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 #ifdef CLITK_USE_PACS_CONNECTION
  52 #include "vvQPacsConnection.h"
  53 #endif
  54 #include "clitkConfiguration.h"
  55 #include "clitkMatrix.h"
  56 #ifdef Q_OS_OSX
  57 # include "vvOSXHelper.h"
  58 #endif
  59
  60 // ITK include
  61 #include <itkImage.h>
  62 #include <itkImageFileReader.h>
  63 #include <itkByteSwapper.h>
  64 #include <itkCommand.h>
  65 #include <itkNumericSeriesFileNames.h>
  66
  67 // VTK include
  68 #include <vtkImageMapper3D.h>
  69 #include <vtkInformation.h>
  70 #include <vtkVersion.h>
  71 #include <vtkImageData.h>
  72 #include <vtkImageActor.h>
  73 #include <vtkCornerAnnotation.h>
  74 #include <vtkRenderWindow.h>
  75 #include <vtkRenderWindowInteractor.h>
  76 #include <vtkRenderer.h>
  77 #include <vtkRendererCollection.h>
  78 #include <vtkWindowToImageFilter.h>
  79 #include <vtkBMPWriter.h>
  80 #include <vtkTIFFWriter.h>
  81 #include <vtkPNMWriter.h>
  82 #include <vtkPNGWriter.h>
  83 #include <vtkJPEGWriter.h>
  84 #include <vtkGenericMovieWriter.h>
  85 #ifdef CLITK_EXPERIMENTAL
  86 #  include <vvAnimatedGIFWriter.h>
  87 #endif
  88 #ifdef VTK_USE_VIDEO_FOR_WINDOWS
  89 #  include <vtkAVIWriter.h>
  90 #endif
  91 #ifdef VTK_USE_FFMPEG_ENCODER
  92 #  include <vtkFFMPEGWriter.h>
  93 #endif
  94 #ifdef VTK_USE_MPEG2_ENCODER
  95 #  include <vtkMPEG2Writer.h>
  96 #endif
  97 #include <vtkMatrix4x4.h>
  98 #include <vtkTransform.h>
  99
 100 // Standard includes
 101 #include <iostream>
 102 #include <fstream>
 103 #include <sstream>
 104 #include <iomanip>
 105
 106 #define COLUMN_TREE 0
 107 #define COLUMN_UL_VIEW 1
 108 #define COLUMN_UR_VIEW 2
 109 #define COLUMN_DL_VIEW 3
 110 #define COLUMN_DR_VIEW 4
 111 #define COLUMN_CLOSE_IMAGE 5
 112 #define COLUMN_RELOAD_IMAGE 6
 113 #define COLUMN_IMAGE_NAME 7
 114
 115 #ifdef CLITK_PRIVATE_FEATURES
 116 #define EXTENSIONS "Images ( *.bmp *.dcm *.png *.jpeg *.jpg *.tif *.mhd *.mha *.hdr *.vox *.his *.xdr *.SCAN *.nii *.nrrd *.nhdr *.refscan *.nii.gz *.usf *.svl)"
 117 #else
 118 #define EXTENSIONS "Images ( *.bmp *.dcm *.png *.jpeg *.jpg *.tif *.mhd *.mha *.hdr *.vox *.his *.xdr *.SCAN *.nii *.nrrd *.nhdr *.refscan *.nii.gz)"
 119 #endif
 120
 121
 122 /*Data Tree values
 123 0,Qt::UserRole full filename
 124 1,Qt::CheckStateRole checkbutton UL View
 125 1,Qt::UserRole overlay, fusion or vector
 126 2,Qt::CheckStateRole checkbutton UR View
 127 3,Qt::CheckStateRole checkbutton DL View
 128 4,Qt::CheckStateRole checkbutton DR View
 129 5,0  short filename
 130 5,Qt::UserRole mSlicerManager id*/
 131
 132 //------------------------------------------------------------------------------
 133 vvMainWindow::vvMainWindow():vvMainWindowBase()
 134 {
 135   setupUi(this); // this sets up the GUI
 136
 137   setDicomClient();
 138
 139   //Qt::WindowFlags flags = windowFlags();
 140   //setWindowFlags(flags | Qt::WindowStaysOnTopHint);
 141
 142   mInputPathName = "";
 143   mMenuTools = menuTools;
 144   //  mMenuSegmentation = menuSegmentation;
 145   mContextMenu = &contextMenu;
 146   mMenuExperimentalTools = menuExperimental;
 147   mMainWidget = this;
 148   mCurrentTime = -1;
 149   mCurrentSelectedImageId = "";
 150   mCurrentPickedImageId = "";
 151   mCurrentPickedImageIndex = 0;
 152
 153   //Init the contextMenu
 154   this->setContextMenuPolicy(Qt::CustomContextMenu);
 155   contextActions.resize(0);
 156   QAction* actionOpen_new_image = contextMenu.addAction(QIcon(QString::fromUtf8(":/common/icons/fileopen.png")),
 157     tr("O&pen new Image"));
 158   connect(actionOpen_new_image,SIGNAL(triggered()),this,SLOT(OpenImages()));
 159   contextActions.push_back(actionOpen_new_image);
 160   contextMenu.addSeparator();
 161
 162   QAction* actionClose_Image = contextMenu.addAction(QIcon(QString::fromUtf8(":/common/icons/exit.png")),
 163     tr("Close Current Image"));
 164   connect(actionClose_Image,SIGNAL(triggered()),this,SLOT(CloseImage()));
 165   contextActions.push_back(actionClose_Image);
 166
 167   QAction* actionReload_image = contextMenu.addAction(QIcon(QString::fromUtf8(":/common/icons/rotateright.png")),
 168     tr("Reload Current Image"));
 169   connect(actionReload_image,SIGNAL(triggered()),this,SLOT(ReloadImage()));
 170   contextActions.push_back(actionReload_image);
 171
 172   QAction* actionSave_image = contextMenu.addAction(QIcon(QString::fromUtf8(":/common/icons/filesave.png")),
 173     tr("Save Current Image"));
 174   connect(actionSave_image,SIGNAL(triggered()),this,SLOT(SaveAs()));
 175   contextActions.push_back(actionSave_image);
 176
 177   QAction* actionSave_state = contextMenu.addAction(QIcon(QString::fromUtf8(":/common/icons/filesave.png")),
 178     tr("Save Current State"));
 179   connect(actionSave_state,SIGNAL(triggered()),this,SLOT(SaveCurrentState()));
 180   contextActions.push_back(actionSave_state);
 181
 182   QAction* actionRead_state = contextMenu.addAction(QIcon(QString::fromUtf8(":/common/icons/filesave.png")),
 183     tr("Read Saved State"));
 184   connect(actionRead_state,SIGNAL(triggered()),this,SLOT(ReadSavedState()));
 185   contextActions.push_back(actionRead_state);
 186
 187   contextMenu.addSeparator();
 188
 189   contextMenu.addAction(actionAdd_VF_to_current_Image);
 190   contextActions.push_back(actionAdd_VF_to_current_Image);
 191
 192   //QAction* actionAdd_Overlay_to_current_Image = menuOverlay->addAction(QIcon(QString::fromUtf8(":/common/icons/GPSup.png")),
 193   //    tr("Add overlay image to current image"));
 194   contextMenu.addAction(actionAdd_overlay_image_to_current_image);
 195   contextActions.push_back(actionAdd_overlay_image_to_current_image);
 196
 197   contextMenu.addAction(actionAdd_fusion_image);
 198   contextActions.push_back(actionAdd_fusion_image);
 199
 200 #ifdef CLITK_EXPERIMENTAL
 201   contextMenu.addAction(actionAdd_USSequence_toCT);
 202   contextActions.push_back(actionAdd_USSequence_toCT);
 203 #endif
 204
 205
 206   contextMenu.addSeparator();
 207   QAction* actionResetMatrix = contextMenu.addAction(QIcon(QString::fromUtf8(":/common/icons/identity.png")),
 208     tr("Reset transformation to identity"));
 209   connect(actionResetMatrix, SIGNAL(triggered()), this,SLOT(ResetTransformationToIdentity()));
 210
 211   //init the DataTree
 212   mSlicerManagers.resize(0);
 213
 214   QStringList header;
 215   header.append("");
 216   header.append("TL");
 217   header.append("TR");
 218   header.append("BL");
 219   header.append("BR");
 220   header.append("");
 221   header.append("");
 222   header.append("Name");
 223
 224   DataTree->setHeaderLabels(header);
 225   DataTree->resizeColumnToContents(COLUMN_TREE);
 226   DataTree->resizeColumnToContents(COLUMN_UL_VIEW);
 227   DataTree->resizeColumnToContents(COLUMN_UR_VIEW);
 228   DataTree->resizeColumnToContents(COLUMN_DL_VIEW);
 229   DataTree->resizeColumnToContents(COLUMN_DR_VIEW);
 230   DataTree->resizeColumnToContents(COLUMN_CLOSE_IMAGE);
 231   DataTree->resizeColumnToContents(COLUMN_RELOAD_IMAGE);
 232   DataTree->resizeColumnToContents(COLUMN_IMAGE_NAME);
 233
 234   viewMode = 1;
 235   documentation = new vvDocumentation();
 236   help_dialog = new vvHelpDialog();
 237   dicomSeriesSelector = new vvDicomSeriesSelector();
 238 #ifdef CLITK_USE_PACS_CONNECTION
 239      PacsConnection = new vvQPacsConnection();
 240 #endif
 241
 242   inverseButton->setEnabled(0);
 243   actionAdd_overlay_image_to_current_image->setEnabled(0);
 244   actionSave_As->setEnabled(0);
 245   actionAdd_VF_to_current_Image->setEnabled(0);
 246   actionAdd_fusion_image->setEnabled(0);
 247   actionAdd_USSequence_toCT->setEnabled(0);
 248
 249   //init the sliders
 250   verticalSliders.push_back(NOVerticalSlider);
 251   verticalSliders.push_back(NEVerticalSlider);
 252   verticalSliders.push_back(SOVerticalSlider);
 253   verticalSliders.push_back(SEVerticalSlider);
 254
 255   for (int i =0; i < 4; i++)
 256     verticalSliders[i]->hide();
 257
 258   horizontalSliders.push_back(NOHorizontalSlider);
 259   horizontalSliders.push_back(NEHorizontalSlider);
 260   horizontalSliders.push_back(SOHorizontalSlider);
 261   horizontalSliders.push_back(SEHorizontalSlider);
 262
 263   for (int i =0; i < 4; i++)
 264     horizontalSliders[i]->hide();
 265
 266
 267   connect(NOVerticalSlider,SIGNAL(valueChanged(int)),this,SLOT(NOVerticalSliderChanged()));
 268   connect(NEVerticalSlider,SIGNAL(valueChanged(int)),this,SLOT(NEVerticalSliderChanged()));
 269   connect(SOVerticalSlider,SIGNAL(valueChanged(int)),this,SLOT(SOVerticalSliderChanged()));
 270   connect(SEVerticalSlider,SIGNAL(valueChanged(int)),this,SLOT(SEVerticalSliderChanged()));
 271
 272   connect(NOHorizontalSlider,SIGNAL(valueChanged(int)),this,SLOT(NOHorizontalSliderMoved()));
 273   connect(NEHorizontalSlider,SIGNAL(valueChanged(int)),this,SLOT(NEHorizontalSliderMoved()));
 274   connect(SOHorizontalSlider,SIGNAL(valueChanged(int)),this,SLOT(SOHorizontalSliderMoved()));
 275   connect(SEHorizontalSlider,SIGNAL(valueChanged(int)),this,SLOT(SEHorizontalSliderMoved()));
 276
 277   //connect everything
 278   connect(actionCompute_mid_position_image,SIGNAL(triggered()),this,SLOT(ComputeMidPosition()));
 279   connect(actionDeformable_Registration,SIGNAL(triggered()),this,SLOT(ComputeDeformableRegistration()));
 280   connect(actionWarp_image_with_vector_field,SIGNAL(triggered()),this,SLOT(WarpImage()));
 281   connect(actionLoad_images,SIGNAL(triggered()),this,SLOT(OpenImages()));
 282   connect(actionOpen_Dicom,SIGNAL(triggered()),this,SLOT(OpenDicom()));
 283   #ifdef CLITK_USE_PACS_CONNECTION
 284 connect(actionConnect_Pacs,SIGNAL(triggered()),this,SLOT(ConnectPacs()));
 285 #endif
 286   //  connect(actionOpen_Dicom_Struct,SIGNAL(triggered()),this,SLOT(OpenDCStructContour()));
 287   connect(actionOpen_VTK_contour,SIGNAL(triggered()),this,SLOT(OpenVTKContour()));
 288   connect(actionOpen_Multiple_Images_As_One,SIGNAL(triggered()),this,SLOT(MergeImages()));
 289   connect(actionSlice_Image_As_Multiple_Images,SIGNAL(triggered()),this,SLOT(SliceImages()));
 290   connect(actionOpen_Image_With_Time,SIGNAL(triggered()),this,SLOT(OpenImageWithTime()));
 291   connect(actionMerge_images_as_n_dim_t, SIGNAL(triggered()), this, SLOT(MergeImagesWithTime()));
 292   connect(actionSave_As,SIGNAL(triggered()),this,SLOT(SaveAs()));
 293   connect(actionSave_current_state,SIGNAL(triggered()),this,SLOT(SaveCurrentState()));
 294   connect(actionRead_saved_state,SIGNAL(triggered()),this,SLOT(ReadSavedState()));
 295   connect(actionExit,SIGNAL(triggered()),this,SLOT(close()));
 296   connect(actionAdd_VF_to_current_Image,SIGNAL(triggered()),this,SLOT(OpenField()));
 297   connect(actionAdd_fusion_image,SIGNAL(triggered()),this,SLOT(SelectFusionImage()));
 298   connect(actionAdd_overlay_image_to_current_image,SIGNAL(triggered()), this,SLOT(SelectOverlayImage()));
 299   connect(actionAdd_USSequence_toCT,SIGNAL(triggered()), this,SLOT(SelectFusionSequence()));
 300   connect(actionNavigation_Help,SIGNAL(triggered()),this,SLOT(ShowHelpDialog()));
 301
 302   QShortcut *shortcutHelp = new QShortcut(QKeySequence(QKeySequence::HelpContents),this);
 303   shortcutHelp->setContext(Qt::ApplicationShortcut);
 304   QObject::connect(shortcutHelp, SIGNAL(activated()), this, SLOT(ShowHelpDialog()));
 305
 306   connect(actionDocumentation,SIGNAL(triggered()),this,SLOT(ShowDocumentation()));
 307   connect(actionRegister_vv,SIGNAL(triggered()),this,SLOT(PopupRegisterForm()));
 308
 309   connect(overlayPanel, SIGNAL(FusionSequenceCorrespondancesButtonPressed()), this, SLOT(SelectFusionSequenceCorrespondances()));
 310
 311
 312   ///////////////////////////////////////////////
 313   connect(actionSegmentation,SIGNAL(triggered()),this,SLOT(SegmentationOnCurrentImage()));
 314   connect(actionSurface_Viewer,SIGNAL(triggered()),this,SLOT(SurfaceViewerLaunch()));
 315   ///////////////////////////////////////////////
 316
 317   actionNorth_East_Window->setEnabled(0);
 318   actionNorth_West_Window->setEnabled(0);
 319   actionSouth_East_Window->setEnabled(0);
 320   actionSouth_West_Window->setEnabled(0);
 321
 322   connect(actionNorth_East_Window,SIGNAL(triggered()),this,SLOT(SaveNEScreenshot()));
 323   connect(actionNorth_West_Window,SIGNAL(triggered()),this,SLOT(SaveNOScreenshot()));
 324   connect(actionSouth_East_Window,SIGNAL(triggered()),this,SLOT(SaveSEScreenshot()));
 325   connect(actionSouth_West_Window,SIGNAL(triggered()),this,SLOT(SaveSOScreenshot()));
 326   connect(actionSave_all_slices,SIGNAL(triggered()),this,SLOT(SaveScreenshotAllSlices()));
 327
 328   connect(DataTree,SIGNAL(itemSelectionChanged()),this,SLOT(ImageInfoChanged()));
 329   connect(DataTree,SIGNAL(itemClicked(QTreeWidgetItem*, int)),this,
 330     SLOT(DisplayChanged(QTreeWidgetItem*, int)));
 331
 332   connect(viewButton,SIGNAL(clicked()),this, SLOT(ChangeViewMode()) );
 333   connect(windowSpinBox,SIGNAL(editingFinished()),this,SLOT(WindowLevelEdited()));
 334   connect(levelSpinBox,SIGNAL(editingFinished()),this,SLOT(WindowLevelEdited()));
 335   connect(colorMapComboBox,SIGNAL(currentIndexChanged(int)),this,SLOT(UpdateColorMap()));
 336   connect(presetComboBox,SIGNAL(currentIndexChanged(int)),this,SLOT(UpdateWindowLevel()));
 337   connect(slicingPresetComboBox, SIGNAL(currentIndexChanged(int)),this,SLOT(UpdateSlicingPreset()));
 338   connect(inverseButton,SIGNAL(clicked()),this,SLOT(SwitchWindowLevel()));
 339   connect(applyWindowLevelToAllButton,SIGNAL(clicked()),this,SLOT(ApplyWindowLevelToAllImages()));
 340
 341   connect(this,SIGNAL(customContextMenuRequested(QPoint)),this,SLOT(ShowContextMenu(QPoint)));
 342
 343   connect(linkPanel,SIGNAL(addLink(QString,QString,bool)),this,SLOT(AddLink(QString,QString,bool)));
 344   connect(linkPanel,SIGNAL(removeLink(QString,QString)),this,SLOT(RemoveLink(QString,QString)));
 345   connect(overlayPanel,SIGNAL(VFPropertyUpdated(int,int,int,int,double,double,double)),this,SLOT(SetVFProperty(int,int,int,int,double,double,double)));
 346   connect(overlayPanel,SIGNAL(OverlayPropertyUpdated(int,int,double,double)),
 347     this,SLOT(SetOverlayProperty(int,int,double,double)));
 348   connect(overlayPanel,SIGNAL(FusionPropertyUpdated(int,int,int,double,double, bool)),
 349     this,SLOT(SetFusionProperty(int,int,int,double,double, bool)));
