vv/vvMainWindow.cxx

   1 /*=========================================================================
   2 Program:   vv                     http://www.creatis.insa-lyon.fr/rio/vv
   3
   4 Authors belong to:
   5 - University of LYON              http://www.universite-lyon.fr/
   6 - Léon Bérard cancer center       http://www.centreleonberard.fr
   7 - CREATIS CNRS laboratory         http://www.creatis.insa-lyon.fr
   8
   9 This software is distributed WITHOUT ANY WARRANTY; without even
  10 the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
  11 PURPOSE.  See the copyright notices for more information.
  12
  13 It is distributed under dual licence
  14
  15 - BSD        See included LICENSE.txt file
  16 - CeCILL-B   http://www.cecill.info/licences/Licence_CeCILL-B_V1-en.html
  17 ===========================================================================**/
  18
  19 #include <algorithm>
  20 #include <QMessageBox>
  21 #include <QInputDialog>
  22 #include <QTimer>
  23 #include "QTreePushButton.h"
  24 #include <QUrl>
  25 #include <QSettings>
  26
  27 // VV include
  28 #include "vvMainWindow.h"
  29 #include "vvHelpDialog.h"
  30 #include "vvRegisterForm.h"
  31 #include "vvDocumentation.h"
  32 #include "vvProgressDialog.h"
  33 #include "vvQDicomSeriesSelector.h"
  34 #include "vvSlicerManager.h"
  35 #include "clitkImageCommon.h"
  36 #include "vvSlicer.h"
  37 #include "vvInteractorStyleNavigator.h"
  38 #include "vvImageWriter.h"
  39 #include "vvSegmentationDialog.h"
  40 #include "vvSurfaceViewerDialog.h"
  41 #include "vvDeformationDialog.h"
  42 #include "vvImageWarp.h"
  43 #include "vvUtils.h"
  44 #include "vvMidPosition.h"
  45 #include "vvMesh.h"
  46 #include "vvStructSelector.h"
  47 #include "vvMeshReader.h"
  48 #include "vvSaveState.h"
  49 #include "vvReadState.h"
  50 #include "clitkConfiguration.h"
  51
  52 // ITK include
  53 #include <itkImage.h>
  54 #include <itkImageFileReader.h>
  55 #include <itkByteSwapper.h>
  56 #include <itkCommand.h>
  57 #include <itkNumericSeriesFileNames.h>
  58
  59 // VTK include
  60 #include <vtkImageData.h>
  61 #include <vtkImageActor.h>
  62 #include <vtkCornerAnnotation.h>
  63 #include <vtkRenderWindow.h>
  64 #include <vtkRenderWindowInteractor.h>
  65 #include <vtkRenderer.h>
  66 #include <vtkRendererCollection.h>
  67 #include <vtkWindowToImageFilter.h>
  68 #include <vtkBMPWriter.h>
  69 #include <vtkTIFFWriter.h>
  70 #include <vtkPNMWriter.h>
  71 #include <vtkPNGWriter.h>
  72 #include <vtkJPEGWriter.h>
  73 #include <vtkGenericMovieWriter.h>
  74 #ifdef CLITK_EXPERIMENTAL
  75 #  include <vvAnimatedGIFWriter.h>
  76 #endif
  77 #ifdef VTK_USE_VIDEO_FOR_WINDOWS
  78 #  include <vtkAVIWriter.h>
  79 #endif
  80 #ifdef VTK_USE_FFMPEG_ENCODER
  81 #  include <vtkFFMPEGWriter.h>
  82 #endif
  83 #ifdef VTK_USE_MPEG2_ENCODER
  84 #  include <vtkMPEG2Writer.h>
  85 #endif
  86 #include <vtkMatrix4x4.h>
  87 #include <vtkTransform.h>
  88
  89 // Standard includes
  90 #include <iostream>
  91 #include <fstream>
  92 #include <sstream>
  93 #include <iomanip>
  94
  95 #define COLUMN_TREE 0
  96 #define COLUMN_UL_VIEW 1
  97 #define COLUMN_UR_VIEW 2
  98 #define COLUMN_DL_VIEW 3
  99 #define COLUMN_DR_VIEW 4
 100 #define COLUMN_CLOSE_IMAGE 5
 101 #define COLUMN_RELOAD_IMAGE 6
 102 #define COLUMN_IMAGE_NAME 7
 103
 104 #ifdef CLITK_PRIVATE_FEATURES
 105 #define EXTENSIONS "Images ( *.bmp *.png *.jpeg *.jpg *.tif *.mhd *.mha *.hdr *.vox *.his *.xdr *.SCAN *.nii *.nrrd *.nhdr *.refscan *.nii.gz *.usf *.svl)"
 106 #else
 107 #define EXTENSIONS "Images ( *.bmp *.png *.jpeg *.jpg *.tif *.mhd *.mha *.hdr *.vox *.his *.xdr *.SCAN *.nii *.nrrd *.nhdr *.refscan *.nii.gz)"
 108 #endif
 109
 110
 111 /*Data Tree values
 112 0,Qt::UserRole full filename
 113 1,Qt::CheckStateRole checkbutton UL View
 114 1,Qt::UserRole overlay, fusion or vector
 115 2,Qt::CheckStateRole checkbutton UR View
 116 3,Qt::CheckStateRole checkbutton DL View
 117 4,Qt::CheckStateRole checkbutton DR View
 118 5,0  short filename
 119 5,Qt::UserRole mSlicerManager id*/
 120
 121 //------------------------------------------------------------------------------
 122 vvMainWindow::vvMainWindow():vvMainWindowBase()
 123 {
 124   setupUi(this); // this sets up the GUI
 125
 126   mInputPathName = "";
 127   mMenuTools = menuTools;
 128   //  mMenuSegmentation = menuSegmentation;
 129   mContextMenu = &contextMenu;
 130   mMenuExperimentalTools = menuExperimental;
 131   mMainWidget = this;
 132   mCurrentTime = -1;
 133   mCurrentSelectedImageId = "";
 134   mCurrentPickedImageId = "";
 135   mCurrentPickedImageIndex = 0;
 136
 137   //Init the contextMenu
 138   this->setContextMenuPolicy(Qt::CustomContextMenu);
 139   contextActions.resize(0);
 140   QAction* actionOpen_new_image = contextMenu.addAction(QIcon(QString::fromUtf8(":/common/icons/fileopen.png")),
 141     tr("O&pen new Image"));
 142   actionOpen_new_image->setShortcut(QKeySequence(tr("Ctrl+O")));
 143   connect(actionOpen_new_image,SIGNAL(triggered()),this,SLOT(OpenImages()));
 144   contextActions.push_back(actionOpen_new_image);
 145   contextMenu.addSeparator();
 146
 147   QAction* actionClose_Image = contextMenu.addAction(QIcon(QString::fromUtf8(":/common/icons/exit.png")),
 148     tr("Close Current Image"));
 149   connect(actionClose_Image,SIGNAL(triggered()),this,SLOT(CloseImage()));
 150   contextActions.push_back(actionClose_Image);
 151
 152   QAction* actionReload_image = contextMenu.addAction(QIcon(QString::fromUtf8(":/common/icons/rotateright.png")),
 153     tr("Reload Current Image"));
 154   connect(actionReload_image,SIGNAL(triggered()),this,SLOT(ReloadImage()));
 155   contextActions.push_back(actionReload_image);
 156
 157   QAction* actionSave_image = contextMenu.addAction(QIcon(QString::fromUtf8(":/common/icons/filesave.png")),
 158     tr("Save Current Image"));
 159   connect(actionSave_image,SIGNAL(triggered()),this,SLOT(SaveAs()));
 160   contextActions.push_back(actionSave_image);
 161
 162   QAction* actionSave_state = contextMenu.addAction(QIcon(QString::fromUtf8(":/common/icons/filesave.png")),
 163     tr("Save Current State"));
 164   connect(actionSave_state,SIGNAL(triggered()),this,SLOT(SaveCurrentState()));
 165   contextActions.push_back(actionSave_state);
 166
 167   QAction* actionRead_state = contextMenu.addAction(QIcon(QString::fromUtf8(":/common/icons/filesave.png")),
 168     tr("Read Saved State"));
 169   connect(actionRead_state,SIGNAL(triggered()),this,SLOT(ReadSavedState()));
 170   contextActions.push_back(actionRead_state);
 171
 172   contextMenu.addSeparator();
 173
 174   contextMenu.addAction(actionAdd_VF_to_current_Image);
 175   contextActions.push_back(actionAdd_VF_to_current_Image);
 176
 177   //QAction* actionAdd_Overlay_to_current_Image = menuOverlay->addAction(QIcon(QString::fromUtf8(":/common/icons/GPSup.png")),
 178   //    tr("Add overlay image to current image"));
 179   contextMenu.addAction(actionAdd_overlay_image_to_current_image);
 180   contextActions.push_back(actionAdd_overlay_image_to_current_image);
 181
 182   contextMenu.addAction(actionAdd_fusion_image);
 183   contextActions.push_back(actionAdd_fusion_image);
 184
 185 #ifdef CLITK_EXPERIMENTAL
 186   contextMenu.addAction(actionAdd_USSequence_toCT);
 187   contextActions.push_back(actionAdd_USSequence_toCT);
 188 #endif
 189
 190
 191   contextMenu.addSeparator();
 192   QAction* actionResetMatrix = contextMenu.addAction(QIcon(QString::fromUtf8(":/common/icons/identity.png")),
 193     tr("Reset transformation to identity"));
 194   connect(actionResetMatrix, SIGNAL(triggered()), this,SLOT(ResetTransformationToIdentity()));
 195
 196   // TRIAL DS
 197   /*
 198   QMenu * m = new QMenu(menubar);
 199   m->setTitle("TOTO");
 200   //  m->setObjectName(QString::fromUtf8("TOTOTO"));
 201   contextMenu.addMenu(m);
 202   QAction * a = m->addAction(QIcon(QString::fromUtf8(":/common/icons/GPSup.png")),
 203   tr("BIDON"));
 204   QAction * b = m->addAction(QIcon(QString::fromUtf8(":/common/icons/GPSup.png")),
 205   tr("BIDON2"));
 206   m->addAction(a);
 207   m->addAction(b);
 208   connect(a,SIGNAL(triggered()),this,SLOT(AddFusionImage()));
 209   */
 210
 211   //init the DataTree
 212   mSlicerManagers.resize(0);
 213
 214   QStringList header;
 215   header.append("");
 216   header.append("TL");
 217   header.append("TR");
 218   header.append("BL");
 219   header.append("BR");
 220   header.append("");
 221   header.append("");
 222   header.append("Name");
 223
 224   DataTree->setHeaderLabels(header);
 225   DataTree->resizeColumnToContents(COLUMN_TREE);
 226   DataTree->resizeColumnToContents(COLUMN_UL_VIEW);
 227   DataTree->resizeColumnToContents(COLUMN_UR_VIEW);
 228   DataTree->resizeColumnToContents(COLUMN_DL_VIEW);
 229   DataTree->resizeColumnToContents(COLUMN_DR_VIEW);
 230   DataTree->resizeColumnToContents(COLUMN_CLOSE_IMAGE);
 231   DataTree->resizeColumnToContents(COLUMN_RELOAD_IMAGE);
 232   DataTree->resizeColumnToContents(COLUMN_IMAGE_NAME);
 233
 234   viewMode = 1;
 235   documentation = new vvDocumentation();
 236   help_dialog = new vvHelpDialog();
 237   dicomSeriesSelector = new vvDicomSeriesSelector();
 238 #ifdef vvPacsConnection
 239   PacsConnection = new vvPacsConnection();
 240 #endif
 241
 242   inverseButton->setEnabled(0);
 243   actionAdd_overlay_image_to_current_image->setEnabled(0);
 244   actionSave_As->setEnabled(0);
 245   actionAdd_VF_to_current_Image->setEnabled(0);
 246   actionAdd_fusion_image->setEnabled(0);
 247   actionAdd_USSequence_toCT->setEnabled(0);
 248
 249   //init the sliders
 250   verticalSliders.push_back(NOVerticalSlider);
 251   verticalSliders.push_back(NEVerticalSlider);
 252   verticalSliders.push_back(SOVerticalSlider);
 253   verticalSliders.push_back(SEVerticalSlider);
 254
 255   for (int i =0; i < 4; i++)
 256     verticalSliders[i]->hide();
 257
 258   horizontalSliders.push_back(NOHorizontalSlider);
 259   horizontalSliders.push_back(NEHorizontalSlider);
 260   horizontalSliders.push_back(SOHorizontalSlider);
 261   horizontalSliders.push_back(SEHorizontalSlider);
 262
 263   for (int i =0; i < 4; i++)
 264     horizontalSliders[i]->hide();
 265
 266
 267   connect(NOVerticalSlider,SIGNAL(valueChanged(int)),this,SLOT(NOVerticalSliderChanged()));
 268   connect(NEVerticalSlider,SIGNAL(valueChanged(int)),this,SLOT(NEVerticalSliderChanged()));
 269   connect(SOVerticalSlider,SIGNAL(valueChanged(int)),this,SLOT(SOVerticalSliderChanged()));
 270   connect(SEVerticalSlider,SIGNAL(valueChanged(int)),this,SLOT(SEVerticalSliderChanged()));
 271
 272   connect(NOHorizontalSlider,SIGNAL(valueChanged(int)),this,SLOT(NOHorizontalSliderMoved()));
 273   connect(NEHorizontalSlider,SIGNAL(valueChanged(int)),this,SLOT(NEHorizontalSliderMoved()));
 274   connect(SOHorizontalSlider,SIGNAL(valueChanged(int)),this,SLOT(SOHorizontalSliderMoved()));
 275   connect(SEHorizontalSlider,SIGNAL(valueChanged(int)),this,SLOT(SEHorizontalSliderMoved()));
 276
 277   //connect everything
 278   connect(actionCompute_mid_position_image,SIGNAL(triggered()),this,SLOT(ComputeMidPosition()));
 279   connect(actionDeformable_Registration,SIGNAL(triggered()),this,SLOT(ComputeDeformableRegistration()));
 280   connect(actionWarp_image_with_vector_field,SIGNAL(triggered()),this,SLOT(WarpImage()));
 281   connect(actionLoad_images,SIGNAL(triggered()),this,SLOT(OpenImages()));
 282   connect(actionOpen_Dicom,SIGNAL(triggered()),this,SLOT(OpenDicom()));
 283   //  connect(actionOpen_Dicom_Struct,SIGNAL(triggered()),this,SLOT(OpenDCStructContour()));
 284   connect(actionOpen_VTK_contour,SIGNAL(triggered()),this,SLOT(OpenVTKContour()));
 285   connect(actionOpen_Multiple_Images_As_One,SIGNAL(triggered()),this,SLOT(MergeImages()));
 286   connect(actionSlice_Image_As_Multiple_Images,SIGNAL(triggered()),this,SLOT(SliceImages()));
 287   connect(actionOpen_Image_With_Time,SIGNAL(triggered()),this,SLOT(OpenImageWithTime()));
 288   connect(actionMerge_images_as_n_dim_t, SIGNAL(triggered()), this, SLOT(MergeImagesWithTime()));
 289   connect(actionSave_As,SIGNAL(triggered()),this,SLOT(SaveAs()));
 290   connect(actionSave_current_state,SIGNAL(triggered()),this,SLOT(SaveCurrentState()));
 291   connect(actionRead_saved_state,SIGNAL(triggered()),this,SLOT(ReadSavedState()));
 292   connect(actionExit,SIGNAL(triggered()),this,SLOT(close()));
 293   connect(actionAdd_VF_to_current_Image,SIGNAL(triggered()),this,SLOT(OpenField()));
 294   connect(actionAdd_fusion_image,SIGNAL(triggered()),this,SLOT(SelectFusionImage()));
 295   connect(actionAdd_overlay_image_to_current_image,SIGNAL(triggered()), this,SLOT(SelectOverlayImage()));
 296   connect(actionAdd_USSequence_toCT,SIGNAL(triggered()), this,SLOT(SelectFusionSequence()));
 297   connect(actionNavigation_Help,SIGNAL(triggered()),this,SLOT(ShowHelpDialog()));
 298   connect(actionDocumentation,SIGNAL(triggered()),this,SLOT(ShowDocumentation()));
 299   connect(actionRegister_vv,SIGNAL(triggered()),this,SLOT(PopupRegisterForm()));
 300
 301   connect(overlayPanel, SIGNAL(FusionSequenceCorrespondancesButtonPressed()), this, SLOT(SelectFusionSequenceCorrespondances()));
 302
 303
 304   ///////////////////////////////////////////////
 305   connect(actionSegmentation,SIGNAL(triggered()),this,SLOT(SegmentationOnCurrentImage()));
 306   connect(actionSurface_Viewer,SIGNAL(triggered()),this,SLOT(SurfaceViewerLaunch()));
 307   ///////////////////////////////////////////////
 308
 309   actionNorth_East_Window->setEnabled(0);
 310   actionNorth_West_Window->setEnabled(0);
 311   actionSouth_East_Window->setEnabled(0);
 312   actionSouth_West_Window->setEnabled(0);
 313
 314   connect(actionNorth_East_Window,SIGNAL(triggered()),this,SLOT(SaveNEScreenshot()));
 315   connect(actionNorth_West_Window,SIGNAL(triggered()),this,SLOT(SaveNOScreenshot()));
 316   connect(actionSouth_East_Window,SIGNAL(triggered()),this,SLOT(SaveSEScreenshot()));
 317   connect(actionSouth_West_Window,SIGNAL(triggered()),this,SLOT(SaveSOScreenshot()));
 318   connect(actionSave_all_slices,SIGNAL(triggered()),this,SLOT(SaveScreenshotAllSlices()));
 319
 320   connect(DataTree,SIGNAL(itemSelectionChanged()),this,SLOT(ImageInfoChanged()));
 321   connect(DataTree,SIGNAL(itemClicked(QTreeWidgetItem*, int)),this,
 322     SLOT(DisplayChanged(QTreeWidgetItem*, int)));
 323
 324   connect(viewButton,SIGNAL(clicked()),this, SLOT(ChangeViewMode()) );
 325   connect(windowSpinBox,SIGNAL(editingFinished()),this,SLOT(WindowLevelEdited()));
 326   connect(levelSpinBox,SIGNAL(editingFinished()),this,SLOT(WindowLevelEdited()));
 327   connect(colorMapComboBox,SIGNAL(currentIndexChanged(int)),this,SLOT(UpdateColorMap()));
 328   connect(presetComboBox,SIGNAL(currentIndexChanged(int)),this,SLOT(UpdateWindowLevel()));
 329   connect(slicingPresetComboBox, SIGNAL(currentIndexChanged(int)),this,SLOT(UpdateSlicingPreset()));
 330   connect(inverseButton,SIGNAL(clicked()),this,SLOT(SwitchWindowLevel()));
 331   connect(applyWindowLevelToAllButton,SIGNAL(clicked()),this,SLOT(ApplyWindowLevelToAllImages()));
 332
 333   connect(this,SIGNAL(customContextMenuRequested(QPoint)),this,SLOT(ShowContextMenu(QPoint)));
 334
 335   connect(linkPanel,SIGNAL(addLink(QString,QString,bool)),this,SLOT(AddLink(QString,QString,bool)));
 336   connect(linkPanel,SIGNAL(removeLink(QString,QString)),this,SLOT(RemoveLink(QString,QString)));
 337   connect(overlayPanel,SIGNAL(VFPropertyUpdated(int,int,int,int,double,double,double)),this,SLOT(SetVFProperty(int,int,int,int,double,double,double)));
 338   connect(overlayPanel,SIGNAL(OverlayPropertyUpdated(int,int,double,double)),
 339     this,SLOT(SetOverlayProperty(int,int,double,double)));
 340   connect(overlayPanel,SIGNAL(FusionPropertyUpdated(int,int,int,double,double, bool)),
 341     this,SLOT(SetFusionProperty(int,int,int,double,double, bool)));
 342   connect(landmarksPanel,SIGNAL(UpdateRenderWindows()),this,SLOT(UpdateRenderWindows()));
 343   connect(landmarksPanel,SIGNAL(SelectedPointChanged()),this,SLOT(GoToLandmark()));
 344
 345   connect(overlayPanel,SIGNAL(FusionSequencePropertyUpdated(int, bool, unsigned int, bool)),
 346     this,SLOT(SetFusionSequenceProperty(int, bool,unsigned int, bool)));
 347
 348
 349   playMode = 0;//pause
 350   mFrameRate = 10;
 351   playButton->setEnabled(0);
 352   frameRateLabel->setEnabled(0);
 353   frameRateSpinBox->setEnabled(0);
 354   connect(playButton, SIGNAL(clicked()),this,SLOT(PlayPause()));
 355   connect(frameRateSpinBox, SIGNAL(valueChanged(int)),this,SLOT(ChangeFrameRate(int)));
 356
 357   goToCursorPushButton->setEnabled(0);
 358   connect(goToCursorPushButton, SIGNAL(clicked()),this,SLOT(GoToCursor()));
 359
 360   NOViewWidget->hide();
 361   NEViewWidget->hide();
 362   SOViewWidget->hide();
 363   SEViewWidget->hide();
 364
 365   //Recently opened files
 366   std::list<std::string> recent_files = GetRecentlyOpenedImages();
 367   recentlyOpenedFilesMenu=NULL;
 368   if ( !recent_files.empty() ) {
 369     createRecentlyOpenedFilesMenu();
 370     updateRecentlyOpenedFilesMenu(recent_files);
 371   }
 372
 373   // Adding all new tools (insertion in the menu)
 374   vvToolManager::GetInstance()->InsertToolsInMenu(this);
 375   vvToolManager::GetInstance()->EnableToolsInMenu(this, false);
 376
 377   if (!CLITK_EXPERIMENTAL)
 378     menuExperimental->menuAction()->setVisible(false);
 379
 380
 381   QTimer * timerMemory = new QTimer(this);
 382   //timerMemory->setInterval(5);
 383   connect(timerMemory, SIGNAL(timeout()), this, SLOT(UpdateMemoryUsage()));
 384   timerMemory->start(2000);
 385
 386 }
 387 //------------------------------------------------------------------------------
 388 void vvMainWindow::show()
 389 {
 390   vvMainWindowBase::show();
 391   PopupRegisterForm(true);
 392 }
 393 //------------------------------------------------------------------------------
 394 void vvMainWindow::UpdateMemoryUsage()
 395 {
 396   //  clitk::PrintMemory(true);
 397   if (clitk::GetMemoryUsageInMb() == 0) infoPanel->setMemoryInMb("NA");
 398   else infoPanel->setMemoryInMb(QString::number(clitk::GetMemoryUsageInMb())+" MiB");
 399 }
 400 //------------------------------------------------------------------------------
 401
 402
 403 //------------------------------------------------------------------------------
 404 void vvMainWindow::createRecentlyOpenedFilesMenu()
 405 {
 406   recentlyOpenedFilesMenu = new QMenu("Recently opened files...");
 407   recentlyOpenedFilesMenu->setIcon(QIcon(QString::fromUtf8(":/common/icons/open.png")));
 408   menuFile->insertMenu(actionOpen_Image_With_Time,recentlyOpenedFilesMenu);
 409   menuFile->insertSeparator(actionOpen_Image_With_Time);
 410 }
 411 //------------------------------------------------------------------------------
 412
 413
 414 //------------------------------------------------------------------------------
 415
 416 void vvMainWindow::updateRecentlyOpenedFilesMenu(const std::list<std::string> &recent_files)
 417 {
 418   if(recentlyOpenedFilesMenu==NULL) {
 419     createRecentlyOpenedFilesMenu();
 420   } else {
 421     recentlyOpenedFilesMenu->clear();
 422   }
 423   for (std::list<std::string>::const_iterator i = recent_files.begin(); i!=recent_files.end(); i++) {
 424     QAction* current=new QAction(QIcon(QString::fromUtf8(":/common/icons/open.png")), i->c_str(),this);
 425     recentlyOpenedFilesMenu->addAction(current);
 426     connect(current,SIGNAL(triggered()),this,SLOT(OpenRecentImage()));
 427   }
 428 }
 429 //------------------------------------------------------------------------------
 430
 431
 432 //------------------------------------------------------------------------------
 433 void vvMainWindow::ComputeMidPosition()
 434 {
 435   bool ok;
 436   int index=GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
 437   int ref = QInputDialog::getInteger(this,"Chose reference phase","Reference phase",0,0,\
 438     mSlicerManagers[index]->GetImage()->GetVTKImages().size()-1,1,&ok);
 439   if (ok) {
 440     vvMidPosition midp;
 441     midp.slicer_manager = mSlicerManagers[index];
 442     midp.reference_image_index = ref;
 443     QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
 444     midp.Update();
 445     if (midp.error)
 446       QMessageBox::warning(this, "Error computing midposition image",midp.error_message.c_str());
