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 #include <QShortcut>
  27
  28 // VV include
  29 #include "vvMainWindow.h"
  30 #include "vvHelpDialog.h"
  31 #include "vvRegisterForm.h"
  32 #include "vvDocumentation.h"
  33 #include "vvProgressDialog.h"
  34 #include "vvQDicomSeriesSelector.h"
  35 #include "vvSlicerManager.h"
  36 #include "clitkImageCommon.h"
  37 #include "vvSlicer.h"
  38 #include "vvInteractorStyleNavigator.h"
  39 #include "vvImageWriter.h"
  40 #include "vvSegmentationDialog.h"
  41 #include "vvSurfaceViewerDialog.h"
  42 #include "vvDeformationDialog.h"
  43 #include "vvImageWarp.h"
  44 #include "vvUtils.h"
  45 #include "vvMidPosition.h"
  46 #include "vvMesh.h"
  47 #include "vvStructSelector.h"
  48 #include "vvMeshReader.h"
  49 #include "vvSaveState.h"
  50 #include "vvReadState.h"
  51 #include "clitkConfiguration.h"
  52 #include "clitkMatrix.h"
  53
  54 // ITK include
  55 #include <itkImage.h>
  56 #include <itkImageFileReader.h>
  57 #include <itkByteSwapper.h>
  58 #include <itkCommand.h>
  59 #include <itkNumericSeriesFileNames.h>
  60
  61 // VTK include
  62 #include <vtkImageMapper3D.h>
  63 #include <vtkInformation.h>
  64 #include <vtkVersion.h>
  65 #include <vtkImageData.h>
  66 #include <vtkImageActor.h>
  67 #include <vtkCornerAnnotation.h>
  68 #include <vtkRenderWindow.h>
  69 #include <vtkRenderWindowInteractor.h>
  70 #include <vtkRenderer.h>
  71 #include <vtkRendererCollection.h>
  72 #include <vtkWindowToImageFilter.h>
  73 #include <vtkBMPWriter.h>
  74 #include <vtkTIFFWriter.h>
  75 #include <vtkPNMWriter.h>
  76 #include <vtkPNGWriter.h>
  77 #include <vtkJPEGWriter.h>
  78 #include <vtkGenericMovieWriter.h>
  79 #ifdef CLITK_EXPERIMENTAL
  80 #  include <vvAnimatedGIFWriter.h>
  81 #endif
  82 #ifdef VTK_USE_VIDEO_FOR_WINDOWS
  83 #  include <vtkAVIWriter.h>
  84 #endif
  85 #ifdef VTK_USE_FFMPEG_ENCODER
  86 #  include <vtkFFMPEGWriter.h>
  87 #endif
  88 #ifdef VTK_USE_MPEG2_ENCODER
  89 #  include <vtkMPEG2Writer.h>
  90 #endif
  91 #include <vtkMatrix4x4.h>
  92 #include <vtkTransform.h>
  93
  94 // Standard includes
  95 #include <iostream>
  96 #include <fstream>
  97 #include <sstream>
  98 #include <iomanip>
  99
 100 #define COLUMN_TREE 0
 101 #define COLUMN_UL_VIEW 1
 102 #define COLUMN_UR_VIEW 2
 103 #define COLUMN_DL_VIEW 3
 104 #define COLUMN_DR_VIEW 4
 105 #define COLUMN_CLOSE_IMAGE 5
 106 #define COLUMN_RELOAD_IMAGE 6
 107 #define COLUMN_IMAGE_NAME 7
 108
 109 #ifdef CLITK_PRIVATE_FEATURES
 110 #define EXTENSIONS "Images ( *.bmp *.dcm *.png *.jpeg *.jpg *.tif *.mhd *.mha *.hdr *.vox *.his *.xdr *.SCAN *.nii *.nrrd *.nhdr *.refscan *.nii.gz *.usf *.svl)"
 111 #else
 112 #define EXTENSIONS "Images ( *.bmp *.dcm *.png *.jpeg *.jpg *.tif *.mhd *.mha *.hdr *.vox *.his *.xdr *.SCAN *.nii *.nrrd *.nhdr *.refscan *.nii.gz)"
 113 #endif
 114
 115
 116 /*Data Tree values
 117 0,Qt::UserRole full filename
 118 1,Qt::CheckStateRole checkbutton UL View
 119 1,Qt::UserRole overlay, fusion or vector
 120 2,Qt::CheckStateRole checkbutton UR View
 121 3,Qt::CheckStateRole checkbutton DL View
 122 4,Qt::CheckStateRole checkbutton DR View
 123 5,0  short filename
 124 5,Qt::UserRole mSlicerManager id*/
 125
 126 //------------------------------------------------------------------------------
 127 vvMainWindow::vvMainWindow():vvMainWindowBase()
 128 {
 129   setupUi(this); // this sets up the GUI
 130
 131   //Qt::WindowFlags flags = windowFlags();
 132   //setWindowFlags(flags | Qt::WindowStaysOnTopHint);
 133
 134   mInputPathName = "";
 135   mMenuTools = menuTools;
 136   //  mMenuSegmentation = menuSegmentation;
 137   mContextMenu = &contextMenu;
 138   mMenuExperimentalTools = menuExperimental;
 139   mMainWidget = this;
 140   mCurrentTime = -1;
 141   mCurrentSelectedImageId = "";
 142   mCurrentPickedImageId = "";
 143   mCurrentPickedImageIndex = 0;
 144
 145   //Init the contextMenu
 146   this->setContextMenuPolicy(Qt::CustomContextMenu);
 147   contextActions.resize(0);
 148   QAction* actionOpen_new_image = contextMenu.addAction(QIcon(QString::fromUtf8(":/common/icons/fileopen.png")),
 149     tr("O&pen new Image"));
 150   actionOpen_new_image->setShortcut(QKeySequence(tr("Ctrl+O")));
 151   connect(actionOpen_new_image,SIGNAL(triggered()),this,SLOT(OpenImages()));
 152   contextActions.push_back(actionOpen_new_image);
 153   contextMenu.addSeparator();
 154
 155   QAction* actionClose_Image = contextMenu.addAction(QIcon(QString::fromUtf8(":/common/icons/exit.png")),
 156     tr("Close Current Image"));
 157   connect(actionClose_Image,SIGNAL(triggered()),this,SLOT(CloseImage()));
 158   contextActions.push_back(actionClose_Image);
 159
 160   QAction* actionReload_image = contextMenu.addAction(QIcon(QString::fromUtf8(":/common/icons/rotateright.png")),
 161     tr("Reload Current Image"));
 162   connect(actionReload_image,SIGNAL(triggered()),this,SLOT(ReloadImage()));
 163   contextActions.push_back(actionReload_image);
 164
 165   QAction* actionSave_image = contextMenu.addAction(QIcon(QString::fromUtf8(":/common/icons/filesave.png")),
 166     tr("Save Current Image"));
 167   connect(actionSave_image,SIGNAL(triggered()),this,SLOT(SaveAs()));
 168   contextActions.push_back(actionSave_image);
 169
 170   QAction* actionSave_state = contextMenu.addAction(QIcon(QString::fromUtf8(":/common/icons/filesave.png")),
 171     tr("Save Current State"));
 172   connect(actionSave_state,SIGNAL(triggered()),this,SLOT(SaveCurrentState()));
 173   contextActions.push_back(actionSave_state);
 174
 175   QAction* actionRead_state = contextMenu.addAction(QIcon(QString::fromUtf8(":/common/icons/filesave.png")),
 176     tr("Read Saved State"));
 177   connect(actionRead_state,SIGNAL(triggered()),this,SLOT(ReadSavedState()));
 178   contextActions.push_back(actionRead_state);
 179
 180   contextMenu.addSeparator();
 181
 182   contextMenu.addAction(actionAdd_VF_to_current_Image);
 183   contextActions.push_back(actionAdd_VF_to_current_Image);
 184
 185   //QAction* actionAdd_Overlay_to_current_Image = menuOverlay->addAction(QIcon(QString::fromUtf8(":/common/icons/GPSup.png")),
 186   //    tr("Add overlay image to current image"));
 187   contextMenu.addAction(actionAdd_overlay_image_to_current_image);
 188   contextActions.push_back(actionAdd_overlay_image_to_current_image);
 189
 190   contextMenu.addAction(actionAdd_fusion_image);
 191   contextActions.push_back(actionAdd_fusion_image);
 192
 193 #ifdef CLITK_EXPERIMENTAL
 194   contextMenu.addAction(actionAdd_USSequence_toCT);
 195   contextActions.push_back(actionAdd_USSequence_toCT);
 196 #endif
 197
 198
 199   contextMenu.addSeparator();
 200   QAction* actionResetMatrix = contextMenu.addAction(QIcon(QString::fromUtf8(":/common/icons/identity.png")),
 201     tr("Reset transformation to identity"));
 202   connect(actionResetMatrix, SIGNAL(triggered()), this,SLOT(ResetTransformationToIdentity()));
 203
 204   // TRIAL DS
 205   /*
 206   QMenu * m = new QMenu(menubar);
 207   m->setTitle("TOTO");
 208   //  m->setObjectName(QString::fromUtf8("TOTOTO"));
 209   contextMenu.addMenu(m);
 210   QAction * a = m->addAction(QIcon(QString::fromUtf8(":/common/icons/GPSup.png")),
 211   tr("BIDON"));
 212   QAction * b = m->addAction(QIcon(QString::fromUtf8(":/common/icons/GPSup.png")),
 213   tr("BIDON2"));
 214   m->addAction(a);
 215   m->addAction(b);
 216   connect(a,SIGNAL(triggered()),this,SLOT(AddFusionImage()));
 217   */
 218
 219   //init the DataTree
 220   mSlicerManagers.resize(0);
 221
 222   QStringList header;
 223   header.append("");
 224   header.append("TL");
 225   header.append("TR");
 226   header.append("BL");
 227   header.append("BR");
 228   header.append("");
 229   header.append("");
 230   header.append("Name");
 231
 232   DataTree->setHeaderLabels(header);
 233   DataTree->resizeColumnToContents(COLUMN_TREE);
 234   DataTree->resizeColumnToContents(COLUMN_UL_VIEW);
 235   DataTree->resizeColumnToContents(COLUMN_UR_VIEW);
 236   DataTree->resizeColumnToContents(COLUMN_DL_VIEW);
 237   DataTree->resizeColumnToContents(COLUMN_DR_VIEW);
 238   DataTree->resizeColumnToContents(COLUMN_CLOSE_IMAGE);
 239   DataTree->resizeColumnToContents(COLUMN_RELOAD_IMAGE);
 240   DataTree->resizeColumnToContents(COLUMN_IMAGE_NAME);
 241
 242   viewMode = 1;
 243   documentation = new vvDocumentation();
 244   help_dialog = new vvHelpDialog();
 245   dicomSeriesSelector = new vvDicomSeriesSelector();
 246
 247   inverseButton->setEnabled(0);
 248   actionAdd_overlay_image_to_current_image->setEnabled(0);
 249   actionSave_As->setEnabled(0);
 250   actionAdd_VF_to_current_Image->setEnabled(0);
 251   actionAdd_fusion_image->setEnabled(0);
 252   actionAdd_USSequence_toCT->setEnabled(0);
 253
 254   //init the sliders
 255   verticalSliders.push_back(NOVerticalSlider);
 256   verticalSliders.push_back(NEVerticalSlider);
 257   verticalSliders.push_back(SOVerticalSlider);
 258   verticalSliders.push_back(SEVerticalSlider);
 259
 260   for (int i =0; i < 4; i++)
 261     verticalSliders[i]->hide();
 262
 263   horizontalSliders.push_back(NOHorizontalSlider);
 264   horizontalSliders.push_back(NEHorizontalSlider);
 265   horizontalSliders.push_back(SOHorizontalSlider);
 266   horizontalSliders.push_back(SEHorizontalSlider);
 267
 268   for (int i =0; i < 4; i++)
 269     horizontalSliders[i]->hide();
 270
 271
 272   connect(NOVerticalSlider,SIGNAL(valueChanged(int)),this,SLOT(NOVerticalSliderChanged()));
 273   connect(NEVerticalSlider,SIGNAL(valueChanged(int)),this,SLOT(NEVerticalSliderChanged()));
 274   connect(SOVerticalSlider,SIGNAL(valueChanged(int)),this,SLOT(SOVerticalSliderChanged()));
 275   connect(SEVerticalSlider,SIGNAL(valueChanged(int)),this,SLOT(SEVerticalSliderChanged()));
 276
 277   connect(NOHorizontalSlider,SIGNAL(valueChanged(int)),this,SLOT(NOHorizontalSliderMoved()));
 278   connect(NEHorizontalSlider,SIGNAL(valueChanged(int)),this,SLOT(NEHorizontalSliderMoved()));
 279   connect(SOHorizontalSlider,SIGNAL(valueChanged(int)),this,SLOT(SOHorizontalSliderMoved()));
 280   connect(SEHorizontalSlider,SIGNAL(valueChanged(int)),this,SLOT(SEHorizontalSliderMoved()));
 281
 282   //connect everything
 283   connect(actionCompute_mid_position_image,SIGNAL(triggered()),this,SLOT(ComputeMidPosition()));
 284   connect(actionDeformable_Registration,SIGNAL(triggered()),this,SLOT(ComputeDeformableRegistration()));
 285   connect(actionWarp_image_with_vector_field,SIGNAL(triggered()),this,SLOT(WarpImage()));
 286   connect(actionLoad_images,SIGNAL(triggered()),this,SLOT(OpenImages()));
 287   connect(actionOpen_Dicom,SIGNAL(triggered()),this,SLOT(OpenDicom()));
 288   //  connect(actionOpen_Dicom_Struct,SIGNAL(triggered()),this,SLOT(OpenDCStructContour()));
 289   connect(actionOpen_VTK_contour,SIGNAL(triggered()),this,SLOT(OpenVTKContour()));
 290   connect(actionOpen_Multiple_Images_As_One,SIGNAL(triggered()),this,SLOT(MergeImages()));
 291   connect(actionSlice_Image_As_Multiple_Images,SIGNAL(triggered()),this,SLOT(SliceImages()));
 292   connect(actionOpen_Image_With_Time,SIGNAL(triggered()),this,SLOT(OpenImageWithTime()));
 293   connect(actionMerge_images_as_n_dim_t, SIGNAL(triggered()), this, SLOT(MergeImagesWithTime()));
 294   connect(actionSave_As,SIGNAL(triggered()),this,SLOT(SaveAs()));
 295   connect(actionSave_current_state,SIGNAL(triggered()),this,SLOT(SaveCurrentState()));
 296   connect(actionRead_saved_state,SIGNAL(triggered()),this,SLOT(ReadSavedState()));
 297   connect(actionExit,SIGNAL(triggered()),this,SLOT(close()));
 298   connect(actionAdd_VF_to_current_Image,SIGNAL(triggered()),this,SLOT(OpenField()));
 299   connect(actionAdd_fusion_image,SIGNAL(triggered()),this,SLOT(SelectFusionImage()));
 300   connect(actionAdd_overlay_image_to_current_image,SIGNAL(triggered()), this,SLOT(SelectOverlayImage()));
 301   connect(actionAdd_USSequence_toCT,SIGNAL(triggered()), this,SLOT(SelectFusionSequence()));
 302   connect(actionNavigation_Help,SIGNAL(triggered()),this,SLOT(ShowHelpDialog()));
 303
 304   QShortcut *shortcutHelp = new QShortcut(QKeySequence(QKeySequence::HelpContents),this);
 305   shortcutHelp->setContext(Qt::ApplicationShortcut);
 306   QObject::connect(shortcutHelp, SIGNAL(activated()), this, SLOT(ShowHelpDialog()));
 307
 308   connect(actionDocumentation,SIGNAL(triggered()),this,SLOT(ShowDocumentation()));
 309   connect(actionRegister_vv,SIGNAL(triggered()),this,SLOT(PopupRegisterForm()));
 310
 311   connect(overlayPanel, SIGNAL(FusionSequenceCorrespondancesButtonPressed()), this, SLOT(SelectFusionSequenceCorrespondances()));
 312
 313
 314   ///////////////////////////////////////////////
 315   connect(actionSegmentation,SIGNAL(triggered()),this,SLOT(SegmentationOnCurrentImage()));
 316   connect(actionSurface_Viewer,SIGNAL(triggered()),this,SLOT(SurfaceViewerLaunch()));
 317   ///////////////////////////////////////////////
 318
 319   actionNorth_East_Window->setEnabled(0);
 320   actionNorth_West_Window->setEnabled(0);
 321   actionSouth_East_Window->setEnabled(0);
 322   actionSouth_West_Window->setEnabled(0);
 323
 324   connect(actionNorth_East_Window,SIGNAL(triggered()),this,SLOT(SaveNEScreenshot()));
 325   connect(actionNorth_West_Window,SIGNAL(triggered()),this,SLOT(SaveNOScreenshot()));
 326   connect(actionSouth_East_Window,SIGNAL(triggered()),this,SLOT(SaveSEScreenshot()));
 327   connect(actionSouth_West_Window,SIGNAL(triggered()),this,SLOT(SaveSOScreenshot()));
 328   connect(actionSave_all_slices,SIGNAL(triggered()),this,SLOT(SaveScreenshotAllSlices()));
 329
 330   connect(DataTree,SIGNAL(itemSelectionChanged()),this,SLOT(ImageInfoChanged()));
 331   connect(DataTree,SIGNAL(itemClicked(QTreeWidgetItem*, int)),this,
 332     SLOT(DisplayChanged(QTreeWidgetItem*, int)));
 333
 334   connect(viewButton,SIGNAL(clicked()),this, SLOT(ChangeViewMode()) );
 335   connect(windowSpinBox,SIGNAL(editingFinished()),this,SLOT(WindowLevelEdited()));
 336   connect(levelSpinBox,SIGNAL(editingFinished()),this,SLOT(WindowLevelEdited()));
 337   connect(colorMapComboBox,SIGNAL(currentIndexChanged(int)),this,SLOT(UpdateColorMap()));
 338   connect(presetComboBox,SIGNAL(currentIndexChanged(int)),this,SLOT(UpdateWindowLevel()));
 339   connect(slicingPresetComboBox, SIGNAL(currentIndexChanged(int)),this,SLOT(UpdateSlicingPreset()));
 340   connect(inverseButton,SIGNAL(clicked()),this,SLOT(SwitchWindowLevel()));
 341   connect(applyWindowLevelToAllButton,SIGNAL(clicked()),this,SLOT(ApplyWindowLevelToAllImages()));
 342
 343   connect(this,SIGNAL(customContextMenuRequested(QPoint)),this,SLOT(ShowContextMenu(QPoint)));
 344
 345   connect(linkPanel,SIGNAL(addLink(QString,QString,bool)),this,SLOT(AddLink(QString,QString,bool)));
 346   connect(linkPanel,SIGNAL(removeLink(QString,QString)),this,SLOT(RemoveLink(QString,QString)));
 347   connect(overlayPanel,SIGNAL(VFPropertyUpdated(int,int,int,int,double,double,double)),this,SLOT(SetVFProperty(int,int,int,int,double,double,double)));
 348   connect(overlayPanel,SIGNAL(OverlayPropertyUpdated(int,int,double,double)),
 349     this,SLOT(SetOverlayProperty(int,int,double,double)));
 350   connect(overlayPanel,SIGNAL(FusionPropertyUpdated(int,int,int,double,double, bool)),
 351     this,SLOT(SetFusionProperty(int,int,int,double,double, bool)));
 352   connect(landmarksPanel,SIGNAL(UpdateRenderWindows()),this,SLOT(UpdateRenderWindows()));
 353   connect(landmarksPanel,SIGNAL(SelectedPointChanged()),this,SLOT(GoToLandmark()));
 354
 355   connect(overlayPanel,SIGNAL(FusionSequencePropertyUpdated(int, bool, unsigned int, bool)),
