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 <vtkImageMapper3D.h>
  62 #include <vtkInformation.h>
  63 #include <vtkVersion.h>
  64 #include <vtkImageData.h>
  65 #include <vtkImageActor.h>
  66 #include <vtkCornerAnnotation.h>
  67 #include <vtkRenderWindow.h>
  68 #include <vtkRenderWindowInteractor.h>
  69 #include <vtkRenderer.h>
  70 #include <vtkRendererCollection.h>
  71 #include <vtkWindowToImageFilter.h>
  72 #include <vtkBMPWriter.h>
  73 #include <vtkTIFFWriter.h>
  74 #include <vtkPNMWriter.h>
  75 #include <vtkPNGWriter.h>
  76 #include <vtkJPEGWriter.h>
  77 #include <vtkGenericMovieWriter.h>
  78 #ifdef CLITK_EXPERIMENTAL
  79 #  include <vvAnimatedGIFWriter.h>
  80 #endif
  81 #ifdef VTK_USE_VIDEO_FOR_WINDOWS
  82 #  include <vtkAVIWriter.h>
  83 #endif
  84 #ifdef VTK_USE_FFMPEG_ENCODER
  85 #  include <vtkFFMPEGWriter.h>
  86 #endif
  87 #ifdef VTK_USE_MPEG2_ENCODER
  88 #  include <vtkMPEG2Writer.h>
  89 #endif
  90 #include <vtkMatrix4x4.h>
  91 #include <vtkTransform.h>
  92
  93 // Standard includes
  94 #include <iostream>
  95 #include <fstream>
  96 #include <sstream>
  97 #include <iomanip>
  98
  99 #define COLUMN_TREE 0
 100 #define COLUMN_UL_VIEW 1
 101 #define COLUMN_UR_VIEW 2
 102 #define COLUMN_DL_VIEW 3
 103 #define COLUMN_DR_VIEW 4
 104 #define COLUMN_CLOSE_IMAGE 5
 105 #define COLUMN_RELOAD_IMAGE 6
 106 #define COLUMN_IMAGE_NAME 7
 107
 108 #ifdef CLITK_PRIVATE_FEATURES
 109 #define EXTENSIONS "Images ( *.bmp *.dcm *.png *.jpeg *.jpg *.tif *.mhd *.mha *.hdr *.vox *.his *.xdr *.SCAN *.nii *.nrrd *.nhdr *.refscan *.nii.gz *.usf *.svl)"
 110 #else
 111 #define EXTENSIONS "Images ( *.bmp *.dcm *.png *.jpeg *.jpg *.tif *.mhd *.mha *.hdr *.vox *.his *.xdr *.SCAN *.nii *.nrrd *.nhdr *.refscan *.nii.gz)"
 112 #endif
 113
 114
 115 /*Data Tree values
 116 0,Qt::UserRole full filename
 117 1,Qt::CheckStateRole checkbutton UL View
 118 1,Qt::UserRole overlay, fusion or vector
 119 2,Qt::CheckStateRole checkbutton UR View
 120 3,Qt::CheckStateRole checkbutton DL View
 121 4,Qt::CheckStateRole checkbutton DR View
 122 5,0  short filename
 123 5,Qt::UserRole mSlicerManager id*/
 124
 125 //------------------------------------------------------------------------------
 126 vvMainWindow::vvMainWindow():vvMainWindowBase()
 127 {
 128   setupUi(this); // this sets up the GUI
 129
 130   mInputPathName = "";
 131   mMenuTools = menuTools;
 132   //  mMenuSegmentation = menuSegmentation;
 133   mContextMenu = &contextMenu;
 134   mMenuExperimentalTools = menuExperimental;
 135   mMainWidget = this;
 136   mCurrentTime = -1;
 137   mCurrentSelectedImageId = "";
 138   mCurrentPickedImageId = "";
 139   mCurrentPickedImageIndex = 0;
 140
 141   //Init the contextMenu
 142   this->setContextMenuPolicy(Qt::CustomContextMenu);
 143   contextActions.resize(0);
 144   QAction* actionOpen_new_image = contextMenu.addAction(QIcon(QString::fromUtf8(":/common/icons/fileopen.png")),
 145     tr("O&pen new Image"));
 146   actionOpen_new_image->setShortcut(QKeySequence(tr("Ctrl+O")));
 147   connect(actionOpen_new_image,SIGNAL(triggered()),this,SLOT(OpenImages()));
 148   contextActions.push_back(actionOpen_new_image);
 149   contextMenu.addSeparator();
 150
 151   QAction* actionClose_Image = contextMenu.addAction(QIcon(QString::fromUtf8(":/common/icons/exit.png")),
 152     tr("Close Current Image"));
 153   connect(actionClose_Image,SIGNAL(triggered()),this,SLOT(CloseImage()));
 154   contextActions.push_back(actionClose_Image);
 155
 156   QAction* actionReload_image = contextMenu.addAction(QIcon(QString::fromUtf8(":/common/icons/rotateright.png")),
 157     tr("Reload Current Image"));
 158   connect(actionReload_image,SIGNAL(triggered()),this,SLOT(ReloadImage()));
 159   contextActions.push_back(actionReload_image);
 160
 161   QAction* actionSave_image = contextMenu.addAction(QIcon(QString::fromUtf8(":/common/icons/filesave.png")),
 162     tr("Save Current Image"));
 163   connect(actionSave_image,SIGNAL(triggered()),this,SLOT(SaveAs()));
 164   contextActions.push_back(actionSave_image);
 165
 166   QAction* actionSave_state = contextMenu.addAction(QIcon(QString::fromUtf8(":/common/icons/filesave.png")),
 167     tr("Save Current State"));
 168   connect(actionSave_state,SIGNAL(triggered()),this,SLOT(SaveCurrentState()));
 169   contextActions.push_back(actionSave_state);
 170
 171   QAction* actionRead_state = contextMenu.addAction(QIcon(QString::fromUtf8(":/common/icons/filesave.png")),
 172     tr("Read Saved State"));
 173   connect(actionRead_state,SIGNAL(triggered()),this,SLOT(ReadSavedState()));
 174   contextActions.push_back(actionRead_state);
 175
 176   contextMenu.addSeparator();
 177
 178   contextMenu.addAction(actionAdd_VF_to_current_Image);
 179   contextActions.push_back(actionAdd_VF_to_current_Image);
 180
 181   //QAction* actionAdd_Overlay_to_current_Image = menuOverlay->addAction(QIcon(QString::fromUtf8(":/common/icons/GPSup.png")),
 182   //    tr("Add overlay image to current image"));
 183   contextMenu.addAction(actionAdd_overlay_image_to_current_image);
 184   contextActions.push_back(actionAdd_overlay_image_to_current_image);
 185
 186   contextMenu.addAction(actionAdd_fusion_image);
 187   contextActions.push_back(actionAdd_fusion_image);
 188
 189 #ifdef CLITK_EXPERIMENTAL
 190   contextMenu.addAction(actionAdd_USSequence_toCT);
 191   contextActions.push_back(actionAdd_USSequence_toCT);
 192 #endif
 193
 194
 195   contextMenu.addSeparator();
 196   QAction* actionResetMatrix = contextMenu.addAction(QIcon(QString::fromUtf8(":/common/icons/identity.png")),
 197     tr("Reset transformation to identity"));
 198   connect(actionResetMatrix, SIGNAL(triggered()), this,SLOT(ResetTransformationToIdentity()));
 199
 200   // TRIAL DS
 201   /*
 202   QMenu * m = new QMenu(menubar);
 203   m->setTitle("TOTO");
 204   //  m->setObjectName(QString::fromUtf8("TOTOTO"));
 205   contextMenu.addMenu(m);
 206   QAction * a = m->addAction(QIcon(QString::fromUtf8(":/common/icons/GPSup.png")),
 207   tr("BIDON"));
 208   QAction * b = m->addAction(QIcon(QString::fromUtf8(":/common/icons/GPSup.png")),
 209   tr("BIDON2"));
 210   m->addAction(a);
 211   m->addAction(b);
 212   connect(a,SIGNAL(triggered()),this,SLOT(AddFusionImage()));
 213   */
 214
 215   //init the DataTree
 216   mSlicerManagers.resize(0);
 217
 218   QStringList header;
 219   header.append("");
 220   header.append("TL");
 221   header.append("TR");
 222   header.append("BL");
 223   header.append("BR");
 224   header.append("");
 225   header.append("");
 226   header.append("Name");
 227
 228   DataTree->setHeaderLabels(header);
 229   DataTree->resizeColumnToContents(COLUMN_TREE);
 230   DataTree->resizeColumnToContents(COLUMN_UL_VIEW);
 231   DataTree->resizeColumnToContents(COLUMN_UR_VIEW);
 232   DataTree->resizeColumnToContents(COLUMN_DL_VIEW);
 233   DataTree->resizeColumnToContents(COLUMN_DR_VIEW);
 234   DataTree->resizeColumnToContents(COLUMN_CLOSE_IMAGE);
 235   DataTree->resizeColumnToContents(COLUMN_RELOAD_IMAGE);
 236   DataTree->resizeColumnToContents(COLUMN_IMAGE_NAME);
 237
 238   viewMode = 1;
 239   documentation = new vvDocumentation();
 240   help_dialog = new vvHelpDialog();
 241   dicomSeriesSelector = new vvDicomSeriesSelector();
 242
 243   inverseButton->setEnabled(0);
 244   actionAdd_overlay_image_to_current_image->setEnabled(0);
 245   actionSave_As->setEnabled(0);
 246   actionAdd_VF_to_current_Image->setEnabled(0);
 247   actionAdd_fusion_image->setEnabled(0);
 248   actionAdd_USSequence_toCT->setEnabled(0);
 249
 250   //init the sliders
 251   verticalSliders.push_back(NOVerticalSlider);
 252   verticalSliders.push_back(NEVerticalSlider);
 253   verticalSliders.push_back(SOVerticalSlider);
 254   verticalSliders.push_back(SEVerticalSlider);
 255
 256   for (int i =0; i < 4; i++)
 257     verticalSliders[i]->hide();
 258
 259   horizontalSliders.push_back(NOHorizontalSlider);
 260   horizontalSliders.push_back(NEHorizontalSlider);
 261   horizontalSliders.push_back(SOHorizontalSlider);
 262   horizontalSliders.push_back(SEHorizontalSlider);
 263
 264   for (int i =0; i < 4; i++)
 265     horizontalSliders[i]->hide();
 266
 267
 268   connect(NOVerticalSlider,SIGNAL(valueChanged(int)),this,SLOT(NOVerticalSliderChanged()));
 269   connect(NEVerticalSlider,SIGNAL(valueChanged(int)),this,SLOT(NEVerticalSliderChanged()));
 270   connect(SOVerticalSlider,SIGNAL(valueChanged(int)),this,SLOT(SOVerticalSliderChanged()));
 271   connect(SEVerticalSlider,SIGNAL(valueChanged(int)),this,SLOT(SEVerticalSliderChanged()));
 272
 273   connect(NOHorizontalSlider,SIGNAL(valueChanged(int)),this,SLOT(NOHorizontalSliderMoved()));
 274   connect(NEHorizontalSlider,SIGNAL(valueChanged(int)),this,SLOT(NEHorizontalSliderMoved()));
 275   connect(SOHorizontalSlider,SIGNAL(valueChanged(int)),this,SLOT(SOHorizontalSliderMoved()));
 276   connect(SEHorizontalSlider,SIGNAL(valueChanged(int)),this,SLOT(SEHorizontalSliderMoved()));
 277
 278   //connect everything
 279   connect(actionCompute_mid_position_image,SIGNAL(triggered()),this,SLOT(ComputeMidPosition()));
 280   connect(actionDeformable_Registration,SIGNAL(triggered()),this,SLOT(ComputeDeformableRegistration()));
 281   connect(actionWarp_image_with_vector_field,SIGNAL(triggered()),this,SLOT(WarpImage()));
 282   connect(actionLoad_images,SIGNAL(triggered()),this,SLOT(OpenImages()));
 283   connect(actionOpen_Dicom,SIGNAL(triggered()),this,SLOT(OpenDicom()));
 284   //  connect(actionOpen_Dicom_Struct,SIGNAL(triggered()),this,SLOT(OpenDCStructContour()));
 285   connect(actionOpen_VTK_contour,SIGNAL(triggered()),this,SLOT(OpenVTKContour()));
 286   connect(actionOpen_Multiple_Images_As_One,SIGNAL(triggered()),this,SLOT(MergeImages()));
 287   connect(actionSlice_Image_As_Multiple_Images,SIGNAL(triggered()),this,SLOT(SliceImages()));
 288   connect(actionOpen_Image_With_Time,SIGNAL(triggered()),this,SLOT(OpenImageWithTime()));
 289   connect(actionMerge_images_as_n_dim_t, SIGNAL(triggered()), this, SLOT(MergeImagesWithTime()));
 290   connect(actionSave_As,SIGNAL(triggered()),this,SLOT(SaveAs()));
 291   connect(actionSave_current_state,SIGNAL(triggered()),this,SLOT(SaveCurrentState()));
 292   connect(actionRead_saved_state,SIGNAL(triggered()),this,SLOT(ReadSavedState()));
 293   connect(actionExit,SIGNAL(triggered()),this,SLOT(close()));
 294   connect(actionAdd_VF_to_current_Image,SIGNAL(triggered()),this,SLOT(OpenField()));
 295   connect(actionAdd_fusion_image,SIGNAL(triggered()),this,SLOT(SelectFusionImage()));
 296   connect(actionAdd_overlay_image_to_current_image,SIGNAL(triggered()), this,SLOT(SelectOverlayImage()));
 297   connect(actionAdd_USSequence_toCT,SIGNAL(triggered()), this,SLOT(SelectFusionSequence()));
 298   connect(actionNavigation_Help,SIGNAL(triggered()),this,SLOT(ShowHelpDialog()));
 299   connect(actionDocumentation,SIGNAL(triggered()),this,SLOT(ShowDocumentation()));
 300   connect(actionRegister_vv,SIGNAL(triggered()),this,SLOT(PopupRegisterForm()));
 301
 302   connect(overlayPanel, SIGNAL(FusionSequenceCorrespondancesButtonPressed()), this, SLOT(SelectFusionSequenceCorrespondances()));
 303
 304
 305   ///////////////////////////////////////////////
 306   connect(actionSegmentation,SIGNAL(triggered()),this,SLOT(SegmentationOnCurrentImage()));
 307   connect(actionSurface_Viewer,SIGNAL(triggered()),this,SLOT(SurfaceViewerLaunch()));
 308   ///////////////////////////////////////////////
 309
 310   actionNorth_East_Window->setEnabled(0);
 311   actionNorth_West_Window->setEnabled(0);
 312   actionSouth_East_Window->setEnabled(0);
 313   actionSouth_West_Window->setEnabled(0);
 314
 315   connect(actionNorth_East_Window,SIGNAL(triggered()),this,SLOT(SaveNEScreenshot()));
 316   connect(actionNorth_West_Window,SIGNAL(triggered()),this,SLOT(SaveNOScreenshot()));
 317   connect(actionSouth_East_Window,SIGNAL(triggered()),this,SLOT(SaveSEScreenshot()));
 318   connect(actionSouth_West_Window,SIGNAL(triggered()),this,SLOT(SaveSOScreenshot()));
 319   connect(actionSave_all_slices,SIGNAL(triggered()),this,SLOT(SaveScreenshotAllSlices()));
 320
 321   connect(DataTree,SIGNAL(itemSelectionChanged()),this,SLOT(ImageInfoChanged()));
 322   connect(DataTree,SIGNAL(itemClicked(QTreeWidgetItem*, int)),this,
 323     SLOT(DisplayChanged(QTreeWidgetItem*, int)));
 324
 325   connect(viewButton,SIGNAL(clicked()),this, SLOT(ChangeViewMode()) );
 326   connect(windowSpinBox,SIGNAL(editingFinished()),this,SLOT(WindowLevelEdited()));
 327   connect(levelSpinBox,SIGNAL(editingFinished()),this,SLOT(WindowLevelEdited()));
 328   connect(colorMapComboBox,SIGNAL(currentIndexChanged(int)),this,SLOT(UpdateColorMap()));
 329   connect(presetComboBox,SIGNAL(currentIndexChanged(int)),this,SLOT(UpdateWindowLevel()));
 330   connect(slicingPresetComboBox, SIGNAL(currentIndexChanged(int)),this,SLOT(UpdateSlicingPreset()));
 331   connect(inverseButton,SIGNAL(clicked()),this,SLOT(SwitchWindowLevel()));
 332   connect(applyWindowLevelToAllButton,SIGNAL(clicked()),this,SLOT(ApplyWindowLevelToAllImages()));
 333
 334   connect(this,SIGNAL(customContextMenuRequested(QPoint)),this,SLOT(ShowContextMenu(QPoint)));
 335
 336   connect(linkPanel,SIGNAL(addLink(QString,QString,bool)),this,SLOT(AddLink(QString,QString,bool)));
 337   connect(linkPanel,SIGNAL(removeLink(QString,QString)),this,SLOT(RemoveLink(QString,QString)));
 338   connect(overlayPanel,SIGNAL(VFPropertyUpdated(int,int,int,int,double,double,double)),this,SLOT(SetVFProperty(int,int,int,int,double,double,double)));
 339   connect(overlayPanel,SIGNAL(OverlayPropertyUpdated(int,int,double,double)),
 340     this,SLOT(SetOverlayProperty(int,int,double,double)));
 341   connect(overlayPanel,SIGNAL(FusionPropertyUpdated(int,int,int,double,double, bool)),
 342     this,SLOT(SetFusionProperty(int,int,int,double,double, bool)));
 343   connect(landmarksPanel,SIGNAL(UpdateRenderWindows()),this,SLOT(UpdateRenderWindows()));
 344   connect(landmarksPanel,SIGNAL(SelectedPointChanged()),this,SLOT(GoToLandmark()));
 345
 346   connect(overlayPanel,SIGNAL(FusionSequencePropertyUpdated(int, bool, unsigned int, bool)),
 347     this,SLOT(SetFusionSequenceProperty(int, bool,unsigned int, bool)));
 348
 349
 350   playMode = 0;//pause
 351   mFrameRate = 10;
 352   playButton->setEnabled(0);
 353   frameRateLabel->setEnabled(0);
 354   frameRateSpinBox->setEnabled(0);
 355   connect(playButton, SIGNAL(clicked()),this,SLOT(PlayPause()));
 356   connect(frameRateSpinBox, SIGNAL(valueChanged(int)),this,SLOT(ChangeFrameRate(int)));
 357
 358   goToCursorPushButton->setEnabled(0);
 359   connect(goToCursorPushButton, SIGNAL(clicked()),this,SLOT(GoToCursor()));
 360
 361   NOViewWidget->hide();
 362   NEViewWidget->hide();
 363   SOViewWidget->hide();
 364   SEViewWidget->hide();
 365
 366   //Recently opened files
 367   std::list<std::string> recent_files = GetRecentlyOpenedImages();
 368   recentlyOpenedFilesMenu=NULL;
 369   if ( !recent_files.empty() ) {
 370     createRecentlyOpenedFilesMenu();
 371     updateRecentlyOpenedFilesMenu(recent_files);
 372   }
 373
 374   // Adding all new tools (insertion in the menu)
 375   vvToolManager::GetInstance()->InsertToolsInMenu(this);
 376   vvToolManager::GetInstance()->EnableToolsInMenu(this, false);
 377
 378   if (!CLITK_EXPERIMENTAL)
 379     menuExperimental->menuAction()->setVisible(false);
 380
 381
 382   QTimer * timerMemory = new QTimer(this);
 383   //timerMemory->setInterval(5);
 384   connect(timerMemory, SIGNAL(timeout()), this, SLOT(UpdateMemoryUsage()));
 385   timerMemory->start(2000);
 386
 387 }
 388 //------------------------------------------------------------------------------
 389 void vvMainWindow::show()
 390 {
 391   vvMainWindowBase::show();
 392   PopupRegisterForm(true);
 393 }
 394 //------------------------------------------------------------------------------
 395 void vvMainWindow::UpdateMemoryUsage()
 396 {
 397   //  clitk::PrintMemory(true);
 398   if (clitk::GetMemoryUsageInMb() == 0) infoPanel->setMemoryInMb("NA");
 399   else infoPanel->setMemoryInMb(QString::number(clitk::GetMemoryUsageInMb())+" MiB");
 400 }
 401 //------------------------------------------------------------------------------
 402
 403
 404 //------------------------------------------------------------------------------
 405 void vvMainWindow::createRecentlyOpenedFilesMenu()
 406 {
 407   recentlyOpenedFilesMenu = new QMenu("Recently opened files...");
 408   recentlyOpenedFilesMenu->setIcon(QIcon(QString::fromUtf8(":/common/icons/open.png")));
 409   menuFile->insertMenu(actionOpen_Image_With_Time,recentlyOpenedFilesMenu);
 410   menuFile->insertSeparator(actionOpen_Image_With_Time);
 411 }
 412 //------------------------------------------------------------------------------
 413
 414
 415 //------------------------------------------------------------------------------
 416
 417 void vvMainWindow::updateRecentlyOpenedFilesMenu(const std::list<std::string> &recent_files)
 418 {
 419   if(recentlyOpenedFilesMenu==NULL) {
 420     createRecentlyOpenedFilesMenu();
 421   } else {
 422     recentlyOpenedFilesMenu->clear();
 423   }
 424   for (std::list<std::string>::const_iterator i = recent_files.begin(); i!=recent_files.end(); i++) {
 425     QAction* current=new QAction(QIcon(QString::fromUtf8(":/common/icons/open.png")), i->c_str(),this);
 426     recentlyOpenedFilesMenu->addAction(current);
 427     connect(current,SIGNAL(triggered()),this,SLOT(OpenRecentImage()));
 428   }
 429 }
 430 //------------------------------------------------------------------------------
 431
 432
 433 //------------------------------------------------------------------------------
 434 void vvMainWindow::ComputeMidPosition()
 435 {
 436   bool ok;
 437   int index=GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
 438   int ref = QInputDialog::getInt(this,"Chose reference phase","Reference phase",0,0,\
 439 mSlicerManagers[index]->GetImage()->GetVTKImages().size()-1,1,&ok);
 440   if (ok) {
 441     vvMidPosition midp;
 442     midp.slicer_manager = mSlicerManagers[index];
 443     midp.reference_image_index = ref;
 444     QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
 445     midp.Update();
 446     if (midp.error)
 447       QMessageBox::warning(this, "Error computing midposition image",midp.error_message.c_str());
 448     else {
 449       QFileInfo info(midp.slicer_manager->GetFileName().c_str());
 450       AddImage(midp.output,info.path().toStdString()+"/"+info.completeBaseName().toStdString()+"_midposition.mhd");
 451     }
 452     QApplication::restoreOverrideCursor();
 453   }
 454 }
 455 //------------------------------------------------------------------------------
 456
 457
 458 //------------------------------------------------------------------------------
 459 void vvMainWindow::AddContour(int image_index, vvMesh::Pointer contour, bool propagation)
 460 {
 461   QTreeWidgetItem *item = new QTreeWidgetItem();
 462   item->setData(0,Qt::UserRole,"filename.vtk");
 463   item->setData(1,Qt::UserRole,tr("contour"));
 464   QBrush brush;
 465   brush.setColor(QColor(contour->r*255,contour->g*255,contour->b*255));
 466   brush.setStyle(Qt::SolidPattern);
 467   item->setData(COLUMN_IMAGE_NAME,Qt::BackgroundRole,brush);
 468   //  item->setData(COLUMN_IMAGE_NAME,Qt::DisplayRole,contour->structure_name.c_str());
 469
 470   for (int j = 1; j <= 4; j++)
 471     item->setData(j,Qt::CheckStateRole,DataTree->topLevelItem(image_index)->data(j,Qt::CheckStateRole));
 472
 473   QTreePushButton* cButton = new QTreePushButton;
 474   cButton->setItem(item);
 475   cButton->setColumn(COLUMN_CLOSE_IMAGE);
 476   cButton->setToolTip(tr("close image"));
 477   cButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/exit.png")));
 478   connect(cButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
 479     this,SLOT(CloseImage(QTreeWidgetItem*, int)));
 480
 481   QTreePushButton* rButton = new QTreePushButton;
 482   rButton->setItem(item);
 483   rButton->setColumn(COLUMN_RELOAD_IMAGE);
 484   rButton->setToolTip(tr("reload image"));
 485   rButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/rotateright.png")));
 486   rButton->setEnabled(false);
 487   //Not implemented
 488   //connect(rButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
 489   //this,SLOT(ReloadImage(QTreeWidgetItem*, int)));