 350   connect(landmarksPanel,SIGNAL(UpdateRenderWindows()),this,SLOT(UpdateRenderWindows()));
 351   connect(landmarksPanel,SIGNAL(SelectedPointChanged()),this,SLOT(GoToLandmark()));
 352
 353   connect(overlayPanel,SIGNAL(FusionSequencePropertyUpdated(int, bool, unsigned int, bool)),
 354     this,SLOT(SetFusionSequenceProperty(int, bool,unsigned int, bool)));
 355
 356
 357   playMode = 0;//pause
 358   mFrameRate = 10;
 359   playButton->setEnabled(0);
 360   frameRateLabel->setEnabled(0);
 361   frameRateSpinBox->setEnabled(0);
 362   connect(playButton, SIGNAL(clicked()),this,SLOT(PlayPause()));
 363   connect(frameRateSpinBox, SIGNAL(valueChanged(int)),this,SLOT(ChangeFrameRate(int)));
 364
 365   goToCursorPushButton->setEnabled(0);
 366   connect(goToCursorPushButton, SIGNAL(clicked()),this,SLOT(GoToCursor()));
 367
 368   NOViewWidget->hide();
 369   NEViewWidget->hide();
 370   SOViewWidget->hide();
 371   SEViewWidget->hide();
 372
 373 #ifdef Q_OS_OSX
 374   disableGLHiDPI(NOViewWidget->winId());
 375   disableGLHiDPI(NEViewWidget->winId());
 376   disableGLHiDPI(SOViewWidget->winId());
 377   disableGLHiDPI(SEViewWidget->winId());
 378 #endif
 379
 380   //Recently opened files
 381   std::list<std::string> recent_files = GetRecentlyOpenedImages();
 382   recentlyOpenedFilesMenu=NULL;
 383   if ( !recent_files.empty() ) {
 384     createRecentlyOpenedFilesMenu();
 385     updateRecentlyOpenedFilesMenu(recent_files);
 386   }
 387
 388   // Adding all new tools (insertion in the menu)
 389   vvToolManager::GetInstance()->InsertToolsInMenu(this);
 390   vvToolManager::GetInstance()->EnableToolsInMenu(this, false);
 391
 392 //#ifndef CLITK_EXPERIMENTAL
 393 //#define CLITK_EXPERIMENTAL 0
 394 //#endif
 395 #ifdef CLITK_EXPERIMENTAL
 396   if (!CLITK_EXPERIMENTAL)
 397     menuExperimental->menuAction()->setVisible(false);
 398 #endif
 399
 400   QTimer * timerMemory = new QTimer(this);
 401   //timerMemory->setInterval(5);
 402   connect(timerMemory, SIGNAL(timeout()), this, SLOT(UpdateMemoryUsage()));
 403   timerMemory->start(2000);
 404 }
 405
 406 //------------------------------------------------------------------------------
 407 void vvMainWindow::show()
 408 {
 409   vvMainWindowBase::show();
 410   PopupRegisterForm(true);
 411 }
 412 //------------------------------------------------------------------------------
 413 void vvMainWindow::UpdateMemoryUsage()
 414 {
 415   //  clitk::PrintMemory(true);
 416   if (clitk::GetMemoryUsageInMb() == 0) infoPanel->setMemoryInMb("NA");
 417   else infoPanel->setMemoryInMb(QString::number(clitk::GetMemoryUsageInMb())+" MiB");
 418 }
 419 //------------------------------------------------------------------------------
 420
 421
 422 //------------------------------------------------------------------------------
 423 void vvMainWindow::createRecentlyOpenedFilesMenu()
 424 {
 425   recentlyOpenedFilesMenu = new QMenu("Recently opened files...");
 426   recentlyOpenedFilesMenu->setIcon(QIcon(QString::fromUtf8(":/common/icons/open.png")));
 427   menuFile->insertMenu(actionOpen_Image_With_Time,recentlyOpenedFilesMenu);
 428   menuFile->insertSeparator(actionOpen_Image_With_Time);
 429 }
 430 //------------------------------------------------------------------------------
 431
 432
 433 //------------------------------------------------------------------------------
 434
 435 void vvMainWindow::updateRecentlyOpenedFilesMenu(const std::list<std::string> &recent_files)
 436 {
 437   if(recentlyOpenedFilesMenu==NULL) {
 438     createRecentlyOpenedFilesMenu();
 439   } else {
 440     recentlyOpenedFilesMenu->clear();
 441   }
 442   for (std::list<std::string>::const_iterator i = recent_files.begin(); i!=recent_files.end(); i++) {
 443     QAction* current=new QAction(QIcon(QString::fromUtf8(":/common/icons/open.png")), i->c_str(),this);
 444     recentlyOpenedFilesMenu->addAction(current);
 445     connect(current,SIGNAL(triggered()),this,SLOT(OpenRecentImage()));
 446   }
 447 }
 448 //------------------------------------------------------------------------------
 449
 450
 451 //------------------------------------------------------------------------------
 452 void vvMainWindow::ComputeMidPosition()
 453 {
 454   bool ok;
 455   int index=GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
 456   int ref = QInputDialog::getInt(this,"Chose reference phase","Reference phase",0,0,\
 457 mSlicerManagers[index]->GetImage()->GetVTKImages().size()-1,1,&ok);
 458   if (ok) {
 459     vvMidPosition midp;
 460     midp.slicer_manager = mSlicerManagers[index];
 461     midp.reference_image_index = ref;
 462     QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
 463     midp.Update();
 464     if (midp.error)
 465       QMessageBox::warning(this, "Error computing midposition image",midp.error_message.c_str());
 466     else {
 467       QFileInfo info(midp.slicer_manager->GetFileName().c_str());
 468       AddImage(midp.output,info.path().toStdString()+"/"+info.completeBaseName().toStdString()+"_midposition.mhd");
 469     }
 470     QApplication::restoreOverrideCursor();
 471   }
 472 }
 473 //------------------------------------------------------------------------------
 474
 475
 476 //------------------------------------------------------------------------------
 477 void vvMainWindow::AddContour(int image_index, vvMesh::Pointer contour, bool propagation)
 478 {
 479   QTreeWidgetItem *item = new QTreeWidgetItem();
 480   item->setData(0,Qt::UserRole,"filename.vtk");
 481   item->setData(1,Qt::UserRole,tr("contour"));
 482   QBrush brush;
 483   brush.setColor(QColor(contour->r*255,contour->g*255,contour->b*255));
 484   brush.setStyle(Qt::SolidPattern);
 485   item->setData(COLUMN_IMAGE_NAME,Qt::BackgroundRole,brush);
 486   item->setData(COLUMN_IMAGE_NAME,Qt::DisplayRole,contour->structure_name.c_str());
 487
 488   for (int j = 1; j <= 4; j++)
 489     item->setData(j,Qt::CheckStateRole,DataTree->topLevelItem(image_index)->data(j,Qt::CheckStateRole));
 490
 491   QTreePushButton* cButton = new QTreePushButton;
 492   cButton->setItem(item);
 493   cButton->setColumn(COLUMN_CLOSE_IMAGE);
 494   cButton->setToolTip(tr("close image"));
 495   cButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/exit.png")));
 496   connect(cButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
 497     this,SLOT(CloseImage(QTreeWidgetItem*, int)));
 498
 499   QTreePushButton* rButton = new QTreePushButton;
 500   rButton->setItem(item);
 501   rButton->setColumn(COLUMN_RELOAD_IMAGE);
 502   rButton->setToolTip(tr("reload image"));
 503   rButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/rotateright.png")));
 504   rButton->setEnabled(false);
 505   //Not implemented
 506   //connect(rButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
 507   //this,SLOT(ReloadImage(QTreeWidgetItem*, int)));
 508
 509   DataTree->topLevelItem(image_index)->setExpanded(1);
 510   DataTree->topLevelItem(image_index)->addChild(item);
 511   DataTree->setItemWidget(item, COLUMN_CLOSE_IMAGE, cButton);
 512   DataTree->setItemWidget(item, COLUMN_RELOAD_IMAGE, rButton);
 513   QString id = DataTree->topLevelItem(image_index)->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString();
 514   item->setData(COLUMN_IMAGE_NAME,Qt::UserRole,id.toStdString().c_str());
 515
 516   UpdateTree();
 517   mSlicerManagers[image_index]->AddContour(contour,propagation);
 518   mSlicerManagers[image_index]->Render();
 519 }
 520 //------------------------------------------------------------------------------
 521
 522
 523 //------------------------------------------------------------------------------
 524 void vvMainWindow::OpenVTKContour()
 525 {
 526   if (mSlicerManagers.size() > 0) {
 527     QString Extensions = "Images ( *.vtk *.obj)";
 528     Extensions += ";;All Files (*)";
 529     QString file = QFileDialog::getOpenFileName(this,tr("Open vtkPolyData"),mInputPathName,Extensions);
 530     if (file.isNull())
 531       return;
 532     QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
 533     int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
 534     vvMeshReader reader;
 535     reader.SetImage(mSlicerManagers[index]->GetImage());
 536     reader.SetModeToVTK();
 537     reader.SetFilename(file.toStdString());
 538     reader.Update();
 539     AddContour(index,reader.GetOutput()[0],false);
 540     QApplication::restoreOverrideCursor();
 541   }
 542 }
 543 //------------------------------------------------------------------------------
 544
 545
 546 //------------------------------------------------------------------------------
 547 void vvMainWindow::AddDCStructContour(int index, QString file)
 548 {
 549   vvMeshReader reader;
 550   reader.SetFilename(file.toStdString());
 551   vvStructSelector selector;
 552   selector.SetStructures(reader.GetROINames());
 553   if (!mSlicerManagers[index]->GetVF().IsNull())
 554     selector.EnablePropagationCheckBox();
 555   if (selector.exec()) {
 556     QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
 557     reader.SetSelectedItems(selector.getSelectedItems());
 558     reader.SetImage(mSlicerManagers[index]->GetImage());
 559     if (selector.PropagationEnabled())
 560       reader.SetPropagationVF(mSlicerManagers[index]->GetVF());
 561     reader.Update();
 562     std::vector<vvMesh::Pointer> contours=reader.GetOutput();
 563     for (std::vector<vvMesh::Pointer>::iterator i=contours.begin();
 564       i!=contours.end(); i++)
 565       AddContour(index,*i,selector.PropagationEnabled());
 566     QApplication::restoreOverrideCursor();
 567   }
 568 }
 569
 570 //------------------------------------------------------------------------------
 571 void vvMainWindow::OpenDCStructContour()
 572 {
 573   if (mSlicerManagers.size() > 0) {
 574     QString Extensions = "Dicom Files ( *.dcm RS*)";
 575     Extensions += ";;All Files (*)";
 576     QString file = QFileDialog::getOpenFileName(this,tr("Merge Images"),mInputPathName,Extensions);
 577     if (file.isNull())
 578       return;
 579     int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
 580     AddDCStructContour(index, file);
 581   }
 582 }
 583 //------------------------------------------------------------------------------
 584
 585
 586 //------------------------------------------------------------------------------
 587 void vvMainWindow::ComputeDeformableRegistration()
 588 {
 589   if (mSlicerManagers.size() > 0) {
 590     int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
 591     vvDeformationDialog dialog(index,mSlicerManagers);
 592     if (dialog.exec()) {
 593       std::string base_name=itksys::SystemTools::GetFilenameWithoutExtension(mSlicerManagers[dialog.GetInputFileIndex()]->GetFileName());
 594       AddField(dialog.GetOutput(),dialog.getFieldFile(),dialog.GetInputFileIndex());
 595       WarpImage(dialog.GetSelectedSlicer(),dialog.GetReferenceFrameIndex());
 596     } else
 597       std::cout << "Error or user cancellation while computing deformation field..." << std::endl;
 598   } else QMessageBox::information(this, "Need to open image","You must open an image first.");
 599 }
 600 //------------------------------------------------------------------------------
 601
 602
 603 //------------------------------------------------------------------------------
 604 void vvMainWindow::WarpImage()
 605 {
 606   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
 607   if (!mSlicerManagers[index]->GetVF().IsNull()) {
 608     bool ok;
 609     int ref = QInputDialog::getInt(this,"Chose reference phase","Reference phase",0,0,\
 610       mSlicerManagers[index]->GetImage()->GetVTKImages().size()-1,1,&ok);
 611     if (ok) {
 612       WarpImage(mSlicerManagers[index],ref);
 613     }
 614   } else
 615     QMessageBox::warning(this,tr("No vector field"),tr("Sorry, can't warp without a vector field"));
 616 }
 617 //------------------------------------------------------------------------------
 618
 619
 620 //------------------------------------------------------------------------------
 621 void vvMainWindow::WarpImage(vvSlicerManager* selected_slicer,int reference_phase)
 622 {
 623   if (!selected_slicer->GetVF().IsNull()) {
 624     QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
 625     QFileInfo info(selected_slicer->GetFileName().c_str());
 626     vvImageWarp warp(selected_slicer->GetImage(),selected_slicer->GetVF(),
 627       reference_phase,this);
 628     if (warp.ComputeWarpedImage()) {
 629       AddImage(warp.GetWarpedImage(),info.path().toStdString()+"/"+info.completeBaseName().toStdString()+"_warped.mhd");
 630       AddImage(warp.GetDiffImage()  ,info.path().toStdString()+"/"+info.completeBaseName().toStdString()+"_diff.mhd");
 631       AddImage(warp.GetJacobianImage()  ,info.path().toStdString()+"/"+info.completeBaseName().toStdString()+"_jacobian.mhd");
 632       QApplication::restoreOverrideCursor();
 633     } else {
 634       QApplication::restoreOverrideCursor();
 635       QMessageBox::warning(this,tr("Different spacings"),tr("The vector field and image spacings must be the same in order to warp."));
 636     }
 637   } else
 638     QMessageBox::warning(this,tr("No vector field"),tr("Sorry, can't warp without a vector field."));
 639 }
 640 //------------------------------------------------------------------------------
 641
 642
 643 //------------------------------------------------------------------------------
 644 vvMainWindow::~vvMainWindow()
 645 {
 646   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
 647     if (mSlicerManagers[i] != NULL)
 648       delete mSlicerManagers[i];
 649   }
 650   delete documentation;
 651   delete help_dialog;
 652   delete dicomSeriesSelector;
 653 }
 654 //------------------------------------------------------------------------------
 655
 656 //------------------------------------------------------------------------------
 657 QTabWidget * vvMainWindow::GetTab()
 658 {
 659   return tabWidget;
 660 }
 661 //------------------------------------------------------------------------------
 662
 663
 664 //------------------------------------------------------------------------------
 665 void vvMainWindow::MergeImages()
 666 {
 667   QString Extensions = EXTENSIONS;