 356     this,SLOT(SetFusionSequenceProperty(int, bool,unsigned int, bool)));
 357
 358
 359   playMode = 0;//pause
 360   mFrameRate = 10;
 361   playButton->setEnabled(0);
 362   frameRateLabel->setEnabled(0);
 363   frameRateSpinBox->setEnabled(0);
 364   connect(playButton, SIGNAL(clicked()),this,SLOT(PlayPause()));
 365   connect(frameRateSpinBox, SIGNAL(valueChanged(int)),this,SLOT(ChangeFrameRate(int)));
 366
 367   goToCursorPushButton->setEnabled(0);
 368   connect(goToCursorPushButton, SIGNAL(clicked()),this,SLOT(GoToCursor()));
 369
 370   NOViewWidget->hide();
 371   NEViewWidget->hide();
 372   SOViewWidget->hide();
 373   SEViewWidget->hide();
 374
 375   //Recently opened files
 376   std::list<std::string> recent_files = GetRecentlyOpenedImages();
 377   recentlyOpenedFilesMenu=NULL;
 378   if ( !recent_files.empty() ) {
 379     createRecentlyOpenedFilesMenu();
 380     updateRecentlyOpenedFilesMenu(recent_files);
 381   }
 382
 383   // Adding all new tools (insertion in the menu)
 384   vvToolManager::GetInstance()->InsertToolsInMenu(this);
 385   vvToolManager::GetInstance()->EnableToolsInMenu(this, false);
 386
 387   if (!CLITK_EXPERIMENTAL)
 388     menuExperimental->menuAction()->setVisible(false);
 389
 390
 391   QTimer * timerMemory = new QTimer(this);
 392   //timerMemory->setInterval(5);
 393   connect(timerMemory, SIGNAL(timeout()), this, SLOT(UpdateMemoryUsage()));
 394   timerMemory->start(2000);
 395
 396 }
 397 //------------------------------------------------------------------------------
 398 void vvMainWindow::show()
 399 {
 400   vvMainWindowBase::show();
 401   PopupRegisterForm(true);
 402 }
 403 //------------------------------------------------------------------------------
 404 void vvMainWindow::UpdateMemoryUsage()
 405 {
 406   //  clitk::PrintMemory(true);
 407   if (clitk::GetMemoryUsageInMb() == 0) infoPanel->setMemoryInMb("NA");
 408   else infoPanel->setMemoryInMb(QString::number(clitk::GetMemoryUsageInMb())+" MiB");
 409 }
 410 //------------------------------------------------------------------------------
 411
 412
 413 //------------------------------------------------------------------------------
 414 void vvMainWindow::createRecentlyOpenedFilesMenu()
 415 {
 416   recentlyOpenedFilesMenu = new QMenu("Recently opened files...");
 417   recentlyOpenedFilesMenu->setIcon(QIcon(QString::fromUtf8(":/common/icons/open.png")));
 418   menuFile->insertMenu(actionOpen_Image_With_Time,recentlyOpenedFilesMenu);
 419   menuFile->insertSeparator(actionOpen_Image_With_Time);
 420 }
 421 //------------------------------------------------------------------------------
 422
 423
 424 //------------------------------------------------------------------------------
 425
 426 void vvMainWindow::updateRecentlyOpenedFilesMenu(const std::list<std::string> &recent_files)
 427 {
 428   if(recentlyOpenedFilesMenu==NULL) {
 429     createRecentlyOpenedFilesMenu();
 430   } else {
 431     recentlyOpenedFilesMenu->clear();
 432   }
 433   for (std::list<std::string>::const_iterator i = recent_files.begin(); i!=recent_files.end(); i++) {
 434     QAction* current=new QAction(QIcon(QString::fromUtf8(":/common/icons/open.png")), i->c_str(),this);
 435     recentlyOpenedFilesMenu->addAction(current);
 436     connect(current,SIGNAL(triggered()),this,SLOT(OpenRecentImage()));
 437   }
 438 }
 439 //------------------------------------------------------------------------------
 440
 441
 442 //------------------------------------------------------------------------------
 443 void vvMainWindow::ComputeMidPosition()
 444 {
 445   bool ok;
 446   int index=GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
 447   int ref = QInputDialog::getInt(this,"Chose reference phase","Reference phase",0,0,\
 448 mSlicerManagers[index]->GetImage()->GetVTKImages().size()-1,1,&ok);
 449   if (ok) {
 450     vvMidPosition midp;
 451     midp.slicer_manager = mSlicerManagers[index];
 452     midp.reference_image_index = ref;
 453     QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
 454     midp.Update();
 455     if (midp.error)
 456       QMessageBox::warning(this, "Error computing midposition image",midp.error_message.c_str());
 457     else {
 458       QFileInfo info(midp.slicer_manager->GetFileName().c_str());
 459       AddImage(midp.output,info.path().toStdString()+"/"+info.completeBaseName().toStdString()+"_midposition.mhd");
 460     }
 461     QApplication::restoreOverrideCursor();
 462   }
 463 }
 464 //------------------------------------------------------------------------------
 465
 466
 467 //------------------------------------------------------------------------------
 468 void vvMainWindow::AddContour(int image_index, vvMesh::Pointer contour, bool propagation)
 469 {
 470   QTreeWidgetItem *item = new QTreeWidgetItem();
 471   item->setData(0,Qt::UserRole,"filename.vtk");
 472   item->setData(1,Qt::UserRole,tr("contour"));
 473   QBrush brush;
 474   brush.setColor(QColor(contour->r*255,contour->g*255,contour->b*255));
 475   brush.setStyle(Qt::SolidPattern);
 476   item->setData(COLUMN_IMAGE_NAME,Qt::BackgroundRole,brush);
 477   //  item->setData(COLUMN_IMAGE_NAME,Qt::DisplayRole,contour->structure_name.c_str());
 478
 479   for (int j = 1; j <= 4; j++)
 480     item->setData(j,Qt::CheckStateRole,DataTree->topLevelItem(image_index)->data(j,Qt::CheckStateRole));
 481
 482   QTreePushButton* cButton = new QTreePushButton;
 483   cButton->setItem(item);
 484   cButton->setColumn(COLUMN_CLOSE_IMAGE);
 485   cButton->setToolTip(tr("close image"));
 486   cButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/exit.png")));
 487   connect(cButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
 488     this,SLOT(CloseImage(QTreeWidgetItem*, int)));
 489
 490   QTreePushButton* rButton = new QTreePushButton;
 491   rButton->setItem(item);
 492   rButton->setColumn(COLUMN_RELOAD_IMAGE);
 493   rButton->setToolTip(tr("reload image"));
 494   rButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/rotateright.png")));
 495   rButton->setEnabled(false);
 496   //Not implemented
 497   //connect(rButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
 498   //this,SLOT(ReloadImage(QTreeWidgetItem*, int)));
 499
 500   DataTree->topLevelItem(image_index)->setExpanded(1);
 501   DataTree->topLevelItem(image_index)->addChild(item);
 502   DataTree->setItemWidget(item, COLUMN_CLOSE_IMAGE, cButton);
 503   DataTree->setItemWidget(item, COLUMN_RELOAD_IMAGE, rButton);
 504   QString id = DataTree->topLevelItem(image_index)->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString();
 505   item->setData(COLUMN_IMAGE_NAME,Qt::UserRole,id.toStdString().c_str());
 506
 507   UpdateTree();
 508   mSlicerManagers[image_index]->AddContour(contour,propagation);
 509   mSlicerManagers[image_index]->Render();
 510 }
 511 //------------------------------------------------------------------------------
 512
 513
 514 //------------------------------------------------------------------------------
 515 void vvMainWindow::OpenVTKContour()
 516 {
 517   if (mSlicerManagers.size() > 0) {
 518     QString Extensions = "Images ( *.vtk *.obj)";
 519     Extensions += ";;All Files (*)";
 520     QString file = QFileDialog::getOpenFileName(this,tr("Open vtkPolyData"),mInputPathName,Extensions);
 521     if (file.isNull())
 522       return;
 523     QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
 524     int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
 525     vvMeshReader reader;
 526     reader.SetImage(mSlicerManagers[index]->GetImage());
 527     reader.SetModeToVTK();
 528     reader.SetFilename(file.toStdString());
 529     reader.Update();
 530     AddContour(index,reader.GetOutput()[0],false);
 531     QApplication::restoreOverrideCursor();
 532   }
 533 }
 534 //------------------------------------------------------------------------------
 535
 536
 537 //------------------------------------------------------------------------------
 538 void vvMainWindow::AddDCStructContour(int index, QString file)
 539 {
 540   vvMeshReader reader;
 541   reader.SetFilename(file.toStdString());
 542   vvStructSelector selector;
 543   selector.SetStructures(reader.GetROINames());
 544   if (!mSlicerManagers[index]->GetVF().IsNull())
 545     selector.EnablePropagationCheckBox();
 546   if (selector.exec()) {
 547     QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
 548     reader.SetSelectedItems(selector.getSelectedItems());
 549     reader.SetImage(mSlicerManagers[index]->GetImage());
 550     if (selector.PropagationEnabled())
 551       reader.SetPropagationVF(mSlicerManagers[index]->GetVF());
 552     reader.Update();
 553     std::vector<vvMesh::Pointer> contours=reader.GetOutput();
 554     for (std::vector<vvMesh::Pointer>::iterator i=contours.begin();
 555       i!=contours.end(); i++)
 556       AddContour(index,*i,selector.PropagationEnabled());
 557     QApplication::restoreOverrideCursor();
 558   }
 559 }
 560
 561 //------------------------------------------------------------------------------
 562 void vvMainWindow::OpenDCStructContour()
 563 {
 564   if (mSlicerManagers.size() > 0) {
 565     QString Extensions = "Dicom Files ( *.dcm RS*)";
 566     Extensions += ";;All Files (*)";
 567     QString file = QFileDialog::getOpenFileName(this,tr("Merge Images"),mInputPathName,Extensions);
 568     if (file.isNull())
 569       return;
 570     int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
 571     AddDCStructContour(index, file);
 572   }
 573 }
 574 //------------------------------------------------------------------------------
 575
 576
 577 //------------------------------------------------------------------------------
 578 void vvMainWindow::ComputeDeformableRegistration()
 579 {
 580   if (mSlicerManagers.size() > 0) {
 581     int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
 582     vvDeformationDialog dialog(index,mSlicerManagers);
 583     if (dialog.exec()) {
 584       std::string base_name=itksys::SystemTools::GetFilenameWithoutExtension(mSlicerManagers[dialog.GetInputFileIndex()]->GetFileName());
 585       AddField(dialog.GetOutput(),dialog.getFieldFile(),dialog.GetInputFileIndex());
 586       WarpImage(dialog.GetSelectedSlicer(),dialog.GetReferenceFrameIndex());
 587     } else
 588       std::cout << "Error or user cancellation while computing deformation field..." << std::endl;
 589   } else QMessageBox::information(this, "Need to open image","You must open an image first.");
 590 }
 591 //------------------------------------------------------------------------------
 592
 593
 594 //------------------------------------------------------------------------------
 595 void vvMainWindow::WarpImage()
 596 {
 597   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
 598   if (!mSlicerManagers[index]->GetVF().IsNull()) {
 599     bool ok;
 600     int ref = QInputDialog::getInt(this,"Chose reference phase","Reference phase",0,0,\
 601       mSlicerManagers[index]->GetImage()->GetVTKImages().size()-1,1,&ok);
 602     if (ok) {
 603       WarpImage(mSlicerManagers[index],ref);
 604     }
 605   } else
 606     QMessageBox::warning(this,tr("No vector field"),tr("Sorry, can't warp without a vector field"));
 607 }
 608 //------------------------------------------------------------------------------
 609
 610
 611 //------------------------------------------------------------------------------
 612 void vvMainWindow::WarpImage(vvSlicerManager* selected_slicer,int reference_phase)
 613 {
 614   if (!selected_slicer->GetVF().IsNull()) {
 615     QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
 616     QFileInfo info(selected_slicer->GetFileName().c_str());
 617     vvImageWarp warp(selected_slicer->GetImage(),selected_slicer->GetVF(),
 618       reference_phase,this);
 619     if (warp.ComputeWarpedImage()) {
 620       AddImage(warp.GetWarpedImage(),info.path().toStdString()+"/"+info.completeBaseName().toStdString()+"_warped.mhd");
 621       AddImage(warp.GetDiffImage()  ,info.path().toStdString()+"/"+info.completeBaseName().toStdString()+"_diff.mhd");
 622       AddImage(warp.GetJacobianImage()  ,info.path().toStdString()+"/"+info.completeBaseName().toStdString()+"_jacobian.mhd");
 623       QApplication::restoreOverrideCursor();
 624     } else {
 625       QApplication::restoreOverrideCursor();
 626       QMessageBox::warning(this,tr("Different spacings"),tr("The vector field and image spacings must be the same in order to warp."));
 627     }
 628   } else
 629     QMessageBox::warning(this,tr("No vector field"),tr("Sorry, can't warp without a vector field."));
 630 }
 631 //------------------------------------------------------------------------------
 632
 633
 634 //------------------------------------------------------------------------------
 635 vvMainWindow::~vvMainWindow()
 636 {
 637   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
 638     if (mSlicerManagers[i] != NULL)
 639       delete mSlicerManagers[i];
 640   }
 641   delete documentation;
 642   delete help_dialog;
 643   delete dicomSeriesSelector;
 644 }
 645 //------------------------------------------------------------------------------
 646
 647 //------------------------------------------------------------------------------
 648 QTabWidget * vvMainWindow::GetTab()
 649 {
 650   return tabWidget;
 651 }
 652 //------------------------------------------------------------------------------
 653
 654
 655 //------------------------------------------------------------------------------
 656 void vvMainWindow::MergeImages()
 657 {
 658   QString Extensions = EXTENSIONS;
 659   Extensions += ";;All Files (*)";
 660   QStringList files = QFileDialog::getOpenFileNames(this,tr("Merge Images"),mInputPathName,Extensions);
 661   if (files.isEmpty())
 662     return;
 663   mInputPathName = itksys::SystemTools::GetFilenamePath(files[0].toStdString()).c_str();
 664   std::vector<std::string> vector;
 665
 666   unsigned int currentDim = 0;
 667   std::vector<double> currentSpacing;
 668   std::vector<int> currentSize;
 669   std::vector<double> currentOrigin;
 670
 671   for (int i = 0; i < files.size(); i++) {
 672     itk::ImageIOBase::Pointer reader = itk::ImageIOFactory::CreateImageIO(
 673       files[i].toStdString().c_str(), itk::ImageIOFactory::ReadMode);
 674     reader->SetFileName(files[i].toStdString().c_str());
 675     reader->ReadImageInformation();
 676     if (reader)        {
 677       //NOViewWidget->hide();
 678       //NEViewWidget->hide();
 679       //SOViewWidget->hide();
 680       //SEViewWidget->hide();
 681       if (i == 0)
 682         currentDim = reader->GetNumberOfDimensions();
 683       bool IsOk = true;
 684       for (unsigned int j = 0; j < currentDim; j++) {
 685         if (i == 0) {
 686           if (j == 0) {
 687             currentSpacing.resize(currentDim);
 688             currentSize.resize(currentDim);
 689             currentOrigin.resize(currentDim);
 690           }
 691           currentOrigin[j] = reader->GetOrigin(j);
 692           currentSpacing[j] = reader->GetSpacing(j);
 693           currentSize[j] = reader->GetDimensions(j);
 694         } else if (currentDim != reader->GetNumberOfDimensions()
 695           || currentSpacing[j] != reader->GetSpacing(j)
 696           || currentSize[j] != (int)reader->GetDimensions(j)
 697           || currentOrigin[j] != reader->GetOrigin(j)) {
 698             QString error = "Cannot read file (too different from others ";
 699             error += files[i].toStdString().c_str();
 700             QMessageBox::information(this,tr("Reading problem"),error);