 447     else {
 448       QFileInfo info(midp.slicer_manager->GetFileName().c_str());
 449       AddImage(midp.output,info.path().toStdString()+"/"+info.completeBaseName().toStdString()+"_midposition.mhd");
 450     }
 451     QApplication::restoreOverrideCursor();
 452   }
 453 }
 454 //------------------------------------------------------------------------------
 455
 456
 457 //------------------------------------------------------------------------------
 458 void vvMainWindow::AddContour(int image_index, vvMesh::Pointer contour, bool propagation)
 459 {
 460   QTreeWidgetItem *item = new QTreeWidgetItem();
 461   item->setData(0,Qt::UserRole,"filename.vtk");
 462   item->setData(1,Qt::UserRole,tr("contour"));
 463   QBrush brush;
 464   brush.setColor(QColor(contour->r*255,contour->g*255,contour->b*255));
 465   brush.setStyle(Qt::SolidPattern);
 466   item->setData(COLUMN_IMAGE_NAME,Qt::BackgroundRole,brush);
 467   //  item->setData(COLUMN_IMAGE_NAME,Qt::DisplayRole,contour->structure_name.c_str());
 468
 469   for (int j = 1; j <= 4; j++)
 470     item->setData(j,Qt::CheckStateRole,DataTree->topLevelItem(image_index)->data(j,Qt::CheckStateRole));
 471
 472   QTreePushButton* cButton = new QTreePushButton;
 473   cButton->setItem(item);
 474   cButton->setColumn(COLUMN_CLOSE_IMAGE);
 475   cButton->setToolTip(tr("close image"));
 476   cButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/exit.png")));
 477   connect(cButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
 478     this,SLOT(CloseImage(QTreeWidgetItem*, int)));
 479
 480   QTreePushButton* rButton = new QTreePushButton;
 481   rButton->setItem(item);
 482   rButton->setColumn(COLUMN_RELOAD_IMAGE);
 483   rButton->setToolTip(tr("reload image"));
 484   rButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/rotateright.png")));
 485   rButton->setEnabled(false);
 486   //Not implemented
 487   //connect(rButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
 488   //this,SLOT(ReloadImage(QTreeWidgetItem*, int)));
 489
 490   DataTree->topLevelItem(image_index)->setExpanded(1);
 491   DataTree->topLevelItem(image_index)->addChild(item);
 492   DataTree->setItemWidget(item, COLUMN_CLOSE_IMAGE, cButton);
 493   DataTree->setItemWidget(item, COLUMN_RELOAD_IMAGE, rButton);
 494   QString id = DataTree->topLevelItem(image_index)->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString();
 495   item->setData(COLUMN_IMAGE_NAME,Qt::UserRole,id.toStdString().c_str());
 496
 497   UpdateTree();
 498   mSlicerManagers[image_index]->AddContour(contour,propagation);
 499   mSlicerManagers[image_index]->Render();
 500 }
 501 //------------------------------------------------------------------------------
 502
 503
 504 //------------------------------------------------------------------------------
 505 void vvMainWindow::OpenVTKContour()
 506 {
 507   if (mSlicerManagers.size() > 0) {
 508     QString Extensions = "Images ( *.vtk *.obj)";
 509     Extensions += ";;All Files (*)";
 510     QString file = QFileDialog::getOpenFileName(this,tr("Open vtkPolyData"),mInputPathName,Extensions);
 511     if (file.isNull())
 512       return;
 513     QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
 514     int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
 515     vvMeshReader reader;
 516     reader.SetImage(mSlicerManagers[index]->GetImage());
 517     reader.SetModeToVTK();
 518     reader.SetFilename(file.toStdString());
 519     reader.Update();
 520     AddContour(index,reader.GetOutput()[0],false);
 521     QApplication::restoreOverrideCursor();
 522   }
 523 }
 524 //------------------------------------------------------------------------------
 525
 526
 527 //------------------------------------------------------------------------------
 528 void vvMainWindow::AddDCStructContour(int index, QString file)
 529 {
 530   vvMeshReader reader;
 531   reader.SetFilename(file.toStdString());
 532   vvStructSelector selector;
 533   selector.SetStructures(reader.GetROINames());
 534   if (!mSlicerManagers[index]->GetVF().IsNull())
 535     selector.EnablePropagationCheckBox();
 536   if (selector.exec()) {
 537     QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
 538     reader.SetSelectedItems(selector.getSelectedItems());
 539     reader.SetImage(mSlicerManagers[index]->GetImage());
 540     if (selector.PropagationEnabled())
 541       reader.SetPropagationVF(mSlicerManagers[index]->GetVF());
 542     reader.Update();
 543     std::vector<vvMesh::Pointer> contours=reader.GetOutput();
 544     for (std::vector<vvMesh::Pointer>::iterator i=contours.begin();
 545       i!=contours.end(); i++)
 546       AddContour(index,*i,selector.PropagationEnabled());
 547     QApplication::restoreOverrideCursor();
 548   }
 549 }
 550
 551 //------------------------------------------------------------------------------
 552 void vvMainWindow::OpenDCStructContour()
 553 {
 554   if (mSlicerManagers.size() > 0) {
 555     QString Extensions = "Dicom Files ( *.dcm RS*)";
 556     Extensions += ";;All Files (*)";
 557     QString file = QFileDialog::getOpenFileName(this,tr("Merge Images"),mInputPathName,Extensions);
 558     if (file.isNull())
 559       return;
 560     int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
 561     AddDCStructContour(index, file);
 562   }
 563 }
 564 //------------------------------------------------------------------------------
 565
 566
 567 //------------------------------------------------------------------------------
 568 void vvMainWindow::ComputeDeformableRegistration()
 569 {
 570   if (mSlicerManagers.size() > 0) {
 571     int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
 572     vvDeformationDialog dialog(index,mSlicerManagers);
 573     if (dialog.exec()) {
 574       std::string base_name=itksys::SystemTools::GetFilenameWithoutExtension(mSlicerManagers[dialog.GetInputFileIndex()]->GetFileName());
 575       AddField(dialog.GetOutput(),dialog.getFieldFile(),dialog.GetInputFileIndex());
 576       WarpImage(dialog.GetSelectedSlicer(),dialog.GetReferenceFrameIndex());
 577     } else
 578       std::cout << "Error or user cancellation while computing deformation field..." << std::endl;
 579   } else QMessageBox::information(this, "Need to open image","You must open an image first.");
 580 }
 581 //------------------------------------------------------------------------------
 582
 583
 584 //------------------------------------------------------------------------------
 585 void vvMainWindow::WarpImage()
 586 {
 587   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
 588   if (!mSlicerManagers[index]->GetVF().IsNull()) {
 589     bool ok;
 590     int ref = QInputDialog::getInteger(this,"Chose reference phase","Reference phase",0,0,\
 591       mSlicerManagers[index]->GetImage()->GetVTKImages().size()-1,1,&ok);
 592     if (ok) {
 593       WarpImage(mSlicerManagers[index],ref);
 594     }
 595   } else
 596     QMessageBox::warning(this,tr("No vector field"),tr("Sorry, can't warp without a vector field"));
 597 }
 598 //------------------------------------------------------------------------------
 599
 600
 601 //------------------------------------------------------------------------------
 602 void vvMainWindow::WarpImage(vvSlicerManager* selected_slicer,int reference_phase)
 603 {
 604   if (!selected_slicer->GetVF().IsNull()) {
 605     QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
 606     QFileInfo info(selected_slicer->GetFileName().c_str());
 607     vvImageWarp warp(selected_slicer->GetImage(),selected_slicer->GetVF(),
 608       reference_phase,this);
 609     if (warp.ComputeWarpedImage()) {
 610       AddImage(warp.GetWarpedImage(),info.path().toStdString()+"/"+info.completeBaseName().toStdString()+"_warped.mhd");
 611       AddImage(warp.GetDiffImage()  ,info.path().toStdString()+"/"+info.completeBaseName().toStdString()+"_diff.mhd");
 612       AddImage(warp.GetJacobianImage()  ,info.path().toStdString()+"/"+info.completeBaseName().toStdString()+"_jacobian.mhd");
 613       QApplication::restoreOverrideCursor();
 614     } else {
 615       QApplication::restoreOverrideCursor();
 616       QMessageBox::warning(this,tr("Different spacings"),tr("The vector field and image spacings must be the same in order to warp."));
 617     }
 618   } else
 619     QMessageBox::warning(this,tr("No vector field"),tr("Sorry, can't warp without a vector field."));
 620 }
 621 //------------------------------------------------------------------------------
 622
 623
 624 //------------------------------------------------------------------------------
 625 vvMainWindow::~vvMainWindow()
 626 {
 627   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
 628     if (mSlicerManagers[i] != NULL)
 629       delete mSlicerManagers[i];
 630   }
 631 }
 632 //------------------------------------------------------------------------------
 633
 634 //------------------------------------------------------------------------------
 635 QTabWidget * vvMainWindow::GetTab()
 636 {
 637   return tabWidget;
 638 }
 639 //------------------------------------------------------------------------------
 640
 641
 642 //------------------------------------------------------------------------------
 643 void vvMainWindow::MergeImages()
 644 {
 645   QString Extensions = EXTENSIONS;
 646   Extensions += ";;All Files (*)";
 647   QStringList files = QFileDialog::getOpenFileNames(this,tr("Merge Images"),mInputPathName,Extensions);
 648   if (files.isEmpty())
 649     return;
 650   mInputPathName = itksys::SystemTools::GetFilenamePath(files[0].toStdString()).c_str();
 651   std::vector<std::string> vector;
 652
 653   unsigned int currentDim = 0;
 654   std::vector<double> currentSpacing;
 655   std::vector<int> currentSize;
 656   std::vector<double> currentOrigin;
 657
 658   for (int i = 0; i < files.size(); i++) {
 659     itk::ImageIOBase::Pointer reader = itk::ImageIOFactory::CreateImageIO(
 660       files[i].toStdString().c_str(), itk::ImageIOFactory::ReadMode);
 661     reader->SetFileName(files[i].toStdString().c_str());
 662     reader->ReadImageInformation();
 663     if (reader)        {
 664       //NOViewWidget->hide();
 665       //NEViewWidget->hide();
 666       //SOViewWidget->hide();
 667       //SEViewWidget->hide();
 668       if (i == 0)
 669         currentDim = reader->GetNumberOfDimensions();
 670       bool IsOk = true;
 671       for (unsigned int j = 0; j < currentDim; j++) {
 672         if (i == 0) {
 673           if (j == 0) {
 674             currentSpacing.resize(currentDim);
 675             currentSize.resize(currentDim);
 676             currentOrigin.resize(currentDim);
 677           }
 678           currentOrigin[j] = reader->GetOrigin(j);
 679           currentSpacing[j] = reader->GetSpacing(j);
 680           currentSize[j] = reader->GetDimensions(j);
 681         } else if (currentDim != reader->GetNumberOfDimensions()
 682           || currentSpacing[j] != reader->GetSpacing(j)
 683           || currentSize[j] != (int)reader->GetDimensions(j)
 684           || currentOrigin[j] != reader->GetOrigin(j)) {
 685             QString error = "Cannot read file (too different from others ";
 686             error += files[i].toStdString().c_str();
 687             QMessageBox::information(this,tr("Reading problem"),error);
 688             IsOk = false;
 689             break;
 690         }
 691       }
 692       if (IsOk)
 693         vector.push_back(files[i].toStdString());
 694     }
 695   }
 696   if (vector.size() > 0)
 697     LoadImages(vector, vvImageReader::MERGED);
 698 }
 699 //------------------------------------------------------------------------------
 700
 701 //------------------------------------------------------------------------------
 702 void vvMainWindow::SliceImages()
 703 {
 704   QString Extensions = EXTENSIONS;
 705   Extensions += ";;All Files (*)";
 706
 707   QStringList files = QFileDialog::getOpenFileNames(this,tr("Slice Images"),mInputPathName,Extensions);
 708   if (files.isEmpty())
 709     return;
 710   mInputPathName = itksys::SystemTools::GetFilenamePath(files[0].toStdString()).c_str();
 711   std::vector<std::string> vector;
 712   for (int i = 0; i < files.size(); i++)
 713     vector.push_back(files[i].toStdString());
 714   LoadImages(vector, vvImageReader::SLICED);
 715 }
 716 //------------------------------------------------------------------------------
 717
 718 //------------------------------------------------------------------------------
 719 void vvMainWindow::MergeImagesWithTime()
 720 {
 721   QString Extensions = EXTENSIONS;
 722   Extensions += ";;All Files (*)";
 723   QStringList files = QFileDialog::getOpenFileNames(this,tr("Merge Images With Time"),mInputPathName,Extensions);
 724   if (files.isEmpty())
 725     return;
 726   mInputPathName = itksys::SystemTools::GetFilenamePath(files[0].toStdString()).c_str();
 727   std::vector<std::string> vector;
 728
 729   for (int i = 0; i < files.size(); i++)
 730     vector.push_back(files[i].toStdString());
 731   sort(vector.begin(),vector.end());
 732   if (vector.size() > 1)
 733     LoadImages(vector, vvImageReader::MERGEDWITHTIME);
 734   else
 735     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.");
 736 }
 737 //------------------------------------------------------------------------------
 738
 739
 740 //------------------------------------------------------------------------------
 741 void vvMainWindow::OpenDicom()
 742 {
 743   std::vector<std::string> files;
 744
 745   //std::cout << "dicomSeriesSelector " << std::endl;
 746   if (dicomSeriesSelector->exec() == QDialog::Accepted) {
 747     files = *(dicomSeriesSelector->GetFilenames());
 748     LoadImages(files, vvImageReader::DICOM);
 749   }
 750 }
 751
 752 #ifdef vvPacsConnection
 753 void vvMainWindow::ConnectPacs()
 754 {
 755   std::vector<std::string> files;
 756
 757   //std::cout << "dicomSeriesSelector " << std::endl;
 758   if (PacsConnection->exec() == QDialog::Accepted) {
 759     files = *(PacsConnection->GetFilenames());
 760     LoadImages(files, vvImageReader::DICOM);
 761   }
 762
 763 }
 764 #endif
 765 //------------------------------------------------------------------------------
 766
 767 //------------------------------------------------------------------------------
 768 void vvMainWindow::OpenImages()
 769 {
 770   QString Extensions = EXTENSIONS;
 771   Extensions += ";;All Files (*)";
 772
 773   QStringList files = QFileDialog::getOpenFileNames(this,tr("Load Images"),mInputPathName,Extensions);
 774   if (files.isEmpty())
 775     return;
 776   mInputPathName = itksys::SystemTools::GetFilenamePath(files[0].toStdString()).c_str();
 777   std::vector<std::string> vector;
 778   for (int i = 0; i < files.size(); i++)
 779     vector.push_back(files[i].toStdString());
 780   LoadImages(vector, vvImageReader::IMAGE);
 781 }
 782 //------------------------------------------------------------------------------
 783 void vvMainWindow::OpenRecentImage()
 784 {
 785   QAction * caller = qobject_cast<QAction*>(sender());
 786   std::vector<std::string> images;
 787   images.push_back(caller->text().toStdString());
 788   mInputPathName = itksys::SystemTools::GetFilenamePath(images[0]).c_str();
 789   LoadImages(images, vvImageReader::IMAGE);
 790 }
 791 //------------------------------------------------------------------------------
 792
 793
 794 //------------------------------------------------------------------------------
 795 void vvMainWindow::OpenImageWithTime()
 796 {
 797   QString Extensions = EXTENSIONS;
 798   Extensions += ";;All Files (*)";
 799
 800   QStringList files = QFileDialog::getOpenFileNames(this,tr("Load Images With Time"),mInputPathName,Extensions);
 801   if (files.isEmpty())
 802     return;
 803   mInputPathName = itksys::SystemTools::GetFilenamePath(files[0].toStdString()).c_str();
 804   std::vector<std::string> vector;
 805   for (int i = 0; i < files.size(); i++) {
 806     vector.push_back(files[i].toStdString());
 807   }
 808   LoadImages(vector, vvImageReader::IMAGEWITHTIME);
 809 }
 810 //------------------------------------------------------------------------------
 811
 812
 813 //------------------------------------------------------------------------------
 814 void vvMainWindow::LoadImages(std::vector<std::string> files, vvImageReader::LoadedImageType filetype)
 815 {
 816   //Separate the way to open images and dicoms
 817   int fileSize;
 818   if (filetype == vvImageReader::IMAGE || filetype == vvImageReader::IMAGEWITHTIME)
 819     fileSize = files.size();
 820   else
 821     fileSize = 1;
 822
 823   // For SLICED, we need the number of slices (ndim and #slices)
 824   std::vector<unsigned int> nSlices;
 825   nSlices.resize(files.size());
 826   std::fill(nSlices.begin(), nSlices.end(), 1);
 827   if (filetype == vvImageReader::SLICED) {
 828     for (int i = 0; i < fileSize; i++) {
 829       itk::ImageIOBase::Pointer header = clitk::readImageHeader(files[i]);
 830       QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
 831       if (!header) {
 832         nSlices[i] = 0;
 833         QString error = "Cannot open file \n";
 834         error += files[i].c_str();
 835         QMessageBox::information(this,tr("Reading problem"),error);
 836         return;
 837       }
 838       if (header->GetNumberOfDimensions() < 3) {
 839         nSlices[i] = 0;
 840         QString error = "Dimension problem. Cannot slice \n";
 841         error += files[i].c_str();
 842         QMessageBox::information(this,tr("Reading problem"),error);
 843         return;
 844       }
 845       nSlices[i] = header->GetDimensions( header->GetNumberOfDimensions()-1 );
 846     }
 847   }
 848
 849   //Only add to the list of recently opened files when a single file is opened,
 850   //to avoid polluting the list of recently opened files
 851   if (files.size() == 1) {
 852     QFileInfo finfo=tr(files[0].c_str());
 853     AddToRecentlyOpenedImages(finfo.absoluteFilePath().toStdString());
 854     updateRecentlyOpenedFilesMenu(GetRecentlyOpenedImages());
 855   }
 856   //init the progress events
 857   QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
 858   vvProgressDialog progress("Opening " + files[0],fileSize>1);
 859   qApp->processEvents();
 860
 861   int numberofsuccesulreads=0;
 862   //open images as 1 or multiples
 863   for (int i = 0; i < fileSize; i++) {
 864     progress.SetText("Opening " + files[i]);
 865     progress.SetProgress(i,fileSize);
 866     qApp->processEvents();
 867
 868     for (unsigned int j = 0; j < nSlices[i]; j++) {
 869       //read the image and put it in mSlicerManagers
 870       vvSlicerManager* imageManager = new vvSlicerManager(4);
 871       qApp->processEvents();
 872
 873       bool SetImageSucceed=false;
 874
 875       // Change filename if an image with the same already exist
 876       int number = GetImageDuplicateFilenameNumber(files[i] + std::string("_slice"));
 877
 878       if (filetype == vvImageReader::IMAGE || filetype == vvImageReader::IMAGEWITHTIME || filetype == vvImageReader::SLICED)
 879         SetImageSucceed = imageManager->SetImage(files[i],filetype, number, j);
 880       else {
 881         SetImageSucceed = imageManager->SetImages(files,filetype, number);
 882       }
 883
 884       if (!SetImageSucceed) {
 885         QApplication::restoreOverrideCursor();
 886         QString error = "Cannot open file \n";
 887         error += imageManager->GetLastError().c_str();
 888         QMessageBox::information(this,tr("Reading problem"),error);
 889         delete imageManager;
 890       } else {
 891         mSlicerManagers.push_back(imageManager);
 892
 893         //create an item in the tree with good settings
 894         QTreeWidgetItem *item = new QTreeWidgetItem();
 895         item->setData(0,Qt::UserRole,files[i].c_str());
 896         QFileInfo fileinfo(imageManager->GetFileName().c_str()); //Do not show the path
 897         item->setData(COLUMN_IMAGE_NAME,Qt::DisplayRole,fileinfo.fileName());
 898         item->setData(1,Qt::UserRole,tr("image"));
 899         item->setToolTip(COLUMN_IMAGE_NAME, imageManager->GetListOfAbsoluteFilePathInOneString("image").c_str());
 900         qApp->processEvents();
 901