 668   Extensions += ";;All Files (*)";
 669   QStringList files = QFileDialog::getOpenFileNames(this,tr("Merge Images"),mInputPathName,Extensions);
 670   if (files.isEmpty())
 671     return;
 672   mInputPathName = itksys::SystemTools::GetFilenamePath(files[0].toStdString()).c_str();
 673   std::vector<std::string> vector;
 674
 675   unsigned int currentDim = 0;
 676   std::vector<double> currentSpacing;
 677   std::vector<int> currentSize;
 678   std::vector<double> currentOrigin;
 679
 680   for (int i = 0; i < files.size(); i++) {
 681     itk::ImageIOBase::Pointer reader = itk::ImageIOFactory::CreateImageIO(
 682       files[i].toStdString().c_str(), itk::ImageIOFactory::ReadMode);
 683     reader->SetFileName(files[i].toStdString().c_str());
 684     reader->ReadImageInformation();
 685     if (reader)        {
 686       //NOViewWidget->hide();
 687       //NEViewWidget->hide();
 688       //SOViewWidget->hide();
 689       //SEViewWidget->hide();
 690       if (i == 0)
 691         currentDim = reader->GetNumberOfDimensions();
 692       bool IsOk = true;
 693       for (unsigned int j = 0; j < currentDim; j++) {
 694         if (i == 0) {
 695           if (j == 0) {
 696             currentSpacing.resize(currentDim);
 697             currentSize.resize(currentDim);
 698             currentOrigin.resize(currentDim);
 699           }
 700           currentOrigin[j] = reader->GetOrigin(j);
 701           currentSpacing[j] = reader->GetSpacing(j);
 702           currentSize[j] = reader->GetDimensions(j);
 703         } else if (currentDim != reader->GetNumberOfDimensions()
 704           || currentSpacing[j] != reader->GetSpacing(j)
 705           || currentSize[j] != (int)reader->GetDimensions(j)
 706           || currentOrigin[j] != reader->GetOrigin(j)) {
 707             QString error = "Cannot read file (too different from others ";
 708             error += files[i].toStdString().c_str();
 709             QMessageBox::information(this,tr("Reading problem"),error);
 710             IsOk = false;
 711             break;
 712         }
 713       }
 714       if (IsOk)
 715         vector.push_back(files[i].toStdString());
 716     }
 717   }
 718   if (vector.size() > 0)
 719     LoadImages(vector, vvImageReader::MERGED);
 720 }
 721 //------------------------------------------------------------------------------
 722
 723 //------------------------------------------------------------------------------
 724 void vvMainWindow::SliceImages()
 725 {
 726   QString Extensions = EXTENSIONS;
 727   Extensions += ";;All Files (*)";
 728
 729   QStringList files = QFileDialog::getOpenFileNames(this,tr("Slice Images"),mInputPathName,Extensions);
 730   if (files.isEmpty())
 731     return;
 732   mInputPathName = itksys::SystemTools::GetFilenamePath(files[0].toStdString()).c_str();
 733   std::vector<std::string> vector;
 734   for (int i = 0; i < files.size(); i++)
 735     vector.push_back(files[i].toStdString());
 736   LoadImages(vector, vvImageReader::SLICED);
 737 }
 738 //------------------------------------------------------------------------------
 739
 740 //------------------------------------------------------------------------------
 741 void vvMainWindow::MergeImagesWithTime()
 742 {
 743   QString Extensions = EXTENSIONS;
 744   Extensions += ";;All Files (*)";
 745   QStringList files = QFileDialog::getOpenFileNames(this,tr("Merge Images With Time"),mInputPathName,Extensions);
 746   if (files.isEmpty())
 747     return;
 748   mInputPathName = itksys::SystemTools::GetFilenamePath(files[0].toStdString()).c_str();
 749   std::vector<std::string> vector;
 750
 751   for (int i = 0; i < files.size(); i++)
 752     vector.push_back(files[i].toStdString());
 753   sort(vector.begin(),vector.end());
 754   if (vector.size() > 1)
 755     LoadImages(vector, vvImageReader::MERGEDWITHTIME);
 756   else
 757     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.");
 758 }
 759 //------------------------------------------------------------------------------
 760
 761
 762 //------------------------------------------------------------------------------
 763 void vvMainWindow::OpenDicom()
 764 {
 765   std::vector<std::string> files;
 766
 767   //std::cout << "dicomSeriesSelector " << std::endl;
 768   if (dicomSeriesSelector->exec() == QDialog::Accepted) {
 769     files = *(dicomSeriesSelector->GetFilenames());
 770     LoadImages(files, vvImageReader::DICOM);
 771   }
 772 }
 773 #ifdef CLITK_USE_PACS_CONNECTION
 774 void vvMainWindow::ConnectPacs()
 775 {
 776   std::vector<std::string> files;
 777
 778   //std::cout << "dicomSeriesSelector " << std::endl;
 779 if (PacsConnection->exec() == QDialog::Accepted) {
 780         for (int i = 0; i < PacsConnection->getSeriesCount(); i++)
 781         {
 782                 files = PacsConnection->getFileNames(i);
 783                 LoadImages(files, vvImageReader::DICOM);
 784         }
 785         PacsConnection->clearMove();
 786   }
 787   }
 788
 789 #endif
 790 //------------------------------------------------------------------------------
 791
 792 //------------------------------------------------------------------------------
 793 void vvMainWindow::OpenImages()
 794 {
 795   QString Extensions = EXTENSIONS;
 796   Extensions += ";;All Files (*)";
 797
 798   QStringList files = QFileDialog::getOpenFileNames(this,tr("Load Images"),mInputPathName,Extensions);
 799   if (files.isEmpty())
 800     return;
 801   mInputPathName = itksys::SystemTools::GetFilenamePath(files[0].toStdString()).c_str();
 802   std::vector<std::string> vector;
 803   for (int i = 0; i < files.size(); i++)
 804     vector.push_back(files[i].toStdString());
 805   LoadImages(vector, vvImageReader::IMAGE);
 806 }
 807 //------------------------------------------------------------------------------
 808 void vvMainWindow::OpenRecentImage()
 809 {
 810   QAction * caller = qobject_cast<QAction*>(sender());
 811   std::vector<std::string> images;
 812   images.push_back(caller->text().toStdString());
 813   mInputPathName = itksys::SystemTools::GetFilenamePath(images[0]).c_str();
 814   LoadImages(images, vvImageReader::IMAGE);
 815 }
 816 //------------------------------------------------------------------------------
 817
 818
 819 //------------------------------------------------------------------------------
 820 void vvMainWindow::OpenImageWithTime()
 821 {
 822   QString Extensions = EXTENSIONS;
 823   Extensions += ";;All Files (*)";
 824
 825   QStringList files = QFileDialog::getOpenFileNames(this,tr("Load Images With Time"),mInputPathName,Extensions);
 826   if (files.isEmpty())
 827     return;
 828   mInputPathName = itksys::SystemTools::GetFilenamePath(files[0].toStdString()).c_str();
 829   std::vector<std::string> vector;
 830   for (int i = 0; i < files.size(); i++) {
 831     vector.push_back(files[i].toStdString());
 832   }
 833   LoadImages(vector, vvImageReader::IMAGEWITHTIME);
 834 }
 835 //------------------------------------------------------------------------------
 836
 837
 838 //------------------------------------------------------------------------------
 839 void vvMainWindow::LoadImages(std::vector<std::string> files, vvImageReader::LoadedImageType filetype)
 840 {
 841   //Separate the way to open images and dicoms
 842   int fileSize;
 843   if (filetype == vvImageReader::IMAGE || filetype == vvImageReader::IMAGEWITHTIME)
 844     fileSize = files.size();
 845   else
 846     fileSize = 1;
 847
 848   // For SLICED, we need the number of slices (ndim and #slices)
 849   std::vector<unsigned int> nSlices;
 850   nSlices.resize(files.size());
 851   std::fill(nSlices.begin(), nSlices.end(), 1);
 852   if (filetype == vvImageReader::SLICED) {
 853     for (int i = 0; i < fileSize; i++) {
 854       itk::ImageIOBase::Pointer header = clitk::readImageHeader(files[i]);
 855       QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
 856       if (!header) {
 857         nSlices[i] = 0;
 858         QString error = "Cannot open file \n";
 859         error += files[i].c_str();
 860         QMessageBox::information(this,tr("Reading problem"),error);
 861         return;
 862       }
 863       if (header->GetNumberOfDimensions() < 3) {
 864         nSlices[i] = 0;
 865         QString error = "Dimension problem. Cannot slice \n";
 866         error += files[i].c_str();
 867         QMessageBox::information(this,tr("Reading problem"),error);
 868         return;
 869       }
 870       nSlices[i] = header->GetDimensions( header->GetNumberOfDimensions()-1 );
 871     }
 872   }
 873
 874   //Only add to the list of recently opened files when a single file is opened,
 875   //to avoid polluting the list of recently opened files
 876   if (files.size() == 1) {
 877     QFileInfo finfo=tr(files[0].c_str());
 878     AddToRecentlyOpenedImages(finfo.absoluteFilePath().toStdString());
 879     updateRecentlyOpenedFilesMenu(GetRecentlyOpenedImages());
 880   }
 881   //init the progress events
 882   QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
 883   vvProgressDialog progress("Opening " + files[0],fileSize>1);
 884   qApp->processEvents();
 885
 886   int numberofsuccesulreads=0;
 887   //open images as 1 or multiples
 888   for (int i = 0; i < fileSize; i++) {
 889     progress.SetText("Opening " + files[i]);
 890     progress.SetProgress(i,fileSize);
 891     qApp->processEvents();
 892
 893     for (unsigned int j = 0; j < nSlices[i]; j++) {
 894       //read the image and put it in mSlicerManagers
 895       vvSlicerManager* imageManager = new vvSlicerManager(4);
 896       qApp->processEvents();
 897
 898       bool SetImageSucceed=false;
 899
 900       // Change filename if an image with the same already exist
 901       int number = GetImageDuplicateFilenameNumber(files[i] + std::string("_slice"));
 902
 903       if (filetype == vvImageReader::IMAGE || filetype == vvImageReader::IMAGEWITHTIME || filetype == vvImageReader::SLICED) {
 904         SetImageSucceed = imageManager->SetImage(files[i],filetype, number, j);
 905       } else {
 906         SetImageSucceed = imageManager->SetImages(files,filetype, number);
 907       }
 908       if (!SetImageSucceed) {
 909         QApplication::restoreOverrideCursor();
 910         QString error = "Cannot open file \n";
 911         error += imageManager->GetLastError().c_str();
 912         QMessageBox::information(this,tr("Reading problem"),error);
 913         delete imageManager;
 914       } else {
 915
 916         mSlicerManagers.push_back(imageManager);
 917
 918         //create an item in the tree with good settings
 919         QTreeWidgetItem *item = new QTreeWidgetItem();
 920         item->setData(0,Qt::UserRole,files[i].c_str());
 921         QFileInfo fileinfo(imageManager->GetFileName().c_str()); //Do not show the path
 922         item->setData(COLUMN_IMAGE_NAME,Qt::DisplayRole,fileinfo.fileName());
 923         item->setData(1,Qt::UserRole,tr("image"));
 924         item->setToolTip(COLUMN_IMAGE_NAME, imageManager->GetListOfAbsoluteFilePathInOneString("image").c_str());
 925         qApp->processEvents();
 926
 927         //Create the buttons for reload and close
 928         qApp->processEvents();
 929         QTreePushButton* cButton = new QTreePushButton;
 930         cButton->setItem(item);
 931         cButton->setColumn(COLUMN_CLOSE_IMAGE);
 932         cButton->setToolTip(tr("close image"));
 933         cButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/exit.png")));
 934         connect(cButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
 935           this,SLOT(CloseImage(QTreeWidgetItem*, int)));
 936
 937         QTreePushButton* rButton = new QTreePushButton;
 938         rButton->setItem(item);
 939         rButton->setColumn(COLUMN_RELOAD_IMAGE);
 940         rButton->setToolTip(tr("reload image"));
 941         rButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/rotateright.png")));
 942         connect(rButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
 943           this,SLOT(ReloadImage(QTreeWidgetItem*, int)));
 944
 945         DataTree->addTopLevelItem(item);
 946         DataTree->setItemWidget(item, COLUMN_CLOSE_IMAGE, cButton);
 947         DataTree->setItemWidget(item, COLUMN_RELOAD_IMAGE, rButton);
 948
 949         //set the id of the image
 950         QString id = QDir::current().absoluteFilePath(files[i].c_str()) + QString::number(mSlicerManagers.size()-1);
 951         item->setData(COLUMN_IMAGE_NAME,Qt::UserRole,id.toStdString().c_str());
 952         mSlicerManagers.back()->SetId(id.toStdString());
 953
 954         linkPanel->addImage(imageManager->GetFileName(), id.toStdString());
 955
 956         connect(mSlicerManagers.back(), SIGNAL(currentImageChanged(std::string)),
 957           this,SLOT(CurrentImageChanged(std::string)));
 958         connect(mSlicerManagers.back(), SIGNAL(currentPickedImageChanged(std::string)),
 959           this, SLOT(CurrentPickedImageChanged(std::string)));
 960         connect(mSlicerManagers.back(), SIGNAL(UpdatePosition(int, double, double, double, double, double, double, double)),
 961           this,SLOT(MousePositionChanged(int,double, double, double, double, double, double, double)));
 962         connect(mSlicerManagers.back(), SIGNAL(UpdateVector(int, double, double, double, double)),
 963           this, SLOT(VectorChanged(int,double,double,double, double)));
 964         connect(mSlicerManagers.back(), SIGNAL(UpdateOverlay(int, double, double)),
 965           this, SLOT(OverlayChanged(int,double,double)));
 966         connect(mSlicerManagers.back(), SIGNAL(UpdateFusion(int, double)),
 967           this, SLOT(FusionChanged(int,double)));
 968         connect(mSlicerManagers.back(), SIGNAL(WindowLevelChanged()),
 969           this,SLOT(WindowLevelChanged()));
 970         connect(mSlicerManagers.back(), SIGNAL(UpdateSlice(int,int)),
 971           this,SLOT(UpdateSlice(int,int)));
 972         connect(mSlicerManagers.back(), SIGNAL(UpdateTSlice(int, int, int)),
 973           this,SLOT(UpdateTSlice(int, int, int)));
 974         connect(mSlicerManagers.back(), SIGNAL(UpdateTSlice(int, int, int)),
 975           this,SLOT(ImageInfoChanged()));
 976         connect(mSlicerManagers.back(), SIGNAL(UpdateSliceRange(int,int,int,int,int)),
