter->Delete();
3405       return;
3406     }
3407
3408     QMessageBox::information(this,tr("Problem saving screenshot !"),tr("Cannot save image.\nPlease set a file extension !!!"));
3409   }
3410 }
3411 //------------------------------------------------------------------------------
3412
3413
3414 //------------------------------------------------------------------------------
3415 void vvMainWindow::GoToCursor()
3416 {
3417   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
3418   for (int column = 1; column < 5; column++) {
3419     if (DataTree->selectedItems()[0]->data(column,Qt::CheckStateRole).toInt() > 1) {
3420       double* cursorPos = mSlicerManagers[index]->GetSlicer(column-1)->GetCursorPosition();
3421       mSlicerManagers[index]->GetSlicer(column-1)->SetCurrentPosition(
3422         cursorPos[0],cursorPos[1],cursorPos[2],cursorPos[3]);
3423       mSlicerManagers[index]->UpdateViews(1,column-1);
3424       mSlicerManagers[index]->UpdateLinked(column-1);
3425       break;
3426     }
3427   }
3428 }
3429 //------------------------------------------------------------------------------
3430
3431 //------------------------------------------------------------------------------
3432 void vvMainWindow::GoToLandmark()
3433 {
3434   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
3435   for (int column = 1; column < 5; column++) {
3436     if (DataTree->selectedItems()[0]->data(column,Qt::CheckStateRole).toInt() > 1) {
3437       double* cursorPos = landmarksPanel->GetSelectedPoint();
3438       mSlicerManagers[index]->GetSlicer(column-1)->SetCurrentPosition(
3439         cursorPos[0],cursorPos[1],cursorPos[2],cursorPos[3]);
3440       mSlicerManagers[index]->UpdateViews(1,column-1);
3441       mSlicerManagers[index]->UpdateLinked(column-1);
3442       break;
3443     }
3444   }
3445 }
3446 //------------------------------------------------------------------------------
3447
3448 //------------------------------------------------------------------------------
3449 void vvMainWindow::PlayPause()
3450 {
3451   if (playMode) {
3452     playMode = 0;
3453     playButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/player_play.png")));
3454     ImageInfoChanged();
3455     return;
3456   } else {
3457     int image_number=DataTree->topLevelItemCount();
3458     bool has_temporal;
3459     for (int i=0; i<image_number; i++)
3460       if (mSlicerManagers[i]->GetSlicer(0)->GetTMax() > 0) {
3461         has_temporal=true;
3462         break;
3463       }
3464       if (has_temporal) {
3465         playMode = 1;
3466         playButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/player_pause.png")));
3467         QTimer::singleShot(1000/mFrameRate, this, SLOT(PlayNext()));
3468       }
3469   }
3470 }
3471 //------------------------------------------------------------------------------
3472
3473 //------------------------------------------------------------------------------
3474 void vvMainWindow::PlayNext()
3475 {
3476   if (playMode && !this->isHidden()) {
3477     int image_number=DataTree->topLevelItemCount();
3478     ///Only play one slicer per SM, and only if the SM is being displayed
3479     for (int i=0; i<image_number; i++)
3480       for (int j=0; j<4; j++)
3481         if (mSlicerManagers[i]->GetSlicer(0)->GetTMax() > 0 &&
3482           DataTree->topLevelItem(i)->data(j+1,Qt::CheckStateRole).toInt() > 0) {
3483             mSlicerManagers[i]->SetNextTSlice(j);
3484             break;
3485         }
3486         QTimer::singleShot(1000/mFrameRate, this, SLOT(PlayNext()));
3487   }
3488 }
3489 //------------------------------------------------------------------------------
3490
3491 void vvMainWindow::ShowLastImage()
3492 {
3493   if (mSlicerManagers.size() > 1) {
3494     QTreeWidgetItem * item=DataTree->topLevelItem(DataTree->topLevelItemCount()-1);
3495     CurrentImageChanged(mSlicerManagers.back()->GetId()); //select new image
3496     item->setData(1,Qt::CheckStateRole,2); //show the new image in the first panel