 701             IsOk = false;
 702             break;
 703         }
 704       }
 705       if (IsOk)
 706         vector.push_back(files[i].toStdString());
 707     }
 708   }
 709   if (vector.size() > 0)
 710     LoadImages(vector, vvImageReader::MERGED);
 711 }
 712 //------------------------------------------------------------------------------
 713
 714 //------------------------------------------------------------------------------
 715 void vvMainWindow::SliceImages()
 716 {
 717   QString Extensions = EXTENSIONS;
 718   Extensions += ";;All Files (*)";
 719
 720   QStringList files = QFileDialog::getOpenFileNames(this,tr("Slice Images"),mInputPathName,Extensions);
 721   if (files.isEmpty())
 722     return;
 723   mInputPathName = itksys::SystemTools::GetFilenamePath(files[0].toStdString()).c_str();
 724   std::vector<std::string> vector;
 725   for (int i = 0; i < files.size(); i++)
 726     vector.push_back(files[i].toStdString());
 727   LoadImages(vector, vvImageReader::SLICED);
 728 }
 729 //------------------------------------------------------------------------------
 730
 731 //------------------------------------------------------------------------------
 732 void vvMainWindow::MergeImagesWithTime()
 733 {
 734   QString Extensions = EXTENSIONS;
 735   Extensions += ";;All Files (*)";
 736   QStringList files = QFileDialog::getOpenFileNames(this,tr("Merge Images With Time"),mInputPathName,Extensions);
 737   if (files.isEmpty())
 738     return;
 739   mInputPathName = itksys::SystemTools::GetFilenamePath(files[0].toStdString()).c_str();
 740   std::vector<std::string> vector;
 741
 742   for (int i = 0; i < files.size(); i++)
 743     vector.push_back(files[i].toStdString());
 744   sort(vector.begin(),vector.end());
 745   if (vector.size() > 1)
 746     LoadImages(vector, vvImageReader::MERGEDWITHTIME);
 747   else
 748     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.");
 749 }
 750 //------------------------------------------------------------------------------
 751
 752
 753 //------------------------------------------------------------------------------
 754 void vvMainWindow::OpenDicom()
 755 {
 756   std::vector<std::string> files;
 757
 758   //std::cout << "dicomSeriesSelector " << std::endl;
 759   if (dicomSeriesSelector->exec() == QDialog::Accepted) {
 760     files = *(dicomSeriesSelector->GetFilenames());
 761     LoadImages(files, vvImageReader::DICOM);
 762   }
 763 }
 764 //------------------------------------------------------------------------------
 765
 766 //------------------------------------------------------------------------------
 767 void vvMainWindow::OpenImages()
 768 {
 769   QString Extensions = EXTENSIONS;
 770   Extensions += ";;All Files (*)";
 771
 772   QStringList files = QFileDialog::getOpenFileNames(this,tr("Load Images"),mInputPathName,Extensions);
 773   if (files.isEmpty())
 774     return;
 775   mInputPathName = itksys::SystemTools::GetFilenamePath(files[0].toStdString()).c_str();
 776   std::vector<std::string> vector;
 777   for (int i = 0; i < files.size(); i++)
 778     vector.push_back(files[i].toStdString());
 779   LoadImages(vector, vvImageReader::IMAGE);
 780 }
 781 //------------------------------------------------------------------------------
 782 void vvMainWindow::OpenRecentImage()
 783 {
 784   QAction * caller = qobject_cast<QAction*>(sender());
 785   std::vector<std::string> images;
 786   images.push_back(caller->text().toStdString());
 787   mInputPathName = itksys::SystemTools::GetFilenamePath(images[0]).c_str();
 788   LoadImages(images, vvImageReader::IMAGE);
 789 }
 790 //------------------------------------------------------------------------------
 791
 792
 793 //------------------------------------------------------------------------------
 794 void vvMainWindow::OpenImageWithTime()
 795 {
 796   QString Extensions = EXTENSIONS;
 797   Extensions += ";;All Files (*)";
 798
 799   QStringList files = QFileDialog::getOpenFileNames(this,tr("Load Images With Time"),mInputPathName,Extensions);
 800   if (files.isEmpty())
 801     return;
 802   mInputPathName = itksys::SystemTools::GetFilenamePath(files[0].toStdString()).c_str();
 803   std::vector<std::string> vector;
 804   for (int i = 0; i < files.size(); i++) {
 805     vector.push_back(files[i].toStdString());
 806   }
 807   LoadImages(vector, vvImageReader::IMAGEWITHTIME);
 808 }
 809 //------------------------------------------------------------------------------
 810
 811
 812 //------------------------------------------------------------------------------
 813 void vvMainWindow::LoadImages(std::vector<std::string> files, vvImageReader::LoadedImageType filetype)
 814 {
 815   //Separate the way to open images and dicoms
 816   int fileSize;
 817   if (filetype == vvImageReader::IMAGE || filetype == vvImageReader::IMAGEWITHTIME)
 818     fileSize = files.size();
 819   else
 820     fileSize = 1;
 821
 822   // For SLICED, we need the number of slices (ndim and #slices)
 823   std::vector<unsigned int> nSlices;
 824   nSlices.resize(files.size());
 825   std::fill(nSlices.begin(), nSlices.end(), 1);
 826   if (filetype == vvImageReader::SLICED) {
 827     for (int i = 0; i < fileSize; i++) {
 828       itk::ImageIOBase::Pointer header = clitk::readImageHeader(files[i]);
 829       QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
 830       if (!header) {
 831         nSlices[i] = 0;
 832         QString error = "Cannot open file \n";
 833         error += files[i].c_str();
 834         QMessageBox::information(this,tr("Reading problem"),error);
 835         return;
 836       }
 837       if (header->GetNumberOfDimensions() < 3) {
 838         nSlices[i] = 0;
 839         QString error = "Dimension problem. Cannot slice \n";
 840         error += files[i].c_str();
 841         QMessageBox::information(this,tr("Reading problem"),error);
 842         return;
 843       }
 844       nSlices[i] = header->GetDimensions( header->GetNumberOfDimensions()-1 );
 845     }
 846   }
 847
 848   //Only add to the list of recently opened files when a single file is opened,
 849   //to avoid polluting the list of recently opened files
 850   if (files.size() == 1) {
 851     QFileInfo finfo=tr(files[0].c_str());
 852     AddToRecentlyOpenedImages(finfo.absoluteFilePath().toStdString());
 853     updateRecentlyOpenedFilesMenu(GetRecentlyOpenedImages());
 854   }
 855   //init the progress events
 856   QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
 857   vvProgressDialog progress("Opening " + files[0],fileSize>1);
 858   qApp->processEvents();
 859
 860   int numberofsuccesulreads=0;
 861   //open images as 1 or multiples
 862   for (int i = 0; i < fileSize; i++) {
 863     progress.SetText("Opening " + files[i]);
 864     progress.SetProgress(i,fileSize);
 865     qApp->processEvents();
 866
 867     for (unsigned int j = 0; j < nSlices[i]; j++) {
 868       //read the image and put it in mSlicerManagers
 869       vvSlicerManager* imageManager = new vvSlicerManager(4);
 870       qApp->processEvents();
 871
 872       bool SetImageSucceed=false;
 873
 874       // Change filename if an image with the same already exist
 875       int number = GetImageDuplicateFilenameNumber(files[i] + std::string("_slice"));
 876
 877       if (filetype == vvImageReader::IMAGE || filetype == vvImageReader::IMAGEWITHTIME || filetype == vvImageReader::SLICED) {
 878         SetImageSucceed = imageManager->SetImage(files[i],filetype, number, j);
 879       } else {
 880         SetImageSucceed = imageManager->SetImages(files,filetype, number);
 881       }
 882       if (!SetImageSucceed) {
 883         QApplication::restoreOverrideCursor();
 884         QString error = "Cannot open file \n";
 885         error += imageManager->GetLastError().c_str();
 886         QMessageBox::information(this,tr("Reading problem"),error);
 887         delete imageManager;
 888       } else {
 889
 890         mSlicerManagers.push_back(imageManager);
 891
 892         //create an item in the tree with good settings
 893         QTreeWidgetItem *item = new QTreeWidgetItem();
 894         item->setData(0,Qt::UserRole,files[i].c_str());
 895         QFileInfo fileinfo(imageManager->GetFileName().c_str()); //Do not show the path
 896         item->setData(COLUMN_IMAGE_NAME,Qt::DisplayRole,fileinfo.fileName());
 897         item->setData(1,Qt::UserRole,tr("image"));
 898         item->setToolTip(COLUMN_IMAGE_NAME, imageManager->GetListOfAbsoluteFilePathInOneString("image").c_str());
 899         qApp->processEvents();
 900
 901         //Create the buttons for reload and close
 902         qApp->processEvents();
 903         QTreePushButton* cButton = new QTreePushButton;
 904         cButton->setItem(item);
 905         cButton->setColumn(COLUMN_CLOSE_IMAGE);
 906         cButton->setToolTip(tr("close image"));
 907         cButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/exit.png")));
 908         connect(cButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
 909           this,SLOT(CloseImage(QTreeWidgetItem*, int)));
 910
 911         QTreePushButton* rButton = new QTreePushButton;
 912         rButton->setItem(item);
 913         rButton->setColumn(COLUMN_RELOAD_IMAGE);
 914         rButton->setToolTip(tr("reload image"));
 915         rButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/rotateright.png")));
 916         connect(rButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
 917           this,SLOT(ReloadImage(QTreeWidgetItem*, int)));
 918
 919         DataTree->addTopLevelItem(item);
 920         DataTree->setItemWidget(item, COLUMN_CLOSE_IMAGE, cButton);
 921         DataTree->setItemWidget(item, COLUMN_RELOAD_IMAGE, rButton);
 922
 923         //set the id of the image
 924         QString id = QDir::current().absoluteFilePath(files[i].c_str()) + QString::number(mSlicerManagers.size()-1);
 925         item->setData(COLUMN_IMAGE_NAME,Qt::UserRole,id.toStdString().c_str());
 926         mSlicerManagers.back()->SetId(id.toStdString());
 927
 928         linkPanel->addImage(imageManager->GetFileName(), id.toStdString());
 929
 930         connect(mSlicerManagers.back(), SIGNAL(currentImageChanged(std::string)),
 931           this,SLOT(CurrentImageChanged(std::string)));
 932         connect(mSlicerManagers.back(), SIGNAL(currentPickedImageChanged(std::string)),
 933           this, SLOT(CurrentPickedImageChanged(std::string)));
 934         connect(mSlicerManagers.back(), SIGNAL(UpdatePosition(int, double, double, double, double, double, double, double)),
 935           this,SLOT(MousePositionChanged(int,double, double, double, double, double, double, double)));
 936         connect(mSlicerManagers.back(), SIGNAL(UpdateVector(int, double, double, double, double)),
 937           this, SLOT(VectorChanged(int,double,double,double, double)));
 938         connect(mSlicerManagers.back(), SIGNAL(UpdateOverlay(int, double, double)),
 939           this, SLOT(OverlayChanged(int,double,double)));
 940         connect(mSlicerManagers.back(), SIGNAL(UpdateFusion(int, double)),
 941           this, SLOT(FusionChanged(int,double)));
 942         connect(mSlicerManagers.back(), SIGNAL(WindowLevelChanged()),
 943           this,SLOT(WindowLevelChanged()));
 944         connect(mSlicerManagers.back(), SIGNAL(UpdateSlice(int,int)),
 945           this,SLOT(UpdateSlice(int,int)));
 946         connect(mSlicerManagers.back(), SIGNAL(UpdateTSlice(int, int, int)),
 947           this,SLOT(UpdateTSlice(int, int, int)));
 948         connect(mSlicerManagers.back(), SIGNAL(UpdateTSlice(int, int, int)),
 949           this,SLOT(ImageInfoChanged()));
 950         connect(mSlicerManagers.back(), SIGNAL(UpdateSliceRange(int,int,int,int,int)),
 951           this,SLOT(UpdateSliceRange(int,int,int,int,int)));
 952         connect(mSlicerManagers.back(), SIGNAL(UpdateLinkManager(std::string,int,double,double,double,int)),
 953           this,SLOT(UpdateLinkManager(std::string,int,double,double,double,int)));
 954         connect(mSlicerManagers.back(), SIGNAL(UpdateLinkedNavigation(std::string,vvSlicerManager*,vvSlicer*)),
 955           this,SLOT(UpdateLinkedNavigation(std::string,vvSlicerManager*,vvSlicer*)));
 956         connect(mSlicerManagers.back(), SIGNAL(ChangeImageWithIndexOffset(vvSlicerManager*,int,int)),
 957           this,SLOT(ChangeImageWithIndexOffset(vvSlicerManager*,int,int)));
 958         connect(mSlicerManagers.back(),SIGNAL(LandmarkAdded()),landmarksPanel,SLOT(AddPoint()));
 959         InitSlicers();
 960         numberofsuccesulreads++;
 961       }
 962     }
 963   }
 964
 965   if (numberofsuccesulreads) {
 966     NOViewWidget->show();
 967     NEViewWidget->show();
 968     SOViewWidget->show();
 969     SEViewWidget->show();
 970     UpdateTree();
 971     InitDisplay();
 972     ShowLastImage();
 973
 974     // Try to guess default WindowLevel
 975     double range[2];
 976     mSlicerManagers.back()->GetImage()->GetFirstVTKImageData()->GetScalarRange(range);
 977     if ((range[0] == 0) && (range[1] == 1)) {
 978       presetComboBox->setCurrentIndex(WL_BINARY);// binary
 979     } else {
 980       // TODO
 981     }
 982   }
 983   QApplication::restoreOverrideCursor();
 984 }
 985 //------------------------------------------------------------------------------
 986
 987 //------------------------------------------------------------------------------
 988 void vvMainWindow::UpdateTree()
 989 {
 990   DataTree->resizeColumnToContents(COLUMN_TREE);
 991   DataTree->resizeColumnToContents(COLUMN_UL_VIEW);
 992   DataTree->resizeColumnToContents(COLUMN_UR_VIEW);
 993   DataTree->resizeColumnToContents(COLUMN_DL_VIEW);
 994   DataTree->resizeColumnToContents(COLUMN_DR_VIEW);
 995   DataTree->resizeColumnToContents(COLUMN_IMAGE_NAME);
 996   DataTree->resizeColumnToContents(COLUMN_CLOSE_IMAGE);
 997   DataTree->resizeColumnToContents(COLUMN_RELOAD_IMAGE);
 998 }
 999 //------------------------------------------------------------------------------
1000
1001 //------------------------------------------------------------------------------
1002 void vvMainWindow::CurrentImageChanged(std::string id)
1003 {
1004   if (id == mCurrentSelectedImageId) return; // Do nothing
1005   int selected = 0;
1006   for (int i = 0; i < DataTree->topLevelItemCount(); i++) {
1007     if (DataTree->topLevelItem(i)->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString().toStdString() == id) {
1008       selected = i;
1009     } else {
1010       DataTree->topLevelItem(i)->setSelected(0);
1011     }
1012     for (int child = 0; child < DataTree->topLevelItem(i)->childCount(); child++)
1013       DataTree->topLevelItem(i)->child(child)->setSelected(0);
1014
1015   }
1016   DataTree->topLevelItem(selected)->setSelected(1);
1017   mCurrentSelectedImageId = id;
1018
1019   landmarksPanel->SetCurrentLandmarks(mSlicerManagers[selected]->GetLandmarks(),
1020                                       mSlicerManagers[selected]->GetTSlice());
1021   landmarksPanel->SetCurrentPath(mInputPathName.toStdString());
1022   landmarksPanel->SetCurrentImage(mSlicerManagers[selected]->GetFileName().c_str());
1023
1024   emit SelectedImageHasChanged(mSlicerManagers[selected]);
1025 }
1026 //------------------------------------------------------------------------------
1027
1028 //------------------------------------------------------------------------------
1029 void vvMainWindow::CurrentPickedImageChanged(std::string id)
1030 {
1031   if (id == mCurrentPickedImageId) return; // Do nothing
1032   int selected = 0;