 490
 491   DataTree->topLevelItem(image_index)->setExpanded(1);
 492   DataTree->topLevelItem(image_index)->addChild(item);
 493   DataTree->setItemWidget(item, COLUMN_CLOSE_IMAGE, cButton);
 494   DataTree->setItemWidget(item, COLUMN_RELOAD_IMAGE, rButton);
 495   QString id = DataTree->topLevelItem(image_index)->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString();
 496   item->setData(COLUMN_IMAGE_NAME,Qt::UserRole,id.toStdString().c_str());
 497
 498   UpdateTree();
 499   mSlicerManagers[image_index]->AddContour(contour,propagation);
 500   mSlicerManagers[image_index]->Render();
 501 }
 502 //------------------------------------------------------------------------------
 503
 504
 505 //------------------------------------------------------------------------------
 506 void vvMainWindow::OpenVTKContour()
 507 {
 508   if (mSlicerManagers.size() > 0) {
 509     QString Extensions = "Images ( *.vtk *.obj)";
 510     Extensions += ";;All Files (*)";
 511     QString file = QFileDialog::getOpenFileName(this,tr("Open vtkPolyData"),mInputPathName,Extensions);
 512     if (file.isNull())
 513       return;
 514     QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
 515     int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
 516     vvMeshReader reader;
 517     reader.SetImage(mSlicerManagers[index]->GetImage());
 518     reader.SetModeToVTK();
 519     reader.SetFilename(file.toStdString());
 520     reader.Update();
 521     AddContour(index,reader.GetOutput()[0],false);
 522     QApplication::restoreOverrideCursor();
 523   }
 524 }
 525 //------------------------------------------------------------------------------
 526
 527
 528 //------------------------------------------------------------------------------
 529 void vvMainWindow::AddDCStructContour(int index, QString file)
 530 {
 531   vvMeshReader reader;
 532   reader.SetFilename(file.toStdString());
 533   vvStructSelector selector;
 534   selector.SetStructures(reader.GetROINames());
 535   if (!mSlicerManagers[index]->GetVF().IsNull())
 536     selector.EnablePropagationCheckBox();
 537   if (selector.exec()) {
 538     QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
 539     reader.SetSelectedItems(selector.getSelectedItems());
 540     reader.SetImage(mSlicerManagers[index]->GetImage());
 541     if (selector.PropagationEnabled())
 542       reader.SetPropagationVF(mSlicerManagers[index]->GetVF());
 543     reader.Update();
 544     std::vector<vvMesh::Pointer> contours=reader.GetOutput();
 545     for (std::vector<vvMesh::Pointer>::iterator i=contours.begin();
 546       i!=contours.end(); i++)
 547       AddContour(index,*i,selector.PropagationEnabled());
 548     QApplication::restoreOverrideCursor();
 549   }
 550 }
 551
 552 //------------------------------------------------------------------------------
 553 void vvMainWindow::OpenDCStructContour()
 554 {
 555   if (mSlicerManagers.size() > 0) {
 556     QString Extensions = "Dicom Files ( *.dcm RS*)";
 557     Extensions += ";;All Files (*)";
 558     QString file = QFileDialog::getOpenFileName(this,tr("Merge Images"),mInputPathName,Extensions);
 559     if (file.isNull())
 560       return;
 561     int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
 562     AddDCStructContour(index, file);
 563   }
 564 }
 565 //------------------------------------------------------------------------------
 566
 567
 568 //------------------------------------------------------------------------------
 569 void vvMainWindow::ComputeDeformableRegistration()
 570 {
 571   if (mSlicerManagers.size() > 0) {
 572     int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
 573     vvDeformationDialog dialog(index,mSlicerManagers);
 574     if (dialog.exec()) {
 575       std::string base_name=itksys::SystemTools::GetFilenameWithoutExtension(mSlicerManagers[dialog.GetInputFileIndex()]->GetFileName());
 576       AddField(dialog.GetOutput(),dialog.getFieldFile(),dialog.GetInputFileIndex());
 577       WarpImage(dialog.GetSelectedSlicer(),dialog.GetReferenceFrameIndex());
 578     } else
 579       std::cout << "Error or user cancellation while computing deformation field..." << std::endl;
 580   } else QMessageBox::information(this, "Need to open image","You must open an image first.");
 581 }
 582 //------------------------------------------------------------------------------
 583
 584
 585 //------------------------------------------------------------------------------
 586 void vvMainWindow::WarpImage()
 587 {
 588   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
 589   if (!mSlicerManagers[index]->GetVF().IsNull()) {
 590     bool ok;
 591     int ref = QInputDialog::getInt(this,"Chose reference phase","Reference phase",0,0,\
 592       mSlicerManagers[index]->GetImage()->GetVTKImages().size()-1,1,&ok);
 593     if (ok) {
 594       WarpImage(mSlicerManagers[index],ref);
 595     }
 596   } else
 597     QMessageBox::warning(this,tr("No vector field"),tr("Sorry, can't warp without a vector field"));
 598 }
 599 //------------------------------------------------------------------------------
 600
 601
 602 //------------------------------------------------------------------------------
 603 void vvMainWindow::WarpImage(vvSlicerManager* selected_slicer,int reference_phase)
 604 {
 605   if (!selected_slicer->GetVF().IsNull()) {
 606     QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
 607     QFileInfo info(selected_slicer->GetFileName().c_str());
 608     vvImageWarp warp(selected_slicer->GetImage(),selected_slicer->GetVF(),
 609       reference_phase,this);
 610     if (warp.ComputeWarpedImage()) {
 611       AddImage(warp.GetWarpedImage(),info.path().toStdString()+"/"+info.completeBaseName().toStdString()+"_warped.mhd");
 612       AddImage(warp.GetDiffImage()  ,info.path().toStdString()+"/"+info.completeBaseName().toStdString()+"_diff.mhd");
 613       AddImage(warp.GetJacobianImage()  ,info.path().toStdString()+"/"+info.completeBaseName().toStdString()+"_jacobian.mhd");
 614       QApplication::restoreOverrideCursor();
 615     } else {
 616       QApplication::restoreOverrideCursor();
 617       QMessageBox::warning(this,tr("Different spacings"),tr("The vector field and image spacings must be the same in order to warp."));
 618     }
 619   } else
 620     QMessageBox::warning(this,tr("No vector field"),tr("Sorry, can't warp without a vector field."));
 621 }
 622 //------------------------------------------------------------------------------
 623
 624
 625 //------------------------------------------------------------------------------
 626 vvMainWindow::~vvMainWindow()
 627 {
 628   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
 629     if (mSlicerManagers[i] != NULL)
 630       delete mSlicerManagers[i];
 631   }
 632 }
 633 //------------------------------------------------------------------------------
 634
 635 //------------------------------------------------------------------------------
 636 QTabWidget * vvMainWindow::GetTab()
 637 {
 638   return tabWidget;
 639 }
 640 //------------------------------------------------------------------------------
 641
 642
 643 //------------------------------------------------------------------------------
 644 void vvMainWindow::MergeImages()
 645 {
 646   QString Extensions = EXTENSIONS;
 647   Extensions += ";;All Files (*)";
 648   QStringList files = QFileDialog::getOpenFileNames(this,tr("Merge Images"),mInputPathName,Extensions);
 649   if (files.isEmpty())
 650     return;
 651   mInputPathName = itksys::SystemTools::GetFilenamePath(files[0].toStdString()).c_str();
 652   std::vector<std::string> vector;
 653
 654   unsigned int currentDim = 0;
 655   std::vector<double> currentSpacing;
 656   std::vector<int> currentSize;
 657   std::vector<double> currentOrigin;
 658
 659   for (int i = 0; i < files.size(); i++) {
 660     itk::ImageIOBase::Pointer reader = itk::ImageIOFactory::CreateImageIO(
 661       files[i].toStdString().c_str(), itk::ImageIOFactory::ReadMode);
 662     reader->SetFileName(files[i].toStdString().c_str());
 663     reader->ReadImageInformation();
 664     if (reader)        {
 665       //NOViewWidget->hide();
 666       //NEViewWidget->hide();
 667       //SOViewWidget->hide();
 668       //SEViewWidget->hide();
 669       if (i == 0)
 670         currentDim = reader->GetNumberOfDimensions();
 671       bool IsOk = true;
 672       for (unsigned int j = 0; j < currentDim; j++) {
 673         if (i == 0) {
 674           if (j == 0) {
 675             currentSpacing.resize(currentDim);
 676             currentSize.resize(currentDim);
 677             currentOrigin.resize(currentDim);
 678           }
 679           currentOrigin[j] = reader->GetOrigin(j);
 680           currentSpacing[j] = reader->GetSpacing(j);
 681           currentSize[j] = reader->GetDimensions(j);
 682         } else if (currentDim != reader->GetNumberOfDimensions()
 683           || currentSpacing[j] != reader->GetSpacing(j)
 684           || currentSize[j] != (int)reader->GetDimensions(j)
 685           || currentOrigin[j] != reader->GetOrigin(j)) {
 686             QString error = "Cannot read file (too different from others ";
 687             error += files[i].toStdString().c_str();
 688             QMessageBox::information(this,tr("Reading problem"),error);
 689             IsOk = false;
 690             break;
 691         }
 692       }
 693       if (IsOk)
 694         vector.push_back(files[i].toStdString());
 695     }
 696   }
 697   if (vector.size() > 0)
 698     LoadImages(vector, vvImageReader::MERGED);
 699 }
 700 //------------------------------------------------------------------------------
 701
 702 //------------------------------------------------------------------------------
 703 void vvMainWindow::SliceImages()
 704 {
 705   QString Extensions = EXTENSIONS;
 706   Extensions += ";;All Files (*)";
 707
 708   QStringList files = QFileDialog::getOpenFileNames(this,tr("Slice Images"),mInputPathName,Extensions);
 709   if (files.isEmpty())
 710     return;
 711   mInputPathName = itksys::SystemTools::GetFilenamePath(files[0].toStdString()).c_str();
 712   std::vector<std::string> vector;
 713   for (int i = 0; i < files.size(); i++)
 714     vector.push_back(files[i].toStdString());
 715   LoadImages(vector, vvImageReader::SLICED);
 716 }
 717 //------------------------------------------------------------------------------
 718
 719 //------------------------------------------------------------------------------
 720 void vvMainWindow::MergeImagesWithTime()
 721 {
 722   QString Extensions = EXTENSIONS;
 723   Extensions += ";;All Files (*)";
 724   QStringList files = QFileDialog::getOpenFileNames(this,tr("Merge Images With Time"),mInputPathName,Extensions);
 725   if (files.isEmpty())
 726     return;
 727   mInputPathName = itksys::SystemTools::GetFilenamePath(files[0].toStdString()).c_str();
 728   std::vector<std::string> vector;
 729
 730   for (int i = 0; i < files.size(); i++)
 731     vector.push_back(files[i].toStdString());
 732   sort(vector.begin(),vector.end());
 733   if (vector.size() > 1)
 734     LoadImages(vector, vvImageReader::MERGEDWITHTIME);
 735   else
 736     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.");
 737 }
 738 //------------------------------------------------------------------------------
 739
 740
 741 //------------------------------------------------------------------------------
 742 void vvMainWindow::OpenDicom()
 743 {
 744   std::vector<std::string> files;
 745
 746   //std::cout << "dicomSeriesSelector " << std::endl;
 747   if (dicomSeriesSelector->exec() == QDialog::Accepted) {
 748     files = *(dicomSeriesSelector->GetFilenames());
 749     LoadImages(files, vvImageReader::DICOM);
 750   }
 751 }
 752 //------------------------------------------------------------------------------
 753
 754 //------------------------------------------------------------------------------
 755 void vvMainWindow::OpenImages()
 756 {
 757   QString Extensions = EXTENSIONS;
 758   Extensions += ";;All Files (*)";
 759
 760   QStringList files = QFileDialog::getOpenFileNames(this,tr("Load Images"),mInputPathName,Extensions);
 761   if (files.isEmpty())
 762     return;
 763   mInputPathName = itksys::SystemTools::GetFilenamePath(files[0].toStdString()).c_str();
 764   std::vector<std::string> vector;
 765   for (int i = 0; i < files.size(); i++)
 766     vector.push_back(files[i].toStdString());
 767   LoadImages(vector, vvImageReader::IMAGE);
 768 }
 769 //------------------------------------------------------------------------------
 770 void vvMainWindow::OpenRecentImage()
 771 {
 772   QAction * caller = qobject_cast<QAction*>(sender());
 773   std::vector<std::string> images;
 774   images.push_back(caller->text().toStdString());
 775   mInputPathName = itksys::SystemTools::GetFilenamePath(images[0]).c_str();
 776   LoadImages(images, vvImageReader::IMAGE);
 777 }
 778 //------------------------------------------------------------------------------
 779
 780
 781 //------------------------------------------------------------------------------
 782 void vvMainWindow::OpenImageWithTime()
 783 {
 784   QString Extensions = EXTENSIONS;
 785   Extensions += ";;All Files (*)";
 786
 787   QStringList files = QFileDialog::getOpenFileNames(this,tr("Load Images With Time"),mInputPathName,Extensions);
 788   if (files.isEmpty())
 789     return;
 790   mInputPathName = itksys::SystemTools::GetFilenamePath(files[0].toStdString()).c_str();
 791   std::vector<std::string> vector;
 792   for (int i = 0; i < files.size(); i++) {
 793     vector.push_back(files[i].toStdString());
 794   }
 795   LoadImages(vector, vvImageReader::IMAGEWITHTIME);
 796 }
 797 //------------------------------------------------------------------------------
 798
 799
 800 //------------------------------------------------------------------------------
 801 void vvMainWindow::LoadImages(std::vector<std::string> files, vvImageReader::LoadedImageType filetype)
 802 {
 803   //Separate the way to open images and dicoms
 804   int fileSize;
 805   if (filetype == vvImageReader::IMAGE || filetype == vvImageReader::IMAGEWITHTIME)
 806     fileSize = files.size();
 807   else
 808     fileSize = 1;
 809
 810   // For SLICED, we need the number of slices (ndim and #slices)
 811   std::vector<unsigned int> nSlices;
 812   nSlices.resize(files.size());
 813   std::fill(nSlices.begin(), nSlices.end(), 1);
 814   if (filetype == vvImageReader::SLICED) {
 815     for (int i = 0; i < fileSize; i++) {
 816       itk::ImageIOBase::Pointer header = clitk::readImageHeader(files[i]);
 817       QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
 818       if (!header) {
 819         nSlices[i] = 0;
 820         QString error = "Cannot open file \n";
 821         error += files[i].c_str();
 822         QMessageBox::information(this,tr("Reading problem"),error);
 823         return;
 824       }
 825       if (header->GetNumberOfDimensions() < 3) {
 826         nSlices[i] = 0;
 827         QString error = "Dimension problem. Cannot slice \n";
 828         error += files[i].c_str();
 829         QMessageBox::information(this,tr("Reading problem"),error);
 830         return;
 831       }
 832       nSlices[i] = header->GetDimensions( header->GetNumberOfDimensions()-1 );
 833     }
 834   }
 835
 836   //Only add to the list of recently opened files when a single file is opened,
 837   //to avoid polluting the list of recently opened files
 838   if (files.size() == 1) {
 839     QFileInfo finfo=tr(files[0].c_str());
 840     AddToRecentlyOpenedImages(finfo.absoluteFilePath().toStdString());
 841     updateRecentlyOpenedFilesMenu(GetRecentlyOpenedImages());
 842   }
 843   //init the progress events
 844   QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
 845   vvProgressDialog progress("Opening " + files[0],fileSize>1);
 846   qApp->processEvents();
 847
 848   int numberofsuccesulreads=0;
 849   //open images as 1 or multiples
 850   for (int i = 0; i < fileSize; i++) {
 851     progress.SetText("Opening " + files[i]);
 852     progress.SetProgress(i,fileSize);
 853     qApp->processEvents();
 854
 855     for (unsigned int j = 0; j < nSlices[i]; j++) {
 856       //read the image and put it in mSlicerManagers
 857       vvSlicerManager* imageManager = new vvSlicerManager(4);
 858       qApp->processEvents();
 859
 860       bool SetImageSucceed=false;
 861
 862       // Change filename if an image with the same already exist
 863       int number = GetImageDuplicateFilenameNumber(files[i] + std::string("_slice"));
 864
 865       if (filetype == vvImageReader::IMAGE || filetype == vvImageReader::IMAGEWITHTIME || filetype == vvImageReader::SLICED) {
 866         SetImageSucceed = imageManager->SetImage(files[i],filetype, number, j);
 867       } else {
 868         SetImageSucceed = imageManager->SetImages(files,filetype, number);
 869       }
 870       if (!SetImageSucceed) {;
 871         QApplication::restoreOverrideCursor();
 872         QString error = "Cannot open file \n";
 873         error += imageManager->GetLastError().c_str();
 874         QMessageBox::information(this,tr("Reading problem"),error);
 875         delete imageManager;
 876       } else {
 877
 878         mSlicerManagers.push_back(imageManager);
 879
 880         //create an item in the tree with good settings
 881         QTreeWidgetItem *item = new QTreeWidgetItem();
 882         item->setData(0,Qt::UserRole,files[i].c_str());
 883         QFileInfo fileinfo(imageManager->GetFileName().c_str()); //Do not show the path
 884         item->setData(COLUMN_IMAGE_NAME,Qt::DisplayRole,fileinfo.fileName());
 885         item->setData(1,Qt::UserRole,tr("image"));
 886         item->setToolTip(COLUMN_IMAGE_NAME, imageManager->GetListOfAbsoluteFilePathInOneString("image").c_str());
 887         qApp->processEvents();
 888
 889         //Create the buttons for reload and close
 890         qApp->processEvents();
 891         QTreePushButton* cButton = new QTreePushButton;
 892         cButton->setItem(item);
 893         cButton->setColumn(COLUMN_CLOSE_IMAGE);
 894         cButton->setToolTip(tr("close image"));
 895         cButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/exit.png")));
 896         connect(cButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
 897           this,SLOT(CloseImage(QTreeWidgetItem*, int)));
 898
 899         QTreePushButton* rButton = new QTreePushButton;
 900         rButton->setItem(item);
 901         rButton->setColumn(COLUMN_RELOAD_IMAGE);
 902         rButton->setToolTip(tr("reload image"));
 903         rButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/rotateright.png")));
 904         connect(rButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
 905           this,SLOT(ReloadImage(QTreeWidgetItem*, int)));
 906
 907         DataTree->addTopLevelItem(item);
 908         DataTree->setItemWidget(item, COLUMN_CLOSE_IMAGE, cButton);
 909         DataTree->setItemWidget(item, COLUMN_RELOAD_IMAGE, rButton);
 910
 911         //set the id of the image
 912         QString id = QDir::current().absoluteFilePath(files[i].c_str()) + QString::number(mSlicerManagers.size()-1);
 913         item->setData(COLUMN_IMAGE_NAME,Qt::UserRole,id.toStdString().c_str());
 914         mSlicerManagers.back()->SetId(id.toStdString());
 915
 916         linkPanel->addImage(imageManager->GetFileName(), id.toStdString());
 917
 918         connect(mSlicerManagers.back(), SIGNAL(currentImageChanged(std::string)),
 919           this,SLOT(CurrentImageChanged(std::string)));
 920         connect(mSlicerManagers.back(), SIGNAL(currentPickedImageChanged(std::string)),
 921           this, SLOT(CurrentPickedImageChanged(std::string)));
 922         connect(mSlicerManagers.back(), SIGNAL(UpdatePosition(int, double, double, double, double, double, double, double)),
 923           this,SLOT(MousePositionChanged(int,double, double, double, double, double, double, double)));
 924         connect(mSlicerManagers.back(), SIGNAL(UpdateVector(int, double, double, double, double)),
 925           this, SLOT(VectorChanged(int,double,double,double, double)));
 926         connect(mSlicerManagers.back(), SIGNAL(UpdateOverlay(int, double, double)),
 927           this, SLOT(OverlayChanged(int,double,double)));