 902         //Create the buttons for reload and close
 903         qApp->processEvents();
 904         QTreePushButton* cButton = new QTreePushButton;
 905         cButton->setItem(item);
 906         cButton->setColumn(COLUMN_CLOSE_IMAGE);
 907         cButton->setToolTip(tr("close image"));
 908         cButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/exit.png")));
 909         connect(cButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
 910           this,SLOT(CloseImage(QTreeWidgetItem*, int)));
 911
 912         QTreePushButton* rButton = new QTreePushButton;
 913         rButton->setItem(item);
 914         rButton->setColumn(COLUMN_RELOAD_IMAGE);
 915         rButton->setToolTip(tr("reload image"));
 916         rButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/rotateright.png")));
 917         connect(rButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
 918           this,SLOT(ReloadImage(QTreeWidgetItem*, int)));
 919
 920         DataTree->addTopLevelItem(item);
 921         DataTree->setItemWidget(item, COLUMN_CLOSE_IMAGE, cButton);
 922         DataTree->setItemWidget(item, COLUMN_RELOAD_IMAGE, rButton);
 923
 924         //set the id of the image
 925         QString id = QDir::current().absoluteFilePath(files[i].c_str()) + QString::number(mSlicerManagers.size()-1);
 926         item->setData(COLUMN_IMAGE_NAME,Qt::UserRole,id.toStdString().c_str());
 927         mSlicerManagers.back()->SetId(id.toStdString());
 928
 929         linkPanel->addImage(imageManager->GetFileName(), id.toStdString());
 930
 931         connect(mSlicerManagers.back(), SIGNAL(currentImageChanged(std::string)),
 932           this,SLOT(CurrentImageChanged(std::string)));
 933         connect(mSlicerManagers.back(), SIGNAL(currentPickedImageChanged(std::string)),
 934           this, SLOT(CurrentPickedImageChanged(std::string)));
 935         connect(mSlicerManagers.back(), SIGNAL(UpdatePosition(int, double, double, double, double, double, double, double)),
 936           this,SLOT(MousePositionChanged(int,double, double, double, double, double, double, double)));
 937         connect(mSlicerManagers.back(), SIGNAL(UpdateVector(int, double, double, double, double)),
 938           this, SLOT(VectorChanged(int,double,double,double, double)));
 939         connect(mSlicerManagers.back(), SIGNAL(UpdateOverlay(int, double, double)),
 940           this, SLOT(OverlayChanged(int,double,double)));
 941         connect(mSlicerManagers.back(), SIGNAL(UpdateFusion(int, double)),
 942           this, SLOT(FusionChanged(int,double)));
 943         connect(mSlicerManagers.back(), SIGNAL(WindowLevelChanged()),
 944           this,SLOT(WindowLevelChanged()));
 945         connect(mSlicerManagers.back(), SIGNAL(UpdateSlice(int,int)),
 946           this,SLOT(UpdateSlice(int,int)));
 947         connect(mSlicerManagers.back(), SIGNAL(UpdateTSlice(int, int, int)),
 948           this,SLOT(UpdateTSlice(int, int, int)));
 949         connect(mSlicerManagers.back(), SIGNAL(UpdateTSlice(int, int, int)),
 950           this,SLOT(ImageInfoChanged()));
 951         connect(mSlicerManagers.back(), SIGNAL(UpdateSliceRange(int,int,int,int,int)),
 952           this,SLOT(UpdateSliceRange(int,int,int,int,int)));
 953         connect(mSlicerManagers.back(), SIGNAL(UpdateLinkManager(std::string,int,double,double,double,int)),
 954           this,SLOT(UpdateLinkManager(std::string,int,double,double,double,int)));
 955         connect(mSlicerManagers.back(), SIGNAL(UpdateLinkedNavigation(std::string,vvSlicerManager*,vvSlicer*)),
 956           this,SLOT(UpdateLinkedNavigation(std::string,vvSlicerManager*,vvSlicer*)));
 957         connect(mSlicerManagers.back(), SIGNAL(ChangeImageWithIndexOffset(vvSlicerManager*,int,int)),
 958           this,SLOT(ChangeImageWithIndexOffset(vvSlicerManager*,int,int)));
 959         connect(mSlicerManagers.back(),SIGNAL(LandmarkAdded()),landmarksPanel,SLOT(AddPoint()));
 960
 961         InitSlicers();
 962         numberofsuccesulreads++;
 963       }
 964     }
 965   }
 966   if (numberofsuccesulreads) {
 967     NOViewWidget->show();
 968     NEViewWidget->show();
 969     SOViewWidget->show();
 970     SEViewWidget->show();
 971     UpdateTree();
 972     InitDisplay();
 973     ShowLastImage();
 974
 975     // Try to guess default WindowLevel
 976     double range[2];
 977     mSlicerManagers.back()->GetImage()->GetFirstVTKImageData()->GetScalarRange(range);
 978     if ((range[0] == 0) && (range[1] == 1)) {
 979       presetComboBox->setCurrentIndex(WL_BINARY);// binary
 980     } else {
 981       // TODO
 982     }
 983   }
 984   QApplication::restoreOverrideCursor();
 985 }
 986 //------------------------------------------------------------------------------
 987
 988 //------------------------------------------------------------------------------
 989 void vvMainWindow::UpdateTree()
 990 {
 991   DataTree->resizeColumnToContents(COLUMN_TREE);
 992   DataTree->resizeColumnToContents(COLUMN_UL_VIEW);
 993   DataTree->resizeColumnToContents(COLUMN_UR_VIEW);
 994   DataTree->resizeColumnToContents(COLUMN_DL_VIEW);
 995   DataTree->resizeColumnToContents(COLUMN_DR_VIEW);
 996   DataTree->resizeColumnToContents(COLUMN_IMAGE_NAME);
 997   DataTree->resizeColumnToContents(COLUMN_CLOSE_IMAGE);
 998   DataTree->resizeColumnToContents(COLUMN_RELOAD_IMAGE);
 999 }
1000 //------------------------------------------------------------------------------
1001
1002 //------------------------------------------------------------------------------
1003 void vvMainWindow::CurrentImageChanged(std::string id)
1004 {
1005   if (id == mCurrentSelectedImageId) return; // Do nothing
1006   int selected = 0;
1007   for (int i = 0; i < DataTree->topLevelItemCount(); i++) {
1008     if (DataTree->topLevelItem(i)->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString().toStdString() == id) {
1009       selected = i;
1010     } else {
1011       DataTree->topLevelItem(i)->setSelected(0);
1012     }
1013     for (int child = 0; child < DataTree->topLevelItem(i)->childCount(); child++)
1014       DataTree->topLevelItem(i)->child(child)->setSelected(0);
1015
1016   }
1017   DataTree->topLevelItem(selected)->setSelected(1);
1018   mCurrentSelectedImageId = id;
1019
1020   landmarksPanel->SetCurrentLandmarks(mSlicerManagers[selected]->GetLandmarks(),
1021                                       mSlicerManagers[selected]->GetTSlice());
1022   landmarksPanel->SetCurrentPath(mInputPathName.toStdString());
1023   landmarksPanel->SetCurrentImage(mSlicerManagers[selected]->GetFileName().c_str());
1024
1025   emit SelectedImageHasChanged(mSlicerManagers[selected]);
1026 }
1027 //------------------------------------------------------------------------------
1028
1029 //------------------------------------------------------------------------------
1030 void vvMainWindow::CurrentPickedImageChanged(std::string id)
1031 {
1032   if (id == mCurrentPickedImageId) return; // Do nothing
1033   int selected = 0;
1034   for (int i = 0; i < DataTree->topLevelItemCount(); i++) {
1035     if (DataTree->topLevelItem(i)->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString().toStdString() == id) {
1036       selected = i;
1037     } else {
1038       DataTree->topLevelItem(i)->setSelected(0);
1039     }
1040     for (int child = 0; child < DataTree->topLevelItem(i)->childCount(); child++)
1041       DataTree->topLevelItem(i)->child(child)->setSelected(0);
1042
1043   }
1044   DataTree->topLevelItem(selected)->setSelected(1);
1045   mCurrentPickedImageId = id;
1046   mCurrentPickedImageIndex = selected;
1047 }
1048 //------------------------------------------------------------------------------
1049
1050 //------------------------------------------------------------------------------
1051 void vvMainWindow::ImageInfoChanged()
1052 {
1053   contextActions[6]->setEnabled(1);
1054   contextActions[5]->setEnabled(1);
1055   actionSave_As->setEnabled(1);
1056   actionAdd_VF_to_current_Image->setEnabled(1);
1057   actionAdd_fusion_image->setEnabled(1);
1058   actionAdd_overlay_image_to_current_image->setEnabled(1);
1059   actionAdd_USSequence_toCT->setEnabled(1);
1060   actionNorth_East_Window->setEnabled(1);
1061   actionNorth_West_Window->setEnabled(1);
1062   actionSouth_East_Window->setEnabled(1);
1063   actionSouth_West_Window->setEnabled(1);
1064   vvToolManager::GetInstance()->EnableToolsInMenu(this, true);
1065   inverseButton->setEnabled(1);
1066
1067   goToCursorPushButton->setEnabled(1);
1068
1069   if (DataTree->selectedItems().size()) {
1070     int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1071
1072     colorMapComboBox->setEnabled(1);
1073     for (int i = 0; i < DataTree->topLevelItem(index)->childCount(); i++) {
1074       if (DataTree->topLevelItem(index)->child(i)->data(1,Qt::UserRole).toString() == "overlay" ||
1075         DataTree->topLevelItem(index)->child(i)->data(1,Qt::UserRole).toString() == "fusion" ||
1076         DataTree->topLevelItem(index)->child(i)->data(1,Qt::UserRole).toString() == "fusionSequence") {
1077           colorMapComboBox->setEnabled(0);
1078           break;
1079       }
1080     }
1081
1082     std::vector<double> origin;
1083     std::vector<double> inputSpacing;
1084     std::vector<int> inputSize;
1085     std::vector<double> sizeMM;
1086     vtkSmartPointer<vtkMatrix4x4> transformation;
1087     int dimension=0;
1088     QString pixelType;
1089     QString inputSizeInBytes;
1090     QString image = DataTree->selectedItems()[0]->data(COLUMN_IMAGE_NAME,Qt::DisplayRole).toString();
1091
1092     int nframes = mSlicerManagers[index]->GetSlicer(0)->GetTMax();
1093
1094     if (nframes > 1 || playMode == 1) {
1095       playButton->setEnabled(1);
1096       frameRateLabel->setEnabled(1);
1097       frameRateSpinBox->setEnabled(1);
1098     } else {
1099       playButton->setEnabled(0);
1100       frameRateLabel->setEnabled(0);
1101       frameRateSpinBox->setEnabled(0);
1102     }
1103
1104     //read image header
1105     int NPixel = 1;
1106
1107     int tSlice = 0;
1108     vvImage::Pointer imageSelected;
1109     if (DataTree->topLevelItem(index) == DataTree->selectedItems()[0]) {
1110       imageSelected = mSlicerManagers[index]->GetSlicer(0)->GetImage();
1111       tSlice = mSlicerManagers[index]->GetSlicer(0)->GetTSlice();
1112     } else if (DataTree->selectedItems()[0]->data(1,Qt::UserRole).toString() == "vector") {
1113       imageSelected = mSlicerManagers[index]->GetSlicer(0)->GetVF();
1114       tSlice = mSlicerManagers[index]->GetSlicer(0)->GetOverlayTSlice();
1115     } else if (DataTree->selectedItems()[0]->data(1,Qt::UserRole).toString() == "overlay") {
1116       imageSelected = mSlicerManagers[index]->GetSlicer(0)->GetOverlay();
1117       tSlice = mSlicerManagers[index]->GetSlicer(0)->GetOverlayTSlice();
1118     } else if (DataTree->selectedItems()[0]->data(1,Qt::UserRole).toString() == "fusion") {
1119       imageSelected = mSlicerManagers[index]->GetSlicer(0)->GetFusion();
1120       tSlice = mSlicerManagers[index]->GetSlicer(0)->GetFusionTSlice();
1121     }
1122     else if (DataTree->selectedItems()[0]->data(1,Qt::UserRole).toString() == "fusionSequence") {
1123       imageSelected = mSlicerManagers[index]->GetSlicer(0)->GetFusion();
1124       tSlice = mSlicerManagers[index]->GetSlicer(0)->GetFusionTSlice();
1125     }
1126     else if (DataTree->selectedItems()[0]->data(1,Qt::UserRole).toString() == "contour") {
1127       imageSelected = mSlicerManagers[index]->GetSlicer(0)->GetImage();
1128       tSlice = mSlicerManagers[index]->GetSlicer(0)->GetTSlice();
1129     }
1130     else {
1131       imageSelected = mSlicerManagers[index]->GetSlicer(0)->GetImage();
1132       tSlice = mSlicerManagers[index]->GetSlicer(0)->GetTSlice();
1133     }
1134
1135     dimension = imageSelected->GetNumberOfDimensions();
1136     origin.resize(dimension);
1137     inputSpacing.resize(dimension);
1138     inputSize.resize(dimension);
1139     sizeMM.resize(dimension);
1140     pixelType = mSlicerManagers[index]->GetImage()->GetScalarTypeAsITKString().c_str();
1141     for (int i = 0; i < dimension; i++) {
1142       origin[i] = imageSelected->GetOrigin()[i];
1143       inputSpacing[i] = imageSelected->GetSpacing()[i];
1144       inputSize[i] = imageSelected->GetSize()[i];
1145       sizeMM[i] = inputSize[i]*inputSpacing[i];
1146       NPixel *= inputSize[i];
1147     }
1148     inputSizeInBytes = GetSizeInBytes(imageSelected->GetActualMemorySize()*1000);
1149
1150     QString dim = QString::number(dimension) + " (";
1151     dim += pixelType + ")";
1152
1153     infoPanel->setFileName(image);
1154     std::string creationImageTimeValue("No creation time");
1155     itk::ExposeMetaData< std::string > (*imageSelected->GetFirstMetaDataDictionary(), "creationImageTime", creationImageTimeValue);
1156     infoPanel->setImageCreationTime(QString(creationImageTimeValue.c_str()));
1157     infoPanel->setDimension(dim);
1158     infoPanel->setSizePixel(GetVectorIntAsString(inputSize));
1159     infoPanel->setSizeMM(GetVectorDoubleAsString(sizeMM));
1160     infoPanel->setOrigin(GetVectorDoubleAsString(origin));
1161     infoPanel->setSpacing(GetVectorDoubleAsString(inputSpacing));
1162     infoPanel->setNPixel(QString::number(NPixel)+" ("+inputSizeInBytes+")");
1163
1164     transformation = imageSelected->GetTransform()[tSlice]->GetMatrix();
1165     infoPanel->setTransformation(Get4x4MatrixDoubleAsString(transformation));
1166
1167     landmarksPanel->SetCurrentLandmarks(mSlicerManagers[index]->GetLandmarks(),
1168                                         mSlicerManagers[index]->GetTSlice());
1169     landmarksPanel->SetCurrentPath(mInputPathName.toStdString());
1170     landmarksPanel->SetCurrentImage(mSlicerManagers[index]->GetFileName().c_str());
1171
1172     overlayPanel->getCurrentImageName(mSlicerManagers[index]->GetFileName().c_str());
1173     for (int i = 0; i < 4; i++) {
1174       if (DataTree->selectedItems()[0]->data(i+1,Qt::CheckStateRole).toInt() > 0 || i == 3) {
1175         mSlicerManagers[index]->UpdateInfoOnCursorPosition(i);
1176         break;
1177       }
1178     }
1179
1180 //     infoPanel->setFileName(image);
1181 //     infoPanel->setDimension(dim);
1182 //     infoPanel->setSizePixel(GetVectorIntAsString(inputSize));
1183 //     infoPanel->setSizeMM(GetVectorDoubleAsString(sizeMM));
1184 //     infoPanel->setOrigin(GetVectorDoubleAsString(origin));
1185 //     infoPanel->setSpacing(GetVectorDoubleAsString(inputSpacing));
1186 //     infoPanel->setNPixel(QString::number(NPixel)+" ("+inputSizeInBytes+")");
1187 //
1188 //     landmarksPanel->SetCurrentLandmarks(mSlicerManagers[index]->GetLandmarks(),
1189 //                                         mSlicerManagers[index]->GetTSlice());
1190 //     landmarksPanel->SetCurrentPath(mInputPathName.toStdString());
1191 //     landmarksPanel->SetCurrentImage(mSlicerManagers[index]->GetFileName().c_str());
1192 //
1193 //     overlayPanel->getCurrentImageName(mSlicerManagers[index]->GetFileName().c_str());
1194 //     for (int i = 0; i < 4; i++) {
1195 //       if (DataTree->selectedItems()[0]->data(i+1,Qt::CheckStateRole).toInt() > 0 || i == 3) {
1196 //         mSlicerManagers[index]->UpdateInfoOnCursorPosition(i);
1197 //         break;
1198 //       }
1199 //     }
1200     WindowLevelChanged();
1201
1202     slicingPresetComboBox->setCurrentIndex(mSlicerManagers[index]->GetSlicingPreset());
1203
1204     if (mSlicerManagers[index]->GetSlicer(0)->GetVF()) {
1205       overlayPanel->getVFName(mSlicerManagers[index]->GetVFName().c_str());
1206       overlayPanel->getVFProperty(mSlicerManagers[index]->GetSlicer(0)->GetVFSubSampling(),
1207         mSlicerManagers[index]->GetSlicer(0)->GetVFScale(),
1208         mSlicerManagers[index]->GetSlicer(0)->GetVFLog());
1209     } else {
1210       overlayPanel->getVFName(mSlicerManagers[index]->GetVFName().c_str());
1211       overlayPanel->getVFProperty(-1,-1,-1);
1212     }
1213     if (mSlicerManagers[index]->GetSlicer(0)->GetOverlay()) {
1214       overlayPanel->getOverlayName(mSlicerManagers[index]->GetOverlayName().c_str());
1215     } else {
1216       overlayPanel->getOverlayName(mSlicerManagers[index]->GetOverlayName().c_str());
1217     }
1218
1219     if (mSlicerManagers[index]->GetSlicer(0)->GetFusion()) {
1220       overlayPanel->getFusionName(mSlicerManagers[index]->GetFusionName().c_str());
1221     } else {
1222       overlayPanel->getFusionName(mSlicerManagers[index]->GetFusionName().c_str());
1223     }
1224   }
1225 }
1226 //------------------------------------------------------------------------------
1227
1228 //------------------------------------------------------------------------------
1229 void vvMainWindow::ShowDocumentation()
1230 {
1231   documentation->show();
1232 }
1233 //------------------------------------------------------------------------------
1234
1235 //------------------------------------------------------------------------------
1236 void vvMainWindow::PopupRegisterForm(bool checkCanPush)
1237 {
1238   vvRegisterForm* registerForm = new vvRegisterForm(QUrl("http://www.creatis.insa-lyon.fr/~dsarrut/vvregister/write.php"), getVVSettingsPath(), getSettingsOptionFormat());
1239   if(!checkCanPush) {
1240     registerForm->show();
1241   } else {
1242     if(registerForm->canPush()) {
1243       registerForm->show();
1244       registerForm->acquitPushed();//too bad if there is not internet connection anymore.
1245     }
1246   }
1247 }
1248 //------------------------------------------------------------------------------
1249
1250 //------------------------------------------------------------------------------
1251 void vvMainWindow::ShowHelpDialog()
1252 {
1253   help_dialog->show();
1254 }
1255 //------------------------------------------------------------------------------
1256
1257 //------------------------------------------------------------------------------
1258 void vvMainWindow::ChangeViewMode()
1259 {
1260   typedef struct _SIZE{
1261     QSplitter* splitter;
1262     QList<int> size1, size2;
1263     int cols[3];
1264   }SplitterSize;
1265   SplitterSize sizes[4];
1266   sizes[0].splitter = OSplitter;
1267   sizes[0].size1.push_back(1);
1268   sizes[0].size1.push_back(0);
1269   sizes[0].size2.push_back(1);
1270   sizes[0].size2.push_back(0);
1271   sizes[0].cols[0] = 2;
1272   sizes[0].cols[1] = 3;
1273   sizes[0].cols[2] = 4;
1274
1275   sizes[1].splitter = ESplitter;
1276   sizes[1].size1.push_back(0);
1277   sizes[1].size1.push_back(1);
1278   sizes[1].size2.push_back(1);
1279   sizes[1].size2.push_back(0);
1280   sizes[1].cols[0] = 1;
1281   sizes[1].cols[1] = 3;
1282   sizes[1].cols[2] = 4;
1283
1284   sizes[2].splitter = OSplitter;
1285   sizes[2].size1.push_back(1);
1286   sizes[2].size1.push_back(0);
1287   sizes[2].size2.push_back(0);
1288   sizes[2].size2.push_back(1);
1289   sizes[2].cols[0] = 1;
1290   sizes[2].cols[1] = 2;
1291   sizes[2].cols[2] = 4;
1292
1293   sizes[3].splitter = ESplitter;
1294   sizes[3].size1.push_back(0);
1295   sizes[3].size1.push_back(1);
1296   sizes[3].size2.push_back(0);
1297   sizes[3].size2.push_back(1);
1298   sizes[3].cols[0] = 1;
1299   sizes[3].cols[1] = 2;
1300   sizes[3].cols[2] = 3;
1301
1302   int slicer = mSlicerManagers[mCurrentPickedImageIndex]->GetSelectedSlicer();
1303   if (viewMode == 1) {
1304     if (slicer >= 0) {
1305       viewMode = 0;
1306       splitter_3->setSizes(sizes[slicer].size1);
1307       sizes[slicer].splitter->setSizes(sizes[slicer].size2);
1308       DataTree->setColumnHidden(sizes[slicer].cols[0],1);
1309       DataTree->setColumnHidden(sizes[slicer].cols[1],1);
1310       DataTree->setColumnHidden(sizes[slicer].cols[2],1);
1311     }
1312   } else {
1313     QList<int> size;
1314     if (slicer >= 0) {
1315       viewMode = 1;
1316       size.push_back(1);
1317       size.push_back(1);
1318       splitter_3->setSizes(size);
1319       sizes[slicer].splitter->setSizes(size);
1320       DataTree->setColumnHidden(sizes[slicer].cols[0],0);
1321       DataTree->setColumnHidden(sizes[slicer].cols[1],0);
1322       DataTree->setColumnHidden(sizes[slicer].cols[2],0);
1323     }
1324   }
1325   UpdateRenderWindows();
1326   /*
1327   ** I don't know why but for both resized QVTKWidget we also need to render
1328   ** the associated Slicer to redraw crosses.