1033   for (int i = 0; i < DataTree->topLevelItemCount(); i++) {
1034     if (DataTree->topLevelItem(i)->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString().toStdString() == id) {
1035       selected = i;
1036     } else {
1037       DataTree->topLevelItem(i)->setSelected(0);
1038     }
1039     for (int child = 0; child < DataTree->topLevelItem(i)->childCount(); child++)
1040       DataTree->topLevelItem(i)->child(child)->setSelected(0);
1041
1042   }
1043   DataTree->topLevelItem(selected)->setSelected(1);
1044   mCurrentPickedImageId = id;
1045   mCurrentPickedImageIndex = selected;
1046 }
1047 //------------------------------------------------------------------------------
1048
1049 //------------------------------------------------------------------------------
1050 void vvMainWindow::ImageInfoChanged()
1051 {
1052   contextActions[6]->setEnabled(1);
1053   contextActions[5]->setEnabled(1);
1054   actionSave_As->setEnabled(1);
1055   actionAdd_VF_to_current_Image->setEnabled(1);
1056   actionAdd_fusion_image->setEnabled(1);
1057   actionAdd_overlay_image_to_current_image->setEnabled(1);
1058   actionAdd_USSequence_toCT->setEnabled(1);
1059   actionNorth_East_Window->setEnabled(1);
1060   actionNorth_West_Window->setEnabled(1);
1061   actionSouth_East_Window->setEnabled(1);
1062   actionSouth_West_Window->setEnabled(1);
1063   vvToolManager::GetInstance()->EnableToolsInMenu(this, true);
1064   inverseButton->setEnabled(1);
1065
1066   goToCursorPushButton->setEnabled(1);
1067
1068   if (DataTree->selectedItems().size()) {
1069     int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1070
1071     colorMapComboBox->setEnabled(1);
1072     for (int i = 0; i < DataTree->topLevelItem(index)->childCount(); i++) {
1073       if (DataTree->topLevelItem(index)->child(i)->data(1,Qt::UserRole).toString() == "overlay" ||
1074         DataTree->topLevelItem(index)->child(i)->data(1,Qt::UserRole).toString() == "fusion" ||
1075         DataTree->topLevelItem(index)->child(i)->data(1,Qt::UserRole).toString() == "fusionSequence") {
1076           colorMapComboBox->setEnabled(0);
1077           break;
1078       }
1079     }
1080
1081     std::vector<double> origin;
1082     std::vector<double> inputSpacing;
1083     std::vector<int> inputSize;
1084     std::vector<double> sizeMM;
1085     vtkSmartPointer<vtkMatrix4x4> transformation;
1086     int dimension=0;
1087     QString pixelType;
1088     QString inputSizeInBytes;
1089     QString image = DataTree->selectedItems()[0]->data(COLUMN_IMAGE_NAME,Qt::DisplayRole).toString();
1090
1091     int nframes = mSlicerManagers[index]->GetSlicer(0)->GetTMax();
1092
1093     if (nframes > 1 || playMode == 1) {
1094       playButton->setEnabled(1);
1095       frameRateLabel->setEnabled(1);
1096       frameRateSpinBox->setEnabled(1);
1097     } else {
1098       playButton->setEnabled(0);
1099       frameRateLabel->setEnabled(0);
1100       frameRateSpinBox->setEnabled(0);
1101     }
1102
1103     //read image header
1104     int NPixel = 1;
1105
1106     int tSlice = 0;
1107     vvImage::Pointer imageSelected;
1108     if (DataTree->topLevelItem(index) == DataTree->selectedItems()[0]) {
1109       imageSelected = mSlicerManagers[index]->GetSlicer(0)->GetImage();
1110       tSlice = mSlicerManagers[index]->GetSlicer(0)->GetTSlice();
1111     } else if (DataTree->selectedItems()[0]->data(1,Qt::UserRole).toString() == "vector") {
1112       imageSelected = mSlicerManagers[index]->GetSlicer(0)->GetVF();
1113       tSlice = mSlicerManagers[index]->GetSlicer(0)->GetOverlayTSlice();
1114     } else if (DataTree->selectedItems()[0]->data(1,Qt::UserRole).toString() == "overlay") {
1115       imageSelected = mSlicerManagers[index]->GetSlicer(0)->GetOverlay();
1116       tSlice = mSlicerManagers[index]->GetSlicer(0)->GetOverlayTSlice();
1117     } else if (DataTree->selectedItems()[0]->data(1,Qt::UserRole).toString() == "fusion") {
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() == "fusionSequence") {
1122       imageSelected = mSlicerManagers[index]->GetSlicer(0)->GetFusion();
1123       tSlice = mSlicerManagers[index]->GetSlicer(0)->GetFusionTSlice();
1124     }
1125     else if (DataTree->selectedItems()[0]->data(1,Qt::UserRole).toString() == "contour") {
1126       imageSelected = mSlicerManagers[index]->GetSlicer(0)->GetImage();
1127       tSlice = mSlicerManagers[index]->GetSlicer(0)->GetTSlice();
1128     }
1129     else {
1130       imageSelected = mSlicerManagers[index]->GetSlicer(0)->GetImage();
1131       tSlice = mSlicerManagers[index]->GetSlicer(0)->GetTSlice();
1132     }
1133
1134     dimension = imageSelected->GetNumberOfDimensions();
1135     origin.resize(dimension);
1136     inputSpacing.resize(dimension);
1137     inputSize.resize(dimension);
1138     sizeMM.resize(dimension);
1139     pixelType = mSlicerManagers[index]->GetImage()->GetScalarTypeAsITKString().c_str();
1140     for (int i = 0; i < dimension; i++) {
1141       origin[i] = imageSelected->GetOrigin()[i];
1142       inputSpacing[i] = imageSelected->GetSpacing()[i];
1143       inputSize[i] = imageSelected->GetSize()[i];
1144       sizeMM[i] = inputSize[i]*inputSpacing[i];
1145       NPixel *= inputSize[i];
1146     }
1147     inputSizeInBytes = GetSizeInBytes(imageSelected->GetActualMemorySize()*1000);
1148
1149     QString dim = QString::number(dimension) + " (";
1150     dim += pixelType + ")";
1151
1152     infoPanel->setFileName(image);
1153     std::string creationImageTimeValue("No creation time");
1154     itk::ExposeMetaData< std::string > (*imageSelected->GetFirstMetaDataDictionary(), "creationImageTime", creationImageTimeValue);
1155     infoPanel->setImageCreationTime(QString(creationImageTimeValue.c_str()));
1156     infoPanel->setDimension(dim);
1157     infoPanel->setSizePixel(GetVectorIntAsString(inputSize));
1158     infoPanel->setSizeMM(GetVectorDoubleAsString(sizeMM));
1159     infoPanel->setOrigin(GetVectorDoubleAsString(origin));
1160     infoPanel->setSpacing(GetVectorDoubleAsString(inputSpacing));
1161     infoPanel->setNPixel(QString::number(NPixel)+" ("+inputSizeInBytes+")");
1162
1163     transformation = imageSelected->GetTransform()[tSlice]->GetMatrix();
1164     infoPanel->setTransformation(clitk::Get4x4MatrixDoubleAsString(transformation).c_str());
1165
1166     landmarksPanel->SetCurrentLandmarks(mSlicerManagers[index]->GetLandmarks(),
1167                                         mSlicerManagers[index]->GetTSlice());
1168     landmarksPanel->SetCurrentPath(mInputPathName.toStdString());
1169     landmarksPanel->SetCurrentImage(mSlicerManagers[index]->GetFileName().c_str());
1170
1171     overlayPanel->getCurrentImageName(mSlicerManagers[index]->GetFileName().c_str());
1172     for (int i = 0; i < 4; i++) {
1173       if (DataTree->selectedItems()[0]->data(i+1,Qt::CheckStateRole).toInt() > 0 || i == 3) {
1174         mSlicerManagers[index]->UpdateInfoOnCursorPosition(i);
1175         break;
1176       }
1177     }
1178
1179 //     infoPanel->setFileName(image);
1180 //     infoPanel->setDimension(dim);
1181 //     infoPanel->setSizePixel(GetVectorIntAsString(inputSize));
1182 //     infoPanel->setSizeMM(GetVectorDoubleAsString(sizeMM));
1183 //     infoPanel->setOrigin(GetVectorDoubleAsString(origin));
1184 //     infoPanel->setSpacing(GetVectorDoubleAsString(inputSpacing));
1185 //     infoPanel->setNPixel(QString::number(NPixel)+" ("+inputSizeInBytes+")");
1186 //
1187 //     landmarksPanel->SetCurrentLandmarks(mSlicerManagers[index]->GetLandmarks(),
1188 //                                         mSlicerManagers[index]->GetTSlice());
1189 //     landmarksPanel->SetCurrentPath(mInputPathName.toStdString());
1190 //     landmarksPanel->SetCurrentImage(mSlicerManagers[index]->GetFileName().c_str());
1191 //
1192 //     overlayPanel->getCurrentImageName(mSlicerManagers[index]->GetFileName().c_str());
1193 //     for (int i = 0; i < 4; i++) {
1194 //       if (DataTree->selectedItems()[0]->data(i+1,Qt::CheckStateRole).toInt() > 0 || i == 3) {
1195 //         mSlicerManagers[index]->UpdateInfoOnCursorPosition(i);
1196 //         break;
1197 //       }
1198 //     }
1199     WindowLevelChanged();
1200
1201     slicingPresetComboBox->setCurrentIndex(mSlicerManagers[index]->GetSlicingPreset());
1202
1203     if (mSlicerManagers[index]->GetSlicer(0)->GetVF()) {
1204       overlayPanel->getVFName(mSlicerManagers[index]->GetVFName().c_str());
1205       overlayPanel->getVFProperty(mSlicerManagers[index]->GetSlicer(0)->GetVFSubSampling(),
1206         mSlicerManagers[index]->GetSlicer(0)->GetVFScale(),
1207         mSlicerManagers[index]->GetSlicer(0)->GetVFLog());
1208     } else {
1209       overlayPanel->getVFName(mSlicerManagers[index]->GetVFName().c_str());
1210       overlayPanel->getVFProperty(-1,-1,-1);
1211     }
1212     if (mSlicerManagers[index]->GetSlicer(0)->GetOverlay()) {
1213       overlayPanel->getOverlayName(mSlicerManagers[index]->GetOverlayName().c_str());
1214     } else {
1215       overlayPanel->getOverlayName(mSlicerManagers[index]->GetOverlayName().c_str());
1216     }
1217
1218     if (mSlicerManagers[index]->GetSlicer(0)->GetFusion()) {
1219       overlayPanel->getFusionName(mSlicerManagers[index]->GetFusionName().c_str());
1220     } else {
1221       overlayPanel->getFusionName(mSlicerManagers[index]->GetFusionName().c_str());
1222     }
1223   }
1224 }
1225 //------------------------------------------------------------------------------
1226
1227 //------------------------------------------------------------------------------
1228 void vvMainWindow::ShowDocumentation()
1229 {
1230   documentation->show();
1231 }
1232 //------------------------------------------------------------------------------
1233
1234 //------------------------------------------------------------------------------
1235 void vvMainWindow::PopupRegisterForm(bool checkCanPush)
1236 {
1237   vvRegisterForm* registerForm = new vvRegisterForm(QUrl("http://www.creatis.insa-lyon.fr/~dsarrut/vvregister/write.php"), getVVSettingsPath(), getSettingsOptionFormat());
1238   if(!checkCanPush) {
1239     registerForm->show();
1240   } else {
1241     if(registerForm->canPush()) {
1242       registerForm->show();
1243       registerForm->acquitPushed();//too bad if there is not internet connection anymore.
1244     }
1245   }
1246 }
1247 //------------------------------------------------------------------------------
1248
1249 //------------------------------------------------------------------------------
1250 void vvMainWindow::ShowHelpDialog()
1251 {
1252   help_dialog->show();
1253 }
1254 //------------------------------------------------------------------------------
1255
1256 //------------------------------------------------------------------------------
1257 void vvMainWindow::ChangeViewMode()
1258 {
1259   typedef struct _SIZE{
1260     QSplitter* splitter;
1261     QList<int> size1, size2;
1262     int cols[3];
1263   }SplitterSize;
1264   SplitterSize sizes[4];
1265   sizes[0].splitter = OSplitter;
1266   sizes[0].size1.push_back(1);
1267   sizes[0].size1.push_back(0);
1268   sizes[0].size2.push_back(1);
1269   sizes[0].size2.push_back(0);
1270   sizes[0].cols[0] = 2;
1271   sizes[0].cols[1] = 3;
1272   sizes[0].cols[2] = 4;
1273
1274   sizes[1].splitter = ESplitter;
1275   sizes[1].size1.push_back(0);
1276   sizes[1].size1.push_back(1);
1277   sizes[1].size2.push_back(1);
1278   sizes[1].size2.push_back(0);
1279   sizes[1].cols[0] = 1;
1280   sizes[1].cols[1] = 3;
1281   sizes[1].cols[2] = 4;
1282
1283   sizes[2].splitter = OSplitter;
1284   sizes[2].size1.push_back(1);
1285   sizes[2].size1.push_back(0);
1286   sizes[2].size2.push_back(0);
1287   sizes[2].size2.push_back(1);
1288   sizes[2].cols[0] = 1;
1289   sizes[2].cols[1] = 2;
1290   sizes[2].cols[2] = 4;
1291
1292   sizes[3].splitter = ESplitter;
1293   sizes[3].size1.push_back(0);
1294   sizes[3].size1.push_back(1);
1295   sizes[3].size2.push_back(0);
1296   sizes[3].size2.push_back(1);
1297   sizes[3].cols[0] = 1;
1298   sizes[3].cols[1] = 2;
1299   sizes[3].cols[2] = 3;
1300
1301   int slicer = mSlicerManagers[mCurrentPickedImageIndex]->GetSelectedSlicer();
1302   if (viewMode == 1) {
1303     if (slicer >= 0) {
1304       viewMode = 0;
1305       splitter_3->setSizes(sizes[slicer].size1);
1306       sizes[slicer].splitter->setSizes(sizes[slicer].size2);
1307       DataTree->setColumnHidden(sizes[slicer].cols[0],1);
1308       DataTree->setColumnHidden(sizes[slicer].cols[1],1);
1309       DataTree->setColumnHidden(sizes[slicer].cols[2],1);
1310     }
1311   } else {
1312     QList<int> size;
1313     if (slicer >= 0) {
1314       viewMode = 1;
1315       size.push_back(1);
1316       size.push_back(1);
1317       splitter_3->setSizes(size);
1318       sizes[slicer].splitter->setSizes(size);
1319       DataTree->setColumnHidden(sizes[slicer].cols[0],0);
1320       DataTree->setColumnHidden(sizes[slicer].cols[1],0);
1321       DataTree->setColumnHidden(sizes[slicer].cols[2],0);
1322     }
1323   }
1324   UpdateRenderWindows();
1325   /*
1326   ** I don't know why but for both resized QVTKWidget we also need to render
1327   ** the associated Slicer to redraw crosses.
1328   */
1329   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
1330     //     if (DataTree->topLevelItem(i)->data(COLUMN_UL_VIEW,Qt::CheckStateRole).toInt() > 1)
1331     mSlicerManagers[i]->GetSlicer(0)->Render();
1332     mSlicerManagers[i]->GetSlicer(1)->Render();
1333     //     if (DataTree->topLevelItem(i)->data(COLUMN_DL_VIEW,Qt::CheckStateRole).toInt() > 1)
1334     mSlicerManagers[i]->GetSlicer(2)->Render();
1335     mSlicerManagers[i]->GetSlicer(3)->Render();
1336   }
1337 }
1338 //------------------------------------------------------------------------------
1339
1340 //------------------------------------------------------------------------------
1341 QString vvMainWindow::GetSizeInBytes(unsigned long size)
1342 {
1343   QString result = "";// QString::number(size);
1344   //result += " bytes (";
1345   if (size > 1000000000) {
1346     size /= 1000000000;
1347     result += QString::number(size);
1348     result += "Gb";//)";
1349   } else if (size > 1000000) {
1350     size /= 1000000;
1351     result += QString::number(size);
1352     result += "Mb";//)";
1353   } else if (size > 1000) {
1354     size /= 1000;
1355     result += QString::number(size);
1356     result += "kb";//)";
1357   }
1358   return result;
1359 }
1360 //------------------------------------------------------------------------------
1361
1362 //------------------------------------------------------------------------------
1363 QString vvMainWindow::GetVectorDoubleAsString(std::vector<double> vectorDouble)
1364 {
1365   QString result;
1366   for (unsigned int i= 0; i < vectorDouble.size(); i++) {
1367     if (i != 0)
1368       result += " ";
1369     result += QString::number(vectorDouble[i]);
1370   }
1371   return result;
1372 }
1373 //------------------------------------------------------------------------------
1374
1375 //------------------------------------------------------------------------------
1376 QString vvMainWindow::GetVectorIntAsString(std::vector<int> vectorInt)
1377 {
1378   QString result;
1379   for (unsigned int i= 0; i < vectorInt.size(); i++) {
1380     if (i != 0)
1381       result += " ";
1382     result += QString::number(vectorInt[i]);
1383   }
1384   return result;
1385 }
1386 //------------------------------------------------------------------------------
1387
1388 //------------------------------------------------------------------------------
1389 //this actually returns the SlicerManager index!