 928         connect(mSlicerManagers.back(), SIGNAL(UpdateFusion(int, double)),
 929           this, SLOT(FusionChanged(int,double)));
 930         connect(mSlicerManagers.back(), SIGNAL(WindowLevelChanged()),
 931           this,SLOT(WindowLevelChanged()));
 932         connect(mSlicerManagers.back(), SIGNAL(UpdateSlice(int,int)),
 933           this,SLOT(UpdateSlice(int,int)));
 934         connect(mSlicerManagers.back(), SIGNAL(UpdateTSlice(int, int, int)),
 935           this,SLOT(UpdateTSlice(int, int, int)));
 936         connect(mSlicerManagers.back(), SIGNAL(UpdateTSlice(int, int, int)),
 937           this,SLOT(ImageInfoChanged()));
 938         connect(mSlicerManagers.back(), SIGNAL(UpdateSliceRange(int,int,int,int,int)),
 939           this,SLOT(UpdateSliceRange(int,int,int,int,int)));
 940         connect(mSlicerManagers.back(), SIGNAL(UpdateLinkManager(std::string,int,double,double,double,int)),
 941           this,SLOT(UpdateLinkManager(std::string,int,double,double,double,int)));
 942         connect(mSlicerManagers.back(), SIGNAL(UpdateLinkedNavigation(std::string,vvSlicerManager*,vvSlicer*)),
 943           this,SLOT(UpdateLinkedNavigation(std::string,vvSlicerManager*,vvSlicer*)));
 944         connect(mSlicerManagers.back(), SIGNAL(ChangeImageWithIndexOffset(vvSlicerManager*,int,int)),
 945           this,SLOT(ChangeImageWithIndexOffset(vvSlicerManager*,int,int)));
 946         connect(mSlicerManagers.back(),SIGNAL(LandmarkAdded()),landmarksPanel,SLOT(AddPoint()));
 947         InitSlicers();
 948         numberofsuccesulreads++;
 949       }
 950     }
 951   }
 952
 953   if (numberofsuccesulreads) {
 954     NOViewWidget->show();
 955     NEViewWidget->show();
 956     SOViewWidget->show();
 957     SEViewWidget->show();
 958     UpdateTree();
 959     InitDisplay();
 960     ShowLastImage();
 961
 962     // Try to guess default WindowLevel
 963     double range[2];
 964     mSlicerManagers.back()->GetImage()->GetFirstVTKImageData()->GetScalarRange(range);
 965     if ((range[0] == 0) && (range[1] == 1)) {
 966       presetComboBox->setCurrentIndex(WL_BINARY);// binary
 967     } else {
 968       // TODO
 969     }
 970   }
 971   QApplication::restoreOverrideCursor();
 972 }
 973 //------------------------------------------------------------------------------
 974
 975 //------------------------------------------------------------------------------
 976 void vvMainWindow::UpdateTree()
 977 {
 978   DataTree->resizeColumnToContents(COLUMN_TREE);
 979   DataTree->resizeColumnToContents(COLUMN_UL_VIEW);
 980   DataTree->resizeColumnToContents(COLUMN_UR_VIEW);
 981   DataTree->resizeColumnToContents(COLUMN_DL_VIEW);
 982   DataTree->resizeColumnToContents(COLUMN_DR_VIEW);
 983   DataTree->resizeColumnToContents(COLUMN_IMAGE_NAME);
 984   DataTree->resizeColumnToContents(COLUMN_CLOSE_IMAGE);
 985   DataTree->resizeColumnToContents(COLUMN_RELOAD_IMAGE);
 986 }
 987 //------------------------------------------------------------------------------
 988
 989 //------------------------------------------------------------------------------
 990 void vvMainWindow::CurrentImageChanged(std::string id)
 991 {
 992   if (id == mCurrentSelectedImageId) return; // Do nothing
 993   int selected = 0;
 994   for (int i = 0; i < DataTree->topLevelItemCount(); i++) {
 995     if (DataTree->topLevelItem(i)->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString().toStdString() == id) {
 996       selected = i;
 997     } else {
 998       DataTree->topLevelItem(i)->setSelected(0);
 999     }
1000     for (int child = 0; child < DataTree->topLevelItem(i)->childCount(); child++)
1001       DataTree->topLevelItem(i)->child(child)->setSelected(0);
1002
1003   }
1004   DataTree->topLevelItem(selected)->setSelected(1);
1005   mCurrentSelectedImageId = id;
1006
1007   landmarksPanel->SetCurrentLandmarks(mSlicerManagers[selected]->GetLandmarks(),
1008                                       mSlicerManagers[selected]->GetTSlice());
1009   landmarksPanel->SetCurrentPath(mInputPathName.toStdString());
1010   landmarksPanel->SetCurrentImage(mSlicerManagers[selected]->GetFileName().c_str());
1011
1012   emit SelectedImageHasChanged(mSlicerManagers[selected]);
1013 }
1014 //------------------------------------------------------------------------------
1015
1016 //------------------------------------------------------------------------------
1017 void vvMainWindow::CurrentPickedImageChanged(std::string id)
1018 {
1019   if (id == mCurrentPickedImageId) return; // Do nothing
1020   int selected = 0;
1021   for (int i = 0; i < DataTree->topLevelItemCount(); i++) {
1022     if (DataTree->topLevelItem(i)->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString().toStdString() == id) {
1023       selected = i;
1024     } else {
1025       DataTree->topLevelItem(i)->setSelected(0);
1026     }
1027     for (int child = 0; child < DataTree->topLevelItem(i)->childCount(); child++)
1028       DataTree->topLevelItem(i)->child(child)->setSelected(0);
1029
1030   }
1031   DataTree->topLevelItem(selected)->setSelected(1);
1032   mCurrentPickedImageId = id;
1033   mCurrentPickedImageIndex = selected;
1034 }
1035 //------------------------------------------------------------------------------
1036
1037 //------------------------------------------------------------------------------
1038 void vvMainWindow::ImageInfoChanged()
1039 {
1040   contextActions[6]->setEnabled(1);
1041   contextActions[5]->setEnabled(1);
1042   actionSave_As->setEnabled(1);
1043   actionAdd_VF_to_current_Image->setEnabled(1);
1044   actionAdd_fusion_image->setEnabled(1);
1045   actionAdd_overlay_image_to_current_image->setEnabled(1);
1046   actionAdd_USSequence_toCT->setEnabled(1);
1047   actionNorth_East_Window->setEnabled(1);
1048   actionNorth_West_Window->setEnabled(1);
1049   actionSouth_East_Window->setEnabled(1);
1050   actionSouth_West_Window->setEnabled(1);
1051   vvToolManager::GetInstance()->EnableToolsInMenu(this, true);
1052   inverseButton->setEnabled(1);
1053
1054   goToCursorPushButton->setEnabled(1);
1055
1056   if (DataTree->selectedItems().size()) {
1057     int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1058
1059     colorMapComboBox->setEnabled(1);
1060     for (int i = 0; i < DataTree->topLevelItem(index)->childCount(); i++) {
1061       if (DataTree->topLevelItem(index)->child(i)->data(1,Qt::UserRole).toString() == "overlay" ||
1062         DataTree->topLevelItem(index)->child(i)->data(1,Qt::UserRole).toString() == "fusion" ||
1063         DataTree->topLevelItem(index)->child(i)->data(1,Qt::UserRole).toString() == "fusionSequence") {
1064           colorMapComboBox->setEnabled(0);
1065           break;
1066       }
1067     }
1068
1069     std::vector<double> origin;
1070     std::vector<double> inputSpacing;
1071     std::vector<int> inputSize;
1072     std::vector<double> sizeMM;
1073     vtkSmartPointer<vtkMatrix4x4> transformation;
1074     int dimension=0;
1075     QString pixelType;
1076     QString inputSizeInBytes;
1077     QString image = DataTree->selectedItems()[0]->data(COLUMN_IMAGE_NAME,Qt::DisplayRole).toString();
1078
1079     int nframes = mSlicerManagers[index]->GetSlicer(0)->GetTMax();
1080
1081     if (nframes > 1 || playMode == 1) {
1082       playButton->setEnabled(1);
1083       frameRateLabel->setEnabled(1);
1084       frameRateSpinBox->setEnabled(1);
1085     } else {
1086       playButton->setEnabled(0);
1087       frameRateLabel->setEnabled(0);
1088       frameRateSpinBox->setEnabled(0);
1089     }
1090
1091     //read image header
1092     int NPixel = 1;
1093
1094     int tSlice = 0;
1095     vvImage::Pointer imageSelected;
1096     if (DataTree->topLevelItem(index) == DataTree->selectedItems()[0]) {
1097       imageSelected = mSlicerManagers[index]->GetSlicer(0)->GetImage();
1098       tSlice = mSlicerManagers[index]->GetSlicer(0)->GetTSlice();
1099     } else if (DataTree->selectedItems()[0]->data(1,Qt::UserRole).toString() == "vector") {
1100       imageSelected = mSlicerManagers[index]->GetSlicer(0)->GetVF();
1101       tSlice = mSlicerManagers[index]->GetSlicer(0)->GetOverlayTSlice();
1102     } else if (DataTree->selectedItems()[0]->data(1,Qt::UserRole).toString() == "overlay") {
1103       imageSelected = mSlicerManagers[index]->GetSlicer(0)->GetOverlay();
1104       tSlice = mSlicerManagers[index]->GetSlicer(0)->GetOverlayTSlice();
1105     } else if (DataTree->selectedItems()[0]->data(1,Qt::UserRole).toString() == "fusion") {
1106       imageSelected = mSlicerManagers[index]->GetSlicer(0)->GetFusion();
1107       tSlice = mSlicerManagers[index]->GetSlicer(0)->GetFusionTSlice();
1108     }
1109     else if (DataTree->selectedItems()[0]->data(1,Qt::UserRole).toString() == "fusionSequence") {
1110       imageSelected = mSlicerManagers[index]->GetSlicer(0)->GetFusion();
1111       tSlice = mSlicerManagers[index]->GetSlicer(0)->GetFusionTSlice();
1112     }
1113     else if (DataTree->selectedItems()[0]->data(1,Qt::UserRole).toString() == "contour") {
1114       imageSelected = mSlicerManagers[index]->GetSlicer(0)->GetImage();
1115       tSlice = mSlicerManagers[index]->GetSlicer(0)->GetTSlice();
1116     }
1117     else {
1118       imageSelected = mSlicerManagers[index]->GetSlicer(0)->GetImage();
1119       tSlice = mSlicerManagers[index]->GetSlicer(0)->GetTSlice();
1120     }
1121
1122     dimension = imageSelected->GetNumberOfDimensions();
1123     origin.resize(dimension);
1124     inputSpacing.resize(dimension);
1125     inputSize.resize(dimension);
1126     sizeMM.resize(dimension);
1127     pixelType = mSlicerManagers[index]->GetImage()->GetScalarTypeAsITKString().c_str();
1128     for (int i = 0; i < dimension; i++) {
1129       origin[i] = imageSelected->GetOrigin()[i];
1130       inputSpacing[i] = imageSelected->GetSpacing()[i];
1131       inputSize[i] = imageSelected->GetSize()[i];
1132       sizeMM[i] = inputSize[i]*inputSpacing[i];
1133       NPixel *= inputSize[i];
1134     }
1135     inputSizeInBytes = GetSizeInBytes(imageSelected->GetActualMemorySize()*1000);
1136
1137     QString dim = QString::number(dimension) + " (";
1138     dim += pixelType + ")";
1139
1140     infoPanel->setFileName(image);
1141     std::string creationImageTimeValue("No creation time");
1142     itk::ExposeMetaData< std::string > (*imageSelected->GetFirstMetaDataDictionary(), "creationImageTime", creationImageTimeValue);
1143     infoPanel->setImageCreationTime(QString(creationImageTimeValue.c_str()));
1144     infoPanel->setDimension(dim);
1145     infoPanel->setSizePixel(GetVectorIntAsString(inputSize));
1146     infoPanel->setSizeMM(GetVectorDoubleAsString(sizeMM));
1147     infoPanel->setOrigin(GetVectorDoubleAsString(origin));
1148     infoPanel->setSpacing(GetVectorDoubleAsString(inputSpacing));
1149     infoPanel->setNPixel(QString::number(NPixel)+" ("+inputSizeInBytes+")");
1150
1151     transformation = imageSelected->GetTransform()[tSlice]->GetMatrix();
1152     infoPanel->setTransformation(clitk::Get4x4MatrixDoubleAsString(transformation).c_str());
1153
1154     landmarksPanel->SetCurrentLandmarks(mSlicerManagers[index]->GetLandmarks(),
1155                                         mSlicerManagers[index]->GetTSlice());
1156     landmarksPanel->SetCurrentPath(mInputPathName.toStdString());
1157     landmarksPanel->SetCurrentImage(mSlicerManagers[index]->GetFileName().c_str());
1158
1159     overlayPanel->getCurrentImageName(mSlicerManagers[index]->GetFileName().c_str());
1160     for (int i = 0; i < 4; i++) {
1161       if (DataTree->selectedItems()[0]->data(i+1,Qt::CheckStateRole).toInt() > 0 || i == 3) {
1162         mSlicerManagers[index]->UpdateInfoOnCursorPosition(i);
1163         break;
1164       }
1165     }
1166
1167 //     infoPanel->setFileName(image);
1168 //     infoPanel->setDimension(dim);
1169 //     infoPanel->setSizePixel(GetVectorIntAsString(inputSize));
1170 //     infoPanel->setSizeMM(GetVectorDoubleAsString(sizeMM));
1171 //     infoPanel->setOrigin(GetVectorDoubleAsString(origin));
1172 //     infoPanel->setSpacing(GetVectorDoubleAsString(inputSpacing));
1173 //     infoPanel->setNPixel(QString::number(NPixel)+" ("+inputSizeInBytes+")");
1174 //
1175 //     landmarksPanel->SetCurrentLandmarks(mSlicerManagers[index]->GetLandmarks(),
1176 //                                         mSlicerManagers[index]->GetTSlice());
1177 //     landmarksPanel->SetCurrentPath(mInputPathName.toStdString());
1178 //     landmarksPanel->SetCurrentImage(mSlicerManagers[index]->GetFileName().c_str());
1179 //
1180 //     overlayPanel->getCurrentImageName(mSlicerManagers[index]->GetFileName().c_str());
1181 //     for (int i = 0; i < 4; i++) {
1182 //       if (DataTree->selectedItems()[0]->data(i+1,Qt::CheckStateRole).toInt() > 0 || i == 3) {
1183 //         mSlicerManagers[index]->UpdateInfoOnCursorPosition(i);
1184 //         break;
1185 //       }
1186 //     }
1187     WindowLevelChanged();
1188
1189     slicingPresetComboBox->setCurrentIndex(mSlicerManagers[index]->GetSlicingPreset());
1190
1191     if (mSlicerManagers[index]->GetSlicer(0)->GetVF()) {
1192       overlayPanel->getVFName(mSlicerManagers[index]->GetVFName().c_str());
1193       overlayPanel->getVFProperty(mSlicerManagers[index]->GetSlicer(0)->GetVFSubSampling(),
1194         mSlicerManagers[index]->GetSlicer(0)->GetVFScale(),
1195         mSlicerManagers[index]->GetSlicer(0)->GetVFLog());
1196     } else {
1197       overlayPanel->getVFName(mSlicerManagers[index]->GetVFName().c_str());
1198       overlayPanel->getVFProperty(-1,-1,-1);
1199     }
1200     if (mSlicerManagers[index]->GetSlicer(0)->GetOverlay()) {
1201       overlayPanel->getOverlayName(mSlicerManagers[index]->GetOverlayName().c_str());
1202     } else {
1203       overlayPanel->getOverlayName(mSlicerManagers[index]->GetOverlayName().c_str());
1204     }
1205
1206     if (mSlicerManagers[index]->GetSlicer(0)->GetFusion()) {
1207       overlayPanel->getFusionName(mSlicerManagers[index]->GetFusionName().c_str());
1208     } else {
1209       overlayPanel->getFusionName(mSlicerManagers[index]->GetFusionName().c_str());
1210     }
1211   }
1212 }
1213 //------------------------------------------------------------------------------
1214
1215 //------------------------------------------------------------------------------
1216 void vvMainWindow::ShowDocumentation()
1217 {
1218   documentation->show();
1219 }
1220 //------------------------------------------------------------------------------
1221
1222 //------------------------------------------------------------------------------
1223 void vvMainWindow::PopupRegisterForm(bool checkCanPush)
1224 {
1225   vvRegisterForm* registerForm = new vvRegisterForm(QUrl("http://www.creatis.insa-lyon.fr/~dsarrut/vvregister/write.php"), getVVSettingsPath(), getSettingsOptionFormat());
1226   if(!checkCanPush) {
1227     registerForm->show();
1228   } else {
1229     if(registerForm->canPush()) {
1230       registerForm->show();
1231       registerForm->acquitPushed();//too bad if there is not internet connection anymore.
1232     }
1233   }
1234 }
1235 //------------------------------------------------------------------------------
1236
1237 //------------------------------------------------------------------------------
1238 void vvMainWindow::ShowHelpDialog()
1239 {
1240   help_dialog->show();
1241 }
1242 //------------------------------------------------------------------------------
1243
1244 //------------------------------------------------------------------------------
1245 void vvMainWindow::ChangeViewMode()
1246 {
1247   typedef struct _SIZE{
1248     QSplitter* splitter;
1249     QList<int> size1, size2;
1250     int cols[3];
1251   }SplitterSize;
1252   SplitterSize sizes[4];
1253   sizes[0].splitter = OSplitter;
1254   sizes[0].size1.push_back(1);
1255   sizes[0].size1.push_back(0);
1256   sizes[0].size2.push_back(1);
1257   sizes[0].size2.push_back(0);
1258   sizes[0].cols[0] = 2;
1259   sizes[0].cols[1] = 3;
1260   sizes[0].cols[2] = 4;
1261
1262   sizes[1].splitter = ESplitter;
1263   sizes[1].size1.push_back(0);
1264   sizes[1].size1.push_back(1);
1265   sizes[1].size2.push_back(1);
1266   sizes[1].size2.push_back(0);
1267   sizes[1].cols[0] = 1;
1268   sizes[1].cols[1] = 3;
1269   sizes[1].cols[2] = 4;
1270
1271   sizes[2].splitter = OSplitter;
1272   sizes[2].size1.push_back(1);
1273   sizes[2].size1.push_back(0);
1274   sizes[2].size2.push_back(0);
1275   sizes[2].size2.push_back(1);
1276   sizes[2].cols[0] = 1;
1277   sizes[2].cols[1] = 2;
1278   sizes[2].cols[2] = 4;
1279
1280   sizes[3].splitter = ESplitter;
1281   sizes[3].size1.push_back(0);
1282   sizes[3].size1.push_back(1);
1283   sizes[3].size2.push_back(0);
1284   sizes[3].size2.push_back(1);
1285   sizes[3].cols[0] = 1;
1286   sizes[3].cols[1] = 2;
1287   sizes[3].cols[2] = 3;
1288
1289   int slicer = mSlicerManagers[mCurrentPickedImageIndex]->GetSelectedSlicer();
1290   if (viewMode == 1) {
1291     if (slicer >= 0) {
1292       viewMode = 0;
1293       splitter_3->setSizes(sizes[slicer].size1);
1294       sizes[slicer].splitter->setSizes(sizes[slicer].size2);
1295       DataTree->setColumnHidden(sizes[slicer].cols[0],1);
1296       DataTree->setColumnHidden(sizes[slicer].cols[1],1);
1297       DataTree->setColumnHidden(sizes[slicer].cols[2],1);
1298     }
1299   } else {
1300     QList<int> size;
1301     if (slicer >= 0) {
1302       viewMode = 1;
1303       size.push_back(1);
1304       size.push_back(1);
1305       splitter_3->setSizes(size);
1306       sizes[slicer].splitter->setSizes(size);
1307       DataTree->setColumnHidden(sizes[slicer].cols[0],0);
1308       DataTree->setColumnHidden(sizes[slicer].cols[1],0);
1309       DataTree->setColumnHidden(sizes[slicer].cols[2],0);
1310     }
1311   }
1312   UpdateRenderWindows();
1313   /*
1314   ** I don't know why but for both resized QVTKWidget we also need to render
1315   ** the associated Slicer to redraw crosses.
1316   */
1317   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
1318     //     if (DataTree->topLevelItem(i)->data(COLUMN_UL_VIEW,Qt::CheckStateRole).toInt() > 1)
1319     mSlicerManagers[i]->GetSlicer(0)->Render();
1320     mSlicerManagers[i]->GetSlicer(1)->Render();
1321     //     if (DataTree->topLevelItem(i)->data(COLUMN_DL_VIEW,Qt::CheckStateRole).toInt() > 1)
1322     mSlicerManagers[i]->GetSlicer(2)->Render();
1323     mSlicerManagers[i]->GetSlicer(3)->Render();
1324   }
1325 }
1326 //------------------------------------------------------------------------------
1327
1328 //------------------------------------------------------------------------------
1329 QString vvMainWindow::GetSizeInBytes(unsigned long size)
1330 {
1331   QString result = "";// QString::number(size);
1332   //result += " bytes (";
1333   if (size > 1000000000) {
1334     size /= 1000000000;
1335     result += QString::number(size);
1336     result += "Gb";//)";
1337   } else if (size > 1000000) {
1338     size /= 1000000;
1339     result += QString::number(size);
1340     result += "Mb";//)";
1341   } else if (size > 1000) {
1342     size /= 1000;
1343     result += QString::number(size);
1344     result += "kb";//)";
1345   }
1346   return result;
1347 }
1348 //------------------------------------------------------------------------------
1349
1350 //------------------------------------------------------------------------------
1351 QString vvMainWindow::GetVectorDoubleAsString(std::vector<double> vectorDouble)
1352 {
1353   QString result;
1354   for (unsigned int i= 0; i < vectorDouble.size(); i++) {
1355     if (i != 0)
1356       result += " ";
1357     result += QString::number(vectorDouble[i]);
1358   }
1359   return result;
1360 }
1361 //------------------------------------------------------------------------------
1362
1363 //------------------------------------------------------------------------------
1364 QString vvMainWindow::GetVectorIntAsString(std::vector<int> vectorInt)
1365 {
1366   QString result;
1367   for (unsigned int i= 0; i < vectorInt.size(); i++) {
1368     if (i != 0)
1369       result += " ";
1370     result += QString::number(vectorInt[i]);
1371   }
1372   return result;
1373 }
1374 //------------------------------------------------------------------------------
1375
1376 //------------------------------------------------------------------------------
1377 //this actually returns the SlicerManager index!