1329   */
1330   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
1331     //     if (DataTree->topLevelItem(i)->data(COLUMN_UL_VIEW,Qt::CheckStateRole).toInt() > 1)
1332     mSlicerManagers[i]->GetSlicer(0)->Render();
1333     mSlicerManagers[i]->GetSlicer(1)->Render();
1334     //     if (DataTree->topLevelItem(i)->data(COLUMN_DL_VIEW,Qt::CheckStateRole).toInt() > 1)
1335     mSlicerManagers[i]->GetSlicer(2)->Render();
1336     mSlicerManagers[i]->GetSlicer(3)->Render();
1337   }
1338 }
1339 //------------------------------------------------------------------------------
1340
1341 //------------------------------------------------------------------------------
1342 QString vvMainWindow::GetSizeInBytes(unsigned long size)
1343 {
1344   QString result = "";// QString::number(size);
1345   //result += " bytes (";
1346   if (size > 1000000000) {
1347     size /= 1000000000;
1348     result += QString::number(size);
1349     result += "Gb";//)";
1350   } else if (size > 1000000) {
1351     size /= 1000000;
1352     result += QString::number(size);
1353     result += "Mb";//)";
1354   } else if (size > 1000) {
1355     size /= 1000;
1356     result += QString::number(size);
1357     result += "kb";//)";
1358   }
1359   return result;
1360 }
1361 //------------------------------------------------------------------------------
1362
1363 //------------------------------------------------------------------------------
1364 QString vvMainWindow::Get4x4MatrixDoubleAsString(vtkSmartPointer<vtkMatrix4x4> matrix, const int precision)
1365 {
1366   std::ostringstream strmatrix;
1367
1368   // Figure out the number of digits of the integer part of the largest absolute value
1369   // for each column
1370   unsigned width[4];
1371   for (unsigned int j = 0; j < 4; j++){
1372     double absmax = 0.;
1373     for (unsigned int i = 0; i < 4; i++)
1374       absmax = std::max(absmax, vnl_math_abs(matrix->GetElement(i, j)));
1375     unsigned ndigits = (unsigned)std::max(0.,std::log10(absmax))+1;
1376     width[j] = precision+ndigits+3;
1377   }
1378
1379   // Output with correct width, aligned to the right
1380   for (unsigned int i = 0; i < 4; i++) {
1381     for (unsigned int j = 0; j < 4; j++) {
1382       strmatrix.setf(ios::fixed,ios::floatfield);
1383       strmatrix.precision(precision);
1384       strmatrix.fill(' ');
1385       strmatrix.width(width[j]);
1386       strmatrix << std::right << matrix->GetElement(i, j);
1387     }
1388     strmatrix << std::endl;
1389   }
1390   QString result = strmatrix.str().c_str();
1391   return result;
1392 }
1393 //------------------------------------------------------------------------------
1394
1395 //------------------------------------------------------------------------------
1396 QString vvMainWindow::GetVectorDoubleAsString(std::vector<double> vectorDouble)
1397 {
1398   QString result;
1399   for (unsigned int i= 0; i < vectorDouble.size(); i++) {
1400     if (i != 0)
1401       result += " ";
1402     result += QString::number(vectorDouble[i]);
1403   }
1404   return result;
1405 }
1406 //------------------------------------------------------------------------------
1407
1408 //------------------------------------------------------------------------------
1409 QString vvMainWindow::GetVectorIntAsString(std::vector<int> vectorInt)
1410 {
1411   QString result;
1412   for (unsigned int i= 0; i < vectorInt.size(); i++) {
1413     if (i != 0)
1414       result += " ";
1415     result += QString::number(vectorInt[i]);
1416   }
1417   return result;
1418 }
1419 //------------------------------------------------------------------------------
1420
1421 //------------------------------------------------------------------------------
1422 //this actually returns the SlicerManager index!
1423 int vvMainWindow::GetSlicerIndexFromItem(QTreeWidgetItem* item)
1424 {
1425   QString id = item->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString();
1426   for (int i = 0; i < DataTree->topLevelItemCount(); i++) {
1427     if (DataTree->topLevelItem(i)->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString() == id)
1428       return i;
1429   }
1430   return -1;
1431 }
1432 //------------------------------------------------------------------------------
1433
1434 //------------------------------------------------------------------------------
1435 QTreeWidgetItem* vvMainWindow::GetItemFromSlicerManager(vvSlicerManager* sm)
1436 {
1437   QString id = sm->GetId().c_str();
1438   for (int i = 0; i < DataTree->topLevelItemCount(); i++) {
1439     if (DataTree->topLevelItem(i)->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString() == id)
1440       return DataTree->topLevelItem(i);
1441   }
1442   return NULL;
1443 }
1444 //------------------------------------------------------------------------------
1445
1446 //------------------------------------------------------------------------------
1447 void vvMainWindow::DisplayChanged(QTreeWidgetItem *clickedItem, int column)
1448 {
1449   if ( column >= COLUMN_CLOSE_IMAGE || column <= 0)
1450     return;
1451
1452   // Get parent information (might be the same item)
1453   int slicerManagerIndex = GetSlicerIndexFromItem(clickedItem);
1454   QTreeWidgetItem* clickedParentItem = DataTree->topLevelItem(slicerManagerIndex);
1455   vvSlicer* clickedSlicer = mSlicerManagers[slicerManagerIndex]->GetSlicer(column-1);
1456
1457   // Go over the complete item tree (only 2 levels, parents and children)
1458   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
1459     // Trick to avoid redoing twice the job for a key (sr)
1460     mSlicerManagers[i]->GetSlicer(column-1)->GetRenderWindow()->GetInteractor()->SetKeySym("Crap");
1461
1462     QTreeWidgetItem* currentParentItem = DataTree->topLevelItem(i);
1463     if(currentParentItem != clickedParentItem) {
1464       // Not the branch of the clicked item, uncheck all
1465
1466       // Parent
1467       currentParentItem->setData(column,Qt::CheckStateRole, 0);
1468       mSlicerManagers[i]->UpdateSlicer(column-1, false);
1469
1470       // Children
1471       for (int iChild = 0; iChild < currentParentItem->childCount(); iChild++) {
1472         currentParentItem->child(iChild)->setData(column,Qt::CheckStateRole, 0);
1473       }
1474     }
1475     else {
1476       // Branch of the clicked one: get check status from actor visibility in slicer
1477       // and toggle the clicked one
1478
1479       // Parent
1480       bool vis = clickedSlicer->GetActorVisibility("image", 0);
1481       bool draw = clickedSlicer->GetRenderer()->GetDraw();
1482
1483       // Update slicer (after getting visibility)
1484       mSlicerManagers[slicerManagerIndex]->UpdateSlicer(column-1, true);
1485       mSlicerManagers[slicerManagerIndex]->UpdateInfoOnCursorPosition(column-1);
1486       DisplaySliders(slicerManagerIndex, column-1);
1487       if(clickedParentItem == clickedItem) {
1488         // Toggle
1489         vis = !draw || !vis;
1490       }
1491       clickedSlicer->SetActorVisibility("image", 0, vis);
1492       clickedParentItem->setData(column, Qt::CheckStateRole, vis?2:0);
1493
1494       // Children
1495       std::map<std::string, int> actorTypeCounts;
1496       for (int iChild = 0; iChild < clickedParentItem->childCount(); iChild++) {
1497         QTreeWidgetItem* currentChildItem = clickedParentItem->child(iChild);
1498         std::string actorType = currentChildItem->data(1,Qt::UserRole).toString().toStdString();
1499         vis = clickedSlicer->GetActorVisibility(actorType, actorTypeCounts[actorType]);
1500         if(currentChildItem == clickedItem) {
1501           // Toggle or force visibility if it was not on this branch so far
1502           vis = !draw || !vis;
1503           clickedSlicer->SetActorVisibility(actorType, actorTypeCounts[actorType], vis);
1504         }
1505         currentChildItem->setData(column, Qt::CheckStateRole, vis?2:0);
1506         actorTypeCounts[actorType]++;
1507       }
1508     }
1509   }
1510
1511   clickedSlicer->Render();
1512 }
1513 //------------------------------------------------------------------------------
1514
1515 void vvMainWindow::InitSlicers()
1516 {
1517   if (mSlicerManagers.size()) {
1518     mSlicerManagers.back()->GenerateDefaultLookupTable();
1519
1520     mSlicerManagers.back()->SetSlicerWindow(0,NOViewWidget->GetRenderWindow());
1521     mSlicerManagers.back()->SetSlicerWindow(1,NEViewWidget->GetRenderWindow());
1522     mSlicerManagers.back()->SetSlicerWindow(2,SOViewWidget->GetRenderWindow());
1523     mSlicerManagers.back()->SetSlicerWindow(3,SEViewWidget->GetRenderWindow());
1524   }
1525 }
1526
1527 //------------------------------------------------------------------------------
1528 void vvMainWindow::InitDisplay()
1529 {
1530   if (mSlicerManagers.size()) {
1531     //BE CAREFUL : this is absolutely necessary to set the interactor style
1532     //in order to have the same style instanciation for all SlicerManagers in
1533     // a same window
1534     for (int j = 0; j < 4; j++) {
1535       vvInteractorStyleNavigator* style = vvInteractorStyleNavigator::New();
1536       style->SetAutoAdjustCameraClippingRange(1);
1537       bool AlreadySelected = false;
1538       for (int i = 0; i < DataTree->topLevelItemCount(); i++) {
1539         mSlicerManagers[i]->SetInteractorStyleNavigator(j,style);
1540
1541         //select the image only if previous are not selected
1542         if (DataTree->topLevelItem(i)->data(j+1,Qt::CheckStateRole).toInt() > 1) {
1543           mSlicerManagers[i]->UpdateSlicer(j,1);
1544           AlreadySelected = true;
1545         } else if (i == DataTree->topLevelItemCount()-1 && !AlreadySelected) {
1546           if (DataTree->selectedItems().size() == 0)
1547             DataTree->topLevelItem(i)->setSelected(1);
1548           DataTree->topLevelItem(i)->setData(j+1,Qt::CheckStateRole,2);
1549           mSlicerManagers[i]->UpdateSlicer(j,1);
1550           DisplaySliders(i,j);
1551         } else {
1552           DataTree->topLevelItem(i)->setData(j+1,Qt::CheckStateRole,0);
1553           mSlicerManagers[i]->UpdateSlicer(j,0);
1554         }
1555       }
1556       style->Delete();
1557     }
1558   }
1559 }
1560 //------------------------------------------------------------------------------
1561
1562 //------------------------------------------------------------------------------
1563 void vvMainWindow::DisplaySliders(int slicer, int window)
1564 {
1565   if(!mSlicerManagers[slicer]->GetSlicer(window)->GetRenderer()->GetDraw())
1566     return;
1567
1568   int range[2];
1569   mSlicerManagers[slicer]->GetSlicer(window)->GetSliceRange(range);
1570   int position = mSlicerManagers[slicer]->GetSlicer(window)->GetSlice();
1571   if (range[1]>0)
1572     verticalSliders[window]->show();
1573   else
1574     verticalSliders[window]->hide();
1575   verticalSliders[window]->setRange(range[0],range[1]);
1576   verticalSliders[window]->setValue(position);
1577
1578   int tRange[2];
1579   tRange[0] = 0;
1580   tRange[1] = mSlicerManagers[slicer]->GetSlicer(window)->GetTMax();
1581   if (tRange[1]>0)
1582     horizontalSliders[window]->show();
1583   else
1584     horizontalSliders[window]->hide();
1585   horizontalSliders[window]->setRange(tRange[0],tRange[1]);
1586   int tPosition = mSlicerManagers[slicer]->GetSlicer(window)->GetMaxCurrentTSlice();
1587   horizontalSliders[window]->setValue(tPosition);
1588 }
1589 //------------------------------------------------------------------------------
1590
1591 //------------------------------------------------------------------------------
1592 void vvMainWindow::CloseImage(QTreeWidgetItem* item, int column)
1593 {
1594   int index = GetSlicerIndexFromItem(item);
1595
1596   if (DataTree->topLevelItem(index) != item) {
1597     QString warning = "Do you really want to close the overlay : ";
1598     warning += item->data(COLUMN_IMAGE_NAME,Qt::DisplayRole).toString();
1599     QMessageBox msgBox(QMessageBox::Warning, tr("Close Overlay"),
1600       warning, 0, this);
1601     msgBox.addButton(tr("Close"), QMessageBox::AcceptRole);
1602     msgBox.addButton(tr("Cancel"), QMessageBox::RejectRole);
1603     if (msgBox.exec() == QMessageBox::AcceptRole) {
1604       std::string overlay_type=item->data(1,Qt::UserRole).toString().toStdString();
1605       int overlay_index=0;
1606       for (int child = 0; child < DataTree->topLevelItem(index)->childCount(); child++) {
1607         if (DataTree->topLevelItem(index)->\
1608           child(child)->data(1,Qt::UserRole).toString().toStdString() == overlay_type)
1609           overlay_index++;
1610         if (DataTree->topLevelItem(index)->child(child) == item) break;
1611       }
1612       if (overlay_type=="fusionSequence") {
1613         //removing the overlay sequence in a fusion sequence visualization mode
1614         //reset the transforms
1615         overlayPanel->getFusionSequenceProperty(-1, false, 0, false);
1616
1617         //unlink and untie the slicer managers
1618         RemoveLink(mSlicerManagers[index]->GetId().c_str(), mSlicerManagers[mSlicerManagers[index]->GetFusionSequenceIndexOfLinkedManager()]->GetId().c_str());
1619         mSlicerManagers[index]->SetFusionSequenceInvolvmentCode(-1);
1620         mSlicerManagers[mSlicerManagers[index]->GetFusionSequenceIndexOfLinkedManager()]->SetFusionSequenceInvolvmentCode(-1);
1621         for (unsigned i=0 ; i<4 ; i++) {
1622             mSlicerManagers[index]->GetSlicer(i)->SetFusionSequenceCode(-1);
1623             mSlicerManagers[mSlicerManagers[index]->GetFusionSequenceIndexOfLinkedManager()]->GetSlicer(i)->SetFusionSequenceCode(-1);
1624         }
1625
1626       }
1627       mSlicerManagers[index]->RemoveActor(overlay_type, overlay_index-1);
1628       mSlicerManagers[index]->SetColorMap(0);
1629       DataTree->topLevelItem(index)->takeChild(DataTree->topLevelItem(index)->indexOfChild(item));
1630       mSlicerManagers[index]->Render();
1631     }
1632   } else if (DataTree->topLevelItemCount() <= 1) {
1633     QString warning = "Do you really want to close the image : ";
1634     warning += item->data(COLUMN_IMAGE_NAME,Qt::DisplayRole).toString();
1635     warning += "\nThis is the last image, you're about to close vv !!!";
1636     QMessageBox msgBox(QMessageBox::Warning, tr("Close Image"),
1637       warning, 0, this);
1638     msgBox.addButton(tr("Close vv"), QMessageBox::AcceptRole);
1639     msgBox.addButton(tr("Cancel"), QMessageBox::RejectRole);
1640     if (msgBox.exec() == QMessageBox::AcceptRole) {
1641       this->close();
1642     }
1643   } else {
1644     QString warning = "Do you really want to close the image : ";
1645     warning += item->data(COLUMN_IMAGE_NAME,Qt::DisplayRole).toString();
1646     QMessageBox msgBox(QMessageBox::Warning, tr("Close Image"),
1647       warning, 0, this);
1648     msgBox.addButton(tr("Close"), QMessageBox::AcceptRole);
1649     msgBox.addButton(tr("Cancel"), QMessageBox::RejectRole);
1650     if (msgBox.exec() == QMessageBox::AcceptRole) {
1651
1652       // Tell tools that we close an image
1653       emit AnImageIsBeingClosed(mSlicerManagers[index]);
1654
1655       std::vector<vvSlicerManager*>::iterator Manageriter = mSlicerManagers.begin();
1656       DataTree->takeTopLevelItem(index);
1657       for (int i = 0; i < index; i++) {
1658         Manageriter++;
1659       }
1660       //if the slicer manager was involved in a fusion sequence visualization...
1661       if ( mSlicerManagers[index]->IsInvolvedInFusionSequence() ) {
1662         //in both cases, close the overlay: find it... and close it
1663         //ideally, I should duplicate the code, and avoid calling CloseImage, since this pops up another interactive box
1664         QTreeWidgetItem* overlayItem;
1665         if (mSlicerManagers[index]->IsMainSequenceOfFusionSequence()) {
1666           for (unsigned i=0 ; i<item->childCount() ; i++) {
1667             overlayItem = item->child(i);
1668             this->CloseImage( overlayItem, 0 );
1669           }
1670         }
1671         else {
1672           QTreeWidgetItem* linkedItem = this->GetItemFromSlicerManager( mSlicerManagers[mSlicerManagers[index]->GetFusionSequenceIndexOfLinkedManager()] );
1673           for (unsigned i=0 ; i<linkedItem->childCount() ; i++) {
1674             overlayItem = linkedItem->child(i);
1675             this->CloseImage( overlayItem, 0 );
1676           }
1677         }
1678
1679         /* -- this is normally already done when closing the overlay.
1680         //reset the transforms
1681         overlayPanel->getFusionSequenceProperty(-1, false, 0, false);
1682
1683         //unlink and untie the slicer managers
1684         RemoveLink(mSlicerManagers[index]->GetId().c_str(), mSlicerManagers[mSlicerManagers[index]->GetFusionSequenceIndexOfLinkedManager()]->GetId().c_str());
1685         mSlicerManagers[index]->SetFusionSequenceInvolvmentCode(-1);
1686         mSlicerManagers[mSlicerManagers[index]->GetFusionSequenceIndexOfLinkedManager()]->SetFusionSequenceInvolvmentCode(-1);
1687         for (unsigned i=0 ; i<4 ; i++) {
1688             mSlicerManagers[index]->GetSlicer(i)->SetFusionSequenceCode(-1);
1689             mSlicerManagers[mSlicerManagers[index]->GetFusionSequenceIndexOfLinkedManager()]->GetSlicer(i)->SetFusionSequenceCode(-1);
1690         }
1691         */
1692       }
1693
1694       linkPanel->removeImage(index);
1695       mSlicerManagers[index]->RemoveActors();
1696
1697       //remove the slicer manager
1698       delete mSlicerManagers[index];
1699       mSlicerManagers.erase(Manageriter);
1700
1701       //
1702       InitDisplay();
1703     }
1704   }
1705   ImageInfoChanged();
1706 }
1707 //------------------------------------------------------------------------------
1708
1709 //------------------------------------------------------------------------------
1710 void vvMainWindow::ReloadImage(QTreeWidgetItem* item, int column)
1711 {
1712   // int index = GetSlicerIndexFromItem(item);
1713   //   QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
1714   //   if (item->data(1,Qt::UserRole).toString() == "vector")
1715   //     mSlicerManagers[index]->ReloadVF();
1716   //   else
1717   //     mSlicerManagers[index]->Reload();
1718
1719   //   QApplication::restoreOverrideCursor();
1720   int index = GetSlicerIndexFromItem(item);
1721   QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
1722   QString role=item->data(1,Qt::UserRole).toString();
1723   if ( role == "vector") {
1724     mSlicerManagers[index]->ReloadVF();
1725   }
1726   else if (role == "overlay") {
1727     mSlicerManagers[index]->ReloadOverlay();
1728   }
1729   else if (role == "fusion") {
1730     mSlicerManagers[index]->ReloadFusion();
1731   }
1732   else if (role == "fusionSequence") {
1733     //both versions of the secondary sequence must be updated.
1734     mSlicerManagers[index]->ReloadFusionSequence();
1735     mSlicerManagers[mSlicerManagers[index]->GetFusionSequenceIndexOfLinkedManager()]->Reload();
1736   }
1737   else {
1738     mSlicerManagers[index]->Reload();
1739     //if we update the secondary sequence, then the overlay of the main sequence should also be updated
1740     if (mSlicerManagers[index]->IsSecondarySequenceOfFusionSequence()) mSlicerManagers[mSlicerManagers[index]->GetFusionSequenceIndexOfLinkedManager()]->ReloadFusionSequence();
1741   }
1742   // Update view and info
1743   ImageInfoChanged();
1744   mSlicerManagers[index]->Render();
1745   QApplication::restoreOverrideCursor();
1746 }
1747 //------------------------------------------------------------------------------
1748
1749 //------------------------------------------------------------------------------
1750 void vvMainWindow::MousePositionChanged(int visibility,double x, double y, double z, double X, double Y, double Z , double value)
1751 {
1752   infoPanel->setCurrentInfo(visibility,x,y,z,X,Y,Z,value);
1753 }
1754 //------------------------------------------------------------------------------
1755
1756 //------------------------------------------------------------------------------
1757 void vvMainWindow::VectorChanged(int visibility,double x, double y, double z, double value)
1758 {
1759   overlayPanel->getCurrentVectorInfo(visibility,x,y,z,value);
1760 }
1761 //------------------------------------------------------------------------------
1762
1763 //------------------------------------------------------------------------------
1764 void vvMainWindow::OverlayChanged(int visibility, double valueOver, double valueRef)
1765 {
1766   overlayPanel->getCurrentOverlayInfo(visibility,valueOver, valueRef);
1767 }
1768 //------------------------------------------------------------------------------
1769
1770 //------------------------------------------------------------------------------
1771 void vvMainWindow::FusionChanged(int visibility, double value)
1772 {
1773   overlayPanel->getCurrentFusionInfo(visibility,value);
1774 }
1775 //------------------------------------------------------------------------------
1776
1777 //------------------------------------------------------------------------------
1778 //called when AddOverlayImage, AddFusionSequence
1779 //or when UpdateWindowLevel() is called ; when slicerManager emits WindowLevelChanged
1780 //when ImageInfoChanged() is called
1781 void vvMainWindow::WindowLevelChanged()
1782 {
1783   // Base image
1784   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1785   if(index==-1) return;
1786   windowSpinBox->setValue(mSlicerManagers[index]->GetColorWindow());
1787   levelSpinBox->setValue(mSlicerManagers[index]->GetColorLevel());
1788   colorMapComboBox->setCurrentIndex(mSlicerManagers[index]->GetColorMap());
1789   presetComboBox->setCurrentIndex(mSlicerManagers[index]->GetPreset());
1790
1791   // Overlay image
1792   if (mSlicerManagers[index]->GetSlicer(0)->GetOverlay())
1793     overlayPanel->getOverlayProperty(mSlicerManagers[index]->GetOverlayColor(),
1794     mSlicerManagers[index]->GetLinkOverlayWindowLevel(),
1795     mSlicerManagers[index]->GetOverlayColorWindow(),
1796     mSlicerManagers[index]->GetOverlayColorLevel());
1797   else
1798     overlayPanel->getOverlayProperty(-1,0,0.,0.);
1799
1800   // Fusion & SequenceFusion image
1801   if (mSlicerManagers[index]->GetSlicer(0)->GetFusion()) {
1802     overlayPanel->getFusionProperty(mSlicerManagers[index]->GetFusionOpacity(),
1803       mSlicerManagers[index]->GetFusionThresholdOpacity(),
1804       mSlicerManagers[index]->GetFusionColorMap(),
1805       mSlicerManagers[index]->GetFusionWindow(),
1806       mSlicerManagers[index]->GetFusionLevel());
1807     if (mSlicerManagers[index]->IsMainSequenceOfFusionSequence()) {
1808       overlayPanel->getFusionSequenceProperty(mSlicerManagers[index]->GetFusionSequenceFrameIndex(),
1809         mSlicerManagers[index]->GetFusionSequenceSpatialSyncFlag(),
1810         mSlicerManagers[index]->GetFusionSequenceNbFrames(),
1811         mSlicerManagers[index]->GetFusionSequenceTemporalSyncFlag());
1812     }
1813   }
1814   else if ( mSlicerManagers[index]->IsSecondarySequenceOfFusionSequence() ) {
1815     //if the image is involved in a fusion sequence, preserve the overlay panel!