3497     DisplayChanged(item,1);
3498   }
3499 }
3500
3501 //------------------------------------------------------------------------------
3502 void vvMainWindow::UpdateRenderWindows()
3503 {
3504   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
3505     mSlicerManagers[i]->GetSlicer(0)->UpdateLandmarks();
3506     mSlicerManagers[i]->GetSlicer(1)->UpdateLandmarks();
3507     mSlicerManagers[i]->GetSlicer(2)->UpdateLandmarks();
3508     mSlicerManagers[i]->GetSlicer(3)->UpdateLandmarks();
3509   }
3510   if (NOViewWidget->GetRenderWindow()) NOViewWidget->GetRenderWindow()->Render();
3511   if (NEViewWidget->GetRenderWindow()) NEViewWidget->GetRenderWindow()->Render();
3512   if (SOViewWidget->GetRenderWindow()) SOViewWidget->GetRenderWindow()->Render();
3513   if (SEViewWidget->GetRenderWindow()) SEViewWidget->GetRenderWindow()->Render();
3514 }
3515 //------------------------------------------------------------------------------
3516
3517 //------------------------------------------------------------------------------
3518 void vvMainWindow::SegmentationOnCurrentImage()
3519 {
3520   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
3521
3522   vvSegmentationDialog segmentation;
3523   segmentation.SetImage(mSlicerManagers[index]->GetSlicer(0)->GetImage());
3524   segmentation.exec();
3525 }
3526 //------------------------------------------------------------------------------
3527
3528 void vvMainWindow::SurfaceViewerLaunch()
3529 {
3530   vvSurfaceViewerDialog surfaceViewer;
3531   surfaceViewer.exec();
3532 }
3533 //------------------------------------------------------------------------------
3534
3535
3536 //------------------------------------------------------------------------------
3537 int vvMainWindow::GetImageDuplicateFilenameNumber(std::string filename)
3538 {
3539   int number=0;
3540   for(unsigned int l=0; l<mSlicerManagers.size(); l++) {
3541     vvSlicerManager * v = mSlicerManagers[l];
3542     if (v->GetBaseFileName() ==
3543       vtksys::SystemTools::GetFilenameName(vtksys::SystemTools::GetFilenameWithoutLastExtension(filename))) {
3544         number = std::max(number, v->GetBaseFileNameNumber()+1);
3545     }
3546   }
3547   return number;
3548 }
3549 //------------------------------------------------------------------------------
3550
3551
3552 //------------------------------------------------------------------------------
3553 vvSlicerManager* vvMainWindow::AddImage(vvImage::Pointer image,std::string filename)
3554 {
3555   // Change filename if another image exist with the same name
3556   int number = GetImageDuplicateFilenameNumber(filename);
3557
3558   // Create new SliceManager
3559   vvSlicerManager* slicer_manager = new vvSlicerManager(4);
3560   slicer_manager->SetImage(image);//, IMAGE, number);
3561   //  filename = filename+"_"+clitk::toString(number);
3562   slicer_manager->SetFilename(filename, number);
3563   mSlicerManagers.push_back(slicer_manager);
3564
3565   //create an item in the tree with good settings
3566   QTreeWidgetItem *item = new QTreeWidgetItem();
3567   item->setData(0,Qt::UserRole,slicer_manager->GetFileName().c_str());//files[i].c_str());
3568   item->setData(1,Qt::UserRole,tr("image"));
3569   item->setData(COLUMN_IMAGE_NAME,Qt::DisplayRole,slicer_manager->GetFileName().c_str());//filename.c_str());
3570   qApp->processEvents();
3571
3572   for (int j = 1; j <= 4; j++) item->setData(j,Qt::CheckStateRole,1);
3573
3574   //Create the buttons for reload and close
3575   qApp->processEvents();
3576   QTreePushButton* cButton = new QTreePushButton;
3577   cButton->setItem(item);
3578   cButton->setColumn(COLUMN_CLOSE_IMAGE);
3579   cButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/exit.png")));
3580   connect(cButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
3581     this,SLOT(CloseImage(QTreeWidgetItem*, int)));
3582
3583   QTreePushButton* rButton = new QTreePushButton;
3584   rButton->setItem(item);
3585   rButton->setColumn(COLUMN_RELOAD_IMAGE);