1378 int vvMainWindow::GetSlicerIndexFromItem(QTreeWidgetItem* item)
1379 {
1380   QString id = item->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString();
1381   for (int i = 0; i < DataTree->topLevelItemCount(); i++) {
1382     if (DataTree->topLevelItem(i)->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString() == id)
1383       return i;
1384   }
1385   return -1;
1386 }
1387 //------------------------------------------------------------------------------
1388
1389 //------------------------------------------------------------------------------
1390 QTreeWidgetItem* vvMainWindow::GetItemFromSlicerManager(vvSlicerManager* sm)
1391 {
1392   QString id = sm->GetId().c_str();
1393   for (int i = 0; i < DataTree->topLevelItemCount(); i++) {
1394     if (DataTree->topLevelItem(i)->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString() == id)
1395       return DataTree->topLevelItem(i);
1396   }
1397   return NULL;
1398 }
1399 //------------------------------------------------------------------------------
1400
1401 //------------------------------------------------------------------------------
1402 void vvMainWindow::DisplayChanged(QTreeWidgetItem *clickedItem, int column)
1403 {
1404   if ( column >= COLUMN_CLOSE_IMAGE || column <= 0)
1405     return;
1406
1407   // Get parent information (might be the same item)
1408   int slicerManagerIndex = GetSlicerIndexFromItem(clickedItem);
1409   QTreeWidgetItem* clickedParentItem = DataTree->topLevelItem(slicerManagerIndex);
1410   vvSlicer* clickedSlicer = mSlicerManagers[slicerManagerIndex]->GetSlicer(column-1);
1411
1412   // Go over the complete item tree (only 2 levels, parents and children)
1413   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
1414     // Trick to avoid redoing twice the job for a key (sr)
1415     mSlicerManagers[i]->GetSlicer(column-1)->GetRenderWindow()->GetInteractor()->SetKeySym("Crap");
1416
1417     QTreeWidgetItem* currentParentItem = DataTree->topLevelItem(i);
1418     if(currentParentItem != clickedParentItem) {
1419       // Not the branch of the clicked item, uncheck all
1420
1421       // Parent
1422       currentParentItem->setData(column,Qt::CheckStateRole, 0);
1423       mSlicerManagers[i]->UpdateSlicer(column-1, false);
1424
1425       // Children
1426       for (int iChild = 0; iChild < currentParentItem->childCount(); iChild++) {
1427         currentParentItem->child(iChild)->setData(column,Qt::CheckStateRole, 0);
1428       }
1429     }
1430     else {
1431       // Branch of the clicked one: get check status from actor visibility in slicer
1432       // and toggle the clicked one
1433
1434       // Parent
1435       bool vis = clickedSlicer->GetActorVisibility("image", 0);
1436       bool draw = clickedSlicer->GetRenderer()->GetDraw();
1437
1438       // Update slicer (after getting visibility)
1439       mSlicerManagers[slicerManagerIndex]->UpdateSlicer(column-1, true);
1440       mSlicerManagers[slicerManagerIndex]->UpdateInfoOnCursorPosition(column-1);
1441       DisplaySliders(slicerManagerIndex, column-1);
1442       if(clickedParentItem == clickedItem) {
1443         // Toggle
1444         vis = !draw || !vis;
1445       }
1446       clickedSlicer->SetActorVisibility("image", 0, vis);
1447       clickedParentItem->setData(column, Qt::CheckStateRole, vis?2:0);
1448
1449       // Children
1450       std::map<std::string, int> actorTypeCounts;
1451       for (int iChild = 0; iChild < clickedParentItem->childCount(); iChild++) {
1452         QTreeWidgetItem* currentChildItem = clickedParentItem->child(iChild);
1453         std::string actorType = currentChildItem->data(1,Qt::UserRole).toString().toStdString();
1454         vis = clickedSlicer->GetActorVisibility(actorType, actorTypeCounts[actorType]);
1455         if(currentChildItem == clickedItem) {
1456           // Toggle or force visibility if it was not on this branch so far
1457           vis = !draw || !vis;
1458           clickedSlicer->SetActorVisibility(actorType, actorTypeCounts[actorType], vis);
1459         }
1460         currentChildItem->setData(column, Qt::CheckStateRole, vis?2:0);
1461         actorTypeCounts[actorType]++;
1462       }
1463     }
1464   }
1465
1466   clickedSlicer->Render();
1467 }
1468 //------------------------------------------------------------------------------
1469
1470 void vvMainWindow::InitSlicers()
1471 {
1472   if (mSlicerManagers.size()) {
1473     mSlicerManagers.back()->GenerateDefaultLookupTable();
1474     mSlicerManagers.back()->SetSlicerWindow(0,NOViewWidget->GetRenderWindow());
1475     mSlicerManagers.back()->SetSlicerWindow(1,NEViewWidget->GetRenderWindow());
1476     mSlicerManagers.back()->SetSlicerWindow(2,SOViewWidget->GetRenderWindow());
1477     mSlicerManagers.back()->SetSlicerWindow(3,SEViewWidget->GetRenderWindow());
1478     mSlicerManagers.back()->Render(); // SR: displayed #slice is wrong without this
1479   }
1480 }
1481
1482 //------------------------------------------------------------------------------
1483 void vvMainWindow::InitDisplay()
1484 {
1485   if (mSlicerManagers.size()) {
1486     //BE CAREFUL : this is absolutely necessary to set the interactor style
1487     //in order to have the same style instanciation for all SlicerManagers in
1488     // a same window
1489     for (int j = 0; j < 4; j++) {
1490       vvInteractorStyleNavigator* style = vvInteractorStyleNavigator::New();
1491       style->SetAutoAdjustCameraClippingRange(1);
1492       bool AlreadySelected = false;
1493       for (int i = 0; i < DataTree->topLevelItemCount(); i++) {
1494         mSlicerManagers[i]->SetInteractorStyleNavigator(j,style);
1495         //select the image only if previous are not selected
1496         if (DataTree->topLevelItem(i)->data(j+1,Qt::CheckStateRole).toInt() > 1) {
1497           mSlicerManagers[i]->UpdateSlicer(j,1);
1498           AlreadySelected = true;
1499         } else if (i == DataTree->topLevelItemCount()-1 && !AlreadySelected) {
1500           if (DataTree->selectedItems().size() == 0) {
1501             DataTree->topLevelItem(i)->setSelected(1);
1502           }
1503           DataTree->topLevelItem(i)->setData(j+1,Qt::CheckStateRole,2);
1504           mSlicerManagers[i]->UpdateSlicer(j,1);
1505           DisplaySliders(i,j);
1506         } else {
1507           DataTree->topLevelItem(i)->setData(j+1,Qt::CheckStateRole,0);
1508           mSlicerManagers[i]->UpdateSlicer(j,0);
1509         }
1510       }
1511       style->Delete();
1512     }
1513   }
1514 }
1515 //------------------------------------------------------------------------------
1516
1517 //------------------------------------------------------------------------------
1518 void vvMainWindow::DisplaySliders(int slicer, int window)
1519 {
1520   if(!mSlicerManagers[slicer]->GetSlicer(window)->GetRenderer()->GetDraw())
1521     return;
1522
1523   int range[2];
1524   mSlicerManagers[slicer]->GetSlicer(window)->GetSliceRange(range);
1525   int position = mSlicerManagers[slicer]->GetSlicer(window)->GetSlice();
1526   if (range[1]>0)
1527     verticalSliders[window]->show();
1528   else
1529     verticalSliders[window]->hide();
1530   verticalSliders[window]->setRange(range[0],range[1]);
1531   verticalSliders[window]->setValue(position);
1532
1533   int tRange[2];
1534   tRange[0] = 0;
1535   tRange[1] = mSlicerManagers[slicer]->GetSlicer(window)->GetTMax();
1536   if (tRange[1]>0)
1537     horizontalSliders[window]->show();
1538   else
1539     horizontalSliders[window]->hide();
1540   horizontalSliders[window]->setRange(tRange[0],tRange[1]);
1541   int tPosition = mSlicerManagers[slicer]->GetSlicer(window)->GetMaxCurrentTSlice();
1542   horizontalSliders[window]->setValue(tPosition);
1543 }
1544 //------------------------------------------------------------------------------
1545
1546 //------------------------------------------------------------------------------
1547 void vvMainWindow::CloseImage(QTreeWidgetItem* item, int column)
1548 {
1549   int index = GetSlicerIndexFromItem(item);
1550
1551   if (DataTree->topLevelItem(index) != item) {
1552     QString warning = "Do you really want to close the overlay : ";
1553     warning += item->data(COLUMN_IMAGE_NAME,Qt::DisplayRole).toString();
1554     QMessageBox msgBox(QMessageBox::Warning, tr("Close Overlay"),
1555       warning, 0, this);
1556     msgBox.addButton(tr("Close"), QMessageBox::AcceptRole);
1557     msgBox.addButton(tr("Cancel"), QMessageBox::RejectRole);
1558     if (msgBox.exec() == QMessageBox::AcceptRole) {
1559       std::string overlay_type=item->data(1,Qt::UserRole).toString().toStdString();
1560       int overlay_index=0;
1561       for (int child = 0; child < DataTree->topLevelItem(index)->childCount(); child++) {
1562         if (DataTree->topLevelItem(index)->\
1563           child(child)->data(1,Qt::UserRole).toString().toStdString() == overlay_type)
1564           overlay_index++;
1565         if (DataTree->topLevelItem(index)->child(child) == item) break;
1566       }
1567       if (overlay_type=="fusionSequence") {
1568         //removing the overlay sequence in a fusion sequence visualization mode
1569         //reset the transforms
1570         overlayPanel->getFusionSequenceProperty(-1, false, 0, false);
1571
1572         //unlink and untie the slicer managers
1573         RemoveLink(mSlicerManagers[index]->GetId().c_str(), mSlicerManagers[mSlicerManagers[index]->GetFusionSequenceIndexOfLinkedManager()]->GetId().c_str());
1574         mSlicerManagers[index]->SetFusionSequenceInvolvmentCode(-1);
1575         mSlicerManagers[mSlicerManagers[index]->GetFusionSequenceIndexOfLinkedManager()]->SetFusionSequenceInvolvmentCode(-1);
1576         for (unsigned i=0 ; i<4 ; i++) {
1577             mSlicerManagers[index]->GetSlicer(i)->SetFusionSequenceCode(-1);
1578             mSlicerManagers[mSlicerManagers[index]->GetFusionSequenceIndexOfLinkedManager()]->GetSlicer(i)->SetFusionSequenceCode(-1);
1579         }
1580
1581       }
1582       mSlicerManagers[index]->RemoveActor(overlay_type, overlay_index-1);
1583       mSlicerManagers[index]->SetColorMap(0);
1584       DataTree->topLevelItem(index)->takeChild(DataTree->topLevelItem(index)->indexOfChild(item));
1585       mSlicerManagers[index]->Render();
1586     }
1587   } else if (DataTree->topLevelItemCount() <= 1) {
1588     QString warning = "Do you really want to close the image : ";
1589     warning += item->data(COLUMN_IMAGE_NAME,Qt::DisplayRole).toString();
1590     warning += "\nThis is the last image, you're about to close vv !!!";
1591     QMessageBox msgBox(QMessageBox::Warning, tr("Close Image"),
1592       warning, 0, this);
1593     msgBox.addButton(tr("Close vv"), QMessageBox::AcceptRole);
1594     msgBox.addButton(tr("Cancel"), QMessageBox::RejectRole);
1595     if (msgBox.exec() == QMessageBox::AcceptRole) {
1596       this->close();
1597     }
1598   } else {
1599     QString warning = "Do you really want to close the image : ";
1600     warning += item->data(COLUMN_IMAGE_NAME,Qt::DisplayRole).toString();
1601     QMessageBox msgBox(QMessageBox::Warning, tr("Close Image"),
1602       warning, 0, this);
1603     msgBox.addButton(tr("Close"), QMessageBox::AcceptRole);
1604     msgBox.addButton(tr("Cancel"), QMessageBox::RejectRole);
1605     if (msgBox.exec() == QMessageBox::AcceptRole) {
1606
1607       // Tell tools that we close an image
1608       emit AnImageIsBeingClosed(mSlicerManagers[index]);
1609
1610       std::vector<vvSlicerManager*>::iterator Manageriter = mSlicerManagers.begin();
1611       DataTree->takeTopLevelItem(index);
1612       for (int i = 0; i < index; i++) {
1613         Manageriter++;
1614       }
1615       //if the slicer manager was involved in a fusion sequence visualization...
1616       if ( mSlicerManagers[index]->IsInvolvedInFusionSequence() ) {
1617         //in both cases, close the overlay: find it... and close it
1618         //ideally, I should duplicate the code, and avoid calling CloseImage, since this pops up another interactive box
1619         QTreeWidgetItem* overlayItem;
1620         if (mSlicerManagers[index]->IsMainSequenceOfFusionSequence()) {
1621           for (unsigned i=0 ; i<item->childCount() ; i++) {
1622             overlayItem = item->child(i);
1623             this->CloseImage( overlayItem, 0 );
1624           }
1625         }
1626         else {
1627           QTreeWidgetItem* linkedItem = this->GetItemFromSlicerManager( mSlicerManagers[mSlicerManagers[index]->GetFusionSequenceIndexOfLinkedManager()] );
1628           for (unsigned i=0 ; i<linkedItem->childCount() ; i++) {
1629             overlayItem = linkedItem->child(i);
1630             this->CloseImage( overlayItem, 0 );
1631           }
1632         }
1633
1634         /* -- this is normally already done when closing the overlay.
1635         //reset the transforms
1636         overlayPanel->getFusionSequenceProperty(-1, false, 0, false);
1637
1638         //unlink and untie the slicer managers
1639         RemoveLink(mSlicerManagers[index]->GetId().c_str(), mSlicerManagers[mSlicerManagers[index]->GetFusionSequenceIndexOfLinkedManager()]->GetId().c_str());
1640         mSlicerManagers[index]->SetFusionSequenceInvolvmentCode(-1);
1641         mSlicerManagers[mSlicerManagers[index]->GetFusionSequenceIndexOfLinkedManager()]->SetFusionSequenceInvolvmentCode(-1);
1642         for (unsigned i=0 ; i<4 ; i++) {
1643             mSlicerManagers[index]->GetSlicer(i)->SetFusionSequenceCode(-1);
1644             mSlicerManagers[mSlicerManagers[index]->GetFusionSequenceIndexOfLinkedManager()]->GetSlicer(i)->SetFusionSequenceCode(-1);
1645         }
1646         */
1647       }
1648
1649       linkPanel->removeImage(index);
1650       mSlicerManagers[index]->RemoveActors();
1651
1652       //remove the slicer manager
1653       delete mSlicerManagers[index];
1654       mSlicerManagers.erase(Manageriter);
1655
1656       //
1657       InitDisplay();
1658     }
1659   }
1660   ImageInfoChanged();
1661 }
1662 //------------------------------------------------------------------------------
1663
1664 //------------------------------------------------------------------------------
1665 void vvMainWindow::ReloadImage(QTreeWidgetItem* item, int column)
1666 {
1667   // int index = GetSlicerIndexFromItem(item);
1668   //   QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
1669   //   if (item->data(1,Qt::UserRole).toString() == "vector")
1670   //     mSlicerManagers[index]->ReloadVF();
1671   //   else
1672   //     mSlicerManagers[index]->Reload();
1673
1674   //   QApplication::restoreOverrideCursor();
1675   int index = GetSlicerIndexFromItem(item);
1676   QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
1677   QString role=item->data(1,Qt::UserRole).toString();
1678   if ( role == "vector") {
1679     mSlicerManagers[index]->ReloadVF();
1680   }
1681   else if (role == "overlay") {
1682     mSlicerManagers[index]->ReloadOverlay();
1683   }
1684   else if (role == "fusion") {
1685     mSlicerManagers[index]->ReloadFusion();
1686   }
1687   else if (role == "fusionSequence") {
1688     //both versions of the secondary sequence must be updated.
1689     mSlicerManagers[index]->ReloadFusionSequence();
1690     mSlicerManagers[mSlicerManagers[index]->GetFusionSequenceIndexOfLinkedManager()]->Reload();
1691   }
1692   else {
1693     mSlicerManagers[index]->Reload();
1694     //if we update the secondary sequence, then the overlay of the main sequence should also be updated
1695     if (mSlicerManagers[index]->IsSecondarySequenceOfFusionSequence()) mSlicerManagers[mSlicerManagers[index]->GetFusionSequenceIndexOfLinkedManager()]->ReloadFusionSequence();
1696   }
1697   // Update view and info
1698   ImageInfoChanged();
1699   mSlicerManagers[index]->Render();
1700   QApplication::restoreOverrideCursor();
1701 }
1702 //------------------------------------------------------------------------------
1703
1704 //------------------------------------------------------------------------------
1705 void vvMainWindow::MousePositionChanged(int visibility,double x, double y, double z, double X, double Y, double Z , double value)
1706 {
1707   infoPanel->setCurrentInfo(visibility,x,y,z,X,Y,Z,value);
1708 }
1709 //------------------------------------------------------------------------------
1710
1711 //------------------------------------------------------------------------------
1712 void vvMainWindow::VectorChanged(int visibility,double x, double y, double z, double value)
1713 {
1714   overlayPanel->getCurrentVectorInfo(visibility,x,y,z,value);
1715 }
1716 //------------------------------------------------------------------------------
1717
1718 //------------------------------------------------------------------------------
1719 void vvMainWindow::OverlayChanged(int visibility, double valueOver, double valueRef)
1720 {
1721   overlayPanel->getCurrentOverlayInfo(visibility,valueOver, valueRef);
1722 }
1723 //------------------------------------------------------------------------------
1724
1725 //------------------------------------------------------------------------------
1726 void vvMainWindow::FusionChanged(int visibility, double value)
1727 {
1728   overlayPanel->getCurrentFusionInfo(visibility,value);
1729 }
1730 //------------------------------------------------------------------------------
1731
1732 //------------------------------------------------------------------------------
1733 //called when AddOverlayImage, AddFusionSequence
1734 //or when UpdateWindowLevel() is called ; when slicerManager emits WindowLevelChanged
1735 //when ImageInfoChanged() is called
1736 void vvMainWindow::WindowLevelChanged()
1737 {
1738   // Base image
1739   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1740   if(index==-1) return;
1741   windowSpinBox->setValue(mSlicerManagers[index]->GetColorWindow());
1742   levelSpinBox->setValue(mSlicerManagers[index]->GetColorLevel());
1743   colorMapComboBox->setCurrentIndex(mSlicerManagers[index]->GetColorMap());
1744   presetComboBox->setCurrentIndex(mSlicerManagers[index]->GetPreset());
1745
1746   // Overlay image
1747   if (mSlicerManagers[index]->GetSlicer(0)->GetOverlay())
1748     overlayPanel->getOverlayProperty(mSlicerManagers[index]->GetOverlayColor(),
1749     mSlicerManagers[index]->GetLinkOverlayWindowLevel(),
1750     mSlicerManagers[index]->GetOverlayColorWindow(),
1751     mSlicerManagers[index]->GetOverlayColorLevel());
1752   else
1753     overlayPanel->getOverlayProperty(-1,0,0.,0.);
1754
1755   // Fusion & SequenceFusion image
1756   if (mSlicerManagers[index]->GetSlicer(0)->GetFusion()) {
1757     overlayPanel->getFusionProperty(mSlicerManagers[index]->GetFusionOpacity(),
1758       mSlicerManagers[index]->GetFusionThresholdOpacity(),
1759       mSlicerManagers[index]->GetFusionColorMap(),
1760       mSlicerManagers[index]->GetFusionWindow(),
1761       mSlicerManagers[index]->GetFusionLevel());
1762     if (mSlicerManagers[index]->IsMainSequenceOfFusionSequence()) {
1763       overlayPanel->getFusionSequenceProperty(mSlicerManagers[index]->GetFusionSequenceFrameIndex(),
1764         mSlicerManagers[index]->GetFusionSequenceSpatialSyncFlag(),
1765         mSlicerManagers[index]->GetFusionSequenceNbFrames(),
1766         mSlicerManagers[index]->GetFusionSequenceTemporalSyncFlag());
1767     }
1768   }
1769   else if ( mSlicerManagers[index]->IsSecondarySequenceOfFusionSequence() ) {
1770     //if the image is involved in a fusion sequence, preserve the overlay panel!