 977           this,SLOT(UpdateSliceRange(int,int,int,int,int)));
 978         connect(mSlicerManagers.back(), SIGNAL(UpdateLinkManager(std::string,int,double,double,double,int)),
 979           this,SLOT(UpdateLinkManager(std::string,int,double,double,double,int)));
 980         connect(mSlicerManagers.back(), SIGNAL(UpdateLinkedNavigation(std::string,vvSlicerManager*,vvSlicer*)),
 981           this,SLOT(UpdateLinkedNavigation(std::string,vvSlicerManager*,vvSlicer*)));
 982         connect(mSlicerManagers.back(), SIGNAL(ChangeImageWithIndexOffset(vvSlicerManager*,int,int)),
 983           this,SLOT(ChangeImageWithIndexOffset(vvSlicerManager*,int,int)));
 984         connect(mSlicerManagers.back(),SIGNAL(LandmarkAdded()),landmarksPanel,SLOT(AddPoint()));
 985         InitSlicers();
 986         numberofsuccesulreads++;
 987       }
 988     }
 989   }
 990
 991   if (numberofsuccesulreads) {
 992     NOViewWidget->show();
 993     NEViewWidget->show();
 994     SOViewWidget->show();
 995     SEViewWidget->show();
 996     UpdateTree();
 997     InitDisplay();
 998     ShowLastImage();
 999
1000     // Try to guess default WindowLevel
1001     double range[2];
1002     mSlicerManagers.back()->GetImage()->GetFirstVTKImageData()->GetScalarRange(range);
1003     if ((range[0] == 0) && (range[1] == 1)) {
1004       presetComboBox->setCurrentIndex(WL_BINARY);// binary
1005     } else {
1006       // TODO
1007     }
1008   }
1009   QApplication::restoreOverrideCursor();
1010 }
1011 //------------------------------------------------------------------------------
1012
1013 //------------------------------------------------------------------------------
1014 void vvMainWindow::UpdateTree()
1015 {
1016   DataTree->resizeColumnToContents(COLUMN_TREE);
1017   DataTree->resizeColumnToContents(COLUMN_UL_VIEW);
1018   DataTree->resizeColumnToContents(COLUMN_UR_VIEW);
1019   DataTree->resizeColumnToContents(COLUMN_DL_VIEW);
1020   DataTree->resizeColumnToContents(COLUMN_DR_VIEW);
1021   DataTree->resizeColumnToContents(COLUMN_IMAGE_NAME);
1022   DataTree->resizeColumnToContents(COLUMN_CLOSE_IMAGE);
1023   DataTree->resizeColumnToContents(COLUMN_RELOAD_IMAGE);
1024 }
1025 //------------------------------------------------------------------------------
1026
1027 //------------------------------------------------------------------------------
1028 void vvMainWindow::CurrentImageChanged(std::string id)
1029 {
1030   if (id == mCurrentSelectedImageId) return; // Do nothing
1031   int selected = 0;
1032   for (int i = 0; i < DataTree->topLevelItemCount(); i++) {
1033     if (DataTree->topLevelItem(i)->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString().toStdString() == id) {
1034       selected = i;
1035     } else {
1036       DataTree->topLevelItem(i)->setSelected(0);
1037     }
1038     for (int child = 0; child < DataTree->topLevelItem(i)->childCount(); child++)
1039       DataTree->topLevelItem(i)->child(child)->setSelected(0);
1040
1041   }
1042   DataTree->topLevelItem(selected)->setSelected(1);
1043   mCurrentSelectedImageId = id;
1044
1045   landmarksPanel->SetCurrentLandmarks(mSlicerManagers[selected]->GetLandmarks(),
1046                                       mSlicerManagers[selected]->GetTSlice());
1047   landmarksPanel->SetCurrentPath(mInputPathName.toStdString());
1048   landmarksPanel->SetCurrentImage(mSlicerManagers[selected]->GetFileName().c_str());
1049
1050   emit SelectedImageHasChanged(mSlicerManagers[selected]);
1051 }
1052 //------------------------------------------------------------------------------
1053
1054 //------------------------------------------------------------------------------
1055 void vvMainWindow::CurrentPickedImageChanged(std::string id)
1056 {
1057   if (id == mCurrentPickedImageId) return; // Do nothing
1058   int selected = 0;
1059   for (int i = 0; i < DataTree->topLevelItemCount(); i++) {
1060     if (DataTree->topLevelItem(i)->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString().toStdString() == id) {
1061       selected = i;
1062     } else {
1063       DataTree->topLevelItem(i)->setSelected(0);
1064     }
1065     for (int child = 0; child < DataTree->topLevelItem(i)->childCount(); child++)
1066       DataTree->topLevelItem(i)->child(child)->setSelected(0);
1067
1068   }
1069   DataTree->topLevelItem(selected)->setSelected(1);
1070   mCurrentPickedImageId = id;
1071   mCurrentPickedImageIndex = selected;
1072 }
1073 //------------------------------------------------------------------------------
1074
1075 //------------------------------------------------------------------------------
1076 void vvMainWindow::ImageInfoChanged()
1077 {
1078   contextActions[6]->setEnabled(1);
1079   contextActions[5]->setEnabled(1);
1080   actionSave_As->setEnabled(1);
1081   actionAdd_VF_to_current_Image->setEnabled(1);
1082   actionAdd_fusion_image->setEnabled(1);
1083   actionAdd_overlay_image_to_current_image->setEnabled(1);
1084   actionAdd_USSequence_toCT->setEnabled(1);
1085   actionNorth_East_Window->setEnabled(1);
1086   actionNorth_West_Window->setEnabled(1);
1087   actionSouth_East_Window->setEnabled(1);
1088   actionSouth_West_Window->setEnabled(1);
1089   vvToolManager::GetInstance()->EnableToolsInMenu(this, true);
1090   inverseButton->setEnabled(1);
1091
1092   goToCursorPushButton->setEnabled(1);
1093
1094   if (DataTree->selectedItems().size()) {
1095     int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1096
1097     colorMapComboBox->setEnabled(1);
1098     for (int i = 0; i < DataTree->topLevelItem(index)->childCount(); i++) {
1099       if (DataTree->topLevelItem(index)->child(i)->data(1,Qt::UserRole).toString() == "overlay" ||
1100         DataTree->topLevelItem(index)->child(i)->data(1,Qt::UserRole).toString() == "fusion" ||
1101         DataTree->topLevelItem(index)->child(i)->data(1,Qt::UserRole).toString() == "fusionSequence") {
1102           colorMapComboBox->setEnabled(0);
1103           break;
1104       }
1105     }
1106
1107     std::vector<double> origin;
1108     std::vector<double> inputSpacing;
1109     std::vector<int> inputSize;
1110     std::vector<double> sizeMM;
1111     vtkSmartPointer<vtkMatrix4x4> transformation;
1112     int dimension=0;
1113     QString pixelType;
1114     QString inputSizeInBytes;
1115     QString image = DataTree->selectedItems()[0]->data(COLUMN_IMAGE_NAME,Qt::DisplayRole).toString();
1116
1117     int nframes = mSlicerManagers[index]->GetSlicer(0)->GetTMax();
1118
1119     if (nframes > 1 || playMode == 1) {
1120       playButton->setEnabled(1);
1121       frameRateLabel->setEnabled(1);
1122       frameRateSpinBox->setEnabled(1);
1123     } else {
1124       playButton->setEnabled(0);
1125       frameRateLabel->setEnabled(0);
1126       frameRateSpinBox->setEnabled(0);
1127     }
1128
1129     //read image header
1130     int NPixel = 1;
1131
1132     int tSlice = 0;
1133     vvImage::Pointer imageSelected;
1134     if (DataTree->topLevelItem(index) == DataTree->selectedItems()[0]) {
1135       imageSelected = mSlicerManagers[index]->GetSlicer(0)->GetImage();
1136       tSlice = mSlicerManagers[index]->GetSlicer(0)->GetTSlice();
1137     } else if (DataTree->selectedItems()[0]->data(1,Qt::UserRole).toString() == "vector") {
1138       imageSelected = mSlicerManagers[index]->GetSlicer(0)->GetVF();
1139       tSlice = mSlicerManagers[index]->GetSlicer(0)->GetOverlayTSlice();
1140     } else if (DataTree->selectedItems()[0]->data(1,Qt::UserRole).toString() == "overlay") {
1141       imageSelected = mSlicerManagers[index]->GetSlicer(0)->GetOverlay();
1142       tSlice = mSlicerManagers[index]->GetSlicer(0)->GetOverlayTSlice();
1143     } else if (DataTree->selectedItems()[0]->data(1,Qt::UserRole).toString() == "fusion") {
1144       imageSelected = mSlicerManagers[index]->GetSlicer(0)->GetFusion();
1145       tSlice = mSlicerManagers[index]->GetSlicer(0)->GetFusionTSlice();
1146     }
1147     else if (DataTree->selectedItems()[0]->data(1,Qt::UserRole).toString() == "fusionSequence") {
1148       imageSelected = mSlicerManagers[index]->GetSlicer(0)->GetFusion();
1149       tSlice = mSlicerManagers[index]->GetSlicer(0)->GetFusionTSlice();
1150     }
1151     else if (DataTree->selectedItems()[0]->data(1,Qt::UserRole).toString() == "contour") {
1152       imageSelected = mSlicerManagers[index]->GetSlicer(0)->GetImage();
1153       tSlice = mSlicerManagers[index]->GetSlicer(0)->GetTSlice();
1154     }
1155     else {
1156       imageSelected = mSlicerManagers[index]->GetSlicer(0)->GetImage();
1157       tSlice = mSlicerManagers[index]->GetSlicer(0)->GetTSlice();
1158     }
1159
1160     dimension = imageSelected->GetNumberOfDimensions();
1161     origin.resize(dimension);
1162     inputSpacing.resize(dimension);
1163     inputSize.resize(dimension);
1164     sizeMM.resize(dimension);
1165     pixelType = mSlicerManagers[index]->GetImage()->GetScalarTypeAsITKString().c_str();
1166     for (int i = 0; i < dimension; i++) {
1167       origin[i] = imageSelected->GetOrigin()[i];
1168       inputSpacing[i] = imageSelected->GetSpacing()[i];
1169       inputSize[i] = imageSelected->GetSize()[i];
1170       sizeMM[i] = inputSize[i]*inputSpacing[i];
1171       NPixel *= inputSize[i];
1172     }
1173     inputSizeInBytes = GetSizeInBytes(imageSelected->GetActualMemorySize()*1000);
1174
1175     QString dim = QString::number(dimension) + " (";
1176     dim += pixelType + ")";
1177
1178     infoPanel->setFileName(image);
1179     std::string creationImageTimeValue("No creation time");
1180     itk::ExposeMetaData< std::string > (*imageSelected->GetFirstMetaDataDictionary(), "creationImageTime", creationImageTimeValue);
1181     infoPanel->setImageCreationTime(QString(creationImageTimeValue.c_str()));
1182     infoPanel->setDimension(dim);
1183     infoPanel->setSizePixel(GetVectorIntAsString(inputSize));
1184     infoPanel->setSizeMM(GetVectorDoubleAsString(sizeMM));
1185     infoPanel->setOrigin(GetVectorDoubleAsString(origin));
1186     infoPanel->setSpacing(GetVectorDoubleAsString(inputSpacing));
1187     infoPanel->setNPixel(QString::number(NPixel)+" ("+inputSizeInBytes+")");
1188
1189     transformation = imageSelected->GetTransform()[tSlice]->GetMatrix();
1190     infoPanel->setTransformation(clitk::Get4x4MatrixDoubleAsString(transformation).c_str());
1191
1192     landmarksPanel->SetCurrentLandmarks(mSlicerManagers[index]->GetLandmarks(),
1193                                         mSlicerManagers[index]->GetTSlice());
1194     landmarksPanel->SetCurrentPath(mInputPathName.toStdString());
1195     landmarksPanel->SetCurrentImage(mSlicerManagers[index]->GetFileName().c_str());
1196
1197     overlayPanel->getCurrentImageName(mSlicerManagers[index]->GetFileName().c_str());
1198     for (int i = 0; i < 4; i++) {
1199       if (DataTree->selectedItems()[0]->data(i+1,Qt::CheckStateRole).toInt() > 0 || i == 3) {
1200         mSlicerManagers[index]->UpdateInfoOnCursorPosition(i);
1201         break;
1202       }
1203     }
1204
1205 //     infoPanel->setFileName(image);
1206 //     infoPanel->setDimension(dim);
1207 //     infoPanel->setSizePixel(GetVectorIntAsString(inputSize));
1208 //     infoPanel->setSizeMM(GetVectorDoubleAsString(sizeMM));
1209 //     infoPanel->setOrigin(GetVectorDoubleAsString(origin));
1210 //     infoPanel->setSpacing(GetVectorDoubleAsString(inputSpacing));
1211 //     infoPanel->setNPixel(QString::number(NPixel)+" ("+inputSizeInBytes+")");
1212 //
1213 //     landmarksPanel->SetCurrentLandmarks(mSlicerManagers[index]->GetLandmarks(),
1214 //                                         mSlicerManagers[index]->GetTSlice());
1215 //     landmarksPanel->SetCurrentPath(mInputPathName.toStdString());
1216 //     landmarksPanel->SetCurrentImage(mSlicerManagers[index]->GetFileName().c_str());
1217 //
1218 //     overlayPanel->getCurrentImageName(mSlicerManagers[index]->GetFileName().c_str());
1219 //     for (int i = 0; i < 4; i++) {
1220 //       if (DataTree->selectedItems()[0]->data(i+1,Qt::CheckStateRole).toInt() > 0 || i == 3) {
1221 //         mSlicerManagers[index]->UpdateInfoOnCursorPosition(i);
1222 //         break;
1223 //       }
1224 //     }
1225     WindowLevelChanged();
1226
1227     slicingPresetComboBox->setCurrentIndex(mSlicerManagers[index]->GetSlicingPreset());
1228
1229     if (mSlicerManagers[index]->GetSlicer(0)->GetVF()) {
1230       overlayPanel->getVFName(mSlicerManagers[index]->GetVFName().c_str());
1231       overlayPanel->getVFProperty(mSlicerManagers[index]->GetSlicer(0)->GetVFSubSampling(),
1232         mSlicerManagers[index]->GetSlicer(0)->GetVFScale(),
1233         mSlicerManagers[index]->GetSlicer(0)->GetVFLog());
1234     } else {
1235       overlayPanel->getVFName(mSlicerManagers[index]->GetVFName().c_str());
1236       overlayPanel->getVFProperty(-1,-1,-1);
1237     }
1238     if (mSlicerManagers[index]->GetSlicer(0)->GetOverlay()) {
1239       overlayPanel->getOverlayName(mSlicerManagers[index]->GetOverlayName().c_str());
1240     } else {
1241       overlayPanel->getOverlayName(mSlicerManagers[index]->GetOverlayName().c_str());
1242     }
1243
1244     if (mSlicerManagers[index]->GetSlicer(0)->GetFusion()) {
1245       overlayPanel->getFusionName(mSlicerManagers[index]->GetFusionName().c_str());
1246     } else {
1247       overlayPanel->getFusionName(mSlicerManagers[index]->GetFusionName().c_str());
1248     }
1249   }
1250 }
1251 //------------------------------------------------------------------------------
1252
1253 //------------------------------------------------------------------------------
1254 void vvMainWindow::ShowDocumentation()
1255 {
1256   documentation->show();
1257 }
1258 //------------------------------------------------------------------------------
1259
1260 //------------------------------------------------------------------------------
1261 void vvMainWindow::PopupRegisterForm(bool checkCanPush)
1262 {
1263   vvRegisterForm* registerForm = new vvRegisterForm(QUrl("http://www.creatis.insa-lyon.fr/~dsarrut/vvregister/write.php"), getVVSettingsPath(), getSettingsOptionFormat());
1264   if(!checkCanPush) {
1265     registerForm->show();
1266   } else {
1267     if(registerForm->canPush()) {
1268       registerForm->show();
1269       registerForm->acquitPushed();//too bad if there is not internet connection anymore.