1390 int vvMainWindow::GetSlicerIndexFromItem(QTreeWidgetItem* item)
1391 {
1392   QString id = item->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString();
1393   for (int i = 0; i < DataTree->topLevelItemCount(); i++) {
1394     if (DataTree->topLevelItem(i)->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString() == id)
1395       return i;
1396   }
1397   return -1;
1398 }
1399 //------------------------------------------------------------------------------
1400
1401 //------------------------------------------------------------------------------
1402 QTreeWidgetItem* vvMainWindow::GetItemFromSlicerManager(vvSlicerManager* sm)
1403 {
1404   QString id = sm->GetId().c_str();
1405   for (int i = 0; i < DataTree->topLevelItemCount(); i++) {
1406     if (DataTree->topLevelItem(i)->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString() == id)
1407       return DataTree->topLevelItem(i);
1408   }
1409   return NULL;
1410 }
1411 //------------------------------------------------------------------------------
1412
1413 //------------------------------------------------------------------------------
1414 void vvMainWindow::DisplayChanged(QTreeWidgetItem *clickedItem, int column)
1415 {
1416   if ( column >= COLUMN_CLOSE_IMAGE || column <= 0)
1417     return;
1418
1419   // Get parent information (might be the same item)
1420   int slicerManagerIndex = GetSlicerIndexFromItem(clickedItem);
1421   QTreeWidgetItem* clickedParentItem = DataTree->topLevelItem(slicerManagerIndex);
1422   vvSlicer* clickedSlicer = mSlicerManagers[slicerManagerIndex]->GetSlicer(column-1);
1423
1424   // Go over the complete item tree (only 2 levels, parents and children)
1425   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
1426     // Trick to avoid redoing twice the job for a key (sr)
1427     mSlicerManagers[i]->GetSlicer(column-1)->GetRenderWindow()->GetInteractor()->SetKeySym("Crap");
1428
1429     QTreeWidgetItem* currentParentItem = DataTree->topLevelItem(i);
1430     if(currentParentItem != clickedParentItem) {
1431       // Not the branch of the clicked item, uncheck all
1432
1433       // Parent
1434       currentParentItem->setData(column,Qt::CheckStateRole, 0);
1435       mSlicerManagers[i]->UpdateSlicer(column-1, false);
1436
1437       // Children
1438       for (int iChild = 0; iChild < currentParentItem->childCount(); iChild++) {
1439         currentParentItem->child(iChild)->setData(column,Qt::CheckStateRole, 0);
1440       }
1441     }
1442     else {
1443       // Branch of the clicked one: get check status from actor visibility in slicer
1444       // and toggle the clicked one
1445
1446       // Parent
1447       bool vis = clickedSlicer->GetActorVisibility("image", 0);
1448       bool draw = clickedSlicer->GetRenderer()->GetDraw();
1449
1450       // Update slicer (after getting visibility)
1451       mSlicerManagers[slicerManagerIndex]->UpdateSlicer(column-1, true);
1452       mSlicerManagers[slicerManagerIndex]->UpdateInfoOnCursorPosition(column-1);
1453       DisplaySliders(slicerManagerIndex, column-1);
1454       if(clickedParentItem == clickedItem) {
1455         // Toggle
1456         vis = !draw || !vis;
1457       }
1458       clickedSlicer->SetActorVisibility("image", 0, vis);
1459       clickedParentItem->setData(column, Qt::CheckStateRole, vis?2:0);
1460
1461       // Children
1462       std::map<std::string, int> actorTypeCounts;
1463       for (int iChild = 0; iChild < clickedParentItem->childCount(); iChild++) {
1464         QTreeWidgetItem* currentChildItem = clickedParentItem->child(iChild);
1465         std::string actorType = currentChildItem->data(1,Qt::UserRole).toString().toStdString();
1466         vis = clickedSlicer->GetActorVisibility(actorType, actorTypeCounts[actorType]);
1467         if(currentChildItem == clickedItem) {
1468           // Toggle or force visibility if it was not on this branch so far
1469           vis = !draw || !vis;
1470           clickedSlicer->SetActorVisibility(actorType, actorTypeCounts[actorType], vis);
1471         }
1472         currentChildItem->setData(column, Qt::CheckStateRole, vis?2:0);
1473         actorTypeCounts[actorType]++;
1474       }
1475     }
1476   }
1477
1478   clickedSlicer->Render();
1479 }
1480 //------------------------------------------------------------------------------
1481
1482 void vvMainWindow::InitSlicers()
1483 {
1484   if (mSlicerManagers.size()) {
1485     mSlicerManagers.back()->GenerateDefaultLookupTable();
1486     mSlicerManagers.back()->SetSlicerWindow(0,NOViewWidget->GetRenderWindow());
1487     mSlicerManagers.back()->SetSlicerWindow(1,NEViewWidget->GetRenderWindow());
1488     mSlicerManagers.back()->SetSlicerWindow(2,SOViewWidget->GetRenderWindow());
1489     mSlicerManagers.back()->SetSlicerWindow(3,SEViewWidget->GetRenderWindow());
1490 #if VTK_MAJOR_VERSION <= 5
1491     mSlicerManagers.back()->Render(); // SR: displayed #slice is wrong without this / TB: With VTK6 and multiple images, all slicers are updated, not only the first
1492 #endif
1493   }
1494 }
1495
1496 //------------------------------------------------------------------------------
1497 void vvMainWindow::InitDisplay()
1498 {
1499   if (mSlicerManagers.size()) {
1500     //BE CAREFUL : this is absolutely necessary to set the interactor style
1501     //in order to have the same style instanciation for all SlicerManagers in
1502     // a same window
1503     for (int j = 0; j < 4; j++) {
1504       vvInteractorStyleNavigator* style = vvInteractorStyleNavigator::New();
1505       style->SetAutoAdjustCameraClippingRange(1);
1506       bool AlreadySelected = false;
1507       for (int i = 0; i < DataTree->topLevelItemCount(); i++) {
1508         mSlicerManagers[i]->SetInteractorStyleNavigator(j,style);
1509         //select the image only if previous are not selected
1510         if (DataTree->topLevelItem(i)->data(j+1,Qt::CheckStateRole).toInt() > 1) {
1511           mSlicerManagers[i]->UpdateSlicer(j,1);
1512           AlreadySelected = true;
1513         } else if (i == DataTree->topLevelItemCount()-1 && !AlreadySelected) {
1514           if (DataTree->selectedItems().size() == 0) {
1515             DataTree->topLevelItem(i)->setSelected(1);
1516           }
1517           DataTree->topLevelItem(i)->setData(j+1,Qt::CheckStateRole,2);
1518           mSlicerManagers[i]->UpdateSlicer(j,1);
1519           DisplaySliders(i,j);
1520         } else {
1521           DataTree->topLevelItem(i)->setData(j+1,Qt::CheckStateRole,0);
1522           mSlicerManagers[i]->UpdateSlicer(j,0);
1523         }
1524       }
1525       style->Delete();
1526     }
1527   }
1528 }
1529 //------------------------------------------------------------------------------
1530
1531 //------------------------------------------------------------------------------
1532 void vvMainWindow::DisplaySliders(int slicer, int window)
1533 {
1534   if(!mSlicerManagers[slicer]->GetSlicer(window)->GetRenderer()->GetDraw())
1535     return;
1536
1537   int range[2];
1538   mSlicerManagers[slicer]->GetSlicer(window)->GetSliceRange(range);
1539   int position = mSlicerManagers[slicer]->GetSlicer(window)->GetSlice();
1540   if (range[1]>0)
1541     verticalSliders[window]->show();
1542   else
1543     verticalSliders[window]->hide();
1544   verticalSliders[window]->setRange(range[0],range[1]);
1545   verticalSliders[window]->setValue(position);
1546
1547   int tRange[2];
1548   tRange[0] = 0;
1549   tRange[1] = mSlicerManagers[slicer]->GetSlicer(window)->GetTMax();
1550   if (tRange[1]>0)
1551     horizontalSliders[window]->show();
1552   else
1553     horizontalSliders[window]->hide();
1554   horizontalSliders[window]->setRange(tRange[0],tRange[1]);
1555   int tPosition = mSlicerManagers[slicer]->GetSlicer(window)->GetMaxCurrentTSlice();
1556   horizontalSliders[window]->setValue(tPosition);
1557 }
1558 //------------------------------------------------------------------------------
1559
1560 //------------------------------------------------------------------------------
1561 void vvMainWindow::CloseImage(QTreeWidgetItem* item, int column)
1562 {
1563   int index = GetSlicerIndexFromItem(item);
1564
1565   if (DataTree->topLevelItem(index) != item) {
1566     QString warning = "Do you really want to close the overlay : ";
1567     warning += item->data(COLUMN_IMAGE_NAME,Qt::DisplayRole).toString();
1568     QMessageBox msgBox(QMessageBox::Warning, tr("Close Overlay"),
1569       warning, 0, this);
1570     msgBox.addButton(tr("Close"), QMessageBox::AcceptRole);
1571     msgBox.addButton(tr("Cancel"), QMessageBox::RejectRole);
1572     if (msgBox.exec() == QMessageBox::AcceptRole) {
1573       std::string overlay_type=item->data(1,Qt::UserRole).toString().toStdString();
1574       int overlay_index=0;
1575       for (int child = 0; child < DataTree->topLevelItem(index)->childCount(); child++) {
1576         if (DataTree->topLevelItem(index)->\
1577           child(child)->data(1,Qt::UserRole).toString().toStdString() == overlay_type)
1578           overlay_index++;
1579         if (DataTree->topLevelItem(index)->child(child) == item) break;
1580       }
1581       if (overlay_type=="fusionSequence") {
1582         //removing the overlay sequence in a fusion sequence visualization mode
1583         //reset the transforms
1584         overlayPanel->getFusionSequenceProperty(-1, false, 0, false);
1585
1586         //unlink and untie the slicer managers
1587         RemoveLink(mSlicerManagers[index]->GetId().c_str(), mSlicerManagers[mSlicerManagers[index]->GetFusionSequenceIndexOfLinkedManager()]->GetId().c_str());
1588         mSlicerManagers[index]->SetFusionSequenceInvolvmentCode(-1);
1589         mSlicerManagers[mSlicerManagers[index]->GetFusionSequenceIndexOfLinkedManager()]->SetFusionSequenceInvolvmentCode(-1);
1590         for (unsigned i=0 ; i<4 ; i++) {
1591             mSlicerManagers[index]->GetSlicer(i)->SetFusionSequenceCode(-1);
1592             mSlicerManagers[mSlicerManagers[index]->GetFusionSequenceIndexOfLinkedManager()]->GetSlicer(i)->SetFusionSequenceCode(-1);
1593         }
1594
1595       }
1596       mSlicerManagers[index]->RemoveActor(overlay_type, overlay_index-1);
1597       mSlicerManagers[index]->SetColorMap(0);
1598       DataTree->topLevelItem(index)->takeChild(DataTree->topLevelItem(index)->indexOfChild(item));
1599       mSlicerManagers[index]->Render();
1600     }
1601   } else if (DataTree->topLevelItemCount() <= 1) {
1602     QString warning = "Do you really want to close the image : ";
1603     warning += item->data(COLUMN_IMAGE_NAME,Qt::DisplayRole).toString();
1604     warning += "\nThis is the last image, you're about to close vv !!!";
1605     QMessageBox msgBox(QMessageBox::Warning, tr("Close Image"),
1606       warning, 0, this);
1607     msgBox.addButton(tr("Close vv"), QMessageBox::AcceptRole);
1608     msgBox.addButton(tr("Cancel"), QMessageBox::RejectRole);
1609     if (msgBox.exec() == QMessageBox::AcceptRole) {
1610       this->close();
1611     }
1612   } else {
1613     QString warning = "Do you really want to close the image : ";
1614     warning += item->data(COLUMN_IMAGE_NAME,Qt::DisplayRole).toString();
1615     QMessageBox msgBox(QMessageBox::Warning, tr("Close Image"),
1616       warning, 0, this);
1617     msgBox.addButton(tr("Close"), QMessageBox::AcceptRole);
1618     msgBox.addButton(tr("Cancel"), QMessageBox::RejectRole);
1619     if (msgBox.exec() == QMessageBox::AcceptRole) {
1620
1621       // Tell tools that we close an image
1622       emit AnImageIsBeingClosed(mSlicerManagers[index]);
1623
1624       std::vector<vvSlicerManager*>::iterator Manageriter = mSlicerManagers.begin();
1625       DataTree->takeTopLevelItem(index);
1626       for (int i = 0; i < index; i++) {
1627         Manageriter++;
1628       }
1629       //if the slicer manager was involved in a fusion sequence visualization...
1630       if ( mSlicerManagers[index]->IsInvolvedInFusionSequence() ) {
1631         //in both cases, close the overlay: find it... and close it
1632         //ideally, I should duplicate the code, and avoid calling CloseImage, since this pops up another interactive box
1633         QTreeWidgetItem* overlayItem;
1634         if (mSlicerManagers[index]->IsMainSequenceOfFusionSequence()) {
1635           for (unsigned i=0 ; i<item->childCount() ; i++) {
1636             overlayItem = item->child(i);
1637             this->CloseImage( overlayItem, 0 );
1638           }
1639         }
1640         else {
1641           QTreeWidgetItem* linkedItem = this->GetItemFromSlicerManager( mSlicerManagers[mSlicerManagers[index]->GetFusionSequenceIndexOfLinkedManager()] );
1642           for (unsigned i=0 ; i<linkedItem->childCount() ; i++) {
1643             overlayItem = linkedItem->child(i);
1644             this->CloseImage( overlayItem, 0 );
1645           }
1646         }
1647
1648         /* -- this is normally already done when closing the overlay.
1649         //reset the transforms
1650         overlayPanel->getFusionSequenceProperty(-1, false, 0, false);
1651
1652         //unlink and untie the slicer managers
1653         RemoveLink(mSlicerManagers[index]->GetId().c_str(), mSlicerManagers[mSlicerManagers[index]->GetFusionSequenceIndexOfLinkedManager()]->GetId().c_str());
1654         mSlicerManagers[index]->SetFusionSequenceInvolvmentCode(-1);
1655         mSlicerManagers[mSlicerManagers[index]->GetFusionSequenceIndexOfLinkedManager()]->SetFusionSequenceInvolvmentCode(-1);
1656         for (unsigned i=0 ; i<4 ; i++) {
1657             mSlicerManagers[index]->GetSlicer(i)->SetFusionSequenceCode(-1);
1658             mSlicerManagers[mSlicerManagers[index]->GetFusionSequenceIndexOfLinkedManager()]->GetSlicer(i)->SetFusionSequenceCode(-1);
1659         }
1660         */
1661       }
1662
1663       linkPanel->removeImage(index);
1664       mSlicerManagers[index]->RemoveActors();
1665
1666       //remove the slicer manager
1667       delete mSlicerManagers[index];
1668       mSlicerManagers.erase(Manageriter);
1669
1670       //
1671       InitDisplay();
1672     }
1673   }
1674   ImageInfoChanged();
1675 }
1676 //------------------------------------------------------------------------------
1677
1678 //------------------------------------------------------------------------------
1679 void vvMainWindow::ReloadImage(QTreeWidgetItem* item, int column)
1680 {
1681   // int index = GetSlicerIndexFromItem(item);
1682   //   QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
1683   //   if (item->data(1,Qt::UserRole).toString() == "vector")
1684   //     mSlicerManagers[index]->ReloadVF();
1685   //   else
1686   //     mSlicerManagers[index]->Reload();
1687
1688   //   QApplication::restoreOverrideCursor();
1689   int index = GetSlicerIndexFromItem(item);
1690   QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
1691   QString role=item->data(1,Qt::UserRole).toString();
1692   if ( role == "vector") {
1693     mSlicerManagers[index]->ReloadVF();
1694   }
1695   else if (role == "overlay") {
1696     mSlicerManagers[index]->ReloadOverlay();
1697   }
1698   else if (role == "fusion") {
1699     mSlicerManagers[index]->ReloadFusion();
1700   }
1701   else if (role == "fusionSequence") {
1702     //both versions of the secondary sequence must be updated.
1703     mSlicerManagers[index]->ReloadFusionSequence();
1704     mSlicerManagers[mSlicerManagers[index]->GetFusionSequenceIndexOfLinkedManager()]->Reload();
1705   }
1706   else {
1707     mSlicerManagers[index]->Reload();
1708     //if we update the secondary sequence, then the overlay of the main sequence should also be updated
1709     if (mSlicerManagers[index]->IsSecondarySequenceOfFusionSequence()) mSlicerManagers[mSlicerManagers[index]->GetFusionSequenceIndexOfLinkedManager()]->ReloadFusionSequence();
1710   }
1711   // Update view and info
1712   ImageInfoChanged();
1713   mSlicerManagers[index]->Render();
1714   QApplication::restoreOverrideCursor();
1715 }
1716 //------------------------------------------------------------------------------
1717
1718 //------------------------------------------------------------------------------
1719 void vvMainWindow::MousePositionChanged(int visibility,double x, double y, double z, double X, double Y, double Z , double value)
1720 {
1721   infoPanel->setCurrentInfo(visibility,x,y,z,X,Y,Z,value);
1722 }
1723 //------------------------------------------------------------------------------
1724
1725 //------------------------------------------------------------------------------
1726 void vvMainWindow::VectorChanged(int visibility,double x, double y, double z, double value)
1727 {
1728   overlayPanel->getCurrentVectorInfo(visibility,x,y,z,value);
1729 }
1730 //------------------------------------------------------------------------------
1731
1732 //------------------------------------------------------------------------------
1733 void vvMainWindow::OverlayChanged(int visibility, double valueOver, double valueRef)
1734 {
1735   overlayPanel->getCurrentOverlayInfo(visibility,valueOver, valueRef);
1736 }
1737 //------------------------------------------------------------------------------
1738
1739 //------------------------------------------------------------------------------
1740 void vvMainWindow::FusionChanged(int visibility, double value)
1741 {
1742   overlayPanel->getCurrentFusionInfo(visibility,value);
1743 }
1744 //------------------------------------------------------------------------------
1745
1746 //------------------------------------------------------------------------------
1747 //called when AddOverlayImage, AddFusionSequence
1748 //or when UpdateWindowLevel() is called ; when slicerManager emits WindowLevelChanged
1749 //when ImageInfoChanged() is called
1750 void vvMainWindow::WindowLevelChanged()
1751 {
1752   // Base image
1753   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1754   if(index==-1) return;
1755   windowSpinBox->setValue(mSlicerManagers[index]->GetColorWindow());
1756   levelSpinBox->setValue(mSlicerManagers[index]->GetColorLevel());
1757   colorMapComboBox->setCurrentIndex(mSlicerManagers[index]->GetColorMap());
1758   presetComboBox->setCurrentIndex(mSlicerManagers[index]->GetPreset());
1759
1760   // Overlay image
1761   if (mSlicerManagers[index]->GetSlicer(0)->GetOverlay())
1762     overlayPanel->getOverlayProperty(mSlicerManagers[index]->GetOverlayColor(),
1763     mSlicerManagers[index]->GetLinkOverlayWindowLevel(),
1764     mSlicerManagers[index]->GetOverlayColorWindow(),
1765     mSlicerManagers[index]->GetOverlayColorLevel());
1766   else
1767     overlayPanel->getOverlayProperty(-1,0,0.,0.);
1768
1769   // Fusion & SequenceFusion image
1770   if (mSlicerManagers[index]->GetSlicer(0)->GetFusion()) {
1771     overlayPanel->getFusionProperty(mSlicerManagers[index]->GetFusionOpacity(),
1772       mSlicerManagers[index]->GetFusionThresholdOpacity(),
1773       mSlicerManagers[index]->GetFusionColorMap(),
1774       mSlicerManagers[index]->GetFusionWindow(),
1775       mSlicerManagers[index]->GetFusionLevel());
1776     if (mSlicerManagers[index]->IsMainSequenceOfFusionSequence()) {
1777       overlayPanel->getFusionSequenceProperty(mSlicerManagers[index]->GetFusionSequenceFrameIndex(),
1778         mSlicerManagers[index]->GetFusionSequenceSpatialSyncFlag(),
1779         mSlicerManagers[index]->GetFusionSequenceNbFrames(),
1780         mSlicerManagers[index]->GetFusionSequenceTemporalSyncFlag());
1781     }
1782   }
1783   else if ( mSlicerManagers[index]->IsSecondarySequenceOfFusionSequence() ) {
1784     //if the image is involved in a fusion sequence, preserve the overlay panel!