1771     int ind = mSlicerManagers[index]->GetFusionSequenceIndexOfLinkedManager();
1772     overlayPanel->getFusionProperty(mSlicerManagers[ind]->GetFusionOpacity(),
1773       mSlicerManagers[ind]->GetFusionThresholdOpacity(),
1774       mSlicerManagers[ind]->GetFusionColorMap(),
1775       mSlicerManagers[ind]->GetFusionWindow(),
1776       mSlicerManagers[ind]->GetFusionLevel());
1777     overlayPanel->getFusionSequenceProperty(mSlicerManagers[ind]->GetFusionSequenceFrameIndex(),
1778       mSlicerManagers[ind]->GetFusionSequenceSpatialSyncFlag(),
1779       mSlicerManagers[ind]->GetFusionSequenceNbFrames(),
1780       mSlicerManagers[ind]->GetFusionSequenceTemporalSyncFlag());
1781   }
1782   else
1783   {
1784     overlayPanel->getFusionProperty(-1, -1, -1, -1, -1);
1785     overlayPanel->getFusionSequenceProperty(-1, false, 0, false);
1786   }
1787 }
1788 //------------------------------------------------------------------------------
1789
1790 //------------------------------------------------------------------------------
1791 void vvMainWindow::WindowLevelEdited()
1792 {
1793   presetComboBox->setCurrentIndex(WL_USER);
1794   UpdateWindowLevel();
1795 }
1796 //------------------------------------------------------------------------------
1797
1798 //------------------------------------------------------------------------------
1799 void vvMainWindow::SetWindowLevel(double w, double l)
1800 {
1801   windowSpinBox->setValue(w);
1802   levelSpinBox->setValue(l);
1803   presetComboBox->setCurrentIndex(WL_USER);
1804   colorMapComboBox->setCurrentIndex(0);
1805   UpdateWindowLevel();
1806 }
1807 //------------------------------------------------------------------------------
1808
1809 //------------------------------------------------------------------------------
1810 void vvMainWindow::UpdateWindowLevel()
1811 {
1812   if (DataTree->selectedItems().size()) {
1813     if (presetComboBox->currentIndex() == WL_VENTILATION) //For ventilation
1814       colorMapComboBox->setCurrentIndex(5);
1815     int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1816     mSlicerManagers[index]->SetColorWindow(windowSpinBox->value());
1817     mSlicerManagers[index]->SetColorLevel(levelSpinBox->value());
1818     mSlicerManagers[index]->SetPreset(presetComboBox->currentIndex());
1819     mSlicerManagers[index]->Render();
1820     WindowLevelChanged();
1821   }
1822 }
1823 //------------------------------------------------------------------------------
1824
1825 //------------------------------------------------------------------------------
1826 void vvMainWindow::UpdateSlicingPreset()
1827 {
1828   if (DataTree->selectedItems().size()) {
1829     int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1830     mSlicerManagers[index]->SetSlicingPreset(vvSlicerManager::SlicingPresetType(slicingPresetComboBox->currentIndex()));
1831   }
1832 }
1833 //------------------------------------------------------------------------------
1834
1835 //------------------------------------------------------------------------------
1836 void vvMainWindow::UpdateColorMap()
1837 {
1838   if (DataTree->selectedItems().size()) {
1839     int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1840     mSlicerManagers[index]->SetColorMap(colorMapComboBox->currentIndex());
1841     mSlicerManagers[index]->Render();
1842   }
1843 }
1844 //------------------------------------------------------------------------------
1845 void vvMainWindow::SwitchWindowLevel()
1846 {
1847   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1848   int window = mSlicerManagers[index]->GetColorWindow();
1849   presetComboBox->setCurrentIndex(WL_USER);
1850   windowSpinBox->setValue(-window);
1851   UpdateWindowLevel();
1852 }
1853 //------------------------------------------------------------------------------
1854
1855 //------------------------------------------------------------------------------
1856 void vvMainWindow::ApplyWindowLevelToAllImages()
1857 {
1858   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1859   if(index==-1) return;
1860   double window = mSlicerManagers[index]->GetColorWindow();
1861   double level = mSlicerManagers[index]->GetColorLevel();
1862
1863   double fusWindow = mSlicerManagers[index]->GetFusionWindow();
1864   double fusLevel = mSlicerManagers[index]->GetFusionLevel();
1865
1866   double overWindow = mSlicerManagers[index]->GetOverlayColorWindow();
1867   double overLevel = mSlicerManagers[index]->GetOverlayColorLevel();
1868
1869   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
1870     if (mSlicerManagers[i] == NULL)
1871       continue;
1872     mSlicerManagers[i]->SetColorWindow(window);
1873     mSlicerManagers[i]->SetColorLevel(level);
1874     mSlicerManagers[i]->SetPreset(WL_USER);
1875     mSlicerManagers[i]->SetFusionWindow(fusWindow);
1876     mSlicerManagers[i]->SetFusionLevel(fusLevel);
1877     mSlicerManagers[i]->SetOverlayColorWindow(overWindow);
1878     mSlicerManagers[i]->SetOverlayColorLevel(overLevel);
1879     mSlicerManagers[i]->Render();
1880   }
1881 }
1882 //------------------------------------------------------------------------------
1883
1884 //------------------------------------------------------------------------------
1885 void vvMainWindow::ApplyWindowToSetOfImages(double window, unsigned int indexMin, unsigned int indexMax)
1886 {
1887   for (unsigned int i = indexMin; i <= indexMax && i < mSlicerManagers.size(); i++) {
1888     if (mSlicerManagers[i] == NULL)
1889       continue;
1890     mSlicerManagers[i]->SetColorWindow(window);
1891     mSlicerManagers[i]->SetPreset(WL_USER);
1892     mSlicerManagers[i]->Render();
1893   }
1894 }
1895 //------------------------------------------------------------------------------
1896
1897 //------------------------------------------------------------------------------
1898 void vvMainWindow::ApplyLevelToSetOfImages(double level, unsigned int indexMin, unsigned int indexMax)
1899 {
1900   for (unsigned int i = indexMin; i <= indexMax && i < mSlicerManagers.size(); i++) {
1901     if (mSlicerManagers[i] == NULL)
1902       continue;
1903     mSlicerManagers[i]->SetColorLevel(level);
1904     mSlicerManagers[i]->SetPreset(WL_USER);
1905     mSlicerManagers[i]->Render();
1906   }
1907 }
1908 //------------------------------------------------------------------------------
1909
1910 //------------------------------------------------------------------------------
1911 void vvMainWindow::UpdateLinkManager(std::string id, int slicer, double x, double y, double z, int temps)
1912 {
1913   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
1914     if (mSlicerManagers[i]->GetId() == id) {
1915       mSlicerManagers[i]->GetSlicer(slicer)->SetCurrentPosition(x,y,z,temps);
1916       mSlicerManagers[i]->UpdateViews(0,slicer);
1917       break;
1918     }
1919   }
1920 }
1921 //------------------------------------------------------------------------------
1922
1923 //------------------------------------------------------------------------------
1924 void vvMainWindow::UpdateLinkedNavigation(std::string id, vvSlicerManager * sm, vvSlicer* refSlicer)
1925 {
1926   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
1927     if (id == mSlicerManagers[i]->GetId()) {
1928       mSlicerManagers[i]->UpdateLinkedNavigation(refSlicer);
1929     }
1930   }
1931 }
1932 //------------------------------------------------------------------------------
1933
1934 //------------------------------------------------------------------------------
1935 void vvMainWindow::ShowContextMenu(QPoint point)
1936 {
1937   if (!DataTree->selectedItems().size()) {
1938     contextActions[1]->setEnabled(0);
1939     contextActions[2]->setEnabled(0);
1940     contextActions[3]->setEnabled(0);
1941     contextActions[4]->setEnabled(0);
1942     contextActions[5]->setEnabled(0);
1943     contextActions[6]->setEnabled(0);
1944   } else {
1945     int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1946     contextActions[1]->setEnabled(1);
1947     contextActions[2]->setEnabled(
1948       DataTree->itemWidget(DataTree->selectedItems()[0],
1949       COLUMN_RELOAD_IMAGE)->isEnabled());
1950     contextActions[3]->setEnabled(1);
1951     contextActions[5]->setEnabled(1);
1952     contextActions[6]->setEnabled(1);
1953
1954     if (mSlicerManagers[index]->GetDimension() < 3)
1955       contextActions[4]->setEnabled(0);
1956     else
1957       contextActions[4]->setEnabled(1);
1958   }
1959   contextMenu.exec(QCursor::pos());
1960 }
1961 //------------------------------------------------------------------------------
1962
1963 //------------------------------------------------------------------------------
1964 void vvMainWindow::CloseImage()
1965 {
1966   CloseImage(DataTree->selectedItems()[0],0);
1967 }
1968 //------------------------------------------------------------------------------
1969
1970 //------------------------------------------------------------------------------
1971 void vvMainWindow::ReloadImage()
1972 {
1973   ReloadImage(DataTree->selectedItems()[0],0);
1974 }
1975 //------------------------------------------------------------------------------
1976
1977 //------------------------------------------------------------------------------
1978 void vvMainWindow::SelectOverlayImage()
1979 {
1980   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1981
1982   //check if one overlay image is added
1983   for (int child = 0; child < DataTree->topLevelItem(index)->childCount(); child++)
1984     if (DataTree->topLevelItem(index)->child(child)->data(1,Qt::UserRole).toString() == "overlay") {
1985       QString error = "Cannot add more than one compared image\n";
1986       error += "Please remove first ";
1987       error += DataTree->topLevelItem(index)->child(child)->data(COLUMN_IMAGE_NAME,Qt::DisplayRole).toString();
1988       QMessageBox::information(this,tr("Problem adding compared image !"),error);
1989       return;
1990     }
1991
1992     QString Extensions = EXTENSIONS;
1993     Extensions += ";;All Files (*)";
1994     QStringList files = QFileDialog::getOpenFileNames(this,tr("Load Overlay image"),mInputPathName,Extensions);
1995     if (files.isEmpty())
1996       return;
1997
1998     std::vector<std::string> vecFileNames;
1999     for (int i = 0; i < files.size(); i++) {
2000       vecFileNames.push_back(files[i].toStdString());
2001     }
2002
2003     AddOverlayImage(index,vecFileNames,vvImageReader::IMAGE);
2004 }
2005 //------------------------------------------------------------------------------
2006
2007 //------------------------------------------------------------------------------
2008 void vvMainWindow::AddOverlayImage(int index, std::vector<std::string> fileNames, vvImageReader::LoadedImageType type)
2009 {
2010   QString file(fileNames[0].c_str());
2011   if (QFile::exists(file))
2012   {
2013     mInputPathName = itksys::SystemTools::GetFilenamePath(file.toStdString()).c_str();
2014     itk::ImageIOBase::Pointer reader = itk::ImageIOFactory::CreateImageIO(
2015       file.toStdString().c_str(), itk::ImageIOFactory::ReadMode);
2016     reader->SetFileName(fileNames[0].c_str());
2017     reader->ReadImageInformation();
2018     std::string component = reader->GetComponentTypeAsString(reader->GetComponentType());
2019     int dimension = reader->GetNumberOfDimensions();
2020     QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
2021     vvProgressDialog progress("Opening " + file.toStdString());
2022     qApp->processEvents();
2023
2024     std::string filename = itksys::SystemTools::GetFilenameWithoutExtension(file.toStdString()).c_str();
2025     if (mSlicerManagers[index]->SetOverlay(fileNames,dimension, component,type)) {
2026       //create an item in the tree with good settings
2027       QTreeWidgetItem *item = new QTreeWidgetItem();
2028       item->setData(0,Qt::UserRole,file.toStdString().c_str());
2029       item->setData(1,Qt::UserRole,tr("overlay"));
2030       QFileInfo fileinfo(file); //Do not show the path
2031       item->setData(COLUMN_IMAGE_NAME,Qt::DisplayRole,fileinfo.fileName());
2032       item->setToolTip(COLUMN_IMAGE_NAME, mSlicerManagers[index]->GetListOfAbsoluteFilePathInOneString("overlay").c_str());
2033       qApp->processEvents();
2034
2035       for (int j = 1; j <= 4; j++) {
2036         item->setData(j,Qt::CheckStateRole,DataTree->topLevelItem(index)->data(j,Qt::CheckStateRole));
2037       }
2038
2039       //Create the buttons for reload and close
2040       qApp->processEvents();
2041       QTreePushButton* cButton = new QTreePushButton;
2042       cButton->setItem(item);
2043       cButton->setColumn(COLUMN_CLOSE_IMAGE);
2044       cButton->setToolTip(tr("close image"));
2045       cButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/exit.png")));
2046       connect(cButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
2047         this,SLOT(CloseImage(QTreeWidgetItem*, int)));
2048
2049       QTreePushButton* rButton = new QTreePushButton;
2050       rButton->setItem(item);
2051       rButton->setColumn(COLUMN_RELOAD_IMAGE);
2052       rButton->setToolTip(tr("reload image"));
2053       rButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/rotateright.png")));
2054       connect(rButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
2055         this,SLOT(ReloadImage(QTreeWidgetItem*, int)));
2056
2057       DataTree->topLevelItem(index)->setExpanded(1);
2058       DataTree->topLevelItem(index)->addChild(item);
2059       DataTree->setItemWidget(item, COLUMN_CLOSE_IMAGE, cButton);
2060       DataTree->setItemWidget(item, COLUMN_RELOAD_IMAGE, rButton);
2061
2062       //set the id of the image
2063       QString id = DataTree->topLevelItem(index)->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString();
2064       item->setData(COLUMN_IMAGE_NAME,Qt::UserRole,id.toStdString().c_str());
2065       UpdateTree();
2066       qApp->processEvents();
2067       ImageInfoChanged();
2068       QApplication::restoreOverrideCursor();
2069
2070       // Update the display to update, e.g., the sliders
2071       for(int i=0; i<4; i++)
2072         DisplaySliders(index, i);
2073     } else {
2074       QApplication::restoreOverrideCursor();
2075       QString error = "Cannot import the new image.\n";
2076       error += mSlicerManagers[index]->GetLastError().c_str();
2077       QMessageBox::information(this,tr("Problem reading image !"),error);
2078     }
2079     WindowLevelChanged();
2080   }
2081   else
2082     QMessageBox::information(this,tr("Problem reading Overlay !"),"File doesn't exist!");
2083 }
2084 //------------------------------------------------------------------------------
2085
2086
2087 //------------------------------------------------------------------------------
2088 void vvMainWindow::AddROI(int index, QString file)
2089 {
2090   /*
2091   // Get slice manager
2092
2093   // Load image
2094
2095   vvImageReader * mReader = new vvImageReader;
2096   mReader->SetInputFilename(filename.toStdString());
2097   mReader->Update(IMAGE);
2098   if (mReader->GetLastError().size() != 0) {
2099   std::cerr << "Error while reading " << filename.toStdString() << std::endl;
2100   QString error = "Cannot open file \n";
2101   error += mReader->GetLastError().c_str();
2102   QMessageBox::information(this,tr("Reading problem"),error);
2103   delete mReader;
2104   return;
2105   }
2106   vvImage::Pointer roi = mReader->GetOutput();
2107
2108   // Create roi in new tool
2109   vvToolStructureSetManager::AddImage(mCurrentSlicerManager, roi);
2110   */
2111 }
2112 //------------------------------------------------------------------------------
2113
2114 //------------------------------------------------------------------------------
2115 void vvMainWindow::SelectFusionImage()
2116 {
2117   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2118
2119   //check if one fusion image is added
2120   for (int child = 0; child < DataTree->topLevelItem(index)->childCount(); child++)
2121     if ( (DataTree->topLevelItem(index)->child(child)->data(1,Qt::UserRole).toString() == "fusion") ||
2122       (DataTree->topLevelItem(index)->child(child)->data(1,Qt::UserRole).toString() == "fusionSequence") ) {
2123         QString error = "Cannot add more than one fusion image\n";
2124         error += "Please remove first ";
2125         error += DataTree->topLevelItem(index)->child(child)->data(COLUMN_IMAGE_NAME,Qt::DisplayRole).toString();
2126         QMessageBox::information(this,tr("Problem adding fusion image !"),error);
2127         return;
2128     }
2129
2130     QString Extensions = EXTENSIONS;
2131     Extensions += ";;All Files (*)";
2132     QStringList files = QFileDialog::getOpenFileNames(this,tr("Load Fusion image"),mInputPathName,Extensions);
2133     if (files.isEmpty())
2134       return;
2135
2136     std::vector<std::string> vecFileNames;
2137     for (int i = 0; i < files.size(); i++) {
2138       vecFileNames.push_back(files[i].toStdString());
2139     }
2140     AddFusionImage(index,vecFileNames,vvImageReader::IMAGE);
2141 }
2142 //------------------------------------------------------------------------------
2143
2144 //------------------------------------------------------------------------------
2145 void vvMainWindow::ResetTransformationToIdentity()
2146 {
2147   std::string actorType = DataTree->selectedItems()[0]->data(1,Qt::UserRole).toString().toStdString();
2148   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2149   mSlicerManagers[index]->ResetTransformationToIdentity(actorType);
2150   ImageInfoChanged();
2151 }
2152 //------------------------------------------------------------------------------
2153
2154 //------------------------------------------------------------------------------
2155 void vvMainWindow::AddFusionImage(int index, std::vector<std::string> fileNames, vvImageReader::LoadedImageType type)
2156 {
2157   QString file(fileNames[0].c_str());
2158   if (QFile::exists(file))
2159   {
2160     mInputPathName = itksys::SystemTools::GetFilenamePath(file.toStdString()).c_str();
2161     itk::ImageIOBase::Pointer reader = itk::ImageIOFactory::CreateImageIO(
2162       file.toStdString().c_str(), itk::ImageIOFactory::ReadMode);
2163     reader->SetFileName(fileNames[0].c_str());
2164     reader->ReadImageInformation();
2165     std::string component = reader->GetComponentTypeAsString(reader->GetComponentType());
2166     int dimension = reader->GetNumberOfDimensions();
2167     QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
2168     vvProgressDialog progress("Opening fusion");
2169     qApp->processEvents();
2170
2171     std::string filename = itksys::SystemTools::GetFilenameWithoutExtension(file.toStdString()).c_str();
2172     if (mSlicerManagers[index]->SetFusion(fileNames,dimension, component,type)) {
2173       //create an item in the tree with good settings
2174       QTreeWidgetItem *item = new QTreeWidgetItem();
2175       item->setData(0,Qt::UserRole,file.toStdString().c_str());
2176       item->setData(1,Qt::UserRole,tr("fusion"));
2177       QFileInfo fileinfo(file); //Do not show the path
2178           item->setData(COLUMN_IMAGE_NAME,Qt::DisplayRole,fileinfo.fileName());
2179           item->setToolTip(COLUMN_IMAGE_NAME, mSlicerManagers[index]->GetListOfAbsoluteFilePathInOneString("fusion").c_str());
2180           qApp->processEvents();
2181
2182       for (int j = 1; j <= 4; j++) {
2183         item->setData(j,Qt::CheckStateRole,DataTree->topLevelItem(index)->data(j,Qt::CheckStateRole));
2184       }
2185
2186       //Create the buttons for reload and close
2187       qApp->processEvents();
2188       QTreePushButton* cButton = new QTreePushButton;
2189       cButton->setItem(item);
2190       cButton->setColumn(COLUMN_CLOSE_IMAGE);
2191       cButton->setToolTip(tr("close image"));
2192       cButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/exit.png")));
2193       connect(cButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
2194         this,SLOT(CloseImage(QTreeWidgetItem*, int)));
2195
2196       QTreePushButton* rButton = new QTreePushButton;
2197       rButton->setItem(item);
2198       rButton->setColumn(COLUMN_RELOAD_IMAGE);
2199       rButton->setToolTip(tr("reload image"));
2200       rButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/rotateright.png")));
2201       connect(rButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
2202         this,SLOT(ReloadImage(QTreeWidgetItem*, int)));
2203
2204       DataTree->topLevelItem(index)->setExpanded(1);
2205       DataTree->topLevelItem(index)->addChild(item);
2206       DataTree->setItemWidget(item, COLUMN_CLOSE_IMAGE, cButton);
2207       DataTree->setItemWidget(item, COLUMN_RELOAD_IMAGE, rButton);
2208
2209       //set the id of the image
2210       QString id = DataTree->topLevelItem(index)->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString();
2211       item->setData(COLUMN_IMAGE_NAME,Qt::UserRole,id.toStdString().c_str());
2212       UpdateTree();
2213       qApp->processEvents();
2214       ImageInfoChanged();
2215       QApplication::restoreOverrideCursor();
2216
2217       // Update the display to update, e.g., the sliders
2218       for(int i=0; i<4; i++)
2219         DisplaySliders(index, i);
2220     } else {
2221       QApplication::restoreOverrideCursor();
2222       QString error = "Cannot import the new image.\n";
2223       error += mSlicerManagers[index]->GetLastError().c_str();
2224       QMessageBox::information(this,tr("Problem reading image !"),error);
2225     }
2226     WindowLevelChanged();
2227   }
2228   else
2229     QMessageBox::information(this,tr("Problem reading Fusion !"),"File doesn't exist!");
2230 }
2231 //------------------------------------------------------------------------------
2232 //------------------------------------------------------------------------------
2233 void vvMainWindow::AddLandmarks(int index, std::vector<std::string> files)
2234 {
2235     if (!landmarksPanel->LoadFromFile(files))
2236       QMessageBox::information(this,tr("Problem reading Landmarks !"),"File doesn't exist!");
2237
2238     landmarksPanel->SetCurrentPath(mInputPathName.toStdString());
2239     landmarksPanel->SetCurrentImage(mSlicerManagers[index]->GetFileName().c_str());
2240 }
2241
2242 //------------------------------------------------------------------------------
2243 void vvMainWindow::OpenField()
2244 {
2245   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2246   //check if a vector field has already been added
2247   for (int child = 0; child < DataTree->topLevelItem(index)->childCount(); child++)
2248     if (DataTree->topLevelItem(index)->child(child)->data(1,Qt::UserRole).toString() == "vector") {
2249       QString error = "Cannot add more than one vector field\n";
2250       error += "Please remove first ";
2251       error += DataTree->topLevelItem(index)->child(child)->data(COLUMN_IMAGE_NAME,Qt::DisplayRole).toString();
2252       QMessageBox::information(this,tr("Problem adding vector field!"),error);
2253       return;
2254     }
2255
2256     QString Extensions = "Images ( *.mhd *.mha *.vf *.nii *.nrrd *.nhdr)";
2257     // Extensions += ";;Images ( *.mha)";
2258     // Extensions += ";;VF Images ( *.vf)";