1816     int ind = mSlicerManagers[index]->GetFusionSequenceIndexOfLinkedManager();
1817     overlayPanel->getFusionProperty(mSlicerManagers[ind]->GetFusionOpacity(),
1818       mSlicerManagers[ind]->GetFusionThresholdOpacity(),
1819       mSlicerManagers[ind]->GetFusionColorMap(),
1820       mSlicerManagers[ind]->GetFusionWindow(),
1821       mSlicerManagers[ind]->GetFusionLevel());
1822     overlayPanel->getFusionSequenceProperty(mSlicerManagers[ind]->GetFusionSequenceFrameIndex(),
1823       mSlicerManagers[ind]->GetFusionSequenceSpatialSyncFlag(),
1824       mSlicerManagers[ind]->GetFusionSequenceNbFrames(),
1825       mSlicerManagers[ind]->GetFusionSequenceTemporalSyncFlag());
1826   }
1827   else
1828   {
1829     overlayPanel->getFusionProperty(-1, -1, -1, -1, -1);
1830     overlayPanel->getFusionSequenceProperty(-1, false, 0, false);
1831   }
1832 }
1833 //------------------------------------------------------------------------------
1834
1835 //------------------------------------------------------------------------------
1836 void vvMainWindow::WindowLevelEdited()
1837 {
1838   presetComboBox->setCurrentIndex(WL_USER);
1839   UpdateWindowLevel();
1840 }
1841 //------------------------------------------------------------------------------
1842
1843 //------------------------------------------------------------------------------
1844 void vvMainWindow::SetWindowLevel(double w, double l)
1845 {
1846   windowSpinBox->setValue(w);
1847   levelSpinBox->setValue(l);
1848   presetComboBox->setCurrentIndex(WL_USER);
1849   colorMapComboBox->setCurrentIndex(0);
1850   UpdateWindowLevel();
1851 }
1852 //------------------------------------------------------------------------------
1853
1854 //------------------------------------------------------------------------------
1855 void vvMainWindow::UpdateWindowLevel()
1856 {
1857   if (DataTree->selectedItems().size()) {
1858     if (presetComboBox->currentIndex() == WL_VENTILATION) //For ventilation
1859       colorMapComboBox->setCurrentIndex(5);
1860     int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1861     mSlicerManagers[index]->SetColorWindow(windowSpinBox->value());
1862     mSlicerManagers[index]->SetColorLevel(levelSpinBox->value());
1863     mSlicerManagers[index]->SetPreset(presetComboBox->currentIndex());
1864     mSlicerManagers[index]->Render();
1865     WindowLevelChanged();
1866   }
1867 }
1868 //------------------------------------------------------------------------------
1869
1870 //------------------------------------------------------------------------------
1871 void vvMainWindow::UpdateSlicingPreset()
1872 {
1873   if (DataTree->selectedItems().size()) {
1874     int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1875     mSlicerManagers[index]->SetSlicingPreset(vvSlicerManager::SlicingPresetType(slicingPresetComboBox->currentIndex()));
1876   }
1877 }
1878 //------------------------------------------------------------------------------
1879
1880 //------------------------------------------------------------------------------
1881 void vvMainWindow::UpdateColorMap()
1882 {
1883   if (DataTree->selectedItems().size()) {
1884     int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1885     mSlicerManagers[index]->SetColorMap(colorMapComboBox->currentIndex());
1886     mSlicerManagers[index]->Render();
1887   }
1888 }
1889 //------------------------------------------------------------------------------
1890 void vvMainWindow::SwitchWindowLevel()
1891 {
1892   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1893   int window = mSlicerManagers[index]->GetColorWindow();
1894   presetComboBox->setCurrentIndex(WL_USER);
1895   windowSpinBox->setValue(-window);
1896   UpdateWindowLevel();
1897 }
1898 //------------------------------------------------------------------------------
1899
1900 //------------------------------------------------------------------------------
1901 void vvMainWindow::ApplyWindowLevelToAllImages()
1902 {
1903   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1904   if(index==-1) return;
1905   double window = mSlicerManagers[index]->GetColorWindow();
1906   double level = mSlicerManagers[index]->GetColorLevel();
1907
1908   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
1909     if (mSlicerManagers[i] == NULL)
1910       continue;
1911     mSlicerManagers[i]->SetColorWindow(window);
1912     mSlicerManagers[i]->SetColorLevel(level);
1913     mSlicerManagers[i]->SetPreset(WL_USER);
1914     mSlicerManagers[i]->Render();
1915   }
1916 }
1917 //------------------------------------------------------------------------------
1918
1919 //------------------------------------------------------------------------------
1920 void vvMainWindow::ApplyWindowToSetOfImages(double window, unsigned int indexMin, unsigned int indexMax)
1921 {
1922   for (unsigned int i = indexMin; i <= indexMax && i < mSlicerManagers.size(); i++) {
1923     if (mSlicerManagers[i] == NULL)
1924       continue;
1925     mSlicerManagers[i]->SetColorWindow(window);
1926     mSlicerManagers[i]->SetPreset(WL_USER);
1927     mSlicerManagers[i]->Render();
1928   }
1929 }
1930 //------------------------------------------------------------------------------
1931
1932 //------------------------------------------------------------------------------
1933 void vvMainWindow::ApplyLevelToSetOfImages(double level, unsigned int indexMin, unsigned int indexMax)
1934 {
1935   for (unsigned int i = indexMin; i <= indexMax && i < mSlicerManagers.size(); i++) {
1936     if (mSlicerManagers[i] == NULL)
1937       continue;
1938     mSlicerManagers[i]->SetColorLevel(level);
1939     mSlicerManagers[i]->SetPreset(WL_USER);
1940     mSlicerManagers[i]->Render();
1941   }
1942 }
1943 //------------------------------------------------------------------------------
1944
1945 //------------------------------------------------------------------------------
1946 void vvMainWindow::UpdateLinkManager(std::string id, int slicer, double x, double y, double z, int temps)
1947 {
1948   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
1949     if (mSlicerManagers[i]->GetId() == id) {
1950       mSlicerManagers[i]->GetSlicer(slicer)->SetCurrentPosition(x,y,z,temps);
1951       mSlicerManagers[i]->UpdateViews(0,slicer);
1952       break;
1953     }
1954   }
1955 }
1956 //------------------------------------------------------------------------------
1957
1958 //------------------------------------------------------------------------------
1959 void vvMainWindow::UpdateLinkedNavigation(std::string id, vvSlicerManager * sm, vvSlicer* refSlicer)
1960 {
1961   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
1962     if (id == mSlicerManagers[i]->GetId()) {
1963       mSlicerManagers[i]->UpdateLinkedNavigation(refSlicer);
1964     }
1965   }
1966 }
1967 //------------------------------------------------------------------------------
1968
1969 //------------------------------------------------------------------------------
1970 void vvMainWindow::ShowContextMenu(QPoint point)
1971 {
1972   if (!DataTree->selectedItems().size()) {
1973     contextActions[1]->setEnabled(0);
1974     contextActions[2]->setEnabled(0);
1975     contextActions[3]->setEnabled(0);
1976     contextActions[4]->setEnabled(0);
1977     contextActions[5]->setEnabled(0);
1978     contextActions[6]->setEnabled(0);
1979   } else {
1980     int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1981     contextActions[1]->setEnabled(1);
1982     contextActions[2]->setEnabled(
1983       DataTree->itemWidget(DataTree->selectedItems()[0],
1984       COLUMN_RELOAD_IMAGE)->isEnabled());
1985     contextActions[3]->setEnabled(1);
1986     contextActions[5]->setEnabled(1);
1987     contextActions[6]->setEnabled(1);
1988
1989     if (mSlicerManagers[index]->GetDimension() < 3)
1990       contextActions[4]->setEnabled(0);
1991     else
1992       contextActions[4]->setEnabled(1);
1993   }
1994   contextMenu.exec(QCursor::pos());
1995 }
1996 //------------------------------------------------------------------------------
1997
1998 //------------------------------------------------------------------------------
1999 void vvMainWindow::CloseImage()
2000 {
2001   CloseImage(DataTree->selectedItems()[0],0);
2002 }
2003 //------------------------------------------------------------------------------
2004
2005 //------------------------------------------------------------------------------
2006 void vvMainWindow::ReloadImage()
2007 {
2008   ReloadImage(DataTree->selectedItems()[0],0);
2009 }
2010 //------------------------------------------------------------------------------
2011
2012 //------------------------------------------------------------------------------
2013 void vvMainWindow::SelectOverlayImage()
2014 {
2015   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2016
2017   //check if one overlay image is added
2018   for (int child = 0; child < DataTree->topLevelItem(index)->childCount(); child++)
2019     if (DataTree->topLevelItem(index)->child(child)->data(1,Qt::UserRole).toString() == "overlay") {
2020       QString error = "Cannot add more than one compared image\n";
2021       error += "Please remove first ";
2022       error += DataTree->topLevelItem(index)->child(child)->data(COLUMN_IMAGE_NAME,Qt::DisplayRole).toString();
2023       QMessageBox::information(this,tr("Problem adding compared image !"),error);
2024       return;
2025     }
2026
2027     QString Extensions = EXTENSIONS;
2028     Extensions += ";;All Files (*)";
2029     QStringList files = QFileDialog::getOpenFileNames(this,tr("Load Overlay image"),mInputPathName,Extensions);
2030     if (files.isEmpty())
2031       return;
2032
2033     std::vector<std::string> vecFileNames;
2034     for (int i = 0; i < files.size(); i++) {
2035       vecFileNames.push_back(files[i].toStdString());
2036     }
2037     AddOverlayImage(index,vecFileNames,vvImageReader::IMAGE);
2038 }
2039 //------------------------------------------------------------------------------
2040
2041 //------------------------------------------------------------------------------
2042 void vvMainWindow::AddOverlayImage(int index, std::vector<std::string> fileNames, vvImageReader::LoadedImageType type)
2043 {
2044   QString file(fileNames[0].c_str());
2045   if (QFile::exists(file))
2046   {
2047     mInputPathName = itksys::SystemTools::GetFilenamePath(file.toStdString()).c_str();
2048     itk::ImageIOBase::Pointer reader = itk::ImageIOFactory::CreateImageIO(
2049       file.toStdString().c_str(), itk::ImageIOFactory::ReadMode);
2050     reader->SetFileName(fileNames[0].c_str());
2051     reader->ReadImageInformation();
2052     std::string component = reader->GetComponentTypeAsString(reader->GetComponentType());
2053     int dimension = reader->GetNumberOfDimensions();
2054     QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
2055     vvProgressDialog progress("Opening " + file.toStdString());
2056     qApp->processEvents();
2057
2058     std::string filename = itksys::SystemTools::GetFilenameWithoutExtension(file.toStdString()).c_str();
2059     if (mSlicerManagers[index]->SetOverlay(fileNames,dimension, component,type)) {
2060       //create an item in the tree with good settings
2061       QTreeWidgetItem *item = new QTreeWidgetItem();
2062       item->setData(0,Qt::UserRole,file.toStdString().c_str());
2063       item->setData(1,Qt::UserRole,tr("overlay"));
2064       QFileInfo fileinfo(file); //Do not show the path
2065       item->setData(COLUMN_IMAGE_NAME,Qt::DisplayRole,fileinfo.fileName());
2066       item->setToolTip(COLUMN_IMAGE_NAME, mSlicerManagers[index]->GetListOfAbsoluteFilePathInOneString("overlay").c_str());
2067       qApp->processEvents();
2068
2069       for (int j = 1; j <= 4; j++) {
2070         item->setData(j,Qt::CheckStateRole,DataTree->topLevelItem(index)->data(j,Qt::CheckStateRole));
2071       }
2072
2073       //Create the buttons for reload and close
2074       qApp->processEvents();
2075       QTreePushButton* cButton = new QTreePushButton;
2076       cButton->setItem(item);
2077       cButton->setColumn(COLUMN_CLOSE_IMAGE);
2078       cButton->setToolTip(tr("close image"));
2079       cButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/exit.png")));
2080       connect(cButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
2081         this,SLOT(CloseImage(QTreeWidgetItem*, int)));
2082
2083       QTreePushButton* rButton = new QTreePushButton;
2084       rButton->setItem(item);
2085       rButton->setColumn(COLUMN_RELOAD_IMAGE);
2086       rButton->setToolTip(tr("reload image"));
2087       rButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/rotateright.png")));
2088       connect(rButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
2089         this,SLOT(ReloadImage(QTreeWidgetItem*, int)));
2090
2091       DataTree->topLevelItem(index)->setExpanded(1);
2092       DataTree->topLevelItem(index)->addChild(item);
2093       DataTree->setItemWidget(item, COLUMN_CLOSE_IMAGE, cButton);
2094       DataTree->setItemWidget(item, COLUMN_RELOAD_IMAGE, rButton);
2095
2096       //set the id of the image
2097       QString id = DataTree->topLevelItem(index)->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString();
2098       item->setData(COLUMN_IMAGE_NAME,Qt::UserRole,id.toStdString().c_str());
2099       UpdateTree();
2100       qApp->processEvents();
2101       ImageInfoChanged();
2102       QApplication::restoreOverrideCursor();
2103
2104       // Update the display to update, e.g., the sliders
2105       for(int i=0; i<4; i++)
2106         DisplaySliders(index, i);
2107     } else {
2108       QApplication::restoreOverrideCursor();
2109       QString error = "Cannot import the new image.\n";
2110       error += mSlicerManagers[index]->GetLastError().c_str();
2111       QMessageBox::information(this,tr("Problem reading image !"),error);
2112     }
2113     WindowLevelChanged();
2114   }
2115   else
2116     QMessageBox::information(this,tr("Problem reading Overlay !"),"File doesn't exist!");
2117 }
2118 //------------------------------------------------------------------------------
2119
2120
2121 //------------------------------------------------------------------------------
2122 void vvMainWindow::AddROI(int index, QString file)
2123 {
2124   /*
2125   // Get slice manager
2126
2127   // Load image
2128
2129   vvImageReader * mReader = new vvImageReader;
2130   mReader->SetInputFilename(filename.toStdString());
2131   mReader->Update(IMAGE);
2132   if (mReader->GetLastError().size() != 0) {
2133   std::cerr << "Error while reading " << filename.toStdString() << std::endl;
2134   QString error = "Cannot open file \n";
2135   error += mReader->GetLastError().c_str();
2136   QMessageBox::information(this,tr("Reading problem"),error);
2137   delete mReader;
2138   return;
2139   }
2140   vvImage::Pointer roi = mReader->GetOutput();
2141
2142   // Create roi in new tool
2143   vvToolStructureSetManager::AddImage(mCurrentSlicerManager, roi);
2144   */
2145 }
2146 //------------------------------------------------------------------------------
2147
2148 //------------------------------------------------------------------------------
2149 void vvMainWindow::SelectFusionImage()
2150 {
2151   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2152
2153   //check if one fusion image is added
2154   for (int child = 0; child < DataTree->topLevelItem(index)->childCount(); child++)
2155     if ( (DataTree->topLevelItem(index)->child(child)->data(1,Qt::UserRole).toString() == "fusion") ||
2156       (DataTree->topLevelItem(index)->child(child)->data(1,Qt::UserRole).toString() == "fusionSequence") ) {
2157         QString error = "Cannot add more than one fusion image\n";
2158         error += "Please remove first ";
2159         error += DataTree->topLevelItem(index)->child(child)->data(COLUMN_IMAGE_NAME,Qt::DisplayRole).toString();
2160         QMessageBox::information(this,tr("Problem adding fusion image !"),error);
2161         return;
2162     }
2163
2164     QString Extensions = EXTENSIONS;
2165     Extensions += ";;All Files (*)";
2166     QStringList files = QFileDialog::getOpenFileNames(this,tr("Load Fusion image"),mInputPathName,Extensions);
2167     if (files.isEmpty())
2168       return;
2169
2170     std::vector<std::string> vecFileNames;
2171     for (int i = 0; i < files.size(); i++) {
2172       vecFileNames.push_back(files[i].toStdString());
2173     }
2174     AddFusionImage(index,vecFileNames,vvImageReader::IMAGE);
2175 }
2176 //------------------------------------------------------------------------------
2177
2178 //------------------------------------------------------------------------------
2179 void vvMainWindow::ResetTransformationToIdentity()
2180 {
2181   std::string actorType = DataTree->selectedItems()[0]->data(1,Qt::UserRole).toString().toStdString();
2182   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2183   mSlicerManagers[index]->ResetTransformationToIdentity(actorType);
2184   ImageInfoChanged();
2185 }
2186 //------------------------------------------------------------------------------
2187
2188 //------------------------------------------------------------------------------
2189 void vvMainWindow::AddFusionImage(int index, std::vector<std::string> fileNames, vvImageReader::LoadedImageType type)
2190 {
2191   QString file(fileNames[0].c_str());
2192   if (QFile::exists(file))
2193   {
2194     mInputPathName = itksys::SystemTools::GetFilenamePath(file.toStdString()).c_str();
2195     itk::ImageIOBase::Pointer reader = itk::ImageIOFactory::CreateImageIO(
2196       file.toStdString().c_str(), itk::ImageIOFactory::ReadMode);
2197     reader->SetFileName(fileNames[0].c_str());
2198     reader->ReadImageInformation();
2199     std::string component = reader->GetComponentTypeAsString(reader->GetComponentType());
2200     int dimension = reader->GetNumberOfDimensions();
2201     QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
2202     vvProgressDialog progress("Opening fusion");
2203     qApp->processEvents();
2204
2205     std::string filename = itksys::SystemTools::GetFilenameWithoutExtension(file.toStdString()).c_str();
2206     if (mSlicerManagers[index]->SetFusion(fileNames,dimension, component,type)) {
2207       //create an item in the tree with good settings
2208       QTreeWidgetItem *item = new QTreeWidgetItem();
2209       item->setData(0,Qt::UserRole,file.toStdString().c_str());
2210       item->setData(1,Qt::UserRole,tr("fusion"));
2211       QFileInfo fileinfo(file); //Do not show the path
2212           item->setData(COLUMN_IMAGE_NAME,Qt::DisplayRole,fileinfo.fileName());
2213           item->setToolTip(COLUMN_IMAGE_NAME, mSlicerManagers[index]->GetListOfAbsoluteFilePathInOneString("fusion").c_str());
2214           qApp->processEvents();
2215
2216       for (int j = 1; j <= 4; j++) {
2217         item->setData(j,Qt::CheckStateRole,DataTree->topLevelItem(index)->data(j,Qt::CheckStateRole));
2218       }
2219
2220       //Create the buttons for reload and close
2221       qApp->processEvents();
2222       QTreePushButton* cButton = new QTreePushButton;
2223       cButton->setItem(item);
2224       cButton->setColumn(COLUMN_CLOSE_IMAGE);
2225       cButton->setToolTip(tr("close image"));
2226       cButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/exit.png")));
2227       connect(cButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
2228         this,SLOT(CloseImage(QTreeWidgetItem*, int)));
2229
2230       QTreePushButton* rButton = new QTreePushButton;
2231       rButton->setItem(item);
2232       rButton->setColumn(COLUMN_RELOAD_IMAGE);
2233       rButton->setToolTip(tr("reload image"));
2234       rButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/rotateright.png")));
2235       connect(rButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
2236         this,SLOT(ReloadImage(QTreeWidgetItem*, int)));
2237
2238       DataTree->topLevelItem(index)->setExpanded(1);
2239       DataTree->topLevelItem(index)->addChild(item);
2240       DataTree->setItemWidget(item, COLUMN_CLOSE_IMAGE, cButton);
2241       DataTree->setItemWidget(item, COLUMN_RELOAD_IMAGE, rButton);
2242
2243       //set the id of the image
2244       QString id = DataTree->topLevelItem(index)->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString();
2245       item->setData(COLUMN_IMAGE_NAME,Qt::UserRole,id.toStdString().c_str());
2246       UpdateTree();
2247       qApp->processEvents();
2248       ImageInfoChanged();
2249       QApplication::restoreOverrideCursor();
2250
2251       // Update the display to update, e.g., the sliders
2252       for(int i=0; i<4; i++)
2253         DisplaySliders(index, i);
2254     } else {
2255       QApplication::restoreOverrideCursor();
2256       QString error = "Cannot import the new image.\n";
2257       error += mSlicerManagers[index]->GetLastError().c_str();
2258       QMessageBox::information(this,tr("Problem reading image !"),error);
2259     }
2260     WindowLevelChanged();
2261   }
2262   else
2263     QMessageBox::information(this,tr("Problem reading Fusion !"),"File doesn't exist!");
2264 }
2265 //------------------------------------------------------------------------------
2266 //------------------------------------------------------------------------------
2267 void vvMainWindow::AddLandmarks(int index, std::vector<std::string> files)
2268 {
2269     if (!landmarksPanel->LoadFromFile(files))
2270       QMessageBox::information(this,tr("Problem reading Landmarks !"),"File doesn't exist!");
2271
2272     landmarksPanel->SetCurrentPath(mInputPathName.toStdString());
2273     landmarksPanel->SetCurrentImage(mSlicerManagers[index]->GetFileName().c_str());
2274 }
2275
2276 //------------------------------------------------------------------------------
2277 void vvMainWindow::OpenField()
2278 {
2279   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2280   //check if a vector field has already been added
2281   for (int child = 0; child < DataTree->topLevelItem(index)->childCount(); child++)
2282     if (DataTree->topLevelItem(index)->child(child)->data(1,Qt::UserRole).toString() == "vector") {
2283       QString error = "Cannot add more than one vector field\n";
2284       error += "Please remove first ";
2285       error += DataTree->topLevelItem(index)->child(child)->data(COLUMN_IMAGE_NAME,Qt::DisplayRole).toString();
2286       QMessageBox::information(this,tr("Problem adding vector field!"),error);
2287       return;
2288     }
2289
2290     QString Extensions = "Images ( *.mhd)";
2291     Extensions += ";;Images ( *.mha)";
2292     Extensions += ";;VF Images ( *.vf)";
2293     Extensions += ";;nii Images ( *.nii)";
2294     Extensions += ";;nrrd Images ( *.nrrd)";
2295     Extensions += ";;nhdr Images ( *.nhdr)";