1270     }
1271   }
1272 }
1273 //------------------------------------------------------------------------------
1274
1275 //------------------------------------------------------------------------------
1276 void vvMainWindow::ShowHelpDialog()
1277 {
1278   help_dialog->show();
1279 }
1280 //------------------------------------------------------------------------------
1281
1282 //------------------------------------------------------------------------------
1283 void vvMainWindow::ChangeViewMode()
1284 {
1285   typedef struct _SIZE{
1286     QSplitter* splitter;
1287     QList<int> size1, size2;
1288     int cols[3];
1289   }SplitterSize;
1290   SplitterSize sizes[4];
1291   sizes[0].splitter = OSplitter;
1292   sizes[0].size1.push_back(1);
1293   sizes[0].size1.push_back(0);
1294   sizes[0].size2.push_back(1);
1295   sizes[0].size2.push_back(0);
1296   sizes[0].cols[0] = 2;
1297   sizes[0].cols[1] = 3;
1298   sizes[0].cols[2] = 4;
1299
1300   sizes[1].splitter = ESplitter;
1301   sizes[1].size1.push_back(0);
1302   sizes[1].size1.push_back(1);
1303   sizes[1].size2.push_back(1);
1304   sizes[1].size2.push_back(0);
1305   sizes[1].cols[0] = 1;
1306   sizes[1].cols[1] = 3;
1307   sizes[1].cols[2] = 4;
1308
1309   sizes[2].splitter = OSplitter;
1310   sizes[2].size1.push_back(1);
1311   sizes[2].size1.push_back(0);
1312   sizes[2].size2.push_back(0);
1313   sizes[2].size2.push_back(1);
1314   sizes[2].cols[0] = 1;
1315   sizes[2].cols[1] = 2;
1316   sizes[2].cols[2] = 4;
1317
1318   sizes[3].splitter = ESplitter;
1319   sizes[3].size1.push_back(0);
1320   sizes[3].size1.push_back(1);
1321   sizes[3].size2.push_back(0);
1322   sizes[3].size2.push_back(1);
1323   sizes[3].cols[0] = 1;
1324   sizes[3].cols[1] = 2;
1325   sizes[3].cols[2] = 3;
1326
1327   int slicer = mSlicerManagers[mCurrentPickedImageIndex]->GetSelectedSlicer();
1328   if (viewMode == 1) {
1329     if (slicer >= 0) {
1330       viewMode = 0;
1331       splitter_3->setSizes(sizes[slicer].size1);
1332       sizes[slicer].splitter->setSizes(sizes[slicer].size2);
1333       DataTree->setColumnHidden(sizes[slicer].cols[0],1);
1334       DataTree->setColumnHidden(sizes[slicer].cols[1],1);
1335       DataTree->setColumnHidden(sizes[slicer].cols[2],1);
1336     }
1337   } else {
1338     QList<int> size;
1339     if (slicer >= 0) {
1340       viewMode = 1;
1341       size.push_back(1);
1342       size.push_back(1);
1343       splitter_3->setSizes(size);
1344       sizes[slicer].splitter->setSizes(size);
1345       DataTree->setColumnHidden(sizes[slicer].cols[0],0);
1346       DataTree->setColumnHidden(sizes[slicer].cols[1],0);
1347       DataTree->setColumnHidden(sizes[slicer].cols[2],0);
1348     }
1349   }
1350   UpdateRenderWindows();
1351   /*
1352   ** I don't know why but for both resized QVTKWidget we also need to render
1353   ** the associated Slicer to redraw crosses.
1354   */
1355   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
1356     //     if (DataTree->topLevelItem(i)->data(COLUMN_UL_VIEW,Qt::CheckStateRole).toInt() > 1)
1357     mSlicerManagers[i]->GetSlicer(0)->Render();
1358     mSlicerManagers[i]->GetSlicer(1)->Render();
1359     //     if (DataTree->topLevelItem(i)->data(COLUMN_DL_VIEW,Qt::CheckStateRole).toInt() > 1)
1360     mSlicerManagers[i]->GetSlicer(2)->Render();
1361     mSlicerManagers[i]->GetSlicer(3)->Render();
1362   }
1363 }
1364 //------------------------------------------------------------------------------
1365
1366 //------------------------------------------------------------------------------
1367 QString vvMainWindow::GetSizeInBytes(unsigned long size)
1368 {
1369   QString result = "";// QString::number(size);
1370   //result += " bytes (";
1371   if (size > 1000000000) {
1372     size /= 1000000000;
1373     result += QString::number(size);
1374     result += "Gb";//)";
1375   } else if (size > 1000000) {
1376     size /= 1000000;
1377     result += QString::number(size);
1378     result += "Mb";//)";
1379   } else if (size > 1000) {
1380     size /= 1000;
1381     result += QString::number(size);
1382     result += "kb";//)";
1383   }
1384   return result;
1385 }
1386 //------------------------------------------------------------------------------
1387
1388 //------------------------------------------------------------------------------
1389 QString vvMainWindow::GetVectorDoubleAsString(std::vector<double> vectorDouble)
1390 {
1391   QString result;
1392   for (unsigned int i= 0; i < vectorDouble.size(); i++) {
1393     if (i != 0)
1394       result += " ";
1395     result += QString::number(vectorDouble[i]);
1396   }
1397   return result;
1398 }
1399 //------------------------------------------------------------------------------
1400
1401 //------------------------------------------------------------------------------
1402 QString vvMainWindow::GetVectorIntAsString(std::vector<int> vectorInt)
1403 {
1404   QString result;
1405   for (unsigned int i= 0; i < vectorInt.size(); i++) {
1406     if (i != 0)
1407       result += " ";
1408     result += QString::number(vectorInt[i]);
1409   }
1410   return result;
1411 }
1412 //------------------------------------------------------------------------------
1413
1414 //------------------------------------------------------------------------------
1415 //this actually returns the SlicerManager index!
1416 int vvMainWindow::GetSlicerIndexFromItem(QTreeWidgetItem* item)
1417 {
1418   QString id = item->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString();
1419   for (int i = 0; i < DataTree->topLevelItemCount(); i++) {
1420     if (DataTree->topLevelItem(i)->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString() == id)
1421       return i;
1422   }
1423   return -1;
1424 }
1425 //------------------------------------------------------------------------------
1426
1427 //------------------------------------------------------------------------------
1428 QTreeWidgetItem* vvMainWindow::GetItemFromSlicerManager(vvSlicerManager* sm)
1429 {
1430   QString id = sm->GetId().c_str();
1431   for (int i = 0; i < DataTree->topLevelItemCount(); i++) {
1432     if (DataTree->topLevelItem(i)->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString() == id)
1433       return DataTree->topLevelItem(i);
1434   }
1435   return NULL;
1436 }
1437 //------------------------------------------------------------------------------
1438
1439 //------------------------------------------------------------------------------
1440 void vvMainWindow::DisplayChanged(QTreeWidgetItem *clickedItem, int column)
1441 {
1442   if ( column >= COLUMN_CLOSE_IMAGE || column <= 0)
1443     return;
1444
1445   // Get parent information (might be the same item)
1446   int slicerManagerIndex = GetSlicerIndexFromItem(clickedItem);
1447   QTreeWidgetItem* clickedParentItem = DataTree->topLevelItem(slicerManagerIndex);
1448   vvSlicer* clickedSlicer = mSlicerManagers[slicerManagerIndex]->GetSlicer(column-1);
1449
1450   // Go over the complete item tree (only 2 levels, parents and children)
1451   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
1452     // Trick to avoid redoing twice the job for a key (sr)
1453     mSlicerManagers[i]->GetSlicer(column-1)->GetRenderWindow()->GetInteractor()->SetKeySym("Crap");
1454
1455     QTreeWidgetItem* currentParentItem = DataTree->topLevelItem(i);
1456     if(currentParentItem != clickedParentItem) {
1457       // Not the branch of the clicked item, uncheck all
1458
1459       // Parent
1460       currentParentItem->setData(column,Qt::CheckStateRole, 0);
1461       mSlicerManagers[i]->UpdateSlicer(column-1, false);
1462
1463       // Children
1464       for (int iChild = 0; iChild < currentParentItem->childCount(); iChild++) {
1465         currentParentItem->child(iChild)->setData(column,Qt::CheckStateRole, 0);
1466       }
1467     }
1468     else {
1469       // Branch of the clicked one: get check status from actor visibility in slicer
1470       // and toggle the clicked one
1471
1472       // Parent
1473       bool vis = clickedSlicer->GetActorVisibility("image", 0);
1474       bool draw = clickedSlicer->GetRenderer()->GetDraw();
1475
1476       // Update slicer (after getting visibility)
1477       mSlicerManagers[slicerManagerIndex]->UpdateSlicer(column-1, true);
1478       mSlicerManagers[slicerManagerIndex]->UpdateInfoOnCursorPosition(column-1);
1479       DisplaySliders(slicerManagerIndex, column-1);
1480       if(clickedParentItem == clickedItem) {
1481         // Toggle
1482         vis = !draw || !vis;
1483       }
1484       clickedSlicer->SetActorVisibility("image", 0, vis);
1485       clickedParentItem->setData(column, Qt::CheckStateRole, vis?2:0);
1486
1487       // Children
1488       std::map<std::string, int> actorTypeCounts;
1489       for (int iChild = 0; iChild < clickedParentItem->childCount(); iChild++) {
1490         QTreeWidgetItem* currentChildItem = clickedParentItem->child(iChild);
1491         std::string actorType = currentChildItem->data(1,Qt::UserRole).toString().toStdString();
1492         vis = clickedSlicer->GetActorVisibility(actorType, actorTypeCounts[actorType]);
1493         if(currentChildItem == clickedItem) {
1494           // Toggle or force visibility if it was not on this branch so far
1495           vis = !draw || !vis;
1496           clickedSlicer->SetActorVisibility(actorType, actorTypeCounts[actorType], vis);
1497         }
1498         currentChildItem->setData(column, Qt::CheckStateRole, vis?2:0);
1499         actorTypeCounts[actorType]++;
1500       }
1501     }
1502   }
1503
1504   clickedSlicer->Render();
1505 }
1506 //------------------------------------------------------------------------------
1507
1508 void vvMainWindow::InitSlicers()
1509 {
1510   if (mSlicerManagers.size()) {
1511     mSlicerManagers.back()->GenerateDefaultLookupTable();
1512     mSlicerManagers.back()->SetSlicerWindow(0,NOViewWidget->GetRenderWindow());
1513     mSlicerManagers.back()->SetSlicerWindow(1,NEViewWidget->GetRenderWindow());
1514     mSlicerManagers.back()->SetSlicerWindow(2,SOViewWidget->GetRenderWindow());
1515     mSlicerManagers.back()->SetSlicerWindow(3,SEViewWidget->GetRenderWindow());
1516 #if VTK_MAJOR_VERSION <= 5
1517     mSlicerManagers.back()->Render(); // SR: displayed #slice is wrong without this / TB: With VTK6 and multiple images, all slicers are updated, not only the first
1518 #endif
1519   }
1520 }
1521
1522 //------------------------------------------------------------------------------
1523 void vvMainWindow::InitDisplay()
1524 {
1525   if (mSlicerManagers.size()) {
1526     //BE CAREFUL : this is absolutely necessary to set the interactor style
1527     //in order to have the same style instanciation for all SlicerManagers in
1528     // a same window
1529     for (int j = 0; j < 4; j++) {
1530       vvInteractorStyleNavigator* style = vvInteractorStyleNavigator::New();
1531       style->SetAutoAdjustCameraClippingRange(1);
1532       bool AlreadySelected = false;
1533       for (int i = 0; i < DataTree->topLevelItemCount(); i++) {
1534         mSlicerManagers[i]->SetInteractorStyleNavigator(j,style);
1535         //select the image only if previous are not selected
1536         if (DataTree->topLevelItem(i)->data(j+1,Qt::CheckStateRole).toInt() > 1) {
1537           mSlicerManagers[i]->UpdateSlicer(j,1);
1538           AlreadySelected = true;
1539         } else if (i == DataTree->topLevelItemCount()-1 && !AlreadySelected) {
1540           if (DataTree->selectedItems().size() == 0) {
1541             DataTree->topLevelItem(i)->setSelected(1);
1542           }
1543           DataTree->topLevelItem(i)->setData(j+1,Qt::CheckStateRole,2);
1544           mSlicerManagers[i]->UpdateSlicer(j,1);
1545           DisplaySliders(i,j);
1546         } else {
1547           DataTree->topLevelItem(i)->setData(j+1,Qt::CheckStateRole,0);
1548           mSlicerManagers[i]->UpdateSlicer(j,0);
1549         }
1550       }
1551       style->Delete();
1552     }
1553   }
1554 }
1555 //------------------------------------------------------------------------------
1556
1557 //------------------------------------------------------------------------------
1558 void vvMainWindow::DisplaySliders(int slicer, int window)
1559 {
1560   if(!mSlicerManagers[slicer]->GetSlicer(window)->GetRenderer()->GetDraw())
1561     return;
1562
1563   int range[2];
1564   mSlicerManagers[slicer]->GetSlicer(window)->GetSliceRange(range);
1565   int position = mSlicerManagers[slicer]->GetSlicer(window)->GetSlice();