2259     // Extensions += ";;nii Images ( *.nii)";
2260     // Extensions += ";;nrrd Images ( *.nrrd)";
2261     // Extensions += ";;nhdr Images ( *.nhdr)";
2262     Extensions += ";;All Files (*)";
2263     QString file = QFileDialog::getOpenFileName(this,tr("Load deformation field"),mInputPathName,Extensions);
2264     if (!file.isEmpty())
2265       AddField(file,index);
2266 }
2267 //------------------------------------------------------------------------------
2268
2269
2270 //------------------------------------------------------------------------------
2271 void vvMainWindow::AddFieldEntry(QString filename,int index,bool from_disk)
2272 {
2273   //create an item in the tree with good settings
2274   QTreeWidgetItem *item = new QTreeWidgetItem();
2275   item->setData(0,Qt::UserRole,filename.toStdString().c_str());
2276   item->setData(1,Qt::UserRole,tr("vector"));
2277   QFileInfo fileinfo(filename); //Do not show the path
2278   item->setData(COLUMN_IMAGE_NAME,Qt::DisplayRole,fileinfo.fileName());
2279   item->setToolTip(COLUMN_IMAGE_NAME, mSlicerManagers[index]->GetListOfAbsoluteFilePathInOneString("vector").c_str());
2280   qApp->processEvents();
2281
2282   for (int j = 1; j <= 4; j++) {
2283     item->setData(j,Qt::CheckStateRole,DataTree->topLevelItem(index)->data(j,Qt::CheckStateRole));
2284   }
2285
2286   //Create the buttons for reload and close
2287   qApp->processEvents();
2288   QTreePushButton* cButton = new QTreePushButton;
2289   cButton->setItem(item);
2290   cButton->setColumn(COLUMN_CLOSE_IMAGE);
2291   cButton->setToolTip(tr("close vector field"));
2292   cButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/exit.png")));
2293   connect(cButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
2294     this,SLOT(CloseImage(QTreeWidgetItem*, int)));
2295
2296   QTreePushButton* rButton = new QTreePushButton;
2297   rButton->setItem(item);
2298   rButton->setColumn(COLUMN_RELOAD_IMAGE);
2299   rButton->setToolTip(tr("reload vector field"));
2300   rButton->setEnabled(from_disk);
2301   rButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/rotateright.png")));
2302   connect(rButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
2303     this,SLOT(ReloadImage(QTreeWidgetItem*, int)));
2304
2305   DataTree->topLevelItem(index)->setExpanded(1);
2306   DataTree->topLevelItem(index)->addChild(item);
2307   DataTree->setItemWidget(item, COLUMN_RELOAD_IMAGE, rButton);
2308   DataTree->setItemWidget(item, COLUMN_CLOSE_IMAGE, cButton);
2309
2310   //set the id of the image
2311   QString id = DataTree->topLevelItem(index)->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString();
2312   item->setData(COLUMN_IMAGE_NAME,Qt::UserRole,id.toStdString().c_str());
2313   UpdateTree();
2314   qApp->processEvents();
2315   ImageInfoChanged();
2316   QApplication::restoreOverrideCursor();
2317 }
2318 //------------------------------------------------------------------------------
2319
2320
2321 //------------------------------------------------------------------------------
2322 void vvMainWindow::AddField(vvImage::Pointer vf,QString file,int index)
2323 {
2324   QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
2325   vvSlicerManager* imageManager = mSlicerManagers[index];
2326   if (imageManager->SetVF(vf,file.toStdString())) {
2327     AddFieldEntry(file,index,false);
2328   } else {
2329     QString error = "Cannot import the vector field for this image.\n";
2330     error += imageManager->GetLastError().c_str();
2331     QMessageBox::information(this,tr("Problem reading VF !"),error);
2332   }
2333   QApplication::restoreOverrideCursor();
2334 }
2335 //------------------------------------------------------------------------------
2336
2337
2338 //------------------------------------------------------------------------------
2339 void vvMainWindow::AddField(QString file,int index)
2340 {
2341   if (QFile::exists(file)) {
2342     mInputPathName = itksys::SystemTools::GetFilenamePath(file.toStdString()).c_str();
2343
2344     //init the progress events
2345     QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
2346     vvProgressDialog progress("Opening " + file.toStdString());
2347     qApp->processEvents();
2348
2349     //read the vector and put it in the current mSlicerManager
2350     vvSlicerManager* imageManager = mSlicerManagers[index];
2351     qApp->processEvents();
2352
2353     std::string filename = itksys::SystemTools::GetFilenameWithoutExtension(file.toStdString()).c_str();
2354     if (imageManager->SetVF(file.toStdString())) {
2355       imageManager->Render();
2356       AddFieldEntry(file,index,true);
2357     } else {
2358       QApplication::restoreOverrideCursor();
2359       QString error = "Cannot import the vector field for this image.\n";
2360       error += imageManager->GetLastError().c_str();
2361       QMessageBox::information(this,tr("Problem reading VF !"),error);
2362     }
2363   } else
2364     QMessageBox::information(this,tr("Problem reading VF !"),"File doesn't exist!");
2365
2366 }
2367 //------------------------------------------------------------------------------
2368
2369
2370 //------------------------------------------------------------------------------
2371 void vvMainWindow::SetVFProperty(int subsampling, int scale, int log, int width, double r, double g, double b)
2372 {
2373   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2374   if (mSlicerManagers[index]->GetSlicer(0)->GetVF()) {
2375     for (int i = 0; i < 4; i++) {
2376       mSlicerManagers[index]->GetSlicer(i)->SetVFSubSampling(subsampling);
2377       mSlicerManagers[index]->GetSlicer(i)->SetVFScale(scale);
2378       mSlicerManagers[index]->GetSlicer(i)->SetVFWidth(width);
2379       mSlicerManagers[index]->GetSlicer(i)->SetVFColor(r,g,b);
2380       if (log > 0)
2381         mSlicerManagers[index]->GetSlicer(i)->SetVFLog(1);
2382       else
2383         mSlicerManagers[index]->GetSlicer(i)->SetVFLog(0);
2384     }
2385   }
2386 }
2387 //------------------------------------------------------------------------------
2388
2389
2390 //------------------------------------------------------------------------------
2391 void vvMainWindow::SetOverlayProperty(int color, int linked, double window, double level)
2392 {
2393   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2394   if (mSlicerManagers[index]->GetSlicer(0)->GetOverlay()) {
2395     mSlicerManagers[index]->SetOverlayColor(color);
2396     mSlicerManagers[index]->SetColorMap(0);
2397     mSlicerManagers[index]->SetLinkOverlayWindowLevel(linked);
2398     mSlicerManagers[index]->SetOverlayColorWindow(window);
2399     mSlicerManagers[index]->SetOverlayColorLevel(level);
2400     mSlicerManagers[index]->Render();
2401   }
2402 }
2403 //------------------------------------------------------------------------------
2404
2405 //------------------------------------------------------------------------------
2406 void vvMainWindow::SetFusionProperty(int opacity, int thresOpacity, int colormap,double window, double level, bool showLegend)
2407 {
2408   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2409   if (mSlicerManagers[index]->GetSlicer(0)->GetFusion()) {
2410     mSlicerManagers[index]->SetFusionColorMap(colormap);
2411     mSlicerManagers[index]->SetFusionOpacity(opacity);
2412     mSlicerManagers[index]->SetFusionThresholdOpacity(thresOpacity);
2413     mSlicerManagers[index]->SetFusionWindow(window);
2414     mSlicerManagers[index]->SetFusionLevel(level);
2415     mSlicerManagers[index]->SetFusionShowLegend(showLegend);
2416     mSlicerManagers[index]->SetColorMap(0);
2417     mSlicerManagers[index]->Render();
2418   }
2419 }
2420 //------------------------------------------------------------------------------
2421
2422
2423 //------------------------------------------------------------------------------
2424 void vvMainWindow::SelectFusionSequence()
2425 {
2426   //get the index of the slicer manager of the main sequence (CT)
2427   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2428   //check if one overlay image is already associated
2429   for (int child = 0; child < DataTree->topLevelItem(index)->childCount(); child++)
2430     if ( (DataTree->topLevelItem(index)->child(child)->data(1,Qt::UserRole).toString() == "fusion") ||
2431       (DataTree->topLevelItem(index)->child(child)->data(1,Qt::UserRole).toString() == "fusionSequence") ) {
2432         QString error = "Cannot add more than one compared image\n";
2433         error += "Please remove first ";
2434         error += DataTree->topLevelItem(index)->child(child)->data(COLUMN_IMAGE_NAME,Qt::DisplayRole).toString();
2435         QMessageBox::information(this,tr("Problem adding compared image !"),error);
2436         return;
2437     }
2438
2439     QString Extensions = EXTENSIONS;
2440     Extensions += ";;All Files (*)";
2441     QStringList files = QFileDialog::getOpenFileNames(this,tr("Load Overlay image sequence"),mInputPathName,Extensions);
2442     if (files.isEmpty())
2443       return;
2444
2445     std::vector<std::string> vecFileNames;
2446     for (int i = 0; i < files.size(); i++) {
2447       vecFileNames.push_back(files[i].toStdString());
2448     }
2449
2450     //associate the secondary sequence (US) to the main one
2451     AddFusionSequence(index,vecFileNames,vvImageReader::MERGEDWITHTIME);
2452 }
2453 //------------------------------------------------------------------------------
2454
2455
2456 //------------------------------------------------------------------------------
2457 void vvMainWindow::SelectFusionSequenceCorrespondances()
2458 {
2459   //make sure the index is right?
2460   //in the end, I should attach the temporal data to the right sequence!
2461   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2462   //in case the other sequence got selected, make sure we select the primary sequence
2463   if ( (!mSlicerManagers[index]->GetSlicer(0)->GetFusion()) && mSlicerManagers[index]->GetFusionSequenceIndexOfLinkedManager()>=0 ) {
2464     index = mSlicerManagers[index]->GetFusionSequenceIndexOfLinkedManager();
2465   }
2466
2467   //open a dialog box to find a file
2468   //QString Extensions = EXTENSIONS;
2469   QString Extensions = ";;All Files (*)";
2470   QString fileName = QFileDialog::getOpenFileName(this,tr("Load respiratory signal for fused sequence"),mInputPathName,Extensions);
2471   if (fileName.isNull())
2472     return;
2473
2474   //read it as a vector of values
2475   vnl_vector<double> tmpVect;
2476
2477   std::ifstream file;
2478   file.open(fileName.toStdString().c_str());
2479   tmpVect.read_ascii(file);
2480   file.close();
2481
2482   //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
2483   bool signalOK = true;
2484   unsigned nbFrameMain = mSlicerManagers[index]->GetImage()->GetTransform().size();
2485   unsigned nbFrameSecondary = mSlicerManagers[index]->GetFusionSequenceNbFrames();
2486   std::cout<<"nbFrameMain = "<<nbFrameMain<<", nbFrameSecondary= "<<nbFrameSecondary<<", signal size: "<<tmpVect.size()<<std::endl;
2487   std::vector<unsigned> temporalCorrespondances;
2488   if ( tmpVect.size() == nbFrameMain + nbFrameSecondary ) {
2489     for (unsigned i=0 ; i<tmpVect.size() ; i++) {
2490       if (i<nbFrameMain) { //first part of the file: i -> index in secondary seq.
2491         if ( tmpVect(i)<nbFrameSecondary ) temporalCorrespondances.push_back(tmpVect(i));
2492         else { signalOK=false; break; } //pointing outside the secondary sequence...
2493       }
2494       else { //first part of the file -> index in secondary seq.
2495         if ( tmpVect(i)<nbFrameMain ) temporalCorrespondances.push_back(tmpVect(i));
2496         else { signalOK=false; break; } //pointing outside the secondary sequence...
2497       }
2498     }
2499   }
2500   else {signalOK=false;}
2501   if (!signalOK) {//else, send a message to signal the failure...
2502     QString error = "The provided temporal correspondances is invalid - check tooltip.\n";
2503     error += "Ignoring file: " + fileName;
2504     QMessageBox::information(this,tr("Problem adding temporal correspondances!"),error);
2505     return;
2506   }
2507   else {
2508     //for convenience, associate this sequence to both the current slicer manager, and to the linked one
2509     mSlicerManagers[index]->SetFusionSequenceCorrespondances(temporalCorrespondances);
2510     mSlicerManagers[ mSlicerManagers[index]->GetFusionSequenceIndexOfLinkedManager() ]->SetFusionSequenceCorrespondances(temporalCorrespondances);
2511     overlayPanel->enableFusionSequenceTemporalSync();
2512   }
2513
2514 }
2515 //------------------------------------------------------------------------------
2516
2517
2518 //------------------------------------------------------------------------------
2519 //when this function is called index is the slicer manager index corresponding to the main sequence (CT)
2520 //the files behind fileNames points to the data for the secondary sequence
2521 void vvMainWindow::AddFusionSequence(int index, std::vector<std::string> fileNames, vvImageReader::LoadedImageType type)
2522 {
2523   QString file(fileNames[0].c_str());
2524   if (QFile::exists(file))
2525   {
2526     mInputPathName = itksys::SystemTools::GetFilenamePath(file.toStdString()).c_str();
2527     itk::ImageIOBase::Pointer reader = itk::ImageIOFactory::CreateImageIO(
2528       file.toStdString().c_str(), itk::ImageIOFactory::ReadMode);
2529     std::sort (fileNames.begin(), fileNames.end());//make sure the files are sorted.
2530     reader->SetFileName(fileNames[0].c_str());
2531     reader->ReadImageInformation();
2532     std::string component = reader->GetComponentTypeAsString(reader->GetComponentType());
2533     int dimension = reader->GetNumberOfDimensions();
2534     QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
2535     vvProgressDialog progress("Opening " + file.toStdString());
2536     qApp->processEvents();
2537
2538     std::string filename = itksys::SystemTools::GetFilenameWithoutExtension(file.toStdString()).c_str();
2539
2540     if (mSlicerManagers[index]->SetFusionSequence(fileNames,dimension, component,type)) {
2541       //create an item in the tree with good settings
2542       QTreeWidgetItem *item = new QTreeWidgetItem();
2543       item->setData(0,Qt::UserRole,file.toStdString().c_str());
2544       item->setData(1,Qt::UserRole,tr("fusionSequence"));
2545
2546       QFileInfo fileinfo(file); //Do not show the path
2547       item->setData(COLUMN_IMAGE_NAME,Qt::DisplayRole,fileinfo.fileName());
2548       item->setToolTip(COLUMN_IMAGE_NAME, mSlicerManagers[index]->GetListOfAbsoluteFilePathInOneString("fusionSequence").c_str());
2549       qApp->processEvents();
2550       for (int j = 1; j <= 4; j++) {
2551         item->setData(j,Qt::CheckStateRole,DataTree->topLevelItem(index)->data(j,Qt::CheckStateRole));
2552       }
2553
2554       //Create the buttons for reload and close
2555       qApp->processEvents();
2556       QTreePushButton* cButton = new QTreePushButton;
2557       cButton->setItem(item);
2558       cButton->setColumn(COLUMN_CLOSE_IMAGE);
2559       cButton->setToolTip(tr("close image"));
2560       cButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/exit.png")));
2561       connect(cButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
2562         this,SLOT(CloseImage(QTreeWidgetItem*, int)));
2563
2564       QTreePushButton* rButton = new QTreePushButton;
2565       rButton->setItem(item);
2566       rButton->setColumn(COLUMN_RELOAD_IMAGE);
2567       rButton->setToolTip(tr("reload image"));
2568       rButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/rotateright.png")));
2569       connect(rButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
2570         this,SLOT(ReloadImage(QTreeWidgetItem*, int)));
2571
2572       DataTree->topLevelItem(index)->setExpanded(1);
2573       DataTree->topLevelItem(index)->addChild(item);
2574       DataTree->setItemWidget(item, COLUMN_CLOSE_IMAGE, cButton);
2575       DataTree->setItemWidget(item, COLUMN_RELOAD_IMAGE, rButton);
2576
2577       //store the original transform matrix
2578       int indexParent = GetSlicerIndexFromItem( DataTree->topLevelItem(index) );
2579       mSlicerManagers[indexParent]->SetFusionSequenceMainTransformMatrix( mSlicerManagers[indexParent]->GetSlicer(0)->GetImage()->GetTransform()[0]->GetMatrix() );
2580
2581       //set the id of the image
2582       QString id = DataTree->topLevelItem(index)->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString();
2583       item->setData(COLUMN_IMAGE_NAME,Qt::UserRole,id.toStdString().c_str());
2584       UpdateTree();
2585       qApp->processEvents();
2586
2587       //ImageInfoChanged();
2588
2589       QApplication::restoreOverrideCursor();
2590       // Update the display to update, e.g., the sliders
2591       for(int i=0; i<4; i++)
2592         DisplaySliders(index, i);
2593
2594
2595       //This loads the secondary sequence (US) as an independent sequence
2596       LoadImages(fileNames, type);
2597       //reset the transforms to identity
2598       //FIX -- and set the thickness of the US slices to a large value (necessary for visualization purposes...)
2599       double sp_x, sp_y, sp_z;
2600       mSlicerManagers[indexParent]->GetImage()->GetVTKImages()[0]->GetSpacing(sp_x, sp_y, sp_z);
2601       sp_z = std::max(sp_x, std::max(sp_y, sp_z)) + 0.5; //
2602       for (unsigned i=0 ; i<mSlicerManagers.back()->GetImage()->GetTransform().size() ; i++) {
2603         sp_x = mSlicerManagers.back()->GetImage()->GetVTKImages()[i]->GetSpacing()[0];
2604         sp_y = mSlicerManagers.back()->GetImage()->GetVTKImages()[i]->GetSpacing()[1];
2605         mSlicerManagers.back()->GetImage()->GetVTKImages()[i]->SetSpacing( sp_x, sp_y, sp_z);
2606         mSlicerManagers.back()->GetImage()->GetTransform()[i]->Identity();
2607         mSlicerManagers.back()->GetImage()->GetTransform()[i]->Update();
2608       }
2609
2610       //automatically link both images...
2611       AddLink(mSlicerManagers[indexParent]->GetId().c_str(), mSlicerManagers.back()->GetId().c_str(), false);
2612
2613       //tie the main and secondary sequences by raising flags and informing each another of their respective SlicerManager indices
2614       mSlicerManagers[indexParent]->SetFusionSequenceIndexOfLinkedManager(mSlicerManagers.size()-1);
2615       mSlicerManagers[indexParent]->SetFusionSequenceInvolvmentCode(0); //main sequence
2616       mSlicerManagers.back()->SetFusionSequenceIndexOfLinkedManager(indexParent);
2617       mSlicerManagers.back()->SetFusionSequenceInvolvmentCode(1); //secondary sequence
2618       for (unsigned i=0 ; i<4 ; i++) {
2619         mSlicerManagers.back()->GetSlicer(i)->SetFusionSequenceCode(1); //flag the slicers of the secondary sequence
2620       }
2621
2622     } else {
2623       QApplication::restoreOverrideCursor();
2624       QString error = "Cannot import the new image.\n";
2625       error += mSlicerManagers[index]->GetLastError().c_str();
2626       QMessageBox::information(this,tr("Problem reading image !"),error);
2627     }
2628     WindowLevelChanged();
2629     ImageInfoChanged(); //this internally calls WindowLevelChanged...
2630   }
2631   else {
2632     QMessageBox::information(this,tr("Problem reading fusion sequence !"),"File doesn't exist!");
2633     return;
2634   }
2635
2636 }
2637 //------------------------------------------------------------------------------
2638
2639
2640 //------------------------------------------------------------------------------
2641 //fusionSequenceFrameIndex and fusionSequenceNbFrames are relative to the secondary sequence (US)
2642 void vvMainWindow::SetFusionSequenceProperty(int fusionSequenceFrameIndex, bool spatialSyncFlag, unsigned int fusionSequenceNbFrames, bool temporalSyncFlag)
2643 {
2644   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2645
2646   if (!mSlicerManagers[index]->IsInvolvedInFusionSequence()) return;
2647
2648   //check if the focus moved to the linked sequence, and in this case, select the master sequence instead
2649   if (!mSlicerManagers[index]->IsMainSequenceOfFusionSequence()) {
2650     index = mSlicerManagers[index]->GetFusionSequenceIndexOfLinkedManager();
2651   }
2652   int secondaryIndex = mSlicerManagers[index]->GetFusionSequenceIndexOfLinkedManager();
2653   if (secondaryIndex==-1) return; //this should never happen
2654   if ( (!mSlicerManagers[index]->IsMainSequenceOfFusionSequence()) ||
2655     (!mSlicerManagers[secondaryIndex]->IsSecondarySequenceOfFusionSequence()) )
2656   {return;} //this should never happen, raise an exception?
2657
2658   if (mSlicerManagers[index]->GetSlicer(0)->GetFusion()) {
2659
2660     //First, if the spatialSync button is unchecked, then reposition the parent sequence (CT) in its original coordinate frame
2661     if ( (!spatialSyncFlag) && (mSlicerManagers[index]->GetFusionSequenceSpatialSyncFlag()) ) {
2662       for ( unsigned i=0 ; i<mSlicerManagers[index]->GetSlicer(0)->GetImage()->GetTransform().size() ; i++ ) {
2663         mSlicerManagers[index]->GetSlicer(0)->GetImage()->GetTransform()[i]->SetMatrix( mSlicerManagers[index]->GetFusionSequenceMainTransformMatrix() );
2664         mSlicerManagers[index]->GetSlicer(0)->GetImage()->GetTransform()[i]->Update();
2665       }
2666
2667       for (int i=0; i<mSlicerManagers[index]->GetNumberOfSlicers(); i++) {
2668         mSlicerManagers[index]->GetSlicer(i)->ForceUpdateDisplayExtent();
2669         mSlicerManagers[index]->GetSlicer(i)->Render();
2670       }
2671     }
2672
2673     //then, update the property values in the slicer manager
2674     mSlicerManagers[index]->SetFusionSequenceLength(fusionSequenceNbFrames);
2675     mSlicerManagers[index]->SetFusionSequenceSpatialSyncFlag(spatialSyncFlag);
2676     mSlicerManagers[index]->SetFusionSequenceTemporalSyncFlag(temporalSyncFlag);
2677     mSlicerManagers[index]->SetFusionSequenceFrameIndex(fusionSequenceFrameIndex);
2678
2679     //select the right frame of the US sequence
2680     mSlicerManagers[index]->SetFusionSequenceTSlice(fusionSequenceFrameIndex); //here, I should only update the overlayed sequence
2681     mSlicerManagers[secondaryIndex]->SetTSlice(fusionSequenceFrameIndex, false); //this should update the secondary sequence (individual version)
2682
2683     //update the horizontal sliders of the main window
2684     overlayPanel->updateFusionSequenceSliderValueFromWindow(fusionSequenceFrameIndex, false);
2685
2686     if (spatialSyncFlag) { //reslice the CT
2687
2688       if (temporalSyncFlag) { //do the temporal synchronisation
2689         int mainSequenceFrameIndex=0;
2690         //estimate the TSlice to set to the CT
2691         unsigned nbFramesMain = mSlicerManagers[index]->GetImage()->GetTransform().size();
2692         mainSequenceFrameIndex = mSlicerManagers[index]->GetFusionSequenceCorrespondances()[ nbFramesMain + fusionSequenceFrameIndex];
2693         //and set it!
2694         mSlicerManagers[index]->SetTSlice(mainSequenceFrameIndex, false);
2695         //warning, there is a loopback, and modification of the TSlice in main sequence forces an update of the TSlice in secondary, etc...