2296     Extensions += ";;All Files (*)";
2297     QString file = QFileDialog::getOpenFileName(this,tr("Load deformation field"),mInputPathName,Extensions);
2298     if (!file.isEmpty())
2299       AddField(file,index);
2300 }
2301 //------------------------------------------------------------------------------
2302
2303
2304 //------------------------------------------------------------------------------
2305 void vvMainWindow::AddFieldEntry(QString filename,int index,bool from_disk)
2306 {
2307   //create an item in the tree with good settings
2308   QTreeWidgetItem *item = new QTreeWidgetItem();
2309   item->setData(0,Qt::UserRole,filename.toStdString().c_str());
2310   item->setData(1,Qt::UserRole,tr("vector"));
2311   QFileInfo fileinfo(filename); //Do not show the path
2312   item->setData(COLUMN_IMAGE_NAME,Qt::DisplayRole,fileinfo.fileName());
2313   item->setToolTip(COLUMN_IMAGE_NAME, mSlicerManagers[index]->GetListOfAbsoluteFilePathInOneString("vector").c_str());
2314   qApp->processEvents();
2315
2316   for (int j = 1; j <= 4; j++) {
2317     item->setData(j,Qt::CheckStateRole,DataTree->topLevelItem(index)->data(j,Qt::CheckStateRole));
2318   }
2319
2320   //Create the buttons for reload and close
2321   qApp->processEvents();
2322   QTreePushButton* cButton = new QTreePushButton;
2323   cButton->setItem(item);
2324   cButton->setColumn(COLUMN_CLOSE_IMAGE);
2325   cButton->setToolTip(tr("close vector field"));
2326   cButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/exit.png")));
2327   connect(cButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
2328     this,SLOT(CloseImage(QTreeWidgetItem*, int)));
2329
2330   QTreePushButton* rButton = new QTreePushButton;
2331   rButton->setItem(item);
2332   rButton->setColumn(COLUMN_RELOAD_IMAGE);
2333   rButton->setToolTip(tr("reload vector field"));
2334   rButton->setEnabled(from_disk);
2335   rButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/rotateright.png")));
2336   connect(rButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
2337     this,SLOT(ReloadImage(QTreeWidgetItem*, int)));
2338
2339   DataTree->topLevelItem(index)->setExpanded(1);
2340   DataTree->topLevelItem(index)->addChild(item);
2341   DataTree->setItemWidget(item, COLUMN_RELOAD_IMAGE, rButton);
2342   DataTree->setItemWidget(item, COLUMN_CLOSE_IMAGE, cButton);
2343
2344   //set the id of the image
2345   QString id = DataTree->topLevelItem(index)->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString();
2346   item->setData(COLUMN_IMAGE_NAME,Qt::UserRole,id.toStdString().c_str());
2347   UpdateTree();
2348   qApp->processEvents();
2349   ImageInfoChanged();
2350   QApplication::restoreOverrideCursor();
2351 }
2352 //------------------------------------------------------------------------------
2353
2354
2355 //------------------------------------------------------------------------------
2356 void vvMainWindow::AddField(vvImage::Pointer vf,QString file,int index)
2357 {
2358   QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
2359   vvSlicerManager* imageManager = mSlicerManagers[index];
2360   if (imageManager->SetVF(vf,file.toStdString())) {
2361     AddFieldEntry(file,index,false);
2362   } else {
2363     QString error = "Cannot import the vector field for this image.\n";
2364     error += imageManager->GetLastError().c_str();
2365     QMessageBox::information(this,tr("Problem reading VF !"),error);
2366   }
2367   QApplication::restoreOverrideCursor();
2368 }
2369 //------------------------------------------------------------------------------
2370
2371
2372 //------------------------------------------------------------------------------
2373 void vvMainWindow::AddField(QString file,int index)
2374 {
2375   if (QFile::exists(file)) {
2376     mInputPathName = itksys::SystemTools::GetFilenamePath(file.toStdString()).c_str();
2377
2378     //init the progress events
2379     QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
2380     vvProgressDialog progress("Opening " + file.toStdString());
2381     qApp->processEvents();
2382
2383     //read the vector and put it in the current mSlicerManager
2384     vvSlicerManager* imageManager = mSlicerManagers[index];
2385     qApp->processEvents();
2386
2387     std::string filename = itksys::SystemTools::GetFilenameWithoutExtension(file.toStdString()).c_str();
2388     if (imageManager->SetVF(file.toStdString())) {
2389       imageManager->Render();
2390       AddFieldEntry(file,index,true);
2391     } else {
2392       QApplication::restoreOverrideCursor();
2393       QString error = "Cannot import the vector field for this image.\n";
2394       error += imageManager->GetLastError().c_str();
2395       QMessageBox::information(this,tr("Problem reading VF !"),error);
2396     }
2397   } else
2398     QMessageBox::information(this,tr("Problem reading VF !"),"File doesn't exist!");
2399
2400 }
2401 //------------------------------------------------------------------------------
2402
2403
2404 //------------------------------------------------------------------------------
2405 void vvMainWindow::SetVFProperty(int subsampling, int scale, int log, int width, double r, double g, double b)
2406 {
2407   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2408   if (mSlicerManagers[index]->GetSlicer(0)->GetVF()) {
2409     for (int i = 0; i < 4; i++) {
2410       mSlicerManagers[index]->GetSlicer(i)->SetVFSubSampling(subsampling);
2411       mSlicerManagers[index]->GetSlicer(i)->SetVFScale(scale);
2412       mSlicerManagers[index]->GetSlicer(i)->SetVFWidth(width);
2413       mSlicerManagers[index]->GetSlicer(i)->SetVFColor(r,g,b);
2414       if (log > 0)
2415         mSlicerManagers[index]->GetSlicer(i)->SetVFLog(1);
2416       else
2417         mSlicerManagers[index]->GetSlicer(i)->SetVFLog(0);
2418     }
2419   }
2420 }
2421 //------------------------------------------------------------------------------
2422
2423
2424 //------------------------------------------------------------------------------
2425 void vvMainWindow::SetOverlayProperty(int color, int linked, double window, double level)
2426 {
2427   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2428   if (mSlicerManagers[index]->GetSlicer(0)->GetOverlay()) {
2429     mSlicerManagers[index]->SetOverlayColor(color);
2430     mSlicerManagers[index]->SetColorMap(0);
2431     mSlicerManagers[index]->SetLinkOverlayWindowLevel(linked);
2432     mSlicerManagers[index]->SetOverlayColorWindow(window);
2433     mSlicerManagers[index]->SetOverlayColorLevel(level);
2434     mSlicerManagers[index]->Render();
2435   }
2436 }
2437 //------------------------------------------------------------------------------
2438
2439 //------------------------------------------------------------------------------
2440 void vvMainWindow::SetFusionProperty(int opacity, int thresOpacity, int colormap,double window, double level, bool showLegend)
2441 {
2442   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2443   if (mSlicerManagers[index]->GetSlicer(0)->GetFusion()) {
2444     mSlicerManagers[index]->SetFusionColorMap(colormap);
2445     mSlicerManagers[index]->SetFusionOpacity(opacity);
2446     mSlicerManagers[index]->SetFusionThresholdOpacity(thresOpacity);
2447     mSlicerManagers[index]->SetFusionWindow(window);
2448     mSlicerManagers[index]->SetFusionLevel(level);
2449     mSlicerManagers[index]->SetFusionShowLegend(showLegend);
2450     mSlicerManagers[index]->SetColorMap(0);
2451     mSlicerManagers[index]->Render();
2452   }
2453 }
2454 //------------------------------------------------------------------------------
2455
2456
2457 //------------------------------------------------------------------------------
2458 void vvMainWindow::SelectFusionSequence()
2459 {
2460   //get the index of the slicer manager of the main sequence (CT)
2461   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2462   //check if one overlay image is already associated
2463   for (int child = 0; child < DataTree->topLevelItem(index)->childCount(); child++)
2464     if ( (DataTree->topLevelItem(index)->child(child)->data(1,Qt::UserRole).toString() == "fusion") ||
2465       (DataTree->topLevelItem(index)->child(child)->data(1,Qt::UserRole).toString() == "fusionSequence") ) {
2466         QString error = "Cannot add more than one compared image\n";
2467         error += "Please remove first ";
2468         error += DataTree->topLevelItem(index)->child(child)->data(COLUMN_IMAGE_NAME,Qt::DisplayRole).toString();
2469         QMessageBox::information(this,tr("Problem adding compared image !"),error);
2470         return;
2471     }
2472
2473     QString Extensions = EXTENSIONS;
2474     Extensions += ";;All Files (*)";
2475     QStringList files = QFileDialog::getOpenFileNames(this,tr("Load Overlay image sequence"),mInputPathName,Extensions);
2476     if (files.isEmpty())
2477       return;
2478
2479     std::vector<std::string> vecFileNames;
2480     for (int i = 0; i < files.size(); i++) {
2481       vecFileNames.push_back(files[i].toStdString());
2482     }
2483
2484     //associate the secondary sequence (US) to the main one
2485     AddFusionSequence(index,vecFileNames,vvImageReader::MERGEDWITHTIME);
2486 }
2487 //------------------------------------------------------------------------------
2488
2489
2490 //------------------------------------------------------------------------------
2491 void vvMainWindow::SelectFusionSequenceCorrespondances() {
2492
2493   //make sure the index is right?
2494   //in the end, I should attach the temporal data to the right sequence!
2495   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2496   //in case the other sequence got selected, make sure we select the primary sequence
2497   if ( (!mSlicerManagers[index]->GetSlicer(0)->GetFusion()) && mSlicerManagers[index]->GetFusionSequenceIndexOfLinkedManager()>=0 ) {
2498     index = mSlicerManagers[index]->GetFusionSequenceIndexOfLinkedManager();
2499   }
2500
2501   //open a dialog box to find a file
2502   //QString Extensions = EXTENSIONS;
2503   QString Extensions = ";;All Files (*)";
2504   QString fileName = QFileDialog::getOpenFileName(this,tr("Load respiratory signal for fused sequence"),mInputPathName,Extensions);
2505   if (fileName.isNull())
2506     return;
2507
2508   //read it as a vector of values
2509   vnl_vector<double> tmpVect;
2510
2511   std::ifstream file;
2512   file.open(fileName.toStdString().c_str());
2513   tmpVect.read_ascii(file);
2514   file.close();
2515
2516   //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
2517   bool signalOK = true;
2518   unsigned nbFrameMain = mSlicerManagers[index]->GetImage()->GetTransform().size();
2519   unsigned nbFrameSecondary = mSlicerManagers[index]->GetFusionSequenceNbFrames();
2520 std::cout<<"nbFrameMain = "<<nbFrameMain<<", nbFrameSecondary= "<<nbFrameSecondary<<", signal size: "<<tmpVect.size()<<std::endl;
2521   std::vector<unsigned> temporalCorrespondances;
2522   if ( tmpVect.size() == nbFrameMain + nbFrameSecondary ) {
2523     for (unsigned i=0 ; i<tmpVect.size() ; i++) {
2524       if (i<nbFrameMain) { //first part of the file: i -> index in secondary seq.
2525         if ( tmpVect(i)<nbFrameSecondary ) temporalCorrespondances.push_back(tmpVect(i));
2526         else { signalOK=false; break; } //pointing outside the secondary sequence...
2527       }
2528       else { //first part of the file -> index in secondary seq.
2529         if ( tmpVect(i)<nbFrameMain ) temporalCorrespondances.push_back(tmpVect(i));
2530         else { signalOK=false; break; } //pointing outside the secondary sequence...
2531       }
2532     }
2533   }
2534   else {signalOK=false;}
2535   if (!signalOK) {//else, send a message to signal the failure...
2536     QString error = "The provided temporal correspondances is invalid - check tooltip.\n";
2537     error += "Ignoring file: " + fileName;
2538     QMessageBox::information(this,tr("Problem adding temporal correspondances!"),error);
2539     return;
2540   }
2541   else {
2542     //for convenience, associate this sequence to both the current slicer manager, and to the linked one
2543     mSlicerManagers[index]->SetFusionSequenceCorrespondances(temporalCorrespondances);
2544     mSlicerManagers[ mSlicerManagers[index]->GetFusionSequenceIndexOfLinkedManager() ]->SetFusionSequenceCorrespondances(temporalCorrespondances);
2545     overlayPanel->enableFusionSequenceTemporalSync();
2546   }
2547
2548 }
2549 //------------------------------------------------------------------------------
2550
2551
2552 //------------------------------------------------------------------------------
2553 //when this function is called index is the slicer manager index corresponding to the main sequence (CT)
2554 //the files behind fileNames points to the data for the secondary sequence
2555 void vvMainWindow::AddFusionSequence(int index, std::vector<std::string> fileNames, vvImageReader::LoadedImageType type)
2556 {
2557   QString file(fileNames[0].c_str());
2558   if (QFile::exists(file))
2559   {
2560     mInputPathName = itksys::SystemTools::GetFilenamePath(file.toStdString()).c_str();
2561     itk::ImageIOBase::Pointer reader = itk::ImageIOFactory::CreateImageIO(
2562       file.toStdString().c_str(), itk::ImageIOFactory::ReadMode);
2563     std::sort (fileNames.begin(), fileNames.end());//make sure the files are sorted.
2564     reader->SetFileName(fileNames[0].c_str());
2565     reader->ReadImageInformation();
2566     std::string component = reader->GetComponentTypeAsString(reader->GetComponentType());
2567     int dimension = reader->GetNumberOfDimensions();
2568     QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
2569     vvProgressDialog progress("Opening " + file.toStdString());
2570     qApp->processEvents();
2571
2572     std::string filename = itksys::SystemTools::GetFilenameWithoutExtension(file.toStdString()).c_str();
2573
2574     if (mSlicerManagers[index]->SetFusionSequence(fileNames,dimension, component,type)) {
2575       //create an item in the tree with good settings
2576       QTreeWidgetItem *item = new QTreeWidgetItem();
2577       item->setData(0,Qt::UserRole,file.toStdString().c_str());
2578       item->setData(1,Qt::UserRole,tr("fusionSequence"));
2579
2580       QFileInfo fileinfo(file); //Do not show the path
2581       item->setData(COLUMN_IMAGE_NAME,Qt::DisplayRole,fileinfo.fileName());
2582       item->setToolTip(COLUMN_IMAGE_NAME, mSlicerManagers[index]->GetListOfAbsoluteFilePathInOneString("fusionSequence").c_str());
2583       qApp->processEvents();
2584       for (int j = 1; j <= 4; j++) {
2585         item->setData(j,Qt::CheckStateRole,DataTree->topLevelItem(index)->data(j,Qt::CheckStateRole));
2586       }
2587
2588       //Create the buttons for reload and close
2589       qApp->processEvents();
2590       QTreePushButton* cButton = new QTreePushButton;
2591       cButton->setItem(item);
2592       cButton->setColumn(COLUMN_CLOSE_IMAGE);
2593       cButton->setToolTip(tr("close image"));
2594       cButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/exit.png")));
2595       connect(cButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
2596         this,SLOT(CloseImage(QTreeWidgetItem*, int)));
2597
2598       QTreePushButton* rButton = new QTreePushButton;
2599       rButton->setItem(item);
2600       rButton->setColumn(COLUMN_RELOAD_IMAGE);
2601       rButton->setToolTip(tr("reload image"));
2602       rButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/rotateright.png")));
2603       connect(rButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
2604         this,SLOT(ReloadImage(QTreeWidgetItem*, int)));
2605
2606       DataTree->topLevelItem(index)->setExpanded(1);
2607       DataTree->topLevelItem(index)->addChild(item);
2608       DataTree->setItemWidget(item, COLUMN_CLOSE_IMAGE, cButton);
2609       DataTree->setItemWidget(item, COLUMN_RELOAD_IMAGE, rButton);
2610
2611       //store the original transform matrix
2612       int indexParent = GetSlicerIndexFromItem( DataTree->topLevelItem(index) );
2613       mSlicerManagers[indexParent]->SetFusionSequenceMainTransformMatrix( mSlicerManagers[indexParent]->GetSlicer(0)->GetImage()->GetTransform()[0]->GetMatrix() );
2614
2615       //set the id of the image
2616       QString id = DataTree->topLevelItem(index)->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString();
2617       item->setData(COLUMN_IMAGE_NAME,Qt::UserRole,id.toStdString().c_str());
2618       UpdateTree();
2619       qApp->processEvents();
2620
2621       //ImageInfoChanged();
2622
2623       QApplication::restoreOverrideCursor();
2624       // Update the display to update, e.g., the sliders
2625       for(int i=0; i<4; i++)
2626         DisplaySliders(index, i);
2627
2628
2629       //This loads the secondary sequence (US) as an independent sequence
2630       LoadImages(fileNames, type);
2631       //reset the transforms to identity
2632       //FIX -- and set the thickness of the US slices to a large value (necessary for visualization purposes...)
2633       double sp_x, sp_y, sp_z;
2634       mSlicerManagers[indexParent]->GetImage()->GetVTKImages()[0]->GetSpacing(sp_x, sp_y, sp_z);
2635       sp_z = std::max(sp_x, std::max(sp_y, sp_z)) + 0.5; //
2636       for (unsigned i=0 ; i<mSlicerManagers.back()->GetImage()->GetTransform().size() ; i++) {
2637         sp_x = mSlicerManagers.back()->GetImage()->GetVTKImages()[i]->GetSpacing()[0];
2638         sp_y = mSlicerManagers.back()->GetImage()->GetVTKImages()[i]->GetSpacing()[1];
2639         mSlicerManagers.back()->GetImage()->GetVTKImages()[i]->SetSpacing( sp_x, sp_y, sp_z);
2640         mSlicerManagers.back()->GetImage()->GetTransform()[i]->Identity();
2641         mSlicerManagers.back()->GetImage()->GetTransform()[i]->Update();
2642       }
2643
2644       //automatically link both images...
2645       AddLink(mSlicerManagers[indexParent]->GetId().c_str(), mSlicerManagers.back()->GetId().c_str(), false);
2646
2647       //tie the main and secondary sequences by raising flags and informing each another of their respective SlicerManager indices
2648       mSlicerManagers[indexParent]->SetFusionSequenceIndexOfLinkedManager(mSlicerManagers.size()-1);
2649       mSlicerManagers[indexParent]->SetFusionSequenceInvolvmentCode(0); //main sequence
2650       mSlicerManagers.back()->SetFusionSequenceIndexOfLinkedManager(indexParent);
2651       mSlicerManagers.back()->SetFusionSequenceInvolvmentCode(1); //secondary sequence
2652       for (unsigned i=0 ; i<4 ; i++) {
2653         mSlicerManagers.back()->GetSlicer(i)->SetFusionSequenceCode(1); //flag the slicers of the secondary sequence
2654       }
2655
2656     } else {
2657       QApplication::restoreOverrideCursor();
2658       QString error = "Cannot import the new image.\n";
2659       error += mSlicerManagers[index]->GetLastError().c_str();
2660       QMessageBox::information(this,tr("Problem reading image !"),error);
2661     }
2662     WindowLevelChanged();
2663     ImageInfoChanged(); //this internally calls WindowLevelChanged...
2664   }
2665   else {
2666     QMessageBox::information(this,tr("Problem reading fusion sequence !"),"File doesn't exist!");
2667     return;
2668   }
2669
2670 }
2671 //------------------------------------------------------------------------------
2672
2673
2674 //------------------------------------------------------------------------------
2675 //fusionSequenceFrameIndex and fusionSequenceNbFrames are relative to the secondary sequence (US)
2676 void vvMainWindow::SetFusionSequenceProperty(int fusionSequenceFrameIndex, bool spatialSyncFlag, unsigned int fusionSequenceNbFrames, bool temporalSyncFlag)
2677 {
2678   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2679
2680   if (!mSlicerManagers[index]->IsInvolvedInFusionSequence()) return;
2681
2682   //check if the focus moved to the linked sequence, and in this case, select the master sequence instead
2683   if (!mSlicerManagers[index]->IsMainSequenceOfFusionSequence()) {
2684     index = mSlicerManagers[index]->GetFusionSequenceIndexOfLinkedManager();
2685   }
2686   int secondaryIndex = mSlicerManagers[index]->GetFusionSequenceIndexOfLinkedManager();
2687   if (secondaryIndex==-1) return; //this should never happen
2688   if ( (!mSlicerManagers[index]->IsMainSequenceOfFusionSequence()) ||
2689     (!mSlicerManagers[secondaryIndex]->IsSecondarySequenceOfFusionSequence()) )
2690   {return;} //this should never happen, raise an exception?
2691
2692   if (mSlicerManagers[index]->GetSlicer(0)->GetFusion()) {
2693
2694     //First, if the spatialSync button is unchecked, then reposition the parent sequence (CT) in its original coordinate frame
2695     if ( (!spatialSyncFlag) && (mSlicerManagers[index]->GetFusionSequenceSpatialSyncFlag()) ) {
2696       for ( unsigned i=0 ; i<mSlicerManagers[index]->GetSlicer(0)->GetImage()->GetTransform().size() ; i++ ) {
2697         mSlicerManagers[index]->GetSlicer(0)->GetImage()->GetTransform()[i]->SetMatrix( mSlicerManagers[index]->GetFusionSequenceMainTransformMatrix() );
2698         mSlicerManagers[index]->GetSlicer(0)->GetImage()->GetTransform()[i]->Update();
2699       }
2700
2701       for (int i=0; i<mSlicerManagers[index]->GetNumberOfSlicers(); i++) {
2702         mSlicerManagers[index]->GetSlicer(i)->ForceUpdateDisplayExtent();
2703         mSlicerManagers[index]->GetSlicer(i)->Render();
2704       }
2705     }
2706
2707     //then, update the property values in the slicer manager
2708     mSlicerManagers[index]->SetFusionSequenceLength(fusionSequenceNbFrames);
2709     mSlicerManagers[index]->SetFusionSequenceSpatialSyncFlag(spatialSyncFlag);
2710     mSlicerManagers[index]->SetFusionSequenceTemporalSyncFlag(temporalSyncFlag);
2711     mSlicerManagers[index]->SetFusionSequenceFrameIndex(fusionSequenceFrameIndex);
2712
2713     //select the right frame of the US sequence
2714     mSlicerManagers[index]->SetFusionSequenceTSlice(fusionSequenceFrameIndex); //here, I should only update the overlayed sequence
2715     mSlicerManagers[secondaryIndex]->SetTSlice(fusionSequenceFrameIndex, false); //this should update the secondary sequence (individual version)
2716
2717     //update the horizontal sliders of the main window
2718     overlayPanel->updateFusionSequenceSliderValueFromWindow(fusionSequenceFrameIndex, false);
2719
2720     if (spatialSyncFlag) { //reslice the CT
2721
2722       if (temporalSyncFlag) { //do the temporal synchronisation
2723         int mainSequenceFrameIndex=0;
2724         //estimate the TSlice to set to the CT
2725         unsigned nbFramesMain = mSlicerManagers[index]->GetImage()->GetTransform().size();
2726         mainSequenceFrameIndex = mSlicerManagers[index]->GetFusionSequenceCorrespondances()[ nbFramesMain + fusionSequenceFrameIndex];
2727         //and set it!