1785     int ind = mSlicerManagers[index]->GetFusionSequenceIndexOfLinkedManager();
1786     overlayPanel->getFusionProperty(mSlicerManagers[ind]->GetFusionOpacity(),
1787       mSlicerManagers[ind]->GetFusionThresholdOpacity(),
1788       mSlicerManagers[ind]->GetFusionColorMap(),
1789       mSlicerManagers[ind]->GetFusionWindow(),
1790       mSlicerManagers[ind]->GetFusionLevel());
1791     overlayPanel->getFusionSequenceProperty(mSlicerManagers[ind]->GetFusionSequenceFrameIndex(),
1792       mSlicerManagers[ind]->GetFusionSequenceSpatialSyncFlag(),
1793       mSlicerManagers[ind]->GetFusionSequenceNbFrames(),
1794       mSlicerManagers[ind]->GetFusionSequenceTemporalSyncFlag());
1795   }
1796   else
1797   {
1798     overlayPanel->getFusionProperty(-1, -1, -1, -1, -1);
1799     overlayPanel->getFusionSequenceProperty(-1, false, 0, false);
1800   }
1801 }
1802 //------------------------------------------------------------------------------
1803
1804 //------------------------------------------------------------------------------
1805 void vvMainWindow::WindowLevelEdited()
1806 {
1807   presetComboBox->setCurrentIndex(WL_USER);
1808   UpdateWindowLevel();
1809 }
1810 //------------------------------------------------------------------------------
1811
1812 //------------------------------------------------------------------------------
1813 void vvMainWindow::SetWindowLevel(double w, double l)
1814 {
1815   windowSpinBox->setValue(w);
1816   levelSpinBox->setValue(l);
1817   presetComboBox->setCurrentIndex(WL_USER);
1818   colorMapComboBox->setCurrentIndex(0);
1819   UpdateWindowLevel();
1820 }
1821 //------------------------------------------------------------------------------
1822
1823 //------------------------------------------------------------------------------
1824 void vvMainWindow::UpdateWindowLevel()
1825 {
1826   if (DataTree->selectedItems().size()) {
1827     if (presetComboBox->currentIndex() == WL_VENTILATION) //For ventilation
1828       colorMapComboBox->setCurrentIndex(5);
1829     int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1830     mSlicerManagers[index]->SetColorWindow(windowSpinBox->value());
1831     mSlicerManagers[index]->SetColorLevel(levelSpinBox->value());
1832     mSlicerManagers[index]->SetPreset(presetComboBox->currentIndex());
1833     mSlicerManagers[index]->Render();
1834     WindowLevelChanged();
1835   }
1836 }
1837 //------------------------------------------------------------------------------
1838
1839 //------------------------------------------------------------------------------
1840 void vvMainWindow::UpdateSlicingPreset()
1841 {
1842   if (DataTree->selectedItems().size()) {
1843     int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1844     mSlicerManagers[index]->SetSlicingPreset(vvSlicerManager::SlicingPresetType(slicingPresetComboBox->currentIndex()));
1845   }
1846 }
1847 //------------------------------------------------------------------------------
1848
1849 //------------------------------------------------------------------------------
1850 void vvMainWindow::UpdateColorMap()
1851 {
1852   if (DataTree->selectedItems().size()) {
1853     int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1854     mSlicerManagers[index]->SetColorMap(colorMapComboBox->currentIndex());
1855     mSlicerManagers[index]->Render();
1856   }
1857 }
1858 //------------------------------------------------------------------------------
1859 void vvMainWindow::SwitchWindowLevel()
1860 {
1861   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1862   int window = mSlicerManagers[index]->GetColorWindow();
1863   presetComboBox->setCurrentIndex(WL_USER);
1864   windowSpinBox->setValue(-window);
1865   UpdateWindowLevel();
1866 }
1867 //------------------------------------------------------------------------------
1868
1869 //------------------------------------------------------------------------------
1870 void vvMainWindow::ApplyWindowLevelToAllImages()
1871 {
1872   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1873   if(index==-1) return;
1874   double window = mSlicerManagers[index]->GetColorWindow();
1875   double level = mSlicerManagers[index]->GetColorLevel();
1876
1877   double fusWindow = mSlicerManagers[index]->GetFusionWindow();
1878   double fusLevel = mSlicerManagers[index]->GetFusionLevel();
1879
1880   double overWindow = mSlicerManagers[index]->GetOverlayColorWindow();
1881   double overLevel = mSlicerManagers[index]->GetOverlayColorLevel();
1882
1883   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
1884     if (mSlicerManagers[i] == NULL)
1885       continue;
1886     mSlicerManagers[i]->SetColorWindow(window);
1887     mSlicerManagers[i]->SetColorLevel(level);
1888     mSlicerManagers[i]->SetPreset(WL_USER);
1889     mSlicerManagers[i]->SetFusionWindow(fusWindow);
1890     mSlicerManagers[i]->SetFusionLevel(fusLevel);
1891     mSlicerManagers[i]->SetOverlayColorWindow(overWindow);
1892     mSlicerManagers[i]->SetOverlayColorLevel(overLevel);
1893     mSlicerManagers[i]->Render();
1894   }
1895 }
1896 //------------------------------------------------------------------------------
1897
1898 //------------------------------------------------------------------------------
1899 void vvMainWindow::ApplyWindowToSetOfImages(double window, unsigned int indexMin, unsigned int indexMax)
1900 {
1901   for (unsigned int i = indexMin; i <= indexMax && i < mSlicerManagers.size(); i++) {
1902     if (mSlicerManagers[i] == NULL)
1903       continue;
1904     mSlicerManagers[i]->SetColorWindow(window);
1905     mSlicerManagers[i]->SetPreset(WL_USER);
1906     mSlicerManagers[i]->Render();
1907   }
1908 }
1909 //------------------------------------------------------------------------------
1910
1911 //------------------------------------------------------------------------------
1912 void vvMainWindow::ApplyLevelToSetOfImages(double level, unsigned int indexMin, unsigned int indexMax)
1913 {
1914   for (unsigned int i = indexMin; i <= indexMax && i < mSlicerManagers.size(); i++) {
1915     if (mSlicerManagers[i] == NULL)
1916       continue;
1917     mSlicerManagers[i]->SetColorLevel(level);
1918     mSlicerManagers[i]->SetPreset(WL_USER);
1919     mSlicerManagers[i]->Render();
1920   }
1921 }
1922 //------------------------------------------------------------------------------
1923
1924 //------------------------------------------------------------------------------
1925 void vvMainWindow::UpdateLinkManager(std::string id, int slicer, double x, double y, double z, int temps)
1926 {
1927   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
1928     if (mSlicerManagers[i]->GetId() == id) {
1929       mSlicerManagers[i]->GetSlicer(slicer)->SetCurrentPosition(x,y,z,temps);
1930       mSlicerManagers[i]->UpdateViews(0,slicer);
1931       break;
1932     }
1933   }
1934 }
1935 //------------------------------------------------------------------------------
1936
1937 //------------------------------------------------------------------------------
1938 void vvMainWindow::UpdateLinkedNavigation(std::string id, vvSlicerManager * sm, vvSlicer* refSlicer)
1939 {
1940   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
1941     if (id == mSlicerManagers[i]->GetId()) {
1942       mSlicerManagers[i]->UpdateLinkedNavigation(refSlicer);
1943     }
1944   }
1945 }
1946 //------------------------------------------------------------------------------
1947
1948 //------------------------------------------------------------------------------
1949 void vvMainWindow::ShowContextMenu(QPoint point)
1950 {
1951   if (!DataTree->selectedItems().size()) {
1952     contextActions[1]->setEnabled(0);
1953     contextActions[2]->setEnabled(0);
1954     contextActions[3]->setEnabled(0);
1955     contextActions[4]->setEnabled(0);
1956     contextActions[5]->setEnabled(0);
1957     contextActions[6]->setEnabled(0);
1958   } else {
1959     int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1960     contextActions[1]->setEnabled(1);
1961     contextActions[2]->setEnabled(
1962       DataTree->itemWidget(DataTree->selectedItems()[0],
1963       COLUMN_RELOAD_IMAGE)->isEnabled());
1964     contextActions[3]->setEnabled(1);
1965     contextActions[5]->setEnabled(1);
1966     contextActions[6]->setEnabled(1);
1967
1968     if (mSlicerManagers[index]->GetDimension() < 3)
1969       contextActions[4]->setEnabled(0);
1970     else
1971       contextActions[4]->setEnabled(1);
1972   }
1973   contextMenu.exec(QCursor::pos());
1974 }
1975 //------------------------------------------------------------------------------
1976
1977 //------------------------------------------------------------------------------
1978 void vvMainWindow::CloseImage()
1979 {
1980   CloseImage(DataTree->selectedItems()[0],0);
1981 }
1982 //------------------------------------------------------------------------------
1983
1984 //------------------------------------------------------------------------------
1985 void vvMainWindow::ReloadImage()
1986 {
1987   ReloadImage(DataTree->selectedItems()[0],0);
1988 }
1989 //------------------------------------------------------------------------------
1990
1991 //------------------------------------------------------------------------------
1992 void vvMainWindow::SelectOverlayImage()
1993 {
1994   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1995
1996   //check if one overlay image is added
1997   for (int child = 0; child < DataTree->topLevelItem(index)->childCount(); child++)
1998     if (DataTree->topLevelItem(index)->child(child)->data(1,Qt::UserRole).toString() == "overlay") {
1999       QString error = "Cannot add more than one compared image\n";
2000       error += "Please remove first ";
2001       error += DataTree->topLevelItem(index)->child(child)->data(COLUMN_IMAGE_NAME,Qt::DisplayRole).toString();
2002       QMessageBox::information(this,tr("Problem adding compared image !"),error);
2003       return;
2004     }
2005
2006     QString Extensions = EXTENSIONS;
2007     Extensions += ";;All Files (*)";
2008     QStringList files = QFileDialog::getOpenFileNames(this,tr("Load Overlay image"),mInputPathName,Extensions);
2009     if (files.isEmpty())
2010       return;
2011
2012     std::vector<std::string> vecFileNames;
2013     for (int i = 0; i < files.size(); i++) {
2014       vecFileNames.push_back(files[i].toStdString());
2015     }
2016
2017     AddOverlayImage(index,vecFileNames,vvImageReader::IMAGE);
2018 }
2019 //------------------------------------------------------------------------------
2020
2021 //------------------------------------------------------------------------------
2022 void vvMainWindow::AddOverlayImage(int index, std::vector<std::string> fileNames, vvImageReader::LoadedImageType type)
2023 {
2024   QString file(fileNames[0].c_str());
2025   if (QFile::exists(file))
2026   {
2027     mInputPathName = itksys::SystemTools::GetFilenamePath(file.toStdString()).c_str();
2028     itk::ImageIOBase::Pointer reader = itk::ImageIOFactory::CreateImageIO(
2029       file.toStdString().c_str(), itk::ImageIOFactory::ReadMode);
2030     reader->SetFileName(fileNames[0].c_str());
2031     reader->ReadImageInformation();
2032     std::string component = reader->GetComponentTypeAsString(reader->GetComponentType());
2033     int dimension = reader->GetNumberOfDimensions();
2034     QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
2035     vvProgressDialog progress("Opening " + file.toStdString());
2036     qApp->processEvents();
2037
2038     std::string filename = itksys::SystemTools::GetFilenameWithoutExtension(file.toStdString()).c_str();
2039     if (mSlicerManagers[index]->SetOverlay(fileNames,dimension, component,type)) {
2040       //create an item in the tree with good settings
2041       QTreeWidgetItem *item = new QTreeWidgetItem();
2042       item->setData(0,Qt::UserRole,file.toStdString().c_str());
2043       item->setData(1,Qt::UserRole,tr("overlay"));
2044       QFileInfo fileinfo(file); //Do not show the path
2045       item->setData(COLUMN_IMAGE_NAME,Qt::DisplayRole,fileinfo.fileName());
2046       item->setToolTip(COLUMN_IMAGE_NAME, mSlicerManagers[index]->GetListOfAbsoluteFilePathInOneString("overlay").c_str());
2047       qApp->processEvents();
2048 #if VTK_MAJOR_VERSION > 5
2049       for ( unsigned int i = 0; i < mSlicerManagers[index]->GetNumberOfSlicers(); i++)
2050         mSlicerManagers[index]->GetSlicer(i)->ForceUpdateDisplayExtent();
2051 #endif
2052
2053       for (int j = 1; j <= 4; j++) {
2054         item->setData(j,Qt::CheckStateRole,DataTree->topLevelItem(index)->data(j,Qt::CheckStateRole));
2055       }
2056
2057       //Create the buttons for reload and close
2058       qApp->processEvents();
2059       QTreePushButton* cButton = new QTreePushButton;
2060       cButton->setItem(item);
2061       cButton->setColumn(COLUMN_CLOSE_IMAGE);
2062       cButton->setToolTip(tr("close image"));
2063       cButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/exit.png")));
2064       connect(cButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
2065         this,SLOT(CloseImage(QTreeWidgetItem*, int)));
2066
2067       QTreePushButton* rButton = new QTreePushButton;
2068       rButton->setItem(item);
2069       rButton->setColumn(COLUMN_RELOAD_IMAGE);
2070       rButton->setToolTip(tr("reload image"));
2071       rButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/rotateright.png")));
2072       connect(rButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
2073         this,SLOT(ReloadImage(QTreeWidgetItem*, int)));
2074
2075       DataTree->topLevelItem(index)->setExpanded(1);
2076       DataTree->topLevelItem(index)->addChild(item);
2077       DataTree->setItemWidget(item, COLUMN_CLOSE_IMAGE, cButton);
2078       DataTree->setItemWidget(item, COLUMN_RELOAD_IMAGE, rButton);
2079
2080       //set the id of the image
2081       QString id = DataTree->topLevelItem(index)->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString();
2082       item->setData(COLUMN_IMAGE_NAME,Qt::UserRole,id.toStdString().c_str());
2083       UpdateTree();
2084       qApp->processEvents();
2085       ImageInfoChanged();
2086       QApplication::restoreOverrideCursor();
2087
2088       // Update the display to update, e.g., the sliders
2089       for(int i=0; i<4; i++)
2090         DisplaySliders(index, i);
2091     } else {
2092       QApplication::restoreOverrideCursor();
2093       QString error = "Cannot import the new image.\n";
2094       error += mSlicerManagers[index]->GetLastError().c_str();
2095       QMessageBox::information(this,tr("Problem reading image !"),error);
2096     }
2097     WindowLevelChanged();
2098   }
2099   else
2100     QMessageBox::information(this,tr("Problem reading Overlay !"),"File doesn't exist!");
2101 }
2102 //------------------------------------------------------------------------------
2103
2104
2105 //------------------------------------------------------------------------------
2106 void vvMainWindow::AddROI(int index, QString file)
2107 {
2108   /*
2109   // Get slice manager
2110
2111   // Load image
2112
2113   vvImageReader * mReader = new vvImageReader;
2114   mReader->SetInputFilename(filename.toStdString());
2115   mReader->Update(IMAGE);
2116   if (mReader->GetLastError().size() != 0) {
2117   std::cerr << "Error while reading " << filename.toStdString() << std::endl;
2118   QString error = "Cannot open file \n";
2119   error += mReader->GetLastError().c_str();
2120   QMessageBox::information(this,tr("Reading problem"),error);
2121   delete mReader;
2122   return;
2123   }
2124   vvImage::Pointer roi = mReader->GetOutput();
2125
2126   // Create roi in new tool
2127   vvToolStructureSetManager::AddImage(mCurrentSlicerManager, roi);
2128   */
2129 }
2130 //------------------------------------------------------------------------------
2131
2132 //------------------------------------------------------------------------------
2133 void vvMainWindow::SelectFusionImage()
2134 {
2135   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2136
2137   //check if one fusion image is added
2138   for (int child = 0; child < DataTree->topLevelItem(index)->childCount(); child++)
2139     if ( (DataTree->topLevelItem(index)->child(child)->data(1,Qt::UserRole).toString() == "fusion") ||
2140       (DataTree->topLevelItem(index)->child(child)->data(1,Qt::UserRole).toString() == "fusionSequence") ) {
2141         QString error = "Cannot add more than one fusion image\n";
2142         error += "Please remove first ";
2143         error += DataTree->topLevelItem(index)->child(child)->data(COLUMN_IMAGE_NAME,Qt::DisplayRole).toString();
2144         QMessageBox::information(this,tr("Problem adding fusion image !"),error);
2145         return;
2146     }
2147
2148     QString Extensions = EXTENSIONS;
2149     Extensions += ";;All Files (*)";
2150     QStringList files = QFileDialog::getOpenFileNames(this,tr("Load Fusion image"),mInputPathName,Extensions);
2151     if (files.isEmpty())
2152       return;
2153
2154     std::vector<std::string> vecFileNames;
2155     for (int i = 0; i < files.size(); i++) {
2156       vecFileNames.push_back(files[i].toStdString());
2157     }
2158     AddFusionImage(index,vecFileNames,vvImageReader::IMAGE);
2159 }
2160 //------------------------------------------------------------------------------
2161
2162 //------------------------------------------------------------------------------
2163 void vvMainWindow::ResetTransformationToIdentity()
2164 {
2165   std::string actorType = DataTree->selectedItems()[0]->data(1,Qt::UserRole).toString().toStdString();
2166   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2167   mSlicerManagers[index]->ResetTransformationToIdentity(actorType);
2168   ImageInfoChanged();
2169 }
2170 //------------------------------------------------------------------------------
2171
2172 //------------------------------------------------------------------------------
2173 void vvMainWindow::AddFusionImage(int index, std::vector<std::string> fileNames, vvImageReader::LoadedImageType type)
2174 {
2175   QString file(fileNames[0].c_str());
2176   if (QFile::exists(file))
2177   {
2178     mInputPathName = itksys::SystemTools::GetFilenamePath(file.toStdString()).c_str();
2179     itk::ImageIOBase::Pointer reader = itk::ImageIOFactory::CreateImageIO(
2180       file.toStdString().c_str(), itk::ImageIOFactory::ReadMode);
2181     reader->SetFileName(fileNames[0].c_str());
2182     reader->ReadImageInformation();
2183     std::string component = reader->GetComponentTypeAsString(reader->GetComponentType());
2184     int dimension = reader->GetNumberOfDimensions();