2696       }
2697
2698
2699       //Set the transform matrix of the parent sequence (typically CT / 4DCT)
2700       vtkSmartPointer<vtkMatrix4x4> tmpMat = vtkSmartPointer<vtkMatrix4x4>::New();
2701       vtkMatrix4x4::Invert( mSlicerManagers[index]->GetFusionSequenceInitialTransformMatrixAtFrame(fusionSequenceFrameIndex), tmpMat );
2702       for ( unsigned i=0 ; i<mSlicerManagers[index]->GetSlicer(0)->GetImage()->GetTransform().size() ; i++ ) {
2703         mSlicerManagers[index]->GetSlicer(0)->GetImage()->GetTransform()[i]->SetMatrix( mSlicerManagers[index]->GetFusionSequenceMainTransformMatrix() );
2704         mSlicerManagers[index]->GetSlicer(0)->GetImage()->GetTransform()[i]->PreMultiply();
2705         mSlicerManagers[index]->GetSlicer(0)->GetImage()->GetTransform()[i]->Concatenate( tmpMat );
2706         mSlicerManagers[index]->GetSlicer(0)->GetImage()->GetTransform()[i]->Update();
2707       }
2708
2709       for (int i=0; i<mSlicerManagers[index]->GetNumberOfSlicers(); i++) {
2710         mSlicerManagers[index]->GetSlicer(i)->ForceUpdateDisplayExtent();
2711         mSlicerManagers[index]->GetSlicer(i)->Render();
2712       }
2713
2714     }
2715
2716   }
2717 }
2718 //------------------------------------------------------------------------------
2719
2720
2721 //------------------------------------------------------------------------------
2722 void vvMainWindow::SaveAs()
2723 {
2724   if (DataTree->selectedItems()[0]->data(1,Qt::UserRole).toString() == "vector") {
2725     QMessageBox::warning(this,tr("Unsupported type"),tr("Sorry, saving a vector field is unsupported for the moment"));
2726     return;
2727   }
2728
2729   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2730   int dimension = mSlicerManagers[index]->GetDimension();
2731   QStringList OutputListeFormat;
2732   OutputListeFormat.clear();
2733   if (dimension == 1) {
2734     OutputListeFormat.push_back(".mhd");
2735     OutputListeFormat.push_back(".mha");
2736   }
2737   if (dimension == 2) {
2738     OutputListeFormat.push_back(".bmp");
2739     OutputListeFormat.push_back(".png");
2740     OutputListeFormat.push_back(".jpeg");
2741     OutputListeFormat.push_back(".tif");
2742     OutputListeFormat.push_back(".mhd");
2743     OutputListeFormat.push_back(".mha");
2744     OutputListeFormat.push_back(".hdr");
2745     OutputListeFormat.push_back(".vox");
2746   } else if (dimension == 3) {
2747     OutputListeFormat.push_back(".mhd");
2748     OutputListeFormat.push_back(".mha");
2749     OutputListeFormat.push_back(".nii");
2750     OutputListeFormat.push_back(".nrrd");
2751     OutputListeFormat.push_back(".nhdr");
2752     OutputListeFormat.push_back(".hdr");
2753     OutputListeFormat.push_back(".vox");
2754   } else if (dimension == 4) {
2755     OutputListeFormat.push_back(".mhd");
2756     OutputListeFormat.push_back(".mha");
2757     OutputListeFormat.push_back(".nii");
2758     OutputListeFormat.push_back(".nrrd");
2759     OutputListeFormat.push_back(".nhdr");
2760   }
2761   QString Extensions = "AllFiles(*.*)";
2762   for (int i = 0; i < OutputListeFormat.count(); i++) {
2763     Extensions += ";;Images ( *";
2764     Extensions += OutputListeFormat[i];
2765     Extensions += ")";
2766   }
2767   QString fileName = QFileDialog::getSaveFileName(this,
2768     tr("Save As"),
2769     mSlicerManagers[index]->GetFileName().c_str(),
2770     Extensions);
2771   if (!fileName.isEmpty()) {
2772     std::string fileformat = itksys::SystemTools::GetFilenameLastExtension(fileName.toStdString());
2773     if (OutputListeFormat.contains(
2774       fileformat.c_str())) {
2775         QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
2776         std::string action = "Saving";
2777         vvProgressDialog progress("Saving "+fileName.toStdString());
2778         qApp->processEvents();
2779         vvImageWriter::Pointer writer = vvImageWriter::New();
2780         writer->SetOutputFileName(fileName.toStdString());
2781         writer->SetInput(mSlicerManagers[index]->GetImage());
2782
2783         // Check on transform and prompt user
2784         writer->SetSaveTransform(false);
2785         bool bId = true;
2786         for(int i=0; i<4; i++)
2787           for(int j=0; j<4; j++) {
2788             // TODO SR and BP: check on the list of transforms and not the first only
2789             double elt = mSlicerManagers[index]->GetImage()->GetTransform()[0]->GetMatrix()->GetElement(i,j);
2790             if(i==j && elt!=1.)
2791               bId = false;
2792             if(i!=j && elt!=0.)
2793               bId = false;
2794           }
2795           if( !bId ) {
2796             QString warning = "The image has an associated linear transform. Do you want to save it along?";
2797             QMessageBox msgBox(QMessageBox::Warning, tr("Save transform"), warning, 0, this);
2798             msgBox.addButton(tr("Yes"), QMessageBox::AcceptRole);
2799             msgBox.addButton(tr("No"), QMessageBox::RejectRole);
2800             if (msgBox.exec() == QMessageBox::AcceptRole)
2801               writer->SetSaveTransform(true);
2802           }
2803
2804           writer->Update();
2805           QApplication::restoreOverrideCursor();
2806           if (writer->GetLastError().size()) {
2807             QString error = "Saving did not succeed\n";
2808             error += writer->GetLastError().c_str();
2809             QMessageBox::information(this,tr("Saving Problem"),error);
2810             SaveAs();
2811           }
2812     } else {
2813       QString error = fileformat.c_str();
2814       if (error.isEmpty())
2815         error += "no file format specified !";
2816       else
2817         error += " format unknown !!!\n";
2818       QMessageBox::information(this,tr("Saving Problem"),error);
2819       SaveAs();
2820     }
2821   }
2822 }
2823 //------------------------------------------------------------------------------
2824
2825 //------------------------------------------------------------------------------
2826 void vvMainWindow::SaveCurrentState()
2827 {
2828   QString Extensions = "XML Files(*.xml)";
2829   QString fileName = QFileDialog::getSaveFileName(this,
2830     tr("Save Current Window State"),
2831     "",
2832     Extensions);
2833
2834   SaveCurrentStateAs(fileName.toStdString());
2835 }
2836 //------------------------------------------------------------------------------
2837
2838 //------------------------------------------------------------------------------
2839 void vvMainWindow::SaveCurrentStateAs(const std::string& stateFile)
2840 {
2841   vvSaveState save_state;
2842   save_state.Run(this, stateFile);
2843 }
2844
2845 //------------------------------------------------------------------------------
2846 void vvMainWindow::ReadSavedState()
2847 {
2848   QString Extensions = "XML Files(*.xml)";
2849   QString fileName = QFileDialog::getOpenFileName(this,
2850     tr("Load Window State"),
2851     "",
2852     Extensions);
2853
2854   ReadSavedStateFile(fileName.toStdString());
2855 }
2856 //------------------------------------------------------------------------------
2857
2858 //------------------------------------------------------------------------------
2859 void vvMainWindow::ReadSavedStateFile(const std::string& stateFile)
2860 {
2861   vvReadState read_state;
2862   read_state.Run(this, stateFile);
2863 }
2864 //------------------------------------------------------------------------------
2865
2866 //------------------------------------------------------------------------------
2867 void vvMainWindow::LinkAllImages()
2868 {
2869   linkPanel->linkAll();
2870 }
2871
2872 //------------------------------------------------------------------------------
2873 void vvMainWindow::AddLink(QString image1,QString image2,bool fromPanel)
2874 {
2875   if (!fromPanel) {
2876     // delegate to linkPanel if call came from elsewhere...
2877     linkPanel->addLinkFromIds(image1, image2);
2878     return;
2879   }
2880
2881   unsigned int sm1 = 0;
2882   unsigned int sm2 = 0;
2883
2884   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
2885     if (image1.toStdString() == mSlicerManagers[i]->GetId()) {
2886       mSlicerManagers[i]->AddLink(image2.toStdString());
2887       sm1 = i;
2888     }
2889     if (image2.toStdString() == mSlicerManagers[i]->GetId()) {
2890       mSlicerManagers[i]->AddLink(image1.toStdString());
2891       sm2 = i;
2892     }
2893   }
2894
2895   if (linkPanel->isLinkAll())   {
2896     emit UpdateLinkedNavigation(mSlicerManagers[sm1]->GetId(), mSlicerManagers[mCurrentPickedImageIndex], mSlicerManagers[mCurrentPickedImageIndex]->GetSlicer(0));
2897     emit UpdateLinkedNavigation(mSlicerManagers[sm2]->GetId(), mSlicerManagers[mCurrentPickedImageIndex], mSlicerManagers[mCurrentPickedImageIndex]->GetSlicer(0));
2898   } else {
2899     emit UpdateLinkedNavigation(mSlicerManagers[sm2]->GetId(), mSlicerManagers[sm1], mSlicerManagers[sm1]->GetSlicer(0));
2900   }
2901 }
2902
2903 //------------------------------------------------------------------------------
2904
2905
2906 //------------------------------------------------------------------------------
2907 void vvMainWindow::RemoveLink(QString image1,QString image2)
2908 {
2909   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
2910     if (image1.toStdString() == mSlicerManagers[i]->GetId()) {
2911       mSlicerManagers[i]->RemoveLink(image2.toStdString());
2912     }
2913     if (image2.toStdString() == mSlicerManagers[i]->GetId()) {
2914       mSlicerManagers[i]->RemoveLink(image1.toStdString());
2915     }
2916   }
2917 }
2918 //------------------------------------------------------------------------------
2919
2920 //------------------------------------------------------------------------------
2921 void vvMainWindow::ChangeImageWithIndexOffset(vvSlicerManager *sm, int slicer, int offset)
2922 {
2923   if(mSlicerManagers.size()==1)
2924     return;
2925
2926   int index = 0;
2927   while(sm != mSlicerManagers[index])
2928     index++;
2929   index = (index+offset+mSlicerManagers.size()) % mSlicerManagers.size();
2930
2931   QTreeWidgetItem* item = GetItemFromSlicerManager(mSlicerManagers[index]);
2932   item->setData(slicer+1,Qt::CheckStateRole,2);         //change checkbox
2933   CurrentImageChanged(mSlicerManagers[index]->GetId()); //select new image
2934   DisplayChanged(item,slicer+1);
2935 }
2936 //------------------------------------------------------------------------------
2937 void vvMainWindow::HorizontalSliderMoved(int value,int column, int slicer_index)
2938 {
2939   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
2940     if (DataTree->topLevelItem(i)->data(column,Qt::CheckStateRole).toInt() > 1) {
2941       //i is the SlicerManager that is in charge of this slicer.
2942       if (mSlicerManagers[i]->IsInvolvedInFusionSequence()) {
2943         //if the slicerManager is involved in a fusionSequence as the secondary sequence, then update the slider position in the overlay panel and everything accordingly
2944         if (mSlicerManagers[i]->IsSecondarySequenceOfFusionSequence()) {
2945           overlayPanel->updateFusionSequenceSliderValueFromWindow(value, true);
2946         }
2947         else { //if this is the primary sequence that has been modified
2948           if (mSlicerManagers[i]->GetFusionSequenceTemporalSyncFlag()) {
2949             //WARNING: for some obscure reason, there are problems when accessing mSlicerManagers[mSlicerManagers[i]->GetFusionSequenceIndexOfLinkedManager()]->GetFusionSequenceFrameIndex();
2950
2951             int estimatedValue=0;
2952             //estimate a corresponding time index for the secondary (US) sequence, and update it accordingly.
2953             estimatedValue = mSlicerManagers[i]->GetFusionSequenceCorrespondances()[ value ];
2954             //TODO: at the moment, there is a loop in TSlice modifications
2955             //modifying sequence 1 causes seq 2 to update, which in turns update seq1...
2956             //I disable control on seq1 at the moment.
2957             //overlayPanel->updateFusionSequenceSliderValueFromWindow(estimatedValue, true);
2958           }
2959         }
2960       }
2961
2962       for (int j = 0; j < 4; j++) {
2963         mSlicerManagers[i]->SetTSliceInSlicer(value,j);
2964       }
2965       mSlicerManagers[i]->GetSlicer(slicer_index)->Render();
2966       break;
2967     }
2968   }
2969 }
2970 //------------------------------------------------------------------------------
2971
2972
2973 //------------------------------------------------------------------------------
2974 void vvMainWindow::NOHorizontalSliderMoved()
2975 {
2976   // if (mCurrentTime == NOHorizontalSlider->value()) return;
2977   HorizontalSliderMoved(NOHorizontalSlider->value(),COLUMN_UL_VIEW,0);
2978   //  mCurrentTime = NOHorizontalSlider->value();
2979 }
2980 //------------------------------------------------------------------------------
2981
2982
2983 //------------------------------------------------------------------------------
2984 void vvMainWindow::NEHorizontalSliderMoved()
2985 {
2986   // if (mCurrentTime == NEHorizontalSlider->value()) return;
2987   HorizontalSliderMoved(NEHorizontalSlider->value(),COLUMN_UR_VIEW,1);
2988   //  mCurrentTime = NEHorizontalSlider->value();
2989 }
2990 //------------------------------------------------------------------------------
2991
2992
2993 //------------------------------------------------------------------------------
2994 void vvMainWindow::SOHorizontalSliderMoved()
2995 {
2996   // if (mCurrentTime == SOHorizontalSlider->value()) return;
2997   HorizontalSliderMoved(SOHorizontalSlider->value(),COLUMN_DL_VIEW,2);
2998   // mCurrentTime = SOHorizontalSlider->value();
2999 }
3000 //------------------------------------------------------------------------------
3001
3002
3003 //------------------------------------------------------------------------------
3004 void vvMainWindow::SEHorizontalSliderMoved()
3005 {
3006   // if (mCurrentTime == SEHorizontalSlider->value()) return;
3007   HorizontalSliderMoved(SEHorizontalSlider->value(),COLUMN_DR_VIEW,3);
3008   // mCurrentTime = SEHorizontalSlider->value();
3009 }
3010 //------------------------------------------------------------------------------
3011
3012 //------------------------------------------------------------------------------
3013 void vvMainWindow::NOVerticalSliderChanged()
3014 {
3015   static int value=-1;
3016   if (value == NOVerticalSlider->value()) return;
3017   else value = NOVerticalSlider->value();
3018   //  int value = NOVerticalSlider->value();
3019   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
3020     if (DataTree->topLevelItem(i)->data(COLUMN_UL_VIEW,Qt::CheckStateRole).toInt() > 1) {
3021       if (mSlicerManagers[i]->GetSlicer(0)->GetSlice() != value) {
3022         mSlicerManagers[i]->GetSlicer(0)->SetSlice(value);
3023         mSlicerManagers[i]->VerticalSliderHasChanged(0, value);
3024
3025         // If nor Update/Render -> slider not work
3026         // only render = ok navigation, but for contour Update needed but slower ?
3027
3028         mSlicerManagers[i]->UpdateSlice(0);  // <-- DS add this. Not too much update ? YES. but needed for ImageContour ...
3029         //mSlicerManagers[i]->GetSlicer(0)->Render(); // <-- DS add this, needed for contour, seems ok ? not too slow ?
3030       }
3031       break;
3032     }
3033   }
3034 }
3035 //------------------------------------------------------------------------------
3036
3037
3038 //------------------------------------------------------------------------------
3039 void vvMainWindow::NEVerticalSliderChanged()
3040 {
3041   static int value=-1;
3042   if (value == NEVerticalSlider->value()) return;
3043   else value = NEVerticalSlider->value();
3044   //  int value = NEVerticalSlider->value();
3045   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
3046     if (DataTree->topLevelItem(i)->data(COLUMN_UR_VIEW,Qt::CheckStateRole).toInt() > 1) {
3047       if (mSlicerManagers[i]->GetSlicer(1)->GetSlice() != value) {
3048         mSlicerManagers[i]->GetSlicer(1)->SetSlice(value);
3049         mSlicerManagers[i]->VerticalSliderHasChanged(1, value);
3050         mSlicerManagers[i]->UpdateSlice(1);
3051         //mSlicerManagers[i]->GetSlicer(1)->Render(); // <-- DS add this, needed for contour, seems ok ? not too slow ?
3052       }
3053       break;
3054     }
3055   }
3056 }
3057 //------------------------------------------------------------------------------
3058
3059
3060 //------------------------------------------------------------------------------
3061 void vvMainWindow::SOVerticalSliderChanged()
3062 {
3063   static int value=-1;
3064   if (value == SOVerticalSlider->value()) return;
3065   else value = SOVerticalSlider->value();
3066   //int value = SOVerticalSlider->value();
3067   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
3068     if (DataTree->topLevelItem(i)->data(COLUMN_DL_VIEW,Qt::CheckStateRole).toInt() > 1) {
3069       if (mSlicerManagers[i]->GetSlicer(2)->GetSlice() != value) {
3070         mSlicerManagers[i]->GetSlicer(2)->SetSlice(value);
3071         mSlicerManagers[i]->VerticalSliderHasChanged(2, value);
3072         mSlicerManagers[i]->UpdateSlice(2);
3073         //mSlicerManagers[i]->GetSlicer(2)->Render(); // <-- DS add this, needed for contour, seems ok ? not too slow ?
3074       }
3075       // else { DD("avoid SOVerticalSlider slicer update"); }
3076       break;
3077     }
3078   }
3079 }
3080 //------------------------------------------------------------------------------
3081
3082
3083 //------------------------------------------------------------------------------
3084 void vvMainWindow::SEVerticalSliderChanged()
3085 {
3086   static int value=-1;
3087   if (value == SEVerticalSlider->value()) return;
3088   else value = SEVerticalSlider->value();
3089   // int value = SEVerticalSlider->value();
3090   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
3091     if (DataTree->topLevelItem(i)->data(COLUMN_DR_VIEW,Qt::CheckStateRole).toInt() > 1) {
3092       if (mSlicerManagers[i]->GetSlicer(3)->GetSlice() != value) {
3093         mSlicerManagers[i]->GetSlicer(3)->SetSlice(value);
3094         mSlicerManagers[i]->VerticalSliderHasChanged(3, value);
3095         mSlicerManagers[i]->UpdateSlice(3);
3096         //mSlicerManagers[i]->GetSlicer(3)->Render(); // <-- DS add this, needed for contour, seems ok ? not too slow ?
