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