1566   if (range[1]>0)
1567     verticalSliders[window]->show();
1568   else
1569     verticalSliders[window]->hide();
1570   verticalSliders[window]->setRange(range[0],range[1]);
1571   verticalSliders[window]->setValue(position);
1572
1573   int tRange[2];
1574   tRange[0] = 0;
1575   tRange[1] = mSlicerManagers[slicer]->GetSlicer(window)->GetTMax();
1576   if (tRange[1]>0)
1577     horizontalSliders[window]->show();
1578   else
1579     horizontalSliders[window]->hide();
1580   horizontalSliders[window]->setRange(tRange[0],tRange[1]);
1581   int tPosition = mSlicerManagers[slicer]->GetSlicer(window)->GetMaxCurrentTSlice();
1582   horizontalSliders[window]->setValue(tPosition);
1583 }
1584 //------------------------------------------------------------------------------
1585
1586 //------------------------------------------------------------------------------
1587 void vvMainWindow::CloseImage(QTreeWidgetItem* item, int column)
1588 {
1589   int index = GetSlicerIndexFromItem(item);
1590
1591   if (DataTree->topLevelItem(index) != item) {
1592     QString warning = "Do you really want to close the overlay : ";
1593     warning += item->data(COLUMN_IMAGE_NAME,Qt::DisplayRole).toString();
1594     QMessageBox msgBox(QMessageBox::Warning, tr("Close Overlay"),
1595       warning, 0, this);
1596     msgBox.addButton(tr("Close"), QMessageBox::AcceptRole);
1597     msgBox.addButton(tr("Cancel"), QMessageBox::RejectRole);
1598     if (msgBox.exec() == QMessageBox::AcceptRole) {
1599       std::string overlay_type=item->data(1,Qt::UserRole).toString().toStdString();
1600       int overlay_index=0;
1601       for (int child = 0; child < DataTree->topLevelItem(index)->childCount(); child++) {
1602         if (DataTree->topLevelItem(index)->\
1603           child(child)->data(1,Qt::UserRole).toString().toStdString() == overlay_type)
1604           overlay_index++;
1605         if (DataTree->topLevelItem(index)->child(child) == item) break;
1606       }
1607       if (overlay_type=="fusionSequence") {
1608         //removing the overlay sequence in a fusion sequence visualization mode
1609         //reset the transforms
1610         overlayPanel->getFusionSequenceProperty(-1, false, 0, false);
1611
1612         //unlink and untie the slicer managers
1613         RemoveLink(mSlicerManagers[index]->GetId().c_str(), mSlicerManagers[mSlicerManagers[index]->GetFusionSequenceIndexOfLinkedManager()]->GetId().c_str());
1614         mSlicerManagers[index]->SetFusionSequenceInvolvmentCode(-1);
1615         mSlicerManagers[mSlicerManagers[index]->GetFusionSequenceIndexOfLinkedManager()]->SetFusionSequenceInvolvmentCode(-1);
1616         for (unsigned i=0 ; i<4 ; i++) {
1617             mSlicerManagers[index]->GetSlicer(i)->SetFusionSequenceCode(-1);
1618             mSlicerManagers[mSlicerManagers[index]->GetFusionSequenceIndexOfLinkedManager()]->GetSlicer(i)->SetFusionSequenceCode(-1);
1619         }
1620
1621       }
1622       mSlicerManagers[index]->RemoveActor(overlay_type, overlay_index-1);
1623       mSlicerManagers[index]->SetColorMap(0);
1624       DataTree->topLevelItem(index)->takeChild(DataTree->topLevelItem(index)->indexOfChild(item));
1625       mSlicerManagers[index]->Render();
1626     }
1627   } else if (DataTree->topLevelItemCount() <= 1) {
1628     QString warning = "Do you really want to close the image : ";
1629     warning += item->data(COLUMN_IMAGE_NAME,Qt::DisplayRole).toString();
1630     warning += "\nThis is the last image, you're about to close vv !!!";
1631     QMessageBox msgBox(QMessageBox::Warning, tr("Close Image"),
1632       warning, 0, this);
1633     msgBox.addButton(tr("Close vv"), QMessageBox::AcceptRole);
1634     msgBox.addButton(tr("Cancel"), QMessageBox::RejectRole);
1635     if (msgBox.exec() == QMessageBox::AcceptRole) {
1636       this->close();
1637     }
1638   } else {
1639     QString warning = "Do you really want to close the image : ";
1640     warning += item->data(COLUMN_IMAGE_NAME,Qt::DisplayRole).toString();
1641     QMessageBox msgBox(QMessageBox::Warning, tr("Close Image"),
1642       warning, 0, this);
1643     msgBox.addButton(tr("Close"), QMessageBox::AcceptRole);
1644     msgBox.addButton(tr("Cancel"), QMessageBox::RejectRole);
1645     if (msgBox.exec() == QMessageBox::AcceptRole) {
1646
1647       // Tell tools that we close an image
1648       emit AnImageIsBeingClosed(mSlicerManagers[index]);
1649
1650       std::vector<vvSlicerManager*>::iterator Manageriter = mSlicerManagers.begin();
1651       DataTree->takeTopLevelItem(index);
1652       for (int i = 0; i < index; i++) {
1653         Manageriter++;
1654       }
1655       //if the slicer manager was involved in a fusion sequence visualization...
1656       if ( mSlicerManagers[index]->IsInvolvedInFusionSequence() ) {
1657         //in both cases, close the overlay: find it... and close it
1658         //ideally, I should duplicate the code, and avoid calling CloseImage, since this pops up another interactive box
1659         QTreeWidgetItem* overlayItem;
1660         if (mSlicerManagers[index]->IsMainSequenceOfFusionSequence()) {
1661           for (unsigned i=0 ; i<item->childCount() ; i++) {
1662             overlayItem = item->child(i);
1663             this->CloseImage( overlayItem, 0 );
1664           }
1665         }
1666         else {
1667           QTreeWidgetItem* linkedItem = this->GetItemFromSlicerManager( mSlicerManagers[mSlicerManagers[index]->GetFusionSequenceIndexOfLinkedManager()] );
1668           for (unsigned i=0 ; i<linkedItem->childCount() ; i++) {
1669             overlayItem = linkedItem->child(i);
1670             this->CloseImage( overlayItem, 0 );
1671           }
1672         }
1673
1674         /* -- this is normally already done when closing the overlay.
1675         //reset the transforms
1676         overlayPanel->getFusionSequenceProperty(-1, false, 0, false);
1677
1678         //unlink and untie the slicer managers
1679         RemoveLink(mSlicerManagers[index]->GetId().c_str(), mSlicerManagers[mSlicerManagers[index]->GetFusionSequenceIndexOfLinkedManager()]->GetId().c_str());
1680         mSlicerManagers[index]->SetFusionSequenceInvolvmentCode(-1);
1681         mSlicerManagers[mSlicerManagers[index]->GetFusionSequenceIndexOfLinkedManager()]->SetFusionSequenceInvolvmentCode(-1);
1682         for (unsigned i=0 ; i<4 ; i++) {
1683             mSlicerManagers[index]->GetSlicer(i)->SetFusionSequenceCode(-1);
1684             mSlicerManagers[mSlicerManagers[index]->GetFusionSequenceIndexOfLinkedManager()]->GetSlicer(i)->SetFusionSequenceCode(-1);
1685         }
1686         */
1687       }
1688
1689       linkPanel->removeImage(index);
1690       mSlicerManagers[index]->RemoveActors();
1691
1692       //remove the slicer manager
1693       delete mSlicerManagers[index];
1694       mSlicerManagers.erase(Manageriter);
1695
1696       //
1697       InitDisplay();
1698     }
1699   }
1700   ImageInfoChanged();
1701 }
1702 //------------------------------------------------------------------------------
1703
1704 //------------------------------------------------------------------------------
1705 void vvMainWindow::ReloadImage(QTreeWidgetItem* item, int column)
1706 {
1707   // int index = GetSlicerIndexFromItem(item);
1708   //   QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
1709   //   if (item->data(1,Qt::UserRole).toString() == "vector")
1710   //     mSlicerManagers[index]->ReloadVF();
1711   //   else
1712   //     mSlicerManagers[index]->Reload();
1713
1714   //   QApplication::restoreOverrideCursor();
1715   int index = GetSlicerIndexFromItem(item);
1716   QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
1717   QString role=item->data(1,Qt::UserRole).toString();
1718   if ( role == "vector") {
1719     mSlicerManagers[index]->ReloadVF();
1720   }
1721   else if (role == "overlay") {
1722     mSlicerManagers[index]->ReloadOverlay();
1723   }
1724   else if (role == "fusion") {
1725     mSlicerManagers[index]->ReloadFusion();
1726   }
1727   else if (role == "fusionSequence") {
1728     //both versions of the secondary sequence must be updated.
1729     mSlicerManagers[index]->ReloadFusionSequence();
1730     mSlicerManagers[mSlicerManagers[index]->GetFusionSequenceIndexOfLinkedManager()]->Reload();
1731   }
1732   else {
1733     mSlicerManagers[index]->Reload();
1734     //if we update the secondary sequence, then the overlay of the main sequence should also be updated
1735     if (mSlicerManagers[index]->IsSecondarySequenceOfFusionSequence()) mSlicerManagers[mSlicerManagers[index]->GetFusionSequenceIndexOfLinkedManager()]->ReloadFusionSequence();
1736   }
1737   // Update view and info
1738   ImageInfoChanged();
1739   mSlicerManagers[index]->Render();
1740   QApplication::restoreOverrideCursor();
1741 }
1742 //------------------------------------------------------------------------------
1743
1744 //------------------------------------------------------------------------------
1745 void vvMainWindow::MousePositionChanged(int visibility,double x, double y, double z, double X, double Y, double Z , double value)
1746 {
1747   infoPanel->setCurrentInfo(visibility,x,y,z,X,Y,Z,value);
1748 }
1749 //------------------------------------------------------------------------------
1750
1751 //------------------------------------------------------------------------------
1752 void vvMainWindow::VectorChanged(int visibility,double x, double y, double z, double value)
1753 {
1754   overlayPanel->getCurrentVectorInfo(visibility,x,y,z,value);
1755 }
1756 //------------------------------------------------------------------------------
1757
1758 //------------------------------------------------------------------------------
1759 void vvMainWindow::OverlayChanged(int visibility, double valueOver, double valueRef)
1760 {
1761   overlayPanel->getCurrentOverlayInfo(visibility,valueOver, valueRef);
1762 }
1763 //------------------------------------------------------------------------------
1764
1765 //------------------------------------------------------------------------------
1766 void vvMainWindow::FusionChanged(int visibility, double value)
1767 {
1768   overlayPanel->getCurrentFusionInfo(visibility,value);
1769 }
1770 //------------------------------------------------------------------------------
1771
1772 //------------------------------------------------------------------------------
1773 //called when AddOverlayImage, AddFusionSequence
1774 //or when UpdateWindowLevel() is called ; when slicerManager emits WindowLevelChanged
1775 //when ImageInfoChanged() is called
1776 void vvMainWindow::WindowLevelChanged()
1777 {
1778   // Base image
1779   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1780   if(index==-1) return;
1781   windowSpinBox->setValue(mSlicerManagers[index]->GetColorWindow());
1782   levelSpinBox->setValue(mSlicerManagers[index]->GetColorLevel());
1783   colorMapComboBox->setCurrentIndex(mSlicerManagers[index]->GetColorMap());
1784   presetComboBox->setCurrentIndex(mSlicerManagers[index]->GetPreset());
1785
1786   // Overlay image
1787   if (mSlicerManagers[index]->GetSlicer(0)->GetOverlay())
1788     overlayPanel->getOverlayProperty(mSlicerManagers[index]->GetOverlayColor(),
1789     mSlicerManagers[index]->GetLinkOverlayWindowLevel(),
1790     mSlicerManagers[index]->GetOverlayColorWindow(),
1791     mSlicerManagers[index]->GetOverlayColorLevel());
1792   else
1793     overlayPanel->getOverlayProperty(-1,0,0.,0.);
1794
1795   // Fusion & SequenceFusion image
1796   if (mSlicerManagers[index]->GetSlicer(0)->GetFusion()) {
1797     overlayPanel->getFusionProperty(mSlicerManagers[index]->GetFusionOpacity(),
1798       mSlicerManagers[index]->GetFusionThresholdOpacity(),
1799       mSlicerManagers[index]->GetFusionColorMap(),
1800       mSlicerManagers[index]->GetFusionWindow(),
1801       mSlicerManagers[index]->GetFusionLevel());
1802     if (mSlicerManagers[index]->IsMainSequenceOfFusionSequence()) {
1803       overlayPanel->getFusionSequenceProperty(mSlicerManagers[index]->GetFusionSequenceFrameIndex(),
1804         mSlicerManagers[index]->GetFusionSequenceSpatialSyncFlag(),
1805         mSlicerManagers[index]->GetFusionSequenceNbFrames(),
1806         mSlicerManagers[index]->GetFusionSequenceTemporalSyncFlag());
1807     }
1808   }
1809   else if ( mSlicerManagers[index]->IsSecondarySequenceOfFusionSequence() ) {
1810     //if the image is involved in a fusion sequence, preserve the overlay panel!