2185     QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
2186     vvProgressDialog progress("Opening fusion");
2187     qApp->processEvents();
2188
2189     std::string filename = itksys::SystemTools::GetFilenameWithoutExtension(file.toStdString()).c_str();
2190     if (mSlicerManagers[index]->SetFusion(fileNames,dimension, component,type)) {
2191       //create an item in the tree with good settings
2192       QTreeWidgetItem *item = new QTreeWidgetItem();
2193       item->setData(0,Qt::UserRole,file.toStdString().c_str());
2194       item->setData(1,Qt::UserRole,tr("fusion"));
2195       QFileInfo fileinfo(file); //Do not show the path
2196           item->setData(COLUMN_IMAGE_NAME,Qt::DisplayRole,fileinfo.fileName());
2197           item->setToolTip(COLUMN_IMAGE_NAME, mSlicerManagers[index]->GetListOfAbsoluteFilePathInOneString("fusion").c_str());
2198           qApp->processEvents();
2199 #if VTK_MAJOR_VERSION > 5
2200       for ( unsigned int i = 0; i < mSlicerManagers[index]->GetNumberOfSlicers(); i++)
2201         mSlicerManagers[index]->GetSlicer(i)->ForceUpdateDisplayExtent();
2202 #endif
2203       for (int j = 1; j <= 4; j++) {
2204         item->setData(j,Qt::CheckStateRole,DataTree->topLevelItem(index)->data(j,Qt::CheckStateRole));
2205       }
2206
2207       //Create the buttons for reload and close
2208       qApp->processEvents();
2209       QTreePushButton* cButton = new QTreePushButton;
2210       cButton->setItem(item);
2211       cButton->setColumn(COLUMN_CLOSE_IMAGE);
2212       cButton->setToolTip(tr("close image"));
2213       cButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/exit.png")));
2214       connect(cButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
2215         this,SLOT(CloseImage(QTreeWidgetItem*, int)));
2216
2217       QTreePushButton* rButton = new QTreePushButton;
2218       rButton->setItem(item);
2219       rButton->setColumn(COLUMN_RELOAD_IMAGE);
2220       rButton->setToolTip(tr("reload image"));
2221       rButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/rotateright.png")));
2222       connect(rButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
2223         this,SLOT(ReloadImage(QTreeWidgetItem*, int)));
2224
2225       DataTree->topLevelItem(index)->setExpanded(1);
2226       DataTree->topLevelItem(index)->addChild(item);
2227       DataTree->setItemWidget(item, COLUMN_CLOSE_IMAGE, cButton);
2228       DataTree->setItemWidget(item, COLUMN_RELOAD_IMAGE, rButton);
2229
2230       //set the id of the image
2231       QString id = DataTree->topLevelItem(index)->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString();
2232       item->setData(COLUMN_IMAGE_NAME,Qt::UserRole,id.toStdString().c_str());
2233       UpdateTree();
2234       qApp->processEvents();
2235       ImageInfoChanged();
2236       QApplication::restoreOverrideCursor();
2237
2238       // Update the display to update, e.g., the sliders
2239       for(int i=0; i<4; i++)
2240         DisplaySliders(index, i);
2241     } else {
2242       QApplication::restoreOverrideCursor();
2243       QString error = "Cannot import the new image.\n";
2244       error += mSlicerManagers[index]->GetLastError().c_str();
2245       QMessageBox::information(this,tr("Problem reading image !"),error);
2246     }
2247     WindowLevelChanged();
2248   }
2249   else
2250     QMessageBox::information(this,tr("Problem reading Fusion !"),"File doesn't exist!");
2251 }
2252 //------------------------------------------------------------------------------
2253 //------------------------------------------------------------------------------
2254 void vvMainWindow::AddLandmarks(int index, std::vector<std::string> files)
2255 {
2256     if (!landmarksPanel->LoadFromFile(files))
2257       QMessageBox::information(this,tr("Problem reading Landmarks !"),"File doesn't exist!");
2258
2259     landmarksPanel->SetCurrentPath(mInputPathName.toStdString());
2260     landmarksPanel->SetCurrentImage(mSlicerManagers[index]->GetFileName().c_str());
2261 }
2262
2263 //------------------------------------------------------------------------------
2264 void vvMainWindow::OpenField()
2265 {
2266   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2267   //check if a vector field has already been added
2268   for (int child = 0; child < DataTree->topLevelItem(index)->childCount(); child++)
2269     if (DataTree->topLevelItem(index)->child(child)->data(1,Qt::UserRole).toString() == "vector") {
2270       QString error = "Cannot add more than one vector field\n";
2271       error += "Please remove first ";
2272       error += DataTree->topLevelItem(index)->child(child)->data(COLUMN_IMAGE_NAME,Qt::DisplayRole).toString();
2273       QMessageBox::information(this,tr("Problem adding vector field!"),error);
2274       return;
2275     }
2276
2277     QString Extensions = "Images ( *.mhd *.mha *.vf *.nii *.nrrd *.nhdr)";
2278     // Extensions += ";;Images ( *.mha)";
2279     // Extensions += ";;VF Images ( *.vf)";
2280     // Extensions += ";;nii Images ( *.nii)";
2281     // Extensions += ";;nrrd Images ( *.nrrd)";
2282     // Extensions += ";;nhdr Images ( *.nhdr)";
2283     Extensions += ";;All Files (*)";
2284     QString file = QFileDialog::getOpenFileName(this,tr("Load deformation field"),mInputPathName,Extensions);
2285     if (!file.isEmpty())
2286       AddField(file,index);
2287 }
2288 //------------------------------------------------------------------------------
2289
2290
2291 //------------------------------------------------------------------------------
2292 void vvMainWindow::AddFieldEntry(QString filename,int index,bool from_disk)
2293 {
2294   //create an item in the tree with good settings
2295   QTreeWidgetItem *item = new QTreeWidgetItem();
2296   item->setData(0,Qt::UserRole,filename.toStdString().c_str());
2297   item->setData(1,Qt::UserRole,tr("vector"));
2298   QFileInfo fileinfo(filename); //Do not show the path
2299   item->setData(COLUMN_IMAGE_NAME,Qt::DisplayRole,fileinfo.fileName());
2300   item->setToolTip(COLUMN_IMAGE_NAME, mSlicerManagers[index]->GetListOfAbsoluteFilePathInOneString("vector").c_str());
2301   qApp->processEvents();
2302
2303   for (int j = 1; j <= 4; j++) {
2304     item->setData(j,Qt::CheckStateRole,DataTree->topLevelItem(index)->data(j,Qt::CheckStateRole));
2305   }
2306
2307   //Create the buttons for reload and close
2308   qApp->processEvents();
2309   QTreePushButton* cButton = new QTreePushButton;
2310   cButton->setItem(item);
2311   cButton->setColumn(COLUMN_CLOSE_IMAGE);
2312   cButton->setToolTip(tr("close vector field"));
2313   cButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/exit.png")));
2314   connect(cButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
2315     this,SLOT(CloseImage(QTreeWidgetItem*, int)));
2316
2317   QTreePushButton* rButton = new QTreePushButton;
2318   rButton->setItem(item);
2319   rButton->setColumn(COLUMN_RELOAD_IMAGE);
2320   rButton->setToolTip(tr("reload vector field"));
2321   rButton->setEnabled(from_disk);
2322   rButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/rotateright.png")));
2323   connect(rButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
2324     this,SLOT(ReloadImage(QTreeWidgetItem*, int)));
2325
2326   DataTree->topLevelItem(index)->setExpanded(1);
2327   DataTree->topLevelItem(index)->addChild(item);
2328   DataTree->setItemWidget(item, COLUMN_RELOAD_IMAGE, rButton);
2329   DataTree->setItemWidget(item, COLUMN_CLOSE_IMAGE, cButton);
2330
2331   //set the id of the image
2332   QString id = DataTree->topLevelItem(index)->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString();
2333   item->setData(COLUMN_IMAGE_NAME,Qt::UserRole,id.toStdString().c_str());
2334   UpdateTree();
2335   qApp->processEvents();
2336   ImageInfoChanged();
2337   QApplication::restoreOverrideCursor();
2338 }
2339 //------------------------------------------------------------------------------
2340
2341
2342 //------------------------------------------------------------------------------
2343 void vvMainWindow::AddField(vvImage::Pointer vf,QString file,int index)
2344 {
2345   QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
2346   vvSlicerManager* imageManager = mSlicerManagers[index];
2347   if (imageManager->SetVF(vf,file.toStdString())) {
2348     AddFieldEntry(file,index,false);
2349 #if VTK_MAJOR_VERSION > 5
2350       for ( unsigned int i = 0; i < mSlicerManagers[index]->GetNumberOfSlicers(); i++)
2351         mSlicerManagers[index]->GetSlicer(i)->ForceUpdateDisplayExtent();
2352 #endif
2353   } else {
2354     QString error = "Cannot import the vector field for this image.\n";
2355     error += imageManager->GetLastError().c_str();
2356     QMessageBox::information(this,tr("Problem reading VF !"),error);
2357   }
2358   QApplication::restoreOverrideCursor();
2359 }
2360 //------------------------------------------------------------------------------
2361
2362
2363 //------------------------------------------------------------------------------
2364 void vvMainWindow::AddField(QString file,int index)
2365 {
2366   if (QFile::exists(file)) {
2367     mInputPathName = itksys::SystemTools::GetFilenamePath(file.toStdString()).c_str();
2368
2369     //init the progress events
2370     QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
2371     vvProgressDialog progress("Opening " + file.toStdString());
2372     qApp->processEvents();
2373
2374     //read the vector and put it in the current mSlicerManager
2375     vvSlicerManager* imageManager = mSlicerManagers[index];
2376     qApp->processEvents();
2377
2378     std::string filename = itksys::SystemTools::GetFilenameWithoutExtension(file.toStdString()).c_str();
2379     if (imageManager->SetVF(file.toStdString())) {
2380       imageManager->Render();
2381       AddFieldEntry(file,index,true);
2382     } else {
2383       QApplication::restoreOverrideCursor();
2384       QString error = "Cannot import the vector field for this image.\n";
2385       error += imageManager->GetLastError().c_str();
2386       QMessageBox::information(this,tr("Problem reading VF !"),error);
2387     }
2388   } else
2389     QMessageBox::information(this,tr("Problem reading VF !"),"File doesn't exist!");
2390
2391 }
2392 //------------------------------------------------------------------------------
2393
2394
2395 //------------------------------------------------------------------------------
2396 void vvMainWindow::SetVFProperty(int subsampling, int scale, int log, int width, double r, double g, double b)
2397 {
2398   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2399   if (mSlicerManagers[index]->GetSlicer(0)->GetVF()) {
2400     for (int i = 0; i < 4; i++) {
2401       mSlicerManagers[index]->GetSlicer(i)->SetVFSubSampling(subsampling);
2402       mSlicerManagers[index]->GetSlicer(i)->SetVFScale(scale);
2403       mSlicerManagers[index]->GetSlicer(i)->SetVFWidth(width);
2404       mSlicerManagers[index]->GetSlicer(i)->SetVFColor(r,g,b);
2405       if (log > 0)
2406         mSlicerManagers[index]->GetSlicer(i)->SetVFLog(1);
2407       else
2408         mSlicerManagers[index]->GetSlicer(i)->SetVFLog(0);
2409     }
2410   }
2411 }
2412 //------------------------------------------------------------------------------
2413
2414
2415 //------------------------------------------------------------------------------
2416 void vvMainWindow::SetOverlayProperty(int color, int linked, double window, double level)
2417 {
2418   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2419   if (mSlicerManagers[index]->GetSlicer(0)->GetOverlay()) {
2420     mSlicerManagers[index]->SetOverlayColor(color);
2421     mSlicerManagers[index]->SetColorMap(0);
2422     mSlicerManagers[index]->SetLinkOverlayWindowLevel(linked);
2423     mSlicerManagers[index]->SetOverlayColorWindow(window);
2424     mSlicerManagers[index]->SetOverlayColorLevel(level);
2425     mSlicerManagers[index]->Render();
2426   }
2427 }
2428 //------------------------------------------------------------------------------
2429
2430 //------------------------------------------------------------------------------
2431 void vvMainWindow::SetFusionProperty(int opacity, int thresOpacity, int colormap,double window, double level, bool showLegend)
2432 {
2433   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2434   if (mSlicerManagers[index]->GetSlicer(0)->GetFusion()) {
2435     mSlicerManagers[index]->SetFusionColorMap(colormap);
2436     mSlicerManagers[index]->SetFusionOpacity(opacity);
2437     mSlicerManagers[index]->SetFusionThresholdOpacity(thresOpacity);
2438     mSlicerManagers[index]->SetFusionWindow(window);
2439     mSlicerManagers[index]->SetFusionLevel(level);
2440     mSlicerManagers[index]->SetFusionShowLegend(showLegend);
2441     mSlicerManagers[index]->SetColorMap(0);
2442     mSlicerManagers[index]->Render();
2443   }
2444 }
2445 //------------------------------------------------------------------------------
2446
2447
2448 //------------------------------------------------------------------------------
2449 void vvMainWindow::SelectFusionSequence()
2450 {
2451   //get the index of the slicer manager of the main sequence (CT)
2452   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2453   //check if one overlay image is already associated
2454   for (int child = 0; child < DataTree->topLevelItem(index)->childCount(); child++)
2455     if ( (DataTree->topLevelItem(index)->child(child)->data(1,Qt::UserRole).toString() == "fusion") ||
2456       (DataTree->topLevelItem(index)->child(child)->data(1,Qt::UserRole).toString() == "fusionSequence") ) {
2457         QString error = "Cannot add more than one compared image\n";
2458         error += "Please remove first ";
2459         error += DataTree->topLevelItem(index)->child(child)->data(COLUMN_IMAGE_NAME,Qt::DisplayRole).toString();
2460         QMessageBox::information(this,tr("Problem adding compared image !"),error);
2461         return;
2462     }
2463
2464     QString Extensions = EXTENSIONS;
2465     Extensions += ";;All Files (*)";
2466     QStringList files = QFileDialog::getOpenFileNames(this,tr("Load Overlay image sequence"),mInputPathName,Extensions);
2467     if (files.isEmpty())
2468       return;
2469
2470     std::vector<std::string> vecFileNames;
2471     for (int i = 0; i < files.size(); i++) {
2472       vecFileNames.push_back(files[i].toStdString());
2473     }
2474
2475     //associate the secondary sequence (US) to the main one
2476     AddFusionSequence(index,vecFileNames,vvImageReader::MERGEDWITHTIME);
2477 }
2478 //------------------------------------------------------------------------------
2479
2480
2481 //------------------------------------------------------------------------------
2482 void vvMainWindow::SelectFusionSequenceCorrespondances()
2483 {
2484   //make sure the index is right?
2485   //in the end, I should attach the temporal data to the right sequence!
2486   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2487   //in case the other sequence got selected, make sure we select the primary sequence
2488   if ( (!mSlicerManagers[index]->GetSlicer(0)->GetFusion()) && mSlicerManagers[index]->GetFusionSequenceIndexOfLinkedManager()>=0 ) {
2489     index = mSlicerManagers[index]->GetFusionSequenceIndexOfLinkedManager();
2490   }
2491
2492   //open a dialog box to find a file
2493   //QString Extensions = EXTENSIONS;
2494   QString Extensions = ";;All Files (*)";
2495   QString fileName = QFileDialog::getOpenFileName(this,tr("Load respiratory signal for fused sequence"),mInputPathName,Extensions);
2496   if (fileName.isNull())
2497     return;
2498
2499   //read it as a vector of values
2500   vnl_vector<double> tmpVect;
2501
2502   std::ifstream file;
2503   file.open(fileName.toStdString().c_str());
2504   tmpVect.read_ascii(file);
2505   file.close();
2506
2507   //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
2508   bool signalOK = true;
2509   unsigned nbFrameMain = mSlicerManagers[index]->GetImage()->GetTransform().size();
2510   unsigned nbFrameSecondary = mSlicerManagers[index]->GetFusionSequenceNbFrames();
2511   std::cout<<"nbFrameMain = "<<nbFrameMain<<", nbFrameSecondary= "<<nbFrameSecondary<<", signal size: "<<tmpVect.size()<<std::endl;
2512   std::vector<unsigned> temporalCorrespondances;
2513   if ( tmpVect.size() == nbFrameMain + nbFrameSecondary ) {
2514     for (unsigned i=0 ; i<tmpVect.size() ; i++) {
2515       if (i<nbFrameMain) { //first part of the file: i -> index in secondary seq.
2516         if ( tmpVect(i)<nbFrameSecondary ) temporalCorrespondances.push_back(tmpVect(i));
2517         else { signalOK=false; break; } //pointing outside the secondary sequence...
2518       }
2519       else { //first part of the file -> index in secondary seq.
2520         if ( tmpVect(i)<nbFrameMain ) temporalCorrespondances.push_back(tmpVect(i));
2521         else { signalOK=false; break; } //pointing outside the secondary sequence...
2522       }
2523     }
2524   }
2525   else {signalOK=false;}
2526   if (!signalOK) {//else, send a message to signal the failure...
2527     QString error = "The provided temporal correspondances is invalid - check tooltip.\n";
2528     error += "Ignoring file: " + fileName;
2529     QMessageBox::information(this,tr("Problem adding temporal correspondances!"),error);
2530     return;
2531   }
2532   else {
2533     //for convenience, associate this sequence to both the current slicer manager, and to the linked one
2534     mSlicerManagers[index]->SetFusionSequenceCorrespondances(temporalCorrespondances);
2535     mSlicerManagers[ mSlicerManagers[index]->GetFusionSequenceIndexOfLinkedManager() ]->SetFusionSequenceCorrespondances(temporalCorrespondances);
2536     overlayPanel->enableFusionSequenceTemporalSync();
2537   }
2538
2539 }
2540 //------------------------------------------------------------------------------
2541
2542
2543 //------------------------------------------------------------------------------
2544 //when this function is called index is the slicer manager index corresponding to the main sequence (CT)
2545 //the files behind fileNames points to the data for the secondary sequence
2546 void vvMainWindow::AddFusionSequence(int index, std::vector<std::string> fileNames, vvImageReader::LoadedImageType type)
2547 {
2548   QString file(fileNames[0].c_str());
2549   if (QFile::exists(file))
2550   {
2551     mInputPathName = itksys::SystemTools::GetFilenamePath(file.toStdString()).c_str();
2552     itk::ImageIOBase::Pointer reader = itk::ImageIOFactory::CreateImageIO(
2553       file.toStdString().c_str(), itk::ImageIOFactory::ReadMode);
2554     std::sort (fileNames.begin(), fileNames.end());//make sure the files are sorted.