2728         mSlicerManagers[index]->SetTSlice(mainSequenceFrameIndex, false);
2729         //warning, there is a loopback, and modification of the TSlice in main sequence forces an update of the TSlice in secondary, etc...
2730       }
2731
2732
2733       //Set the transform matrix of the parent sequence (typically CT / 4DCT)
2734       vtkSmartPointer<vtkMatrix4x4> tmpMat = vtkSmartPointer<vtkMatrix4x4>::New();
2735       vtkMatrix4x4::Invert( mSlicerManagers[index]->GetFusionSequenceInitialTransformMatrixAtFrame(fusionSequenceFrameIndex), tmpMat );
2736       for ( unsigned i=0 ; i<mSlicerManagers[index]->GetSlicer(0)->GetImage()->GetTransform().size() ; i++ ) {
2737         mSlicerManagers[index]->GetSlicer(0)->GetImage()->GetTransform()[i]->SetMatrix( mSlicerManagers[index]->GetFusionSequenceMainTransformMatrix() );
2738         mSlicerManagers[index]->GetSlicer(0)->GetImage()->GetTransform()[i]->PreMultiply();
2739         mSlicerManagers[index]->GetSlicer(0)->GetImage()->GetTransform()[i]->Concatenate( tmpMat );
2740         mSlicerManagers[index]->GetSlicer(0)->GetImage()->GetTransform()[i]->Update();
2741       }
2742
2743       for (int i=0; i<mSlicerManagers[index]->GetNumberOfSlicers(); i++) {
2744         mSlicerManagers[index]->GetSlicer(i)->ForceUpdateDisplayExtent();
2745         mSlicerManagers[index]->GetSlicer(i)->Render();
2746       }
2747
2748     }
2749
2750   }
2751 }
2752 //------------------------------------------------------------------------------
2753
2754
2755 //------------------------------------------------------------------------------
2756 void vvMainWindow::SaveAs()
2757 {
2758   if (DataTree->selectedItems()[0]->data(1,Qt::UserRole).toString() == "vector") {
2759     QMessageBox::warning(this,tr("Unsupported type"),tr("Sorry, saving a vector field is unsupported for the moment"));
2760     return;
2761   }
2762
2763   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2764   int dimension = mSlicerManagers[index]->GetDimension();
2765   QStringList OutputListeFormat;
2766   OutputListeFormat.clear();
2767   if (dimension == 1) {
2768     OutputListeFormat.push_back(".mhd");
2769     OutputListeFormat.push_back(".mha");
2770   }
2771   if (dimension == 2) {
2772     OutputListeFormat.push_back(".bmp");
2773     OutputListeFormat.push_back(".png");
2774     OutputListeFormat.push_back(".jpeg");
2775     OutputListeFormat.push_back(".tif");
2776     OutputListeFormat.push_back(".mhd");
2777     OutputListeFormat.push_back(".mha");
2778     OutputListeFormat.push_back(".hdr");
2779     OutputListeFormat.push_back(".vox");
2780   } else if (dimension == 3) {
2781     OutputListeFormat.push_back(".mhd");
2782     OutputListeFormat.push_back(".mha");
2783     OutputListeFormat.push_back(".nii");
2784     OutputListeFormat.push_back(".nrrd");
2785     OutputListeFormat.push_back(".nhdr");
2786     OutputListeFormat.push_back(".hdr");
2787     OutputListeFormat.push_back(".vox");
2788   } else if (dimension == 4) {
2789     OutputListeFormat.push_back(".mhd");
2790     OutputListeFormat.push_back(".mha");
2791     OutputListeFormat.push_back(".nii");
2792     OutputListeFormat.push_back(".nrrd");
2793     OutputListeFormat.push_back(".nhdr");
2794   }
2795   QString Extensions = "AllFiles(*.*)";
2796   for (int i = 0; i < OutputListeFormat.count(); i++) {
2797     Extensions += ";;Images ( *";
2798     Extensions += OutputListeFormat[i];
2799     Extensions += ")";
2800   }
2801   QString fileName = QFileDialog::getSaveFileName(this,
2802     tr("Save As"),
2803     mSlicerManagers[index]->GetFileName().c_str(),
2804     Extensions);
2805   if (!fileName.isEmpty()) {
2806     std::string fileformat = itksys::SystemTools::GetFilenameLastExtension(fileName.toStdString());
2807     if (OutputListeFormat.contains(
2808       fileformat.c_str())) {
2809         QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
2810         std::string action = "Saving";
2811         vvProgressDialog progress("Saving "+fileName.toStdString());
2812         qApp->processEvents();
2813         vvImageWriter::Pointer writer = vvImageWriter::New();
2814         writer->SetOutputFileName(fileName.toStdString());
2815         writer->SetInput(mSlicerManagers[index]->GetImage());
2816
2817         // Check on transform and prompt user
2818         writer->SetSaveTransform(false);
2819         bool bId = true;
2820         for(int i=0; i<4; i++)
2821           for(int j=0; j<4; j++) {
2822             // TODO SR and BP: check on the list of transforms and not the first only
2823             double elt = mSlicerManagers[index]->GetImage()->GetTransform()[0]->GetMatrix()->GetElement(i,j);
2824             if(i==j && elt!=1.)
2825               bId = false;
2826             if(i!=j && elt!=0.)
2827               bId = false;
2828           }
2829           if( !bId ) {
2830             QString warning = "The image has an associated linear transform. Do you want to save it along?";
2831             QMessageBox msgBox(QMessageBox::Warning, tr("Save transform"), warning, 0, this);
2832             msgBox.addButton(tr("Yes"), QMessageBox::AcceptRole);
2833             msgBox.addButton(tr("No"), QMessageBox::RejectRole);
2834             if (msgBox.exec() == QMessageBox::AcceptRole)
2835               writer->SetSaveTransform(true);
2836           }
2837
2838           writer->Update();
2839           QApplication::restoreOverrideCursor();
2840           if (writer->GetLastError().size()) {
2841             QString error = "Saving did not succeed\n";
2842             error += writer->GetLastError().c_str();
2843             QMessageBox::information(this,tr("Saving Problem"),error);
2844             SaveAs();
2845           }
2846     } else {
2847       QString error = fileformat.c_str();
2848       if (error.isEmpty())
2849         error += "no file format specified !";
2850       else
2851         error += " format unknown !!!\n";
2852       QMessageBox::information(this,tr("Saving Problem"),error);
2853       SaveAs();
2854     }
2855   }
2856 }
2857 //------------------------------------------------------------------------------
2858
2859 //------------------------------------------------------------------------------
2860 void vvMainWindow::SaveCurrentState()
2861 {
2862   QString Extensions = "XML Files(*.xml)";
2863   QString fileName = QFileDialog::getSaveFileName(this,
2864     tr("Save Current Window State"),
2865     "",
2866     Extensions);
2867
2868   SaveCurrentStateAs(fileName.toStdString());
2869 }
2870 //------------------------------------------------------------------------------
2871
2872 //------------------------------------------------------------------------------
2873 void vvMainWindow::SaveCurrentStateAs(const std::string& stateFile)
2874 {
2875   vvSaveState save_state;
2876   save_state.Run(this, stateFile);
2877 }
2878
2879 //------------------------------------------------------------------------------
2880 void vvMainWindow::ReadSavedState()
2881 {
2882   QString Extensions = "XML Files(*.xml)";
2883   QString fileName = QFileDialog::getOpenFileName(this,
2884     tr("Load Window State"),
2885     "",
2886     Extensions);
2887
2888   ReadSavedStateFile(fileName.toStdString());
2889 }
2890 //------------------------------------------------------------------------------
2891
2892 //------------------------------------------------------------------------------
2893 void vvMainWindow::ReadSavedStateFile(const std::string& stateFile)
2894 {
2895   vvReadState read_state;
2896   read_state.Run(this, stateFile);
2897 }
2898 //------------------------------------------------------------------------------
2899
2900 //------------------------------------------------------------------------------
2901 void vvMainWindow::LinkAllImages()
2902 {
2903   linkPanel->linkAll();
2904 }
2905
2906 //------------------------------------------------------------------------------
2907 void vvMainWindow::AddLink(QString image1,QString image2,bool fromPanel)
2908 {
2909   if (!fromPanel) {
2910     // delegate to linkPanel if call came from elsewhere...
2911     linkPanel->addLinkFromIds(image1, image2);
2912     return;
2913   }
2914
2915   unsigned int sm1 = 0;
2916   unsigned int sm2 = 0;
2917
2918   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
2919     if (image1.toStdString() == mSlicerManagers[i]->GetId()) {
2920       mSlicerManagers[i]->AddLink(image2.toStdString());
2921       sm1 = i;
2922     }
2923     if (image2.toStdString() == mSlicerManagers[i]->GetId()) {
2924       mSlicerManagers[i]->AddLink(image1.toStdString());
2925       sm2 = i;
2926     }
2927   }
2928
2929   if (linkPanel->isLinkAll())   {
2930     emit UpdateLinkedNavigation(mSlicerManagers[sm1]->GetId(), mSlicerManagers[mCurrentPickedImageIndex], mSlicerManagers[mCurrentPickedImageIndex]->GetSlicer(0));
2931     emit UpdateLinkedNavigation(mSlicerManagers[sm2]->GetId(), mSlicerManagers[mCurrentPickedImageIndex], mSlicerManagers[mCurrentPickedImageIndex]->GetSlicer(0));
2932   } else {
2933     emit UpdateLinkedNavigation(mSlicerManagers[sm2]->GetId(), mSlicerManagers[sm1], mSlicerManagers[sm1]->GetSlicer(0));
2934   }
2935 }
2936
2937 //------------------------------------------------------------------------------
2938
2939
2940 //------------------------------------------------------------------------------
2941 void vvMainWindow::RemoveLink(QString image1,QString image2)
2942 {
2943   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
2944     if (image1.toStdString() == mSlicerManagers[i]->GetId()) {
2945       mSlicerManagers[i]->RemoveLink(image2.toStdString());
2946     }
2947     if (image2.toStdString() == mSlicerManagers[i]->GetId()) {
2948       mSlicerManagers[i]->RemoveLink(image1.toStdString());
2949     }
2950   }
2951 }
2952 //------------------------------------------------------------------------------
2953
2954 //------------------------------------------------------------------------------
2955 void vvMainWindow::ChangeImageWithIndexOffset(vvSlicerManager *sm, int slicer, int offset)
2956 {
2957   if(mSlicerManagers.size()==1)
2958     return;
2959
2960   int index = 0;
2961   while(sm != mSlicerManagers[index])
2962     index++;
2963   index = (index+offset+mSlicerManagers.size()) % mSlicerManagers.size();
2964
2965   QTreeWidgetItem* item = GetItemFromSlicerManager(mSlicerManagers[index]);
2966   item->setData(slicer+1,Qt::CheckStateRole,2);         //change checkbox
2967   CurrentImageChanged(mSlicerManagers[index]->GetId()); //select new image
2968   DisplayChanged(item,slicer+1);
2969 }
2970 //------------------------------------------------------------------------------
2971 void vvMainWindow::HorizontalSliderMoved(int value,int column, int slicer_index)
2972 {
2973   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
2974     if (DataTree->topLevelItem(i)->data(column,Qt::CheckStateRole).toInt() > 1) {
2975       //i is the SlicerManager that is in charge of this slicer.
2976       if (mSlicerManagers[i]->IsInvolvedInFusionSequence()) {
2977         //if the slicerManager is involved in a fusionSequence as the secondary sequence, then update the slider position in the overlay panel and everything accordingly
2978         if (mSlicerManagers[i]->IsSecondarySequenceOfFusionSequence()) {
2979           overlayPanel->updateFusionSequenceSliderValueFromWindow(value, true);
2980         }
2981         else { //if this is the primary sequence that has been modified
2982           if (mSlicerManagers[i]->GetFusionSequenceTemporalSyncFlag()) {
2983             //WARNING: for some obscure reason, there are problems when accessing mSlicerManagers[mSlicerManagers[i]->GetFusionSequenceIndexOfLinkedManager()]->GetFusionSequenceFrameIndex();
2984
2985             int estimatedValue=0;
2986             //estimate a corresponding time index for the secondary (US) sequence, and update it accordingly.
2987             estimatedValue = mSlicerManagers[i]->GetFusionSequenceCorrespondances()[ value ];
2988             //TODO: at the moment, there is a loop in TSlice modifications
2989             //modifying sequence 1 causes seq 2 to update, which in turns update seq1...
2990             //I disable control on seq1 at the moment.
2991             //overlayPanel->updateFusionSequenceSliderValueFromWindow(estimatedValue, true);
2992           }
2993         }
2994       }
2995
2996       for (int j = 0; j < 4; j++) {
2997         mSlicerManagers[i]->SetTSliceInSlicer(value,j);
2998       }
2999       mSlicerManagers[i]->GetSlicer(slicer_index)->Render();
3000       break;
3001     }
3002   }
3003 }
3004 //------------------------------------------------------------------------------
3005
3006
3007 //------------------------------------------------------------------------------
3008 void vvMainWindow::NOHorizontalSliderMoved()
3009 {
3010   // if (mCurrentTime == NOHorizontalSlider->value()) return;
3011   HorizontalSliderMoved(NOHorizontalSlider->value(),COLUMN_UL_VIEW,0);
3012   //  mCurrentTime = NOHorizontalSlider->value();
3013 }
3014 //------------------------------------------------------------------------------
3015
3016
3017 //------------------------------------------------------------------------------
3018 void vvMainWindow::NEHorizontalSliderMoved()
3019 {
3020   // if (mCurrentTime == NEHorizontalSlider->value()) return;
3021   HorizontalSliderMoved(NEHorizontalSlider->value(),COLUMN_UR_VIEW,1);
3022   //  mCurrentTime = NEHorizontalSlider->value();
3023 }
3024 //------------------------------------------------------------------------------
3025
3026
3027 //------------------------------------------------------------------------------
3028 void vvMainWindow::SOHorizontalSliderMoved()
3029 {
3030   // if (mCurrentTime == SOHorizontalSlider->value()) return;
3031   HorizontalSliderMoved(SOHorizontalSlider->value(),COLUMN_DL_VIEW,2);
3032   // mCurrentTime = SOHorizontalSlider->value();
3033 }
3034 //------------------------------------------------------------------------------
3035
3036
3037 //------------------------------------------------------------------------------
3038 void vvMainWindow::SEHorizontalSliderMoved()
3039 {
3040   // if (mCurrentTime == SEHorizontalSlider->value()) return;
3041   HorizontalSliderMoved(SEHorizontalSlider->value(),COLUMN_DR_VIEW,3);
3042   // mCurrentTime = SEHorizontalSlider->value();
3043 }
3044 //------------------------------------------------------------------------------
3045
3046 //------------------------------------------------------------------------------
3047 void vvMainWindow::NOVerticalSliderChanged()
3048 {
3049   static int value=-1;
3050   if (value == NOVerticalSlider->value()) return;
3051   else value = NOVerticalSlider->value();
3052   //  int value = NOVerticalSlider->value();
3053   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
3054     if (DataTree->topLevelItem(i)->data(COLUMN_UL_VIEW,Qt::CheckStateRole).toInt() > 1) {
3055       if (mSlicerManagers[i]->GetSlicer(0)->GetSlice() != value) {
3056         mSlicerManagers[i]->GetSlicer(0)->SetSlice(value);
3057         mSlicerManagers[i]->VerticalSliderHasChanged(0, value);
3058
3059         // If nor Update/Render -> slider not work
3060         // only render = ok navigation, but for contour Update needed but slower ?
3061
3062         mSlicerManagers[i]->UpdateSlice(0);  // <-- DS add this. Not too much update ? YES. but needed for ImageContour ...
3063         //mSlicerManagers[i]->GetSlicer(0)->Render(); // <-- DS add this, needed for contour, seems ok ? not too slow ?
3064       }
3065       break;
3066     }
3067   }
3068 }
3069 //------------------------------------------------------------------------------
3070
3071
3072 //------------------------------------------------------------------------------
3073 void vvMainWindow::NEVerticalSliderChanged()
3074 {
3075   static int value=-1;
3076   if (value == NEVerticalSlider->value()) return;
3077   else value = NEVerticalSlider->value();
3078   //  int value = NEVerticalSlider->value();
3079   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
3080     if (DataTree->topLevelItem(i)->data(COLUMN_UR_VIEW,Qt::CheckStateRole).toInt() > 1) {
3081       if (mSlicerManagers[i]->GetSlicer(1)->GetSlice() != value) {
3082         mSlicerManagers[i]->GetSlicer(1)->SetSlice(value);
3083         mSlicerManagers[i]->VerticalSliderHasChanged(1, value);
3084         mSlicerManagers[i]->UpdateSlice(1);
3085         //mSlicerManagers[i]->GetSlicer(1)->Render(); // <-- DS add this, needed for contour, seems ok ? not too slow ?
3086       }
3087       break;
3088     }
3089   }
3090 }
3091 //------------------------------------------------------------------------------
3092
3093
3094 //------------------------------------------------------------------------------
3095 void vvMainWindow::SOVerticalSliderChanged()
3096 {
3097   static int value=-1;
3098   if (value == SOVerticalSlider->value()) return;
3099   else value = SOVerticalSlider->value();
3100   //int value = SOVerticalSlider->value();
3101   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
3102     if (DataTree->topLevelItem(i)->data(COLUMN_DL_VIEW,Qt::CheckStateRole).toInt() > 1) {
3103       if (mSlicerManagers[i]->GetSlicer(2)->GetSlice() != value) {
3104         mSlicerManagers[i]->GetSlicer(2)->SetSlice(value);
3105         mSlicerManagers[i]->VerticalSliderHasChanged(2, value);
3106         mSlicerManagers[i]->UpdateSlice(2);
3107         //mSlicerManagers[i]->GetSlicer(2)->Render(); // <-- DS add this, needed for contour, seems ok ? not too slow ?
3108       }
3109       // else { DD("avoid SOVerticalSlider slicer update"); }
3110       break;
3111     }
3112   }
3113 }
3114 //------------------------------------------------------------------------------
3115
3116
3117 //------------------------------------------------------------------------------
3118 void vvMainWindow::SEVerticalSliderChanged()
3119 {
3120   static int value=-1;
3121   if (value == SEVerticalSlider->value()) return;
3122   else value = SEVerticalSlider->value();
3123   // int value = SEVerticalSlider->value();
3124   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
3125     if (DataTree->topLevelItem(i)->data(COLUMN_DR_VIEW,Qt::CheckStateRole).toInt() > 1) {
3126       if (mSlicerManagers[i]->GetSlicer(3)->GetSlice() != value) {
3127         mSlicerManagers[i]->GetSlicer(3)->SetSlice(value);
3128         mSlicerManagers[i]->VerticalSliderHasChanged(3, value);
3129         mSlicerManagers[i]->UpdateSlice(3);
3130         //mSlicerManagers[i]->GetSlicer(3)->Render(); // <-- DS add this, needed for contour, seems ok ? not too slow ?