1811     int ind = mSlicerManagers[index]->GetFusionSequenceIndexOfLinkedManager();
1812     overlayPanel->getFusionProperty(mSlicerManagers[ind]->GetFusionOpacity(),
1813       mSlicerManagers[ind]->GetFusionThresholdOpacity(),
1814       mSlicerManagers[ind]->GetFusionColorMap(),
1815       mSlicerManagers[ind]->GetFusionWindow(),
1816       mSlicerManagers[ind]->GetFusionLevel());
1817     overlayPanel->getFusionSequenceProperty(mSlicerManagers[ind]->GetFusionSequenceFrameIndex(),
1818       mSlicerManagers[ind]->GetFusionSequenceSpatialSyncFlag(),
1819       mSlicerManagers[ind]->GetFusionSequenceNbFrames(),
1820       mSlicerManagers[ind]->GetFusionSequenceTemporalSyncFlag());
1821   }
1822   else
1823   {
1824     overlayPanel->getFusionProperty(-1, -1, -1, -1, -1);
1825     overlayPanel->getFusionSequenceProperty(-1, false, 0, false);
1826   }
1827 }
1828 //------------------------------------------------------------------------------
1829
1830 //------------------------------------------------------------------------------
1831 void vvMainWindow::WindowLevelEdited()
1832 {
1833   presetComboBox->setCurrentIndex(WL_USER);
1834   UpdateWindowLevel();
1835 }
1836 //------------------------------------------------------------------------------
1837
1838 //------------------------------------------------------------------------------
1839 void vvMainWindow::SetWindowLevel(double w, double l)
1840 {
1841   windowSpinBox->setValue(w);
1842   levelSpinBox->setValue(l);
1843   presetComboBox->setCurrentIndex(WL_USER);
1844   colorMapComboBox->setCurrentIndex(0);
1845   UpdateWindowLevel();
1846 }
1847 //------------------------------------------------------------------------------
1848
1849 //------------------------------------------------------------------------------
1850 void vvMainWindow::UpdateWindowLevel()
1851 {
1852   if (DataTree->selectedItems().size()) {
1853     if (presetComboBox->currentIndex() == WL_VENTILATION) //For ventilation
1854       colorMapComboBox->setCurrentIndex(5);
1855     int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1856     mSlicerManagers[index]->SetColorWindow(windowSpinBox->value());
1857     mSlicerManagers[index]->SetColorLevel(levelSpinBox->value());
1858     mSlicerManagers[index]->SetPreset(presetComboBox->currentIndex());
1859     mSlicerManagers[index]->Render();
1860     WindowLevelChanged();
1861   }
1862 }
1863 //------------------------------------------------------------------------------
1864
1865 //------------------------------------------------------------------------------
1866 void vvMainWindow::UpdateSlicingPreset()
1867 {
1868   if (DataTree->selectedItems().size()) {
1869     int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1870     mSlicerManagers[index]->SetSlicingPreset(vvSlicerManager::SlicingPresetType(slicingPresetComboBox->currentIndex()));
1871   }
1872 }
1873 //------------------------------------------------------------------------------
1874
1875 //------------------------------------------------------------------------------
1876 void vvMainWindow::UpdateColorMap()
1877 {
1878   if (DataTree->selectedItems().size()) {
1879     int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1880     mSlicerManagers[index]->SetColorMap(colorMapComboBox->currentIndex());
1881     mSlicerManagers[index]->Render();
1882   }
1883 }
1884 //------------------------------------------------------------------------------
1885 void vvMainWindow::SwitchWindowLevel()
1886 {
1887   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1888   int window = mSlicerManagers[index]->GetColorWindow();
1889   presetComboBox->setCurrentIndex(WL_USER);
1890   windowSpinBox->setValue(-window);
1891   UpdateWindowLevel();
1892 }
1893 //------------------------------------------------------------------------------
1894
1895 //------------------------------------------------------------------------------
1896 void vvMainWindow::ApplyWindowLevelToAllImages()
1897 {
1898   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1899   if(index==-1) return;
1900   double window = mSlicerManagers[index]->GetColorWindow();
1901   double level = mSlicerManagers[index]->GetColorLevel();
1902
1903   double fusWindow = mSlicerManagers[index]->GetFusionWindow();
1904   double fusLevel = mSlicerManagers[index]->GetFusionLevel();
1905
1906   double overWindow = mSlicerManagers[index]->GetOverlayColorWindow();
1907   double overLevel = mSlicerManagers[index]->GetOverlayColorLevel();
1908
1909   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
1910     if (mSlicerManagers[i] == NULL)
1911       continue;
1912     mSlicerManagers[i]->SetColorWindow(window);
1913     mSlicerManagers[i]->SetColorLevel(level);
1914     mSlicerManagers[i]->SetPreset(WL_USER);
1915     mSlicerManagers[i]->SetFusionWindow(fusWindow);
1916     mSlicerManagers[i]->SetFusionLevel(fusLevel);
1917     mSlicerManagers[i]->SetOverlayColorWindow(overWindow);
1918     mSlicerManagers[i]->SetOverlayColorLevel(overLevel);
1919     mSlicerManagers[i]->Render();
1920   }
1921 }
1922 //------------------------------------------------------------------------------
1923
1924 //------------------------------------------------------------------------------
1925 void vvMainWindow::ApplyWindowToSetOfImages(double window, unsigned int indexMin, unsigned int indexMax)
1926 {
1927   for (unsigned int i = indexMin; i <= indexMax && i < mSlicerManagers.size(); i++) {
1928     if (mSlicerManagers[i] == NULL)
1929       continue;
1930     SetWindowLevel(window, mSlicerManagers[i]->GetColorLevel());
1931     mSlicerManagers[i]->SetColorWindow(window);
1932     mSlicerManagers[i]->SetPreset(WL_USER);
1933     mSlicerManagers[i]->Render();
1934   }
1935 }
1936 //------------------------------------------------------------------------------
1937
1938 //------------------------------------------------------------------------------
1939 void vvMainWindow::ApplyLevelToSetOfImages(double level, unsigned int indexMin, unsigned int indexMax)
1940 {
1941   for (unsigned int i = indexMin; i <= indexMax && i < mSlicerManagers.size(); i++) {
1942     if (mSlicerManagers[i] == NULL)
1943       continue;
1944     SetWindowLevel(mSlicerManagers[i]->GetColorWindow(), level);
1945     mSlicerManagers[i]->SetColorLevel(level);
1946     mSlicerManagers[i]->SetPreset(WL_USER);
1947     mSlicerManagers[i]->Render();
1948   }
1949 }
1950 //------------------------------------------------------------------------------
1951
1952 //------------------------------------------------------------------------------
1953 void vvMainWindow::UpdateLinkManager(std::string id, int slicer, double x, double y, double z, int temps)
1954 {
1955   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
1956     if (mSlicerManagers[i]->GetId() == id) {
1957       mSlicerManagers[i]->GetSlicer(slicer)->SetCurrentPosition(x,y,z,temps);
1958       mSlicerManagers[i]->UpdateViews(0,slicer);
1959       break;
1960     }
1961   }
1962 }
1963 //------------------------------------------------------------------------------
1964
1965 //------------------------------------------------------------------------------
1966 void vvMainWindow::UpdateLinkedNavigation(std::string id, vvSlicerManager * sm, vvSlicer* refSlicer)
1967 {
1968   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
1969     if (id == mSlicerManagers[i]->GetId()) {
1970       mSlicerManagers[i]->UpdateLinkedNavigation(refSlicer);
1971     }
1972   }
1973 }
1974 //------------------------------------------------------------------------------
1975
1976 //------------------------------------------------------------------------------
1977 void vvMainWindow::ShowContextMenu(QPoint point)
1978 {
1979   if (!DataTree->selectedItems().size()) {
1980     contextActions[1]->setEnabled(0);
1981     contextActions[2]->setEnabled(0);
1982     contextActions[3]->setEnabled(0);
1983     contextActions[4]->setEnabled(0);
1984     contextActions[5]->setEnabled(0);
1985     contextActions[6]->setEnabled(0);
1986   } else {
1987     int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1988     contextActions[1]->setEnabled(1);
1989     contextActions[2]->setEnabled(
1990       DataTree->itemWidget(DataTree->selectedItems()[0],
1991       COLUMN_RELOAD_IMAGE)->isEnabled());
1992     contextActions[3]->setEnabled(1);
1993     contextActions[5]->setEnabled(1);
1994     contextActions[6]->setEnabled(1);
1995
1996     if (mSlicerManagers[index]->GetDimension() < 3)
1997       contextActions[4]->setEnabled(0);
1998     else
1999       contextActions[4]->setEnabled(1);
2000   }
2001   contextMenu.exec(QCursor::pos());
2002 }
2003 //------------------------------------------------------------------------------
2004
2005 //------------------------------------------------------------------------------
2006 void vvMainWindow::CloseImage()
2007 {
2008   CloseImage(DataTree->selectedItems()[0],0);
2009 }
2010 //------------------------------------------------------------------------------
2011
2012 //------------------------------------------------------------------------------
2013 void vvMainWindow::ReloadImage()
2014 {
2015   ReloadImage(DataTree->selectedItems()[0],0);
2016 }
2017 //------------------------------------------------------------------------------
2018
2019 //------------------------------------------------------------------------------
2020 void vvMainWindow::SelectOverlayImage()
2021 {
2022   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2023
2024   if (!(CheckAddedImage(index, "overlay")))
2025     return;
2026
2027   QString Extensions = EXTENSIONS;
2028   Extensions += ";;All Files (*)";
2029   QStringList files = QFileDialog::getOpenFileNames(this,tr("Load Overlay image"),mInputPathName,Extensions);
2030   if (files.isEmpty())
2031     return;
2032
2033   std::vector<std::string> vecFileNames;
2034   for (int i = 0; i < files.size(); i++) {
2035     vecFileNames.push_back(files[i].toStdString());
2036   }
2037
2038   AddOverlayImage(index,vecFileNames,vvImageReader::IMAGE);
2039 }
2040 //------------------------------------------------------------------------------
2041
2042 //------------------------------------------------------------------------------
2043 bool vvMainWindow::CheckAddedImage(int index, QString imageType)
2044 {
2045   //check if one overlay image is added
2046   for (int child = 0; child < DataTree->topLevelItem(index)->childCount(); child++)
2047     if (DataTree->topLevelItem(index)->child(child)->data(1,Qt::UserRole).toString().compare(imageType) == 0) {
2048       QString error = "Cannot add more than one compared image\n";
2049       error += "Please remove first ";
2050       error += DataTree->topLevelItem(index)->child(child)->data(COLUMN_IMAGE_NAME,Qt::DisplayRole).toString();
2051       QMessageBox::information(this,tr("Problem adding compared image !"),error);
2052       return false;
2053     }
2054     return true;
2055 }
2056 //------------------------------------------------------------------------------
2057
2058 //------------------------------------------------------------------------------
2059 void vvMainWindow::AddOverlayImage(int index, std::vector<std::string> fileNames, vvImageReader::LoadedImageType type)
2060 {
2061   QString file(fileNames[0].c_str());
2062   if (QFile::exists(file))
2063   {
2064     mInputPathName = itksys::SystemTools::GetFilenamePath(file.toStdString()).c_str();
2065     itk::ImageIOBase::Pointer reader = itk::ImageIOFactory::CreateImageIO(
2066       file.toStdString().c_str(), itk::ImageIOFactory::ReadMode);
2067     reader->SetFileName(fileNames[0].c_str());
2068     reader->ReadImageInformation();
2069     std::string component = reader->GetComponentTypeAsString(reader->GetComponentType());
2070     int dimension = reader->GetNumberOfDimensions();
2071     QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
2072     vvProgressDialog progress("Opening " + file.toStdString());
2073     qApp->processEvents();
2074
2075     std::string filename = itksys::SystemTools::GetFilenameWithoutExtension(file.toStdString()).c_str();
2076     if (mSlicerManagers[index]->SetOverlay(fileNames,dimension, component,type)) {
2077       //create an item in the tree with good settings
2078       QTreeWidgetItem *item = new QTreeWidgetItem();
2079       item->setData(0,Qt::UserRole,file.toStdString().c_str());
2080       item->setData(1,Qt::UserRole,tr("overlay"));
2081       QFileInfo fileinfo(file); //Do not show the path
2082       item->setData(COLUMN_IMAGE_NAME,Qt::DisplayRole,fileinfo.fileName());
2083       item->setToolTip(COLUMN_IMAGE_NAME, mSlicerManagers[index]->GetListOfAbsoluteFilePathInOneString("overlay").c_str());
2084       qApp->processEvents();
2085 #if VTK_MAJOR_VERSION > 5
2086       for ( unsigned int i = 0; i < mSlicerManagers[index]->GetNumberOfSlicers(); i++)
2087         mSlicerManagers[index]->GetSlicer(i)->ForceUpdateDisplayExtent();
2088 #endif
2089
2090       for (int j = 1; j <= 4; j++) {
2091         item->setData(j,Qt::CheckStateRole,DataTree->topLevelItem(index)->data(j,Qt::CheckStateRole));
2092       }
2093
2094       //Create the buttons for reload and close
2095       qApp->processEvents();
2096       QTreePushButton* cButton = new QTreePushButton;
2097       cButton->setItem(item);
2098       cButton->setColumn(COLUMN_CLOSE_IMAGE);
2099       cButton->setToolTip(tr("close image"));
2100       cButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/exit.png")));
2101       connect(cButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
2102         this,SLOT(CloseImage(QTreeWidgetItem*, int)));
2103
2104       QTreePushButton* rButton = new QTreePushButton;
2105       rButton->setItem(item);
2106       rButton->setColumn(COLUMN_RELOAD_IMAGE);
2107       rButton->setToolTip(tr("reload image"));
2108       rButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/rotateright.png")));
2109       connect(rButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
2110         this,SLOT(ReloadImage(QTreeWidgetItem*, int)));
2111
2112       DataTree->topLevelItem(index)->setExpanded(1);
2113       DataTree->topLevelItem(index)->addChild(item);
2114       DataTree->setItemWidget(item, COLUMN_CLOSE_IMAGE, cButton);
2115       DataTree->setItemWidget(item, COLUMN_RELOAD_IMAGE, rButton);
2116
2117       //set the id of the image
2118       QString id = DataTree->topLevelItem(index)->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString();