3097       }
3098       break;
3099     }
3100   }
3101 }
3102 //------------------------------------------------------------------------------
3103
3104
3105 //------------------------------------------------------------------------------
3106 void vvMainWindow::UpdateSlice(int slicer, int slice)
3107 {
3108   // DD("vvMainWindow::UpdateSlice");
3109   //   DD(slicer);
3110   //   DD(slice);
3111   if (slicer == 0) {
3112     //    if (slice != NOVerticalSlider->value())
3113     NOVerticalSlider->setValue(slice);
3114   } else {
3115     if (slicer == 1)
3116       NEVerticalSlider->setValue(slice);
3117     else {
3118       if (slicer == 2)
3119         SOVerticalSlider->setValue(slice);
3120       else {
3121         if (slicer == 3)
3122           SEVerticalSlider->setValue(slice);
3123       }
3124     }
3125   }
3126   // DD("vvMainWindow:UpdateSlice END");
3127 }
3128 //------------------------------------------------------------------------------
3129
3130
3131 //------------------------------------------------------------------------------
3132 void vvMainWindow::UpdateTSlice(int slicer, int slice, int code)
3133 {
3134   //FusionSequence: the slider value should be updated for slicers which show the same sequence as requested
3135   bool doUpdate=false;
3136   if (code==-1) doUpdate=true;
3137   else {
3138     for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
3139       if (DataTree->topLevelItem(i)->data(slicer+1,Qt::CheckStateRole).toInt() > 1) {
3140         //i is the active SlicerManager
3141         if (mSlicerManagers[i]->GetFusionSequenceInvolvmentCode()==code) doUpdate=true;
3142         break;
3143       }
3144     }
3145   }
3146   if (!doUpdate) return;
3147
3148   switch (slicer) {
3149   case 0:
3150     if (NOHorizontalSlider->value()==slice) return;
3151     NOHorizontalSlider->setValue(slice);
3152     break;
3153   case 1:
3154     if (NEHorizontalSlider->value()==slice) return;
3155     NEHorizontalSlider->setValue(slice);
3156     break;
3157   case 2:
3158     if (SOHorizontalSlider->value()==slice) return;
3159     SOHorizontalSlider->setValue(slice);
3160     break;
3161   case 3:
3162     if (SEHorizontalSlider->value()==slice) return;
3163     SEHorizontalSlider->setValue(slice);
3164     break;
3165   }
3166 }
3167 //------------------------------------------------------------------------------
3168
3169
3170 //------------------------------------------------------------------------------
3171 void vvMainWindow::UpdateSliceRange(int slicer, int min, int max, int tmin, int tmax)
3172 {
3173   //int position = int((min+max)/2);
3174   int position = mSlicerManagers[mCurrentPickedImageIndex]->GetSlicer(slicer)->GetSlice();
3175   if (slicer == 0) {
3176     NOVerticalSlider->setRange(min,max);
3177     NOHorizontalSlider->setRange(tmin,tmax);
3178     NOVerticalSlider->setValue(position);
3179   } else if (slicer == 1) {
3180     NEVerticalSlider->setRange(min,max);
3181     NEHorizontalSlider->setRange(tmin,tmax);
3182     NEVerticalSlider->setValue(position);
3183   } else if (slicer == 2) {
3184     SOVerticalSlider->setRange(min,max);
3185     SOHorizontalSlider->setRange(tmin,tmax);
3186     SOVerticalSlider->setValue(position);
3187   } else if (slicer == 3) {
3188     SEVerticalSlider->setRange(min,max);
3189     SEHorizontalSlider->setRange(tmin,tmax);
3190     SEVerticalSlider->setValue(position);
3191   }
3192 }
3193 //------------------------------------------------------------------------------
3194
3195
3196 //------------------------------------------------------------------------------
3197 void vvMainWindow::SaveNOScreenshot()
3198 {
3199   SaveScreenshot(NOViewWidget);
3200 }
3201 //------------------------------------------------------------------------------
3202
3203
3204 //------------------------------------------------------------------------------
3205 void vvMainWindow::SaveNEScreenshot()
3206 {
3207   SaveScreenshot(NEViewWidget);
3208 }
3209 //------------------------------------------------------------------------------
3210
3211
3212 //------------------------------------------------------------------------------
3213 void vvMainWindow::SaveSOScreenshot()
3214 {
3215   SaveScreenshot(SOViewWidget);
3216 }
3217 //------------------------------------------------------------------------------
3218
3219
3220 //------------------------------------------------------------------------------
3221 void vvMainWindow::SaveSEScreenshot()
3222 {
3223   SaveScreenshot(SEViewWidget);
3224 }
3225 //------------------------------------------------------------------------------
3226
3227
3228 //------------------------------------------------------------------------------
3229 void vvMainWindow::SaveScreenshotAllSlices()
3230 {
3231   QVTKWidget *widget = NOViewWidget;
3232
3233   int index = 0;// GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
3234   vvSlicerManager * SM = mSlicerManagers[index];
3235   vvImage * image = SM->GetImage();
3236   vvSlicer * slicer = SM->GetSlicer(0);
3237   int orientation = slicer->GetOrientation();
3238   int nbSlices = image->GetSize()[orientation];
3239   vtkSmartPointer<vtkRenderWindow>  renderWindow = widget->GetRenderWindow();
3240
3241   // Select filename base
3242   QString filename = QFileDialog::getSaveFileName(this,
3243     tr("Save As (filename will be completed by slice number)"),
3244     itksys::SystemTools::GetFilenamePath(mSlicerManagers[index]->GetFileName()).c_str(),
3245     "Images( *.png);;Images( *.jpg)");
3246
3247   // Loop on slices
3248   for(int i=0; i<nbSlices; i++) {
3249     // Change the slice
3250     slicer->SetSlice(i); // -> change the slice of the current slicer
3251     SM->UpdateSlice(0); // --> this one emit UpdateSlice
3252     QCoreApplication::flush(); // -> needed to force display of contours
3253
3254     // Screenshot
3255     vtkSmartPointer<vtkWindowToImageFilter> windowToImageFilter = vtkSmartPointer<vtkWindowToImageFilter>::New();
3256     windowToImageFilter->SetInput(renderWindow);
3257     windowToImageFilter->SetMagnification(1);
3258     windowToImageFilter->SetInputBufferTypeToRGBA(); //also record the alpha (transparency) channel
3259     windowToImageFilter->Update();
3260
3261     vtkSmartPointer<vtkPNGWriter> writer = vtkSmartPointer<vtkPNGWriter>::New();
3262     std::string fn = itksys::SystemTools::GetFilenameWithoutLastExtension(filename.toStdString());
3263     std::string num = clitk::toString(i);
3264     if (i<10) num = "0"+num;
3265     if (i<100) num = "0"+num;
3266     if (i<1000) num = "0"+num;
3267
3268     fn = itksys::SystemTools::GetFilenamePath(filename.toStdString()) + "/"+ fn
3269       + "_" + num + itksys::SystemTools::GetFilenameLastExtension(filename.toStdString());
3270     writer->SetFileName(fn.c_str());
3271 #if VTK_MAJOR_VERSION <= 5
3272     writer->SetInput(windowToImageFilter->GetOutput());
3273 #else
3274     writer->SetInputConnection(windowToImageFilter->GetOutputPort());
3275 #endif
3276     writer->Write();
3277   }
3278 }
3279 //------------------------------------------------------------------------------
3280
3281
3282 //------------------------------------------------------------------------------
3283 void vvMainWindow::SaveScreenshot(QVTKWidget *widget)
3284 {
3285   QString Extensions = "Images( *.png);;";
3286   Extensions += "Images( *.jpg);;";
3287   Extensions += "Images( *.bmp);;";
3288   Extensions += "Images( *.tif);;";
3289   Extensions += "Images( *.ppm)";
3290 #if defined(VTK_USE_FFMPEG_ENCODER) || defined(VTK_USE_VIDEO_FOR_WINDOWS)
3291   Extensions += ";;Video( *.avi)";
3292 #endif
3293 #ifdef VTK_USE_MPEG2_ENCODER
3294   Extensions += ";;Video( *.mpg)";
3295 #endif
3296 #ifdef CLITK_EXPERIMENTAL
3297   Extensions += ";;Video( *.gif)";
3298 #endif
3299
3300   int smIndex=GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
3301   QString fileName = QFileDialog::getSaveFileName(this,
3302     tr("Save As"),
3303     itksys::SystemTools::GetFilenamePath(mSlicerManagers[smIndex]->GetFileName()).c_str(),
3304     Extensions);
3305
3306   if (!fileName.isEmpty()) {
3307     vtkSmartPointer<vtkWindowToImageFilter> w2i = vtkSmartPointer<vtkWindowToImageFilter>::New();
3308     w2i->SetInput(widget->GetRenderWindow());
3309     w2i->Update();
3310     vtkImageData *image = w2i->GetOutput();
3311
3312     std::string ext(itksys::SystemTools::GetFilenameLastExtension(fileName.toStdString()));
3313
3314     // Image
3315     vtkImageWriter *imgwriter = NULL;
3316     if (ext==".bmp")
3317       imgwriter = vtkBMPWriter::New();
3318     else if (ext==".tif")
3319       imgwriter = vtkTIFFWriter::New();
3320     else if (ext==".ppm")
3321       imgwriter = vtkPNMWriter::New();
3322     else if (ext==".png")
3323       imgwriter = vtkPNGWriter::New();
3324     else if (ext==".jpg")
3325       imgwriter = vtkJPEGWriter::New();
3326
3327     // Snapshot image if not null
3328     if(imgwriter!=NULL) {
3329 #if VTK_MAJOR_VERSION <= 5
3330       imgwriter->SetInput(image);
3331 #else
3332       imgwriter->SetInputConnection(w2i->GetOutputPort());
3333 #endif
3334       imgwriter->SetFileName(fileName.toStdString().c_str());
3335       imgwriter->Write();
3336       return;
3337     }
3338
3339     // Video
3340     vtkGenericMovieWriter *vidwriter = NULL;
3341 #if CLITK_EXPERIMENTAL == 1
3342     if (ext==".gif") {
3343       vvAnimatedGIFWriter *gif = vvAnimatedGIFWriter::New();
3344       vidwriter = gif;
3345
3346       // FPS
3347       bool ok;
3348       int fps = QInputDialog::getInt(this, tr("Number of frames per second"),
3349         tr("FPS:"), 5, 0, 1000, 1, &ok);
3350       if(ok)
3351         gif->SetRate(fps);
3352
3353       // Loops
3354       int loops = QInputDialog::getInt(this, tr("Loops"),
3355         tr("Number of loops (0 means infinite):"), 0, 0, 1000000000, 1, &ok);
3356       if(ok)
3357         gif->SetLoops(loops);
3358
3359       // Dithering
3360       QString msg = "Would you like to activate dithering?";
3361       QMessageBox msgBox(QMessageBox::Question, tr("Dithering"),msg, 0, this);
3362       msgBox.addButton(tr("Yes"), QMessageBox::AcceptRole);
3363       msgBox.addButton(tr("No"), QMessageBox::RejectRole);
3364       gif->SetDither(msgBox.exec() == QMessageBox::AcceptRole);
3365     }
3366 #endif
3367 #ifdef VTK_USE_VIDEO_FOR_WINDOWS
3368     if (ext==".avi") {
3369       vtkAVIWriter *mpg = vtkAVIWriter::New();
3370       vidwriter = mpg;
3371       mpg->SetQuality(2);
3372       bool ok;
3373       int fps = QInputDialog::getInteger(this, tr("Number of frames per second"),
3374         tr("FPS:"), 5, 0, 1024, 1, &ok);
3375       if(!ok)
3376         fps = 5;
3377       mpg->SetRate(fps);
3378     }
3379 #endif
3380 #ifdef VTK_USE_FFMPEG_ENCODER
3381     if (ext==".avi") {
3382       vtkFFMPEGWriter *mpg = vtkFFMPEGWriter::New();
3383       vidwriter = mpg;
3384       mpg->SetQuality(2);
3385       bool ok;
3386       int fps = QInputDialog::getInteger(this, tr("Number of frames per second"),
3387         tr("FPS:"), 5, 0, 1024, 1, &ok);
3388       if(!ok)
3389         fps = 5;
3390       mpg->SetRate(fps);
3391       mpg->SetBitRateTolerance(int(ceil(12.0*1024*1024/fps)));
3392     }
3393 #endif
3394 #ifdef VTK_USE_MPEG2_ENCODER
3395     if (ext==".mpg") {
3396       vtkMPEG2Writer *mpg = vtkMPEG2Writer::New();
3397       vidwriter = mpg;
3398     }
3399 #endif
3400
3401     // Take video if not null
3402     if(vidwriter!=NULL){
3403 #if VTK_MAJOR_VERSION <= 5
3404       vidwriter->SetInput(image);
3405 #else
3406       vidwriter->SetInputConnection(w2i->GetOutputPort());
3407 #endif
3408       vidwriter->SetFileName(fileName.toStdString().c_str());
3409       vidwriter->Start();
3410       int nSlice = mSlicerManagers[smIndex]->GetSlicer(0)->GetTMax();
3411       for(int i=0; i<=nSlice; i++) {
3412         mSlicerManagers[smIndex]->SetNextTSlice(0);
3413         vtkSmartPointer<vtkWindowToImageFilter> w2i = vtkSmartPointer<vtkWindowToImageFilter>::New();
3414         w2i->SetInput(widget->GetRenderWindow());
3415         w2i->Update();
3416 #if VTK_MAJOR_VERSION <= 5
3417         vidwriter->SetInput(w2i->GetOutput());
3418 #else
3419         vidwriter->SetInputConnection(w2i->GetOutputPort());
3420 #endif
3421         vidwriter->Write();
3422       }
3423       vidwriter->End();
3424       vidwriter->Delete();
3425       return;
3426     }
3427
3428     QMessageBox::information(this,tr("Problem saving screenshot !"),tr("Cannot save image.\nPlease set a file extension !!!"));
3429   }
3430 }
3431 //------------------------------------------------------------------------------
3432
3433
3434 //------------------------------------------------------------------------------
3435 void vvMainWindow::GoToCursor()
3436 {
3437   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
3438   for (int column = 1; column < 5; column++) {
3439     if (DataTree->selectedItems()[0]->data(column,Qt::CheckStateRole).toInt() > 1) {
3440       double* cursorPos = mSlicerManagers[index]->GetSlicer(column-1)->GetCursorPosition();
3441       mSlicerManagers[index]->GetSlicer(column-1)->SetCurrentPosition(
3442         cursorPos[0],cursorPos[1],cursorPos[2],cursorPos[3]);
3443       mSlicerManagers[index]->UpdateViews(1,column-1);
3444       mSlicerManagers[index]->UpdateLinked(column-1);
3445       break;
3446     }
3447   }
3448 }
3449 //------------------------------------------------------------------------------
3450
3451 //------------------------------------------------------------------------------
3452 void vvMainWindow::GoToLandmark()
3453 {
3454   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
3455   for (int column = 1; column < 5; column++) {
3456     if (DataTree->selectedItems()[0]->data(column,Qt::CheckStateRole).toInt() > 1) {
3457       double* cursorPos = landmarksPanel->GetSelectedPoint();
3458       mSlicerManagers[index]->GetSlicer(column-1)->SetCurrentPosition(
3459         cursorPos[0],cursorPos[1],cursorPos[2],cursorPos[3]);
3460       mSlicerManagers[index]->UpdateViews(1,column-1);
3461       mSlicerManagers[index]->UpdateLinked(column-1);
3462       break;
3463     }
3464   }
3465 }
3466 //------------------------------------------------------------------------------
3467
3468 //------------------------------------------------------------------------------
3469 void vvMainWindow::PlayPause()
3470 {
3471   if (playMode) {
3472     playMode = 0;
3473     playButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/player_play.png")));
3474     ImageInfoChanged();
3475     return;
3476   } else {
3477     int image_number=DataTree->topLevelItemCount();
3478     bool has_temporal;
3479     for (int i=0; i<image_number; i++)
3480       if (mSlicerManagers[i]->GetSlicer(0)->GetTMax() > 0) {
3481         has_temporal=true;
3482         break;
3483       }
3484       if (has_temporal) {
3485         playMode = 1;
3486         playButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/player_pause.png")));
3487         QTimer::singleShot(1000/mFrameRate, this, SLOT(PlayNext()));
3488       }
3489   }
3490 }
3491 //------------------------------------------------------------------------------
3492
3493 //------------------------------------------------------------------------------
3494 void vvMainWindow::PlayNext()
3495 {
3496   if (playMode && !this->isHidden()) {
3497     int image_number=DataTree->topLevelItemCount();
3498     ///Only play one slicer per SM, and only if the SM is being displayed
3499     for (int i=0; i<image_number; i++)
3500       for (int j=0; j<4; j++)
3501         if (mSlicerManagers[i]->GetSlicer(0)->GetTMax() > 0 &&
3502           DataTree->topLevelItem(i)->data(j+1,Qt::CheckStateRole).toInt() > 0) {
3503             mSlicerManagers[i]->SetNextTSlice(j);
3504             break;
3505         }
3506         QTimer::singleShot(1000/mFrameRate, this, SLOT(PlayNext()));
3507   }
3508 }
3509 //------------------------------------------------------------------------------
3510
3511 void vvMainWindow::ShowLastImage()
3512 {
3513   if (mSlicerManagers.size() > 1) {
3514     QTreeWidgetItem * item=DataTree->topLevelItem(DataTree->topLevelItemCount()-1);
3515     CurrentImageChanged(mSlicerManagers.back()->GetId()); //select new image
3516     item->setData(1,Qt::CheckStateRole,2); //show the new image in the first panel
3517     //mSlicerManagers[GetSlicerIndexFromItem(item)]->GetSlicer(0)->SetActorVisibility("image", 0, 1); //Set the Last Image visibles
3518     DisplayChanged(item,1);
3519   }
3520 }
3521
3522 //------------------------------------------------------------------------------
3523 void vvMainWindow::UpdateRenderWindows()
3524 {
3525   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
3526     mSlicerManagers[i]->GetSlicer(0)->UpdateLandmarks();
3527     mSlicerManagers[i]->GetSlicer(1)->UpdateLandmarks();
3528     mSlicerManagers[i]->GetSlicer(2)->UpdateLandmarks();
3529     mSlicerManagers[i]->GetSlicer(3)->UpdateLandmarks();
3530   }
3531   if (NOViewWidget->GetRenderWindow()) NOViewWidget->GetRenderWindow()->Render();
3532   if (NEViewWidget->GetRenderWindow()) NEViewWidget->GetRenderWindow()->Render();
3533   if (SOViewWidget->GetRenderWindow()) SOViewWidget->GetRenderWindow()->Render();
3534   if (SEViewWidget->GetRenderWindow()) SEViewWidget->GetRenderWindow()->Render();
3535 }
3536 //------------------------------------------------------------------------------
3537
3538 //------------------------------------------------------------------------------
3539 void vvMainWindow::SegmentationOnCurrentImage()
3540 {
3541   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
3542
3543   vvSegmentationDialog segmentation;
3544   segmentation.SetImage(mSlicerManagers[index]->GetSlicer(0)->GetImage());
3545   segmentation.exec();
3546 }
3547 //------------------------------------------------------------------------------
3548
3549 void vvMainWindow::SurfaceViewerLaunch()
3550 {
3551   vvSurfaceViewerDialog surfaceViewer;
3552   surfaceViewer.exec();
3553 }
3554 //------------------------------------------------------------------------------
3555
3556
3557 //------------------------------------------------------------------------------
3558 int vvMainWindow::GetImageDuplicateFilenameNumber(std::string filename)
3559 {
3560   int number=0;
3561   for(unsigned int l=0; l<mSlicerManagers.size(); l++) {
3562     vvSlicerManager * v = mSlicerManagers[l];
3563     if (v->GetBaseFileName() ==
3564       vtksys::SystemTools::GetFilenameName(vtksys::SystemTools::GetFilenameWithoutLastExtension(filename))) {
3565         number = std::max(number, v->GetBaseFileNameNumber()+1);
3566     }
3567   }
3568   return number;
3569 }
3570 //------------------------------------------------------------------------------
3571
3572
3573 //------------------------------------------------------------------------------
3574 vvSlicerManager* vvMainWindow::AddImage(vvImage::Pointer image,std::string filename)
3575 {
3576   // Change filename if another image exist with the same name
3577   int number = GetImageDuplicateFilenameNumber(filename);
3578
3579   // Create new SliceManager
3580   vvSlicerManager* slicer_manager = new vvSlicerManager(4);
3581   slicer_manager->SetImage(image);//, IMAGE, number);
3582   //  filename = filename+"_"+clitk::toString(number);
3583   slicer_manager->SetFilename(filename, number);
3584   mSlicerManagers.push_back(slicer_manager);
3585
3586   //create an item in the tree with good settings
3587   QTreeWidgetItem *item = new QTreeWidgetItem();
3588   item->setData(0,Qt::UserRole,slicer_manager->GetFileName().c_str());//files[i].c_str());
3589   item->setData(1,Qt::UserRole,tr("image"));
3590   item->setData(COLUMN_IMAGE_NAME,Qt::DisplayRole,slicer_manager->GetFileName().c_str());//filename.c_str());
3591   qApp->processEvents();
3592
3593   for (int j = 1; j <= 4; j++) item->setData(j,Qt::CheckStateRole,1);
3594
3595   //Create the buttons for reload and close
3596   qApp->processEvents();
3597   QTreePushButton* cButton = new QTreePushButton;
3598   cButton->setItem(item);
3599   cButton->setColumn(COLUMN_CLOSE_IMAGE);
3600   cButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/exit.png")));
3601   connect(cButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
3602     this,SLOT(CloseImage(QTreeWidgetItem*, int)));
3603
3604   QTreePushButton* rButton = new QTreePushButton;
3605   rButton->setItem(item);
3606   rButton->setColumn(COLUMN_RELOAD_IMAGE);
3607   rButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/rotateright.png")));
3608   rButton->setEnabled(0);
3609   connect(rButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
3610     this,SLOT(ReloadImage(QTreeWidgetItem*, int)));
3611
3612   DataTree->addTopLevelItem(item);
3613   DataTree->setItemWidget(item, COLUMN_CLOSE_IMAGE, cButton);
3614   DataTree->setItemWidget(item, COLUMN_RELOAD_IMAGE, rButton);
3615
3616   //set the id of the image
3617   QString id = QDir::current().absoluteFilePath(slicer_manager->GetFileName().c_str()) + QString::number(mSlicerManagers.size()-1);
3618   item->setData(COLUMN_IMAGE_NAME,Qt::UserRole,id.toStdString().c_str());
3619   mSlicerManagers.back()->SetId(id.toStdString());
3620
3621   linkPanel->addImage(slicer_manager->GetFileName().c_str()// filename
3622     , id.toStdString());
3623
3624   connect(mSlicerManagers.back(), SIGNAL(currentImageChanged(std::string)),
3625     this, SLOT(CurrentImageChanged(std::string)));
3626   connect(mSlicerManagers.back(), SIGNAL(currentPickedImageChanged(std::string)),
3627     this, SLOT(CurrentPickedImageChanged(std::string)));
3628   connect(mSlicerManagers.back(), SIGNAL(UpdatePosition(int, double, double, double, double, double, double, double)),
3629     this, SLOT(MousePositionChanged(int,double, double, double, double, double, double, double)));
3630   connect(mSlicerManagers.back(), SIGNAL(UpdateVector(int, double, double, double, double)),
3631     this, SLOT(VectorChanged(int,double,double,double, double)));
3632   connect(mSlicerManagers.back(), SIGNAL(UpdateOverlay(int, double, double)),
3633     this, SLOT(OverlayChanged(int,double,double)));
3634   connect(mSlicerManagers.back(), SIGNAL(UpdateFusion(int, double)),
3635     this, SLOT(FusionChanged(int,double)));
3636   //connect(mSlicerManagers.back(), SIGNAL(UpdateFusionSequence(int, bool, unsigned int)),
3637   //  this, SLOT(FusionSequenceChanged(int, bool, unsigned int)));
3638   connect(mSlicerManagers.back(), SIGNAL(WindowLevelChanged()),
3639     this,SLOT(WindowLevelChanged()));
3640   connect(mSlicerManagers.back(), SIGNAL(UpdateSlice(int,int)),
3641     this,SLOT(UpdateSlice(int,int)));
3642   connect(mSlicerManagers.back(), SIGNAL(UpdateTSlice(int, int, int)),
3643     this,SLOT(UpdateTSlice(int, int, int)));
3644   connect(mSlicerManagers.back(), SIGNAL(UpdateTSlice(int, int, int)),
3645     this,SLOT(ImageInfoChanged()));
3646   connect(mSlicerManagers.back(), SIGNAL(UpdateSliceRange(int,int,int,int,int)),
3647     this,SLOT(UpdateSliceRange(int,int,int,int,int)));
3648   connect(mSlicerManagers.back(), SIGNAL(UpdateLinkManager(std::string,int,double,double,double,int)),
3649     this,SLOT(UpdateLinkManager(std::string,int,double,double,double,int)));
3650   connect(mSlicerManagers.back(), SIGNAL(UpdateLinkedNavigation(std::string,vvSlicerManager*,vvSlicer*)),
3651     this,SLOT(UpdateLinkedNavigation(std::string,vvSlicerManager*,vvSlicer*)));
3652   connect(mSlicerManagers.back(), SIGNAL(ChangeImageWithIndexOffset(vvSlicerManager*,int,int)),
3653     this,SLOT(ChangeImageWithIndexOffset(vvSlicerManager*,int,int)));
3654   connect(mSlicerManagers.back(), SIGNAL(LandmarkAdded()),landmarksPanel,SLOT(AddPoint()));
3655
3656
3657
3658   InitSlicers();
3659   UpdateTree();
3660   qApp->processEvents();
3661   InitDisplay();
3662   ShowLastImage();
3663   qApp->processEvents();
3664   // End
3665   ImageInfoChanged();
3666   return slicer_manager;
3667 }
3668 //------------------------------------------------------------------------------
3669
3670
3671 //------------------------------------------------------------------------------
3672 void vvMainWindow::UpdateCurrentSlicer()
3673 {
3674   int index = -1;
3675   if (DataTree->selectedItems().size() > 0) {
3676     index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
3677   }
3678   mSlicerManagerCurrentIndex = index;
3679 }
3680 //------------------------------------------------------------------------------