3131       }
3132       break;
3133     }
3134   }
3135 }
3136 //------------------------------------------------------------------------------
3137
3138
3139 //------------------------------------------------------------------------------
3140 void vvMainWindow::UpdateSlice(int slicer, int slice)
3141 {
3142   // DD("vvMainWindow::UpdateSlice");
3143   //   DD(slicer);
3144   //   DD(slice);
3145   if (slicer == 0) {
3146     //    if (slice != NOVerticalSlider->value())
3147     NOVerticalSlider->setValue(slice);
3148   } else {
3149     if (slicer == 1)
3150       NEVerticalSlider->setValue(slice);
3151     else {
3152       if (slicer == 2)
3153         SOVerticalSlider->setValue(slice);
3154       else {
3155         if (slicer == 3)
3156           SEVerticalSlider->setValue(slice);
3157       }
3158     }
3159   }
3160   // DD("vvMainWindow:UpdateSlice END");
3161 }
3162 //------------------------------------------------------------------------------
3163
3164
3165 //------------------------------------------------------------------------------
3166 void vvMainWindow::UpdateTSlice(int slicer, int slice, int code)
3167 {
3168   //FusionSequence: the slider value should be updated for slicers which show the same sequence as requested
3169   bool doUpdate=false;
3170   if (code==-1) doUpdate=true;
3171   else {
3172     for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
3173       if (DataTree->topLevelItem(i)->data(slicer+1,Qt::CheckStateRole).toInt() > 1) {
3174         //i is the active SlicerManager
3175         if (mSlicerManagers[i]->GetFusionSequenceInvolvmentCode()==code) doUpdate=true;
3176         break;
3177       }
3178     }
3179   }
3180   if (!doUpdate) return;
3181
3182   switch (slicer) {
3183   case 0:
3184     if (NOHorizontalSlider->value()==slice) return;
3185     NOHorizontalSlider->setValue(slice);
3186     break;
3187   case 1:
3188     if (NEHorizontalSlider->value()==slice) return;
3189     NEHorizontalSlider->setValue(slice);
3190     break;
3191   case 2:
3192     if (SOHorizontalSlider->value()==slice) return;
3193     SOHorizontalSlider->setValue(slice);
3194     break;
3195   case 3:
3196     if (SEHorizontalSlider->value()==slice) return;
3197     SEHorizontalSlider->setValue(slice);
3198     break;
3199   }
3200 }
3201 //------------------------------------------------------------------------------
3202
3203
3204 //------------------------------------------------------------------------------
3205 void vvMainWindow::UpdateSliceRange(int slicer, int min, int max, int tmin, int tmax)
3206 {
3207   //int position = int((min+max)/2);
3208   int position = mSlicerManagers[mCurrentPickedImageIndex]->GetSlicer(slicer)->GetSlice();
3209   if (slicer == 0) {
3210     NOVerticalSlider->setRange(min,max);
3211     NOHorizontalSlider->setRange(tmin,tmax);
3212     NOVerticalSlider->setValue(position);
3213   } else if (slicer == 1) {
3214     NEVerticalSlider->setRange(min,max);
3215     NEHorizontalSlider->setRange(tmin,tmax);
3216     NEVerticalSlider->setValue(position);
3217   } else if (slicer == 2) {
3218     SOVerticalSlider->setRange(min,max);
3219     SOHorizontalSlider->setRange(tmin,tmax);
3220     SOVerticalSlider->setValue(position);
3221   } else if (slicer == 3) {
3222     SEVerticalSlider->setRange(min,max);
3223     SEHorizontalSlider->setRange(tmin,tmax);
3224     SEVerticalSlider->setValue(position);
3225   }
3226 }
3227 //------------------------------------------------------------------------------
3228
3229
3230 //------------------------------------------------------------------------------
3231 void vvMainWindow::SaveNOScreenshot()
3232 {
3233   SaveScreenshot(NOViewWidget);
3234 }
3235 //------------------------------------------------------------------------------
3236
3237
3238 //------------------------------------------------------------------------------
3239 void vvMainWindow::SaveNEScreenshot()
3240 {
3241   SaveScreenshot(NEViewWidget);
3242 }
3243 //------------------------------------------------------------------------------
3244
3245
3246 //------------------------------------------------------------------------------
3247 void vvMainWindow::SaveSOScreenshot()
3248 {
3249   SaveScreenshot(SOViewWidget);
3250 }
3251 //------------------------------------------------------------------------------
3252
3253
3254 //------------------------------------------------------------------------------
3255 void vvMainWindow::SaveSEScreenshot()
3256 {
3257   SaveScreenshot(SEViewWidget);
3258 }
3259 //------------------------------------------------------------------------------
3260
3261
3262 //------------------------------------------------------------------------------
3263 void vvMainWindow::SaveScreenshotAllSlices()
3264 {
3265   QVTKWidget *widget = NOViewWidget;
3266
3267   int index = 0;// GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
3268   vvSlicerManager * SM = mSlicerManagers[index];
3269   vvImage * image = SM->GetImage();
3270   vvSlicer * slicer = SM->GetSlicer(0);
3271   int orientation = slicer->GetOrientation();
3272   int nbSlices = image->GetSize()[orientation];
3273   vtkSmartPointer<vtkRenderWindow>  renderWindow = widget->GetRenderWindow();
3274
3275   // Select filename base
3276   QString filename = QFileDialog::getSaveFileName(this,
3277     tr("Save As (filename will be completed by slice number)"),
3278     itksys::SystemTools::GetFilenamePath(mSlicerManagers[index]->GetFileName()).c_str(),
3279     "Images( *.png);;Images( *.jpg)");
3280
3281   // Loop on slices
3282   for(int i=0; i<nbSlices; i++) {
3283     // Change the slice
3284     slicer->SetSlice(i); // -> change the slice of the current slicer
3285     SM->UpdateSlice(0); // --> this one emit UpdateSlice
3286     QCoreApplication::flush(); // -> needed to force display of contours
3287
3288     // Screenshot
3289     vtkSmartPointer<vtkWindowToImageFilter> windowToImageFilter = vtkSmartPointer<vtkWindowToImageFilter>::New();
3290     windowToImageFilter->SetInput(renderWindow);
3291     windowToImageFilter->SetMagnification(1);
3292     windowToImageFilter->SetInputBufferTypeToRGBA(); //also record the alpha (transparency) channel
3293     windowToImageFilter->Update();
3294
3295     vtkSmartPointer<vtkPNGWriter> writer = vtkSmartPointer<vtkPNGWriter>::New();
3296     std::string fn = itksys::SystemTools::GetFilenameWithoutLastExtension(filename.toStdString());
3297     std::string num = clitk::toString(i);
3298     if (i<10) num = "0"+num;
3299     if (i<100) num = "0"+num;
3300     if (i<1000) num = "0"+num;
3301
3302     fn = itksys::SystemTools::GetFilenamePath(filename.toStdString()) + "/"+ fn
3303       + "_" + num + itksys::SystemTools::GetFilenameLastExtension(filename.toStdString());
3304     writer->SetFileName(fn.c_str());
3305     writer->SetInput(windowToImageFilter->GetOutput());
3306     writer->Write();
3307   }
3308 }
3309 //------------------------------------------------------------------------------
3310
3311
3312 //------------------------------------------------------------------------------
3313 void vvMainWindow::SaveScreenshot(QVTKWidget *widget)
3314 {
3315   QString Extensions = "Images( *.png);;";
3316   Extensions += "Images( *.jpg);;";
3317   Extensions += "Images( *.bmp);;";
3318   Extensions += "Images( *.tif);;";
3319   Extensions += "Images( *.ppm)";
3320 #if defined(VTK_USE_FFMPEG_ENCODER) || defined(VTK_USE_VIDEO_FOR_WINDOWS)
3321   Extensions += ";;Video( *.avi)";
3322 #endif
3323 #ifdef VTK_USE_MPEG2_ENCODER
3324   Extensions += ";;Video( *.mpg)";
3325 #endif
3326 #ifdef CLITK_EXPERIMENTAL
3327   Extensions += ";;Video( *.gif)";
3328 #endif
3329
3330   int smIndex=GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
3331   QString fileName = QFileDialog::getSaveFileName(this,
3332     tr("Save As"),
3333     itksys::SystemTools::GetFilenamePath(mSlicerManagers[smIndex]->GetFileName()).c_str(),
3334     Extensions);
3335
3336   if (!fileName.isEmpty()) {
3337     vtkSmartPointer<vtkWindowToImageFilter> w2i = vtkSmartPointer<vtkWindowToImageFilter>::New();
3338     w2i->SetInput(widget->GetRenderWindow());
3339     w2i->Update();
3340     vtkImageData *image = w2i->GetOutput();
3341
3342     std::string ext(itksys::SystemTools::GetFilenameLastExtension(fileName.toStdString()));
3343
3344     // Image
3345     vtkImageWriter *imgwriter = NULL;
3346     if (ext==".bmp")
3347       imgwriter = vtkBMPWriter::New();
3348     else if (ext==".tif")
3349       imgwriter = vtkTIFFWriter::New();
3350     else if (ext==".ppm")
3351       imgwriter = vtkPNMWriter::New();
3352     else if (ext==".png")
3353       imgwriter = vtkPNGWriter::New();
3354     else if (ext==".jpg")
3355       imgwriter = vtkJPEGWriter::New();
3356
3357     // Snapshot image if not null
3358     if(imgwriter!=NULL) {
3359       imgwriter->SetInput(image);
3360       imgwriter->SetFileName(fileName.toStdString().c_str());
3361       imgwriter->Write();
3362       return;
3363     }
3364
3365     // Video
3366     vtkGenericMovieWriter *vidwriter = NULL;
3367 #if CLITK_EXPERIMENTAL == 1
3368     if (ext==".gif") {
3369       vvAnimatedGIFWriter *gif = vvAnimatedGIFWriter::New();
3370       vidwriter = gif;
3371
3372       // FPS
3373       bool ok;
3374       int fps = QInputDialog::getInteger(this, tr("Number of frames per second"),
3375         tr("FPS:"), 5, 0, 1000, 1, &ok);
3376       if(ok)
3377         gif->SetRate(fps);
3378
3379       // Loops
3380       int loops = QInputDialog::getInteger(this, tr("Loops"),
3381         tr("Number of loops (0 means infinite):"), 0, 0, 1000000000, 1, &ok);
3382       if(ok)
3383         gif->SetLoops(loops);
3384
3385       // Dithering
3386       QString msg = "Would you like to activate dithering?";
3387       QMessageBox msgBox(QMessageBox::Question, tr("Dithering"),msg, 0, this);
3388       msgBox.addButton(tr("Yes"), QMessageBox::AcceptRole);
3389       msgBox.addButton(tr("No"), QMessageBox::RejectRole);
3390       gif->SetDither(msgBox.exec() == QMessageBox::AcceptRole);
3391     }
3392 #endif
3393 #ifdef VTK_USE_VIDEO_FOR_WINDOWS
3394     if (ext==".avi") {
3395       vtkAVIWriter *mpg = vtkAVIWriter::New();
3396       vidwriter = mpg;
3397       mpg->SetQuality(2);
3398       bool ok;
3399       int fps = QInputDialog::getInteger(this, tr("Number of frames per second"),
3400         tr("FPS:"), 5, 0, 1024, 1, &ok);
3401       if(!ok)
3402         fps = 5;
3403       mpg->SetRate(fps);
3404     }
3405 #endif
3406 #ifdef VTK_USE_FFMPEG_ENCODER
3407     if (ext==".avi") {
3408       vtkFFMPEGWriter *mpg = vtkFFMPEGWriter::New();
3409       vidwriter = mpg;
3410       mpg->SetQuality(2);
3411       bool ok;
3412       int fps = QInputDialog::getInteger(this, tr("Number of frames per second"),
3413         tr("FPS:"), 5, 0, 1024, 1, &ok);
3414       if(!ok)
3415         fps = 5;
3416       mpg->SetRate(fps);
3417       mpg->SetBitRateTolerance(int(ceil(12.0*1024*1024/fps)));
3418     }
3419 #endif
3420 #ifdef VTK_USE_MPEG2_ENCODER
3421     if (ext==".mpg") {
3422       vtkMPEG2Writer *mpg = vtkMPEG2Writer::New();
3423       vidwriter = mpg;
3424     }
3425 #endif
3426
3427     // Take video if not null
3428     if(vidwriter!=NULL){
3429       vidwriter->SetInput(image);
3430       vidwriter->SetFileName(fileName.toStdString().c_str());
3431       vidwriter->Start();
3432       int nSlice = mSlicerManagers[smIndex]->GetSlicer(0)->GetTMax();
3433       for(int i=0; i<=nSlice; i++) {
3434         mSlicerManagers[smIndex]->SetNextTSlice(0);
3435         vtkSmartPointer<vtkWindowToImageFilter> w2i = vtkSmartPointer<vtkWindowToImageFilter>::New();
3436         w2i->SetInput(widget->GetRenderWindow());
3437         w2i->Update();
3438         vidwriter->SetInput(w2i->GetOutput());
3439         vidwriter->Write();
3440       }
3441       vidwriter->End();
3442       vidwriter->Delete();
3443       return;
3444     }
3445
3446     QMessageBox::information(this,tr("Problem saving screenshot !"),tr("Cannot save image.\nPlease set a file extension !!!"));
3447   }
3448 }
3449 //------------------------------------------------------------------------------
3450
3451
3452 //------------------------------------------------------------------------------
3453 void vvMainWindow::GoToCursor()
3454 {
3455   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
3456   for (int column = 1; column < 5; column++) {
3457     if (DataTree->selectedItems()[0]->data(column,Qt::CheckStateRole).toInt() > 1) {
3458       double* cursorPos = mSlicerManagers[index]->GetSlicer(column-1)->GetCursorPosition();
3459       mSlicerManagers[index]->GetSlicer(column-1)->SetCurrentPosition(
3460         cursorPos[0],cursorPos[1],cursorPos[2],cursorPos[3]);
3461       mSlicerManagers[index]->UpdateViews(1,column-1);
3462       mSlicerManagers[index]->UpdateLinked(column-1);
3463       break;
3464     }
3465   }
3466 }
3467 //------------------------------------------------------------------------------
3468
3469 //------------------------------------------------------------------------------
3470 void vvMainWindow::GoToLandmark()
3471 {
3472   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
3473   for (int column = 1; column < 5; column++) {
3474     if (DataTree->selectedItems()[0]->data(column,Qt::CheckStateRole).toInt() > 1) {
3475       double* cursorPos = landmarksPanel->GetSelectedPoint();
3476       mSlicerManagers[index]->GetSlicer(column-1)->SetCurrentPosition(
3477         cursorPos[0],cursorPos[1],cursorPos[2],cursorPos[3]);
3478       mSlicerManagers[index]->UpdateViews(1,column-1);
3479       mSlicerManagers[index]->UpdateLinked(column-1);
3480       break;
3481     }
3482   }
3483 }
3484 //------------------------------------------------------------------------------
3485
3486 //------------------------------------------------------------------------------
3487 void vvMainWindow::PlayPause()
3488 {
3489   if (playMode) {
3490     playMode = 0;
3491     playButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/player_play.png")));
3492     ImageInfoChanged();
3493     return;
3494   } else {
3495     int image_number=DataTree->topLevelItemCount();
3496     bool has_temporal;
3497     for (int i=0; i<image_number; i++)
3498       if (mSlicerManagers[i]->GetSlicer(0)->GetTMax() > 0) {
3499         has_temporal=true;
3500         break;
3501       }
3502       if (has_temporal) {
3503         playMode = 1;
3504         playButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/player_pause.png")));
3505         QTimer::singleShot(1000/mFrameRate, this, SLOT(PlayNext()));
3506       }
3507   }
3508 }
3509 //------------------------------------------------------------------------------
3510
3511 //------------------------------------------------------------------------------
3512 void vvMainWindow::PlayNext()
3513 {
3514   if (playMode && !this->isHidden()) {
3515     int image_number=DataTree->topLevelItemCount();
3516     ///Only play one slicer per SM, and only if the SM is being displayed
3517     for (int i=0; i<image_number; i++)
3518       for (int j=0; j<4; j++)
3519         if (mSlicerManagers[i]->GetSlicer(0)->GetTMax() > 0 &&
3520           DataTree->topLevelItem(i)->data(j+1,Qt::CheckStateRole).toInt() > 0) {
3521             mSlicerManagers[i]->SetNextTSlice(j);
3522             break;
3523         }
3524         QTimer::singleShot(1000/mFrameRate, this, SLOT(PlayNext()));
3525   }
3526 }
3527 //------------------------------------------------------------------------------
3528
3529 void vvMainWindow::ShowLastImage()
3530 {
3531   if (mSlicerManagers.size() > 1) {
3532     QTreeWidgetItem * item=DataTree->topLevelItem(DataTree->topLevelItemCount()-1);
3533     CurrentImageChanged(mSlicerManagers.back()->GetId()); //select new image
3534     item->setData(1,Qt::CheckStateRole,2); //show the new image in the first panel
3535     DisplayChanged(item,1);
3536   }
3537 }
3538
3539 //------------------------------------------------------------------------------
3540 void vvMainWindow::UpdateRenderWindows()
3541 {
3542   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
3543     mSlicerManagers[i]->GetSlicer(0)->UpdateLandmarks();
3544     mSlicerManagers[i]->GetSlicer(1)->UpdateLandmarks();
3545     mSlicerManagers[i]->GetSlicer(2)->UpdateLandmarks();
3546     mSlicerManagers[i]->GetSlicer(3)->UpdateLandmarks();
3547   }
3548   if (NOViewWidget->GetRenderWindow()) NOViewWidget->GetRenderWindow()->Render();
3549   if (NEViewWidget->GetRenderWindow()) NEViewWidget->GetRenderWindow()->Render();
3550   if (SOViewWidget->GetRenderWindow()) SOViewWidget->GetRenderWindow()->Render();
3551   if (SEViewWidget->GetRenderWindow()) SEViewWidget->GetRenderWindow()->Render();
3552 }
3553 //------------------------------------------------------------------------------
3554
3555 //------------------------------------------------------------------------------
3556 void vvMainWindow::SegmentationOnCurrentImage()
3557 {
3558   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
3559
3560   vvSegmentationDialog segmentation;
3561   segmentation.SetImage(mSlicerManagers[index]->GetSlicer(0)->GetImage());
3562   segmentation.exec();
3563 }
3564 //------------------------------------------------------------------------------
3565
3566 void vvMainWindow::SurfaceViewerLaunch()
3567 {
3568   vvSurfaceViewerDialog surfaceViewer;
3569   surfaceViewer.exec();
3570 }
3571 //------------------------------------------------------------------------------
3572
3573
3574 //------------------------------------------------------------------------------
3575 int vvMainWindow::GetImageDuplicateFilenameNumber(std::string filename)
3576 {
3577   int number=0;
3578   for(unsigned int l=0; l<mSlicerManagers.size(); l++) {
3579     vvSlicerManager * v = mSlicerManagers[l];
3580     if (v->GetBaseFileName() ==
3581       vtksys::SystemTools::GetFilenameName(vtksys::SystemTools::GetFilenameWithoutLastExtension(filename))) {
3582         number = std::max(number, v->GetBaseFileNameNumber()+1);
3583     }
3584   }
3585   return number;
3586 }
3587 //------------------------------------------------------------------------------
3588
3589
3590 //------------------------------------------------------------------------------
3591 vvSlicerManager* vvMainWindow::AddImage(vvImage::Pointer image,std::string filename)
3592 {
3593   // Change filename if another image exist with the same name
3594   int number = GetImageDuplicateFilenameNumber(filename);
3595
3596   // Create new SliceManager
3597   vvSlicerManager* slicer_manager = new vvSlicerManager(4);
3598   slicer_manager->SetImage(image);//, IMAGE, number);
3599   //  filename = filename+"_"+clitk::toString(number);
3600   slicer_manager->SetFilename(filename, number);
3601   mSlicerManagers.push_back(slicer_manager);
3602
3603   //create an item in the tree with good settings
3604   QTreeWidgetItem *item = new QTreeWidgetItem();
3605   item->setData(0,Qt::UserRole,slicer_manager->GetFileName().c_str());//files[i].c_str());
3606   item->setData(1,Qt::UserRole,tr("image"));
3607   item->setData(COLUMN_IMAGE_NAME,Qt::DisplayRole,slicer_manager->GetFileName().c_str());//filename.c_str());
3608   qApp->processEvents();
3609
3610   for (int j = 1; j <= 4; j++) item->setData(j,Qt::CheckStateRole,1);
3611
3612   //Create the buttons for reload and close
3613   qApp->processEvents();
3614   QTreePushButton* cButton = new QTreePushButton;
3615   cButton->setItem(item);
3616   cButton->setColumn(COLUMN_CLOSE_IMAGE);
3617   cButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/exit.png")));
3618   connect(cButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
3619     this,SLOT(CloseImage(QTreeWidgetItem*, int)));
3620
3621   QTreePushButton* rButton = new QTreePushButton;
3622   rButton->setItem(item);
3623   rButton->setColumn(COLUMN_RELOAD_IMAGE);
3624   rButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/rotateright.png")));
3625   rButton->setEnabled(0);
3626   connect(rButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
3627     this,SLOT(ReloadImage(QTreeWidgetItem*, int)));
3628
3629   DataTree->addTopLevelItem(item);
3630   DataTree->setItemWidget(item, COLUMN_CLOSE_IMAGE, cButton);
3631   DataTree->setItemWidget(item, COLUMN_RELOAD_IMAGE, rButton);
3632
3633   //set the id of the image
3634   QString id = QDir::current().absoluteFilePath(slicer_manager->GetFileName().c_str()) + QString::number(mSlicerManagers.size()-1);
3635   item->setData(COLUMN_IMAGE_NAME,Qt::UserRole,id.toStdString().c_str());
3636   mSlicerManagers.back()->SetId(id.toStdString());
3637
3638   linkPanel->addImage(slicer_manager->GetFileName().c_str()// filename
3639     , id.toStdString());
3640
3641   connect(mSlicerManagers.back(), SIGNAL(currentImageChanged(std::string)),
3642     this, SLOT(CurrentImageChanged(std::string)));
3643   connect(mSlicerManagers.back(), SIGNAL(currentPickedImageChanged(std::string)),
3644     this, SLOT(CurrentPickedImageChanged(std::string)));
3645   connect(mSlicerManagers.back(), SIGNAL(UpdatePosition(int, double, double, double, double, double, double, double)),
3646     this, SLOT(MousePositionChanged(int,double, double, double, double, double, double, double)));
3647   connect(mSlicerManagers.back(), SIGNAL(UpdateVector(int, double, double, double, double)),
3648     this, SLOT(VectorChanged(int,double,double,double, double)));
3649   connect(mSlicerManagers.back(), SIGNAL(UpdateOverlay(int, double, double)),
3650     this, SLOT(OverlayChanged(int,double,double)));
3651   connect(mSlicerManagers.back(), SIGNAL(UpdateFusion(int, double)),
3652     this, SLOT(FusionChanged(int,double)));
3653   //connect(mSlicerManagers.back(), SIGNAL(UpdateFusionSequence(int, bool, unsigned int)),
3654   //  this, SLOT(FusionSequenceChanged(int, bool, unsigned int)));
3655   connect(mSlicerManagers.back(), SIGNAL(WindowLevelChanged()),
3656     this,SLOT(WindowLevelChanged()));
3657   connect(mSlicerManagers.back(), SIGNAL(UpdateSlice(int,int)),
3658     this,SLOT(UpdateSlice(int,int)));
3659   connect(mSlicerManagers.back(), SIGNAL(UpdateTSlice(int, int, int)),
3660     this,SLOT(UpdateTSlice(int, int, int)));
3661   connect(mSlicerManagers.back(), SIGNAL(UpdateTSlice(int, int, int)),
3662     this,SLOT(ImageInfoChanged()));
3663   connect(mSlicerManagers.back(), SIGNAL(UpdateSliceRange(int,int,int,int,int)),
3664     this,SLOT(UpdateSliceRange(int,int,int,int,int)));
3665   connect(mSlicerManagers.back(), SIGNAL(UpdateLinkManager(std::string,int,double,double,double,int)),
3666     this,SLOT(UpdateLinkManager(std::string,int,double,double,double,int)));
3667   connect(mSlicerManagers.back(), SIGNAL(UpdateLinkedNavigation(std::string,vvSlicerManager*,vvSlicer*)),
3668     this,SLOT(UpdateLinkedNavigation(std::string,vvSlicerManager*,vvSlicer*)));
3669   connect(mSlicerManagers.back(), SIGNAL(ChangeImageWithIndexOffset(vvSlicerManager*,int,int)),
3670     this,SLOT(ChangeImageWithIndexOffset(vvSlicerManager*,int,int)));
3671   connect(mSlicerManagers.back(), SIGNAL(LandmarkAdded()),landmarksPanel,SLOT(AddPoint()));
3672
3673
3674   UpdateTree();
3675   qApp->processEvents();
3676   InitSlicers();
3677   ShowLastImage();
3678   InitDisplay();
3679   qApp->processEvents();
3680
3681   // End
3682   ImageInfoChanged();
3683   return slicer_manager;
3684 }
3685 //------------------------------------------------------------------------------
3686
3687
3688 //------------------------------------------------------------------------------
3689 void vvMainWindow::UpdateCurrentSlicer()
3690 {
3691   int index = -1;
3692   if (DataTree->selectedItems().size() > 0) {
3693     index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
3694   }
3695   mSlicerManagerCurrentIndex = index;
3696 }
3697 //------------------------------------------------------------------------------
3698