2119       item->setData(COLUMN_IMAGE_NAME,Qt::UserRole,id.toStdString().c_str());
2120       UpdateTree();
2121       qApp->processEvents();
2122       ImageInfoChanged();
2123       QApplication::restoreOverrideCursor();
2124
2125       // Update the display to update, e.g., the sliders
2126       for(int i=0; i<4; i++)
2127         DisplaySliders(index, i);
2128     } else {
2129       QApplication::restoreOverrideCursor();
2130       QString error = "Cannot import the new image.\n";
2131       error += mSlicerManagers[index]->GetLastError().c_str();
2132       QMessageBox::information(this,tr("Problem reading image !"),error);
2133     }
2134     WindowLevelChanged();
2135   }
2136   else
2137     QMessageBox::information(this,tr("Problem reading Overlay !"),"File doesn't exist!");
2138 }
2139 //------------------------------------------------------------------------------
2140
2141
2142 //------------------------------------------------------------------------------
2143 void vvMainWindow::AddROI(int index, QString file)
2144 {
2145   /*
2146   // Get slice manager
2147
2148   // Load image
2149
2150   vvImageReader * mReader = new vvImageReader;
2151   mReader->SetInputFilename(filename.toStdString());
2152   mReader->Update(IMAGE);
2153   if (mReader->GetLastError().size() != 0) {
2154   std::cerr << "Error while reading " << filename.toStdString() << std::endl;
2155   QString error = "Cannot open file \n";
2156   error += mReader->GetLastError().c_str();
2157   QMessageBox::information(this,tr("Reading problem"),error);
2158   delete mReader;
2159   return;
2160   }
2161   vvImage::Pointer roi = mReader->GetOutput();
2162
2163   // Create roi in new tool
2164   vvToolStructureSetManager::AddImage(mCurrentSlicerManager, roi);
2165   */
2166 }
2167 //------------------------------------------------------------------------------
2168
2169 //------------------------------------------------------------------------------
2170 void vvMainWindow::SelectFusionImage()
2171 {
2172   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2173
2174   if (!(CheckAddedImage(index, "fusion")) || !(CheckAddedImage(index, "fusionSequence")))
2175     return;
2176
2177   QString Extensions = EXTENSIONS;
2178   Extensions += ";;All Files (*)";
2179   QStringList files = QFileDialog::getOpenFileNames(this,tr("Load Fusion image"),mInputPathName,Extensions);
2180   if (files.isEmpty())
2181     return;
2182
2183   std::vector<std::string> vecFileNames;
2184   for (int i = 0; i < files.size(); i++) {
2185     vecFileNames.push_back(files[i].toStdString());
2186   }
2187   AddFusionImage(index,vecFileNames,vvImageReader::IMAGE);
2188 }
2189 //------------------------------------------------------------------------------
2190
2191 //------------------------------------------------------------------------------
2192 void vvMainWindow::ResetTransformationToIdentity()
2193 {
2194   std::string actorType = DataTree->selectedItems()[0]->data(1,Qt::UserRole).toString().toStdString();
2195   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2196   mSlicerManagers[index]->ResetTransformationToIdentity(actorType);
2197   ImageInfoChanged();
2198 }
2199 //------------------------------------------------------------------------------
2200
2201 //------------------------------------------------------------------------------
2202 void vvMainWindow::AddFusionImage(int index, std::vector<std::string> fileNames, vvImageReader::LoadedImageType type)
2203 {
2204   QString file(fileNames[0].c_str());
2205   if (QFile::exists(file))
2206   {
2207     mInputPathName = itksys::SystemTools::GetFilenamePath(file.toStdString()).c_str();
2208     itk::ImageIOBase::Pointer reader = itk::ImageIOFactory::CreateImageIO(
2209       file.toStdString().c_str(), itk::ImageIOFactory::ReadMode);
2210     reader->SetFileName(fileNames[0].c_str());
2211     reader->ReadImageInformation();
2212     std::string component = reader->GetComponentTypeAsString(reader->GetComponentType());
2213     int dimension = reader->GetNumberOfDimensions();
2214     QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
2215     vvProgressDialog progress("Opening fusion");
2216     qApp->processEvents();
2217
2218     std::string filename = itksys::SystemTools::GetFilenameWithoutExtension(file.toStdString()).c_str();
2219     if (mSlicerManagers[index]->SetFusion(fileNames,dimension, component,type)) {
2220       //create an item in the tree with good settings
2221       QTreeWidgetItem *item = new QTreeWidgetItem();
2222       item->setData(0,Qt::UserRole,file.toStdString().c_str());
2223       item->setData(1,Qt::UserRole,tr("fusion"));
2224       QFileInfo fileinfo(file); //Do not show the path
2225           item->setData(COLUMN_IMAGE_NAME,Qt::DisplayRole,fileinfo.fileName());
2226           item->setToolTip(COLUMN_IMAGE_NAME, mSlicerManagers[index]->GetListOfAbsoluteFilePathInOneString("fusion").c_str());
2227           qApp->processEvents();
2228 #if VTK_MAJOR_VERSION > 5
2229       for ( unsigned int i = 0; i < mSlicerManagers[index]->GetNumberOfSlicers(); i++)
2230         mSlicerManagers[index]->GetSlicer(i)->ForceUpdateDisplayExtent();
2231 #endif
2232       for (int j = 1; j <= 4; j++) {
2233         item->setData(j,Qt::CheckStateRole,DataTree->topLevelItem(index)->data(j,Qt::CheckStateRole));
2234       }
2235
2236       //Create the buttons for reload and close
2237       qApp->processEvents();
2238       QTreePushButton* cButton = new QTreePushButton;
2239       cButton->setItem(item);
2240       cButton->setColumn(COLUMN_CLOSE_IMAGE);
2241       cButton->setToolTip(tr("close image"));
2242       cButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/exit.png")));
2243       connect(cButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
2244         this,SLOT(CloseImage(QTreeWidgetItem*, int)));
2245
2246       QTreePushButton* rButton = new QTreePushButton;
2247       rButton->setItem(item);
2248       rButton->setColumn(COLUMN_RELOAD_IMAGE);
2249       rButton->setToolTip(tr("reload image"));
2250       rButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/rotateright.png")));
2251       connect(rButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
2252         this,SLOT(ReloadImage(QTreeWidgetItem*, int)));
2253
2254       DataTree->topLevelItem(index)->setExpanded(1);
2255       DataTree->topLevelItem(index)->addChild(item);
2256       DataTree->setItemWidget(item, COLUMN_CLOSE_IMAGE, cButton);
2257       DataTree->setItemWidget(item, COLUMN_RELOAD_IMAGE, rButton);
2258
2259       //set the id of the image
2260       QString id = DataTree->topLevelItem(index)->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString();
2261       item->setData(COLUMN_IMAGE_NAME,Qt::UserRole,id.toStdString().c_str());
2262       UpdateTree();
2263       qApp->processEvents();
2264       ImageInfoChanged();
2265       QApplication::restoreOverrideCursor();
2266
2267       // Update the display to update, e.g., the sliders
2268       for(int i=0; i<4; i++)
2269         DisplaySliders(index, i);
2270     } else {
2271       QApplication::restoreOverrideCursor();
2272       QString error = "Cannot import the new image.\n";
2273       error += mSlicerManagers[index]->GetLastError().c_str();
2274       QMessageBox::information(this,tr("Problem reading image !"),error);
2275     }
2276     WindowLevelChanged();
2277   }
2278   else
2279     QMessageBox::information(this,tr("Problem reading Fusion !"),"File doesn't exist!");
2280 }
2281 //------------------------------------------------------------------------------
2282 //------------------------------------------------------------------------------
2283 void vvMainWindow::AddLandmarks(int index, std::vector<std::string> files)
2284 {
2285     if (!landmarksPanel->LoadFromFile(files))
2286       QMessageBox::information(this,tr("Problem reading Landmarks !"),"File doesn't exist!");
2287
2288     landmarksPanel->SetCurrentPath(mInputPathName.toStdString());
2289     landmarksPanel->SetCurrentImage(mSlicerManagers[index]->GetFileName().c_str());
2290 }
2291
2292 //------------------------------------------------------------------------------
2293 void vvMainWindow::OpenField()
2294 {
2295   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2296
2297   if (!(CheckAddedImage(index, "vector")))
2298     return;
2299
2300   QString Extensions = "Images ( *.mhd *.mha *.vf *.nii *.nrrd *.nhdr)";
2301   // Extensions += ";;Images ( *.mha)";
2302   // Extensions += ";;VF Images ( *.vf)";
2303   // Extensions += ";;nii Images ( *.nii)";
2304   // Extensions += ";;nrrd Images ( *.nrrd)";
2305   // Extensions += ";;nhdr Images ( *.nhdr)";
2306   Extensions += ";;All Files (*)";
2307   QString file = QFileDialog::getOpenFileName(this,tr("Load deformation field"),mInputPathName,Extensions);
2308   if (!file.isEmpty())
2309     AddField(file,index);
2310 }
2311 //------------------------------------------------------------------------------
2312
2313
2314 //------------------------------------------------------------------------------
2315 void vvMainWindow::AddFieldEntry(QString filename,int index,bool from_disk)
2316 {
2317   //create an item in the tree with good settings
2318   QTreeWidgetItem *item = new QTreeWidgetItem();
2319   item->setData(0,Qt::UserRole,filename.toStdString().c_str());
2320   item->setData(1,Qt::UserRole,tr("vector"));
2321   QFileInfo fileinfo(filename); //Do not show the path
2322   item->setData(COLUMN_IMAGE_NAME,Qt::DisplayRole,fileinfo.fileName());
2323   item->setToolTip(COLUMN_IMAGE_NAME, mSlicerManagers[index]->GetListOfAbsoluteFilePathInOneString("vector").c_str());
2324   qApp->processEvents();
2325
2326   for (int j = 1; j <= 4; j++) {
2327     item->setData(j,Qt::CheckStateRole,DataTree->topLevelItem(index)->data(j,Qt::CheckStateRole));
2328   }
2329
2330   //Create the buttons for reload and close
2331   qApp->processEvents();
2332   QTreePushButton* cButton = new QTreePushButton;
2333   cButton->setItem(item);
2334   cButton->setColumn(COLUMN_CLOSE_IMAGE);
2335   cButton->setToolTip(tr("close vector field"));
2336   cButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/exit.png")));
2337   connect(cButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
2338     this,SLOT(CloseImage(QTreeWidgetItem*, int)));
2339
2340   QTreePushButton* rButton = new QTreePushButton;
2341   rButton->setItem(item);
2342   rButton->setColumn(COLUMN_RELOAD_IMAGE);
2343   rButton->setToolTip(tr("reload vector field"));
2344   rButton->setEnabled(from_disk);
2345   rButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/rotateright.png")));
2346   connect(rButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
2347     this,SLOT(ReloadImage(QTreeWidgetItem*, int)));
2348
2349   DataTree->topLevelItem(index)->setExpanded(1);
2350   DataTree->topLevelItem(index)->addChild(item);
2351   DataTree->setItemWidget(item, COLUMN_RELOAD_IMAGE, rButton);
2352   DataTree->setItemWidget(item, COLUMN_CLOSE_IMAGE, cButton);
2353
2354   //set the id of the image
2355   QString id = DataTree->topLevelItem(index)->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString();
2356   item->setData(COLUMN_IMAGE_NAME,Qt::UserRole,id.toStdString().c_str());
2357   UpdateTree();
2358   qApp->processEvents();
2359   ImageInfoChanged();
2360   QApplication::restoreOverrideCursor();
2361 }
2362 //------------------------------------------------------------------------------
2363
2364
2365 //------------------------------------------------------------------------------
2366 void vvMainWindow::AddField(vvImage::Pointer vf,QString file,int index)
2367 {
2368   QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
2369   vvSlicerManager* imageManager = mSlicerManagers[index];
2370   if (imageManager->SetVF(vf,file.toStdString())) {
2371     AddFieldEntry(file,index,false);
2372 #if VTK_MAJOR_VERSION > 5
2373       for ( unsigned int i = 0; i < mSlicerManagers[index]->GetNumberOfSlicers(); i++)
2374         mSlicerManagers[index]->GetSlicer(i)->ForceUpdateDisplayExtent();
2375 #endif
2376   } else {
2377     QString error = "Cannot import the vector field for this image.\n";
2378     error += imageManager->GetLastError().c_str();
2379     QMessageBox::information(this,tr("Problem reading VF !"),error);
2380   }
2381   QApplication::restoreOverrideCursor();
2382 }
2383 //------------------------------------------------------------------------------
2384
2385
2386 //------------------------------------------------------------------------------
2387 void vvMainWindow::AddField(QString file,int index)
2388 {
2389   if (QFile::exists(file)) {
2390     mInputPathName = itksys::SystemTools::GetFilenamePath(file.toStdString()).c_str();
2391
2392     //init the progress events
2393     QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
2394     vvProgressDialog progress("Opening " + file.toStdString());
2395     qApp->processEvents();
2396
2397     //read the vector and put it in the current mSlicerManager
2398     vvSlicerManager* imageManager = mSlicerManagers[index];
2399     qApp->processEvents();
2400
2401     std::string filename = itksys::SystemTools::GetFilenameWithoutExtension(file.toStdString()).c_str();
2402     if (imageManager->SetVF(file.toStdString())) {
2403       imageManager->Render();
2404       AddFieldEntry(file,index,true);
2405     } else {
2406       QApplication::restoreOverrideCursor();
2407       QString error = "Cannot import the vector field for this image.\n";
2408       error += imageManager->GetLastError().c_str();
2409       QMessageBox::information(this,tr("Problem reading VF !"),error);
2410     }
2411   } else
2412     QMessageBox::information(this,tr("Problem reading VF !"),"File doesn't exist!");
2413
2414 }
2415 //------------------------------------------------------------------------------
2416
2417
2418 //------------------------------------------------------------------------------
2419 void vvMainWindow::SetVFProperty(int subsampling, int scale, int log, int width, double r, double g, double b)
2420 {
2421   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2422   if (mSlicerManagers[index]->GetSlicer(0)->GetVF()) {
2423     for (int i = 0; i < 4; i++) {
2424       mSlicerManagers[index]->GetSlicer(i)->SetVFSubSampling(subsampling);
2425       mSlicerManagers[index]->GetSlicer(i)->SetVFScale(scale);
2426       mSlicerManagers[index]->GetSlicer(i)->SetVFWidth(width);
2427       mSlicerManagers[index]->GetSlicer(i)->SetVFColor(r,g,b);
2428       if (log > 0)
2429         mSlicerManagers