2555     reader->SetFileName(fileNames[0].c_str());
2556     reader->ReadImageInformation();
2557     std::string component = reader->GetComponentTypeAsString(reader->GetComponentType());
2558     int dimension = reader->GetNumberOfDimensions();
2559     QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
2560     vvProgressDialog progress("Opening " + file.toStdString());
2561     qApp->processEvents();
2562
2563     std::string filename = itksys::SystemTools::GetFilenameWithoutExtension(file.toStdString()).c_str();
2564
2565     if (mSlicerManagers[index]->SetFusionSequence(fileNames,dimension, component,type)) {
2566       //create an item in the tree with good settings
2567       QTreeWidgetItem *item = new QTreeWidgetItem();
2568       item->setData(0,Qt::UserRole,file.toStdString().c_str());
2569       item->setData(1,Qt::UserRole,tr("fusionSequence"));
2570
2571       QFileInfo fileinfo(file); //Do not show the path
2572       item->setData(COLUMN_IMAGE_NAME,Qt::DisplayRole,fileinfo.fileName());
2573       item->setToolTip(COLUMN_IMAGE_NAME, mSlicerManagers[index]->GetListOfAbsoluteFilePathInOneString("fusionSequence").c_str());
2574       qApp->processEvents();
2575 #if VTK_MAJOR_VERSION > 5
2576       for ( unsigned int i = 0; i < mSlicerManagers[index]->GetNumberOfSlicers(); i++)
2577         mSlicerManagers[index]->GetSlicer(i)->ForceUpdateDisplayExtent();
2578 #endif
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 #if VTK_MAJOR_VERSION <= 5
3301     writer->SetInput(windowToImageFilter->GetOutput());
3302 #else
3303     writer->SetInputConnection(windowToImageFilter->GetOutputPort());
3304 #endif
3305     writer->Write();
3306   }
3307 }
3308 //------------------------------------------------------------------------------
3309
3310
3311 //------------------------------------------------------------------------------
3312 void vvMainWindow::SaveScreenshot(QVTKWidget *widget)
3313 {
3314   QString Extensions = "Images( *.png);;";
3315   Extensions += "Images( *.jpg);;";
3316   Extensions += "Images( *.bmp);;";
3317   Extensions += "Images( *.tif);;";
3318   Extensions += "Images( *.ppm)";
3319 #if defined(VTK_USE_FFMPEG_ENCODER) || defined(VTK_USE_VIDEO_FOR_WINDOWS)
3320   Extensions += ";;Video( *.avi)";
3321 #endif
3322 #ifdef VTK_USE_MPEG2_ENCODER
3323   Extensions += ";;Video( *.mpg)";
3324 #endif
3325 #ifdef CLITK_EXPERIMENTAL
3326   Extensions += ";;Video( *.gif)";
3327 #endif
3328
3329   int smIndex=GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
3330   QString fileName = QFileDialog::getSaveFileName(this,
3331     tr("Save As"),
3332     itksys::SystemTools::GetFilenamePath(mSlicerManagers[smIndex]->GetFileName()).c_str(),
3333     Extensions);
3334
3335   if (!fileName.isEmpty()) {
3336     vtkSmartPointer<vtkWindowToImageFilter> w2i = vtkSmartPointer<vtkWindowToImageFilter>::New();
3337     w2i->SetInput(widget->GetRenderWindow());
3338     w2i->Update();
3339     vtkImageData *image = w2i->GetOutput();
3340
3341     std::string ext(itksys::SystemTools::GetFilenameLastExtension(fileName.toStdString()));
3342
3343     // Image
3344     vtkImageWriter *imgwriter = NULL;
3345     if (ext==".bmp")
3346       imgwriter = vtkBMPWriter::New();
3347     else if (ext==".tif")
3348       imgwriter = vtkTIFFWriter::New();
3349     else if (ext==".ppm")
3350       imgwriter = vtkPNMWriter::New();
3351     else if (ext==".png")
3352       imgwriter = vtkPNGWriter::New();
3353     else if (ext==".jpg")
3354       imgwriter = vtkJPEGWriter::New();
3355
3356     // Snapshot image if not null
3357     if(imgwriter!=NULL) {
3358 #if VTK_MAJOR_VERSION <= 5
3359       imgwriter->SetInput(image);
3360 #else
3361       imgwriter->SetInputConnection(w2i->GetOutputPort());
3362 #endif
3363       imgwriter->SetFileName(fileName.toStdString().c_str());
3364       imgwriter->Write();
3365       return;
3366     }
3367
3368     // Video
3369     vtkGenericMovieWriter *vidwriter = NULL;
3370 #if CLITK_EXPERIMENTAL == 1
3371     if (ext==".gif") {
3372       vvAnimatedGIFWriter *gif = vvAnimatedGIFWriter::New();
3373       vidwriter = gif;
3374
3375       // FPS
3376       bool ok;
3377       int fps = QInputDialog::getInt(this, tr("Number of frames per second"),
3378         tr("FPS:"), 5, 0, 1000, 1, &ok);
3379       if(ok)
3380         gif->SetRate(fps);
3381
3382       // Loops
3383       int loops = QInputDialog::getInt(this, tr("Loops"),
3384         tr("Number of loops (0 means infinite):"), 0, 0, 1000000000, 1, &ok);
3385       if(ok)
3386         gif->SetLoops(loops);
3387
3388       // Dithering
3389       QString msg = "Would you like to activate dithering?";
3390       QMessageBox msgBox(QMessageBox::Question, tr("Dithering"),msg, 0, this);
3391       msgBox.addButton(tr("Yes"), QMessageBox::AcceptRole);
3392       msgBox.addButton(tr("No"), QMessageBox::RejectRole);
3393       gif->SetDither(msgBox.exec() == QMessageBox::AcceptRole);
3394     }
3395 #endif
3396 #ifdef VTK_USE_VIDEO_FOR_WINDOWS
3397     if (ext==".avi") {
3398       vtkAVIWriter *mpg = vtkAVIWriter::New();
3399       vidwriter = mpg;
3400       mpg->SetQuality(2);
3401       bool ok;
3402       int fps = QInputDialog::getInteger(this, tr("Number of frames per second"),
3403         tr("FPS:"), 5, 0, 1024, 1, &ok);
3404       if(!ok)
3405         fps = 5;
3406       mpg->SetRate(fps);
3407     }
3408 #endif
3409 #ifdef VTK_USE_FFMPEG_ENCODER
3410     if (ext==".avi") {
3411       vtkFFMPEGWriter *mpg = vtkFFMPEGWriter::New();
3412       vidwriter = mpg;
3413       mpg->SetQuality(2);
3414       bool ok;
3415       int fps = QInputDialog::getInteger(this, tr("Number of frames per second"),
3416         tr("FPS:"), 5, 0, 1024, 1, &ok);
3417       if(!ok)
3418         fps = 5;
3419       mpg->SetRate(fps);
3420       mpg->SetBitRateTolerance(int(ceil(12.0*1024*1024/fps)));
3421     }
3422 #endif
3423 #ifdef VTK_USE_MPEG2_ENCODER
3424     if (ext==".mpg") {
3425       vtkMPEG2Writer *mpg = vtkMPEG2Writer::New();
3426       vidwriter = mpg;
3427     }
3428 #endif
3429
3430     // Take video if not null
3431     if(vidwriter!=NULL){
3432 #if VTK_MAJOR_VERSION <= 5
3433       vidwriter->SetInput(image);
3434 #else
3435       vidwriter->SetInputConnection(w2i->GetOutputPort());
3436 #endif
3437       vidwriter->SetFileName(fileName.toStdString().c_str());
3438       vidwriter->Start();
3439       int nSlice = mSlicerManagers[smIndex]->GetSlicer(0)->GetTMax();
3440       for(int i=0; i<=nSlice; i++) {
3441         mSlicerManagers[smIndex]->SetNextTSlice(0);
3442         vtkSmartPointer<vtkWindowToImageFilter> w2i = vtkSmartPointer<vtkWindowToImageFilter>::New();
3443         w2i->SetInput(widget->GetRenderWindow());
3444         w2i->Update();
3445 #if VTK_MAJOR_VERSION <= 5
3446         vidwriter->SetInput(w2i->GetOutput());
3447 #else
3448         vidwriter->SetInputConnection(w2i->GetOutputPort());
3449 #endif
3450         vidwriter->Write();
3451       }
3452       vidwriter->End();
3453       vidwriter->Delete();
3454       return;
3455     }
3456
3457     QMessageBox::information(this,tr("Problem saving screenshot !"),tr("Cannot save image.\nPlease set a file extension !!!"));
3458   }
3459 }
3460 //------------------------------------------------------------------------------
3461
3462
3463 //------------------------------------------------------------------------------
3464 void vvMainWindow::GoToCursor()
3465 {
3466   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
3467   for (int column = 1; column < 5; column++) {
3468     if (DataTree->selectedItems()[0]->data(column,Qt::CheckStateRole).toInt() > 1) {
3469       double* cursorPos = mSlicerManagers[index]->GetSlicer(column-1)->GetCursorPosition();
3470       mSlicerManagers[index]->GetSlicer(column-1)->SetCurrentPosition(
3471         cursorPos[0],cursorPos[1],cursorPos[2],cursorPos[3]);
3472       mSlicerManagers[index]->UpdateViews(1,column-1);
3473       mSlicerManagers[index]->UpdateLinked(column-1);
3474       break;
3475     }
3476   }
3477 }
3478 //------------------------------------------------------------------------------
3479
3480 //------------------------------------------------------------------------------
3481 void vvMainWindow::GoToLandmark()
3482 {
3483   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
3484   for (int column = 1; column < 5; column++) {
3485     if (DataTree->selectedItems()[0]->data(column,Qt::CheckStateRole).toInt() > 1) {
3486       double* cursorPos = landmarksPanel->GetSelectedPoint();
3487       mSlicerManagers[index]->GetSlicer(column-1)->SetCurrentPosition(
3488         cursorPos[0],cursorPos[1],cursorPos[2],cursorPos[3]);
3489       mSlicerManagers[index]->UpdateViews(1,column-1);
3490       mSlicerManagers[index]->UpdateLinked(column-1);
3491       break;
3492     }
3493   }
3494 }
3495 //------------------------------------------------------------------------------
3496
3497 //------------------------------------------------------------------------------
3498 void vvMainWindow::PlayPause()
3499 {
3500   if (playMode) {
3501     playMode = 0;
3502     playButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/player_play.png")));
3503     ImageInfoChanged();
3504     return;
3505   } else {
3506     int image_number=DataTree->topLevelItemCount();
3507     bool has_temporal;
3508     for (int i=0; i<image_number; i++)
3509       if (mSlicerManagers[i]->GetSlicer(0)->GetTMax() > 0) {
3510         has_temporal=true;
3511         break;
3512       }
3513       if (has_temporal) {
3514         playMode = 1;
3515         playButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/player_pause.png")));
3516         QTimer::singleShot(1000/mFrameRate, this, SLOT(PlayNext()));
3517       }
3518   }
3519 }
3520 //------------------------------------------------------------------------------
3521
3522 //------------------------------------------------------------------------------
3523 void vvMainWindow::PlayNext()
3524 {
3525   if (playMode && !this->isHidden()) {
3526     int image_number=DataTree->topLevelItemCount();
3527     ///Only play one slicer per SM, and only if the SM is being displayed
3528     for (int i=0; i<image_number; i++)
3529       for (int j=0; j<4; j++)
3530         if (mSlicerManagers[i]->GetSlicer(0)->GetTMax() > 0 &&
3531           DataTree->topLevelItem(i)->data(j+1,Qt::CheckStateRole).toInt() > 0) {
3532             mSlicerManagers[i]->SetNextTSlice(j);
3533             break;
3534         }
3535         QTimer::singleShot(1000/mFrameRate, this, SLOT(PlayNext()));
3536   }
3537 }
3538 //------------------------------------------------------------------------------
3539
3540 void vvMainWindow::ShowLastImage()
3541 {
3542   if (mSlicerManagers.size() > 1) {
3543     QTreeWidgetItem * item=DataTree->topLevelItem(DataTree->topLevelItemCount()-1);
3544     CurrentImageChanged(mSlicerManagers.back()->GetId()); //select new image
3545     item->setData(1,Qt::CheckStateRole,2); //show the new image in the first panel
3546     //mSlicerManagers[GetSlicerIndexFromItem(item)]->GetSlicer(0)->SetActorVisibility("image", 0, 1); //Set the Last Image visibles
3547     DisplayChanged(item,1);
3548   }
3549 }
3550
3551 //------------------------------------------------------------------------------
3552 void vvMainWindow::UpdateRenderWindows()
3553 {
3554   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
3555       for (unsigned int j = 0; j < 4; ++j) {
3556         mSlicerManagers[i]->GetSlicer(j)->RemoveLandmarks();
3557         mSlicerManagers[i]->GetSlicer(j)->DisplayLandmarks();
3558       }
3559   }
3560   if (NOViewWidget->GetRenderWindow()) NOViewWidget->GetRenderWindow()->Render();
3561   if (NEViewWidget->GetRenderWindow()) NEViewWidget->GetRenderWindow()->Render();
3562   if (SOViewWidget->GetRenderWindow()) SOViewWidget->GetRenderWindow()->Render();
3563   if (SEViewWidget->GetRenderWindow()) SEViewWidget->GetRenderWindow()->Render();
3564 }
3565 //------------------------------------------------------------------------------
3566
3567 //------------------------------------------------------------------------------
3568 void vvMainWindow::SegmentationOnCurrentImage()
3569 {
3570   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
3571
3572   vvSegmentationDialog segmentation;
3573   segmentation.SetImage(mSlicerManagers[index]->GetSlicer(0)->GetImage());
3574   segmentation.exec();
3575 }
3576 //------------------------------------------------------------------------------
3577
3578 void vvMainWindow::SurfaceViewerLaunch()
3579 {
3580   vvSurfaceViewerDialog surfaceViewer;
3581   surfaceViewer.exec();
3582 }
3583 //------------------------------------------------------------------------------
3584
3585
3586 //------------------------------------------------------------------------------
3587 int vvMainWindow::GetImageDuplicateFilenameNumber(std::string filename)
3588 {
3589   int number=0;
3590   for(unsigned int l=0; l<mSlicerManagers.size(); l++) {
3591     vvSlicerManager * v = mSlicerManagers[l];
3592     if (v->GetBaseFileName() ==
3593       vtksys::SystemTools::GetFilenameName(vtksys::SystemTools::GetFilenameWithoutLastExtension(filename))) {
3594         number = std::max(number, v->GetBaseFileNameNumber()+1);
3595     }
3596   }
3597   return number;
3598 }
3599 //------------------------------------------------------------------------------
3600
3601
3602 //------------------------------------------------------------------------------
3603 vvSlicerManager* vvMainWindow::AddImage(vvImage::Pointer image,std::string filename)
3604 {
3605   // Change filename if another image exist with the same name
3606   int number = GetImageDuplicateFilenameNumber(filename);
3607
3608   // Create new SliceManager
3609   vvSlicerManager* slicer_manager = new vvSlicerManager(4);
3610   slicer_manager->SetImage(image);//, IMAGE, number);
3611   //  filename = filename+"_"+clitk::toString(number);
3612   slicer_manager->SetFilename(filename, number);
3613   mSlicerManagers.push_back(slicer_manager);
3614
3615   //create an item in the tree with good settings
3616   QTreeWidgetItem *item = new QTreeWidgetItem();
3617   item->setData(0,Qt::UserRole,slicer_manager->GetFileName().c_str());//files[i].c_str());
3618   item->setData(1,Qt::UserRole,tr("image"));
3619   item->setData(COLUMN_IMAGE_NAME,Qt::DisplayRole,slicer_manager->GetFileName().c_str());//filename.c_str());
3620   qApp->processEvents();
3621
3622   for (int j = 1; j <= 4; j++) item->setData(j,Qt::CheckStateRole,1);
3623
3624   //Create the buttons for reload and close
3625   qApp->processEvents();
3626   QTreePushButton* cButton = new QTreePushButton;
3627   cButton->setItem(item);
3628   cButton->setColumn(COLUMN_CLOSE_IMAGE);
3629   cButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/exit.png")));
3630   connect(cButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
3631     this,SLOT(CloseImage(QTreeWidgetItem*, int)));
3632
3633   QTreePushButton* rButton = new QTreePushButton;
3634   rButton->setItem(item);
3635   rButton->setColumn(COLUMN_RELOAD_IMAGE);
3636   rButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/rotateright.png")));
3637   rButton->setEnabled(0);
3638   connect(rButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
3639     this,SLOT(ReloadImage(QTreeWidgetItem*, int)));
3640
3641   DataTree->addTopLevelItem(item);
3642   DataTree->setItemWidget(item, COLUMN_CLOSE_IMAGE, cButton);
3643   DataTree->setItemWidget(item, COLUMN_RELOAD_IMAGE, rButton);
3644
3645   //set the id of the image
3646   QString id = QDir::current().absoluteFilePath(slicer_manager->GetFileName().c_str()) + QString::number(mSlicerManagers.size()-1);
3647   item->setData(COLUMN_IMAGE_NAME,Qt::UserRole,id.toStdString().c_str());
3648   mSlicerManagers.back()->SetId(id.toStdString());
3649
3650   linkPanel->addImage(slicer_manager->GetFileName().c_str()// filename
3651     , id.toStdString());
3652
3653   connect(mSlicerManagers.back(), SIGNAL(currentImageChanged(std::string)),
3654     this, SLOT(CurrentImageChanged(std::string)));
3655   connect(mSlicerManagers.back(), SIGNAL(currentPickedImageChanged(std::string)),
3656     this, SLOT(CurrentPickedImageChanged(std::string)));
3657   connect(mSlicerManagers.back(), SIGNAL(UpdatePosition(int, double, double, double, double, double, double, double)),
3658     this, SLOT(MousePositionChanged(int,double, double, double, double, double, double, double)));
3659   connect(mSlicerManagers.back(), SIGNAL(UpdateVector(int, double, double, double, double)),
3660     this, SLOT(VectorChanged(int,double,double,double, double)));
3661   connect(mSlicerManagers.back(), SIGNAL(UpdateOverlay(int, double, double)),
3662     this, SLOT(OverlayChanged(int,double,double)));
3663   connect(mSlicerManagers.back(), SIGNAL(UpdateFusion(int, double)),
3664     this, SLOT(FusionChanged(int,double)));
3665   //connect(mSlicerManagers.back(), SIGNAL(UpdateFusionSequence(int, bool, unsigned int)),
3666   //  this, SLOT(FusionSequenceChanged(int, bool, unsigned int)));
3667   connect(mSlicerManagers.back(), SIGNAL(WindowLevelChanged()),
3668     this,SLOT(WindowLevelChanged()));
3669   connect(mSlicerManagers.back(), SIGNAL(UpdateSlice(int,int)),
3670     this,SLOT(UpdateSlice(int,int)));
3671   connect(mSlicerManagers.back(), SIGNAL(UpdateTSlice(int, int, int)),
3672     this,SLOT(UpdateTSlice(int, int, int)));
3673   connect(mSlicerManagers.back(), SIGNAL(UpdateTSlice(int, int, int)),
3674     this,SLOT(ImageInfoChanged()));
3675   connect(mSlicerManagers.back(), SIGNAL(UpdateSliceRange(int,int,int,int,int)),
3676     this,SLOT(UpdateSliceRange(int,int,int,int,int)));
3677   connect(mSlicerManagers.back(), SIGNAL(UpdateLinkManager(std::string,int,double,double,double,int)),
3678     this,SLOT(UpdateLinkManager(std::string,int,double,double,double,int)));
3679   connect(mSlicerManagers.back(), SIGNAL(UpdateLinkedNavigation(std::string,vvSlicerManager*,vvSlicer*)),
3680     this,SLOT(UpdateLinkedNavigation(std::string,vvSlicerManager*,vvSlicer*)));
3681   connect(mSlicerManagers.back(), SIGNAL(ChangeImageWithIndexOffset(vvSlicerManager*,int,int)),
3682     this,SLOT(ChangeImageWithIndexOffset(vvSlicerManager*,int,int)));
3683   connect(mSlicerManagers.back(), SIGNAL(LandmarkAdded()),landmarksPanel,SLOT(AddPoint()));
3684
3685
3686
3687   InitSlicers();
3688   UpdateTree();
3689   qApp->processEvents();
3690   InitDisplay();
3691   ShowLastImage();
3692   qApp->processEvents();
3693   // End
3694   ImageInfoChanged();
3695   return slicer_manager;
3696 }
3697 //------------------------------------------------------------------------------
3698
3699
3700 //------------------------------------------------------------------------------
3701 void vvMainWindow::UpdateCurrentSlicer()
3702 {
3703   int index = -1;
3704   if (DataTree->selectedItems().size() > 0) {
3705     index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
3706   }
3707   mSlicerManagerCurrentIndex = index;
3708 }
3709 //------------------------------------------------------------------------------