3586   rButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/rotateright.png")));
3587   rButton->setEnabled(0);
3588   connect(rButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
3589     this,SLOT(ReloadImage(QTreeWidgetItem*, int)));
3590
3591   DataTree->addTopLevelItem(item);
3592   DataTree->setItemWidget(item, COLUMN_CLOSE_IMAGE, cButton);
3593   DataTree->setItemWidget(item, COLUMN_RELOAD_IMAGE, rButton);
3594
3595   //set the id of the image
3596   QString id = QDir::current().absoluteFilePath(slicer_manager->GetFileName().c_str()) + QString::number(mSlicerManagers.size()-1);
3597   item->setData(COLUMN_IMAGE_NAME,Qt::UserRole,id.toStdString().c_str());
3598   mSlicerManagers.back()->SetId(id.toStdString());
3599
3600   linkPanel->addImage(slicer_manager->GetFileName().c_str()// filename
3601     , id.toStdString());
3602
3603   connect(mSlicerManagers.back(), SIGNAL(currentImageChanged(std::string)),
3604     this, SLOT(CurrentImageChanged(std::string)));
3605   connect(mSlicerManagers.back(), SIGNAL(currentPickedImageChanged(std::string)),
3606     this, SLOT(CurrentPickedImageChanged(std::string)));
3607   connect(mSlicerManagers.back(), SIGNAL(UpdatePosition(int, double, double, double, double, double, double, double)),
3608     this, SLOT(MousePositionChanged(int,double, double, double, double, double, double, double)));
3609   connect(mSlicerManagers.back(), SIGNAL(UpdateVector(int, double, double, double, double)),
3610     this, SLOT(VectorChanged(int,double,double,double, double)));
3611   connect(mSlicerManagers.back(), SIGNAL(UpdateOverlay(int, double, double)),
3612     this, SLOT(OverlayChanged(int,double,double)));
3613   connect(mSlicerManagers.back(), SIGNAL(UpdateFusion(int, double)),
3614     this, SLOT(FusionChanged(int,double)));
3615   //connect(mSlicerManagers.back(), SIGNAL(UpdateFusionSequence(int, bool, unsigned int)),
3616   //  this, SLOT(FusionSequenceChanged(int, bool, unsigned int)));
3617   connect(mSlicerManagers.back(), SIGNAL(WindowLevelChanged()),
3618     this,SLOT(WindowLevelChanged()));
3619   connect(mSlicerManagers.back(), SIGNAL(UpdateSlice(int,int)),
3620     this,SLOT(UpdateSlice(int,int)));
3621   connect(mSlicerManagers.back(), SIGNAL(UpdateTSlice(int, int, int)),
3622     this,SLOT(UpdateTSlice(int, int, int)));
3623   connect(mSlicerManagers.back(), SIGNAL(UpdateTSlice(int, int, int)),
3624     this,SLOT(ImageInfoChanged()));
3625   connect(mSlicerManagers.back(), SIGNAL(UpdateSliceRange(int,int,int,int,int)),
3626     this,SLOT(UpdateSliceRange(int,int,int,int,int)));
3627   connect(mSlicerManagers.back(), SIGNAL(UpdateLinkManager(std::string,int,double,double,double,int)),
3628     this,SLOT(UpdateLinkManager(std::string,int,double,double,double,int)));
3629   connect(mSlicerManagers.back(), SIGNAL(UpdateLinkedNavigation(std::string,vvSlicerManager*,vvSlicer*)),
3630     this,SLOT(UpdateLinkedNavigation(std::string,vvSlicerManager*,vvSlicer*)));
3631   connect(mSlicerManagers.back(), SIGNAL(ChangeImageWithIndexOffset(vvSlicerManager*,int,int)),
3632     this,SLOT(ChangeImageWithIndexOffset(vvSlicerManager*,int,int)));
3633   connect(mSlicerManagers.back(), SIGNAL(LandmarkAdded()),landmarksPanel,SLOT(AddPoint()));
3634
3635
3636   UpdateTree();
3637   qApp->processEvents();
3638   InitSlicers();
3639   ShowLastImage();
3640   InitDisplay();
3641   qApp->processEvents();
3642
3643   // End
3644   ImageInfoChanged();
3645   return slicer_manager;
3646 }
3647 //------------------------------------------------------------------------------
3648
3649
3650 //------------------------------------------------------------------------------
3651 void vvMainWindow::UpdateCurrentSlicer()
3652 {
3653   int index = -1;
3654   if (DataTree->selectedItems().size() > 0) {
3655     index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
3656   }
3657   mSlicerManagerCurrentIndex = index;
3658 }
3659 //------------------------------------------------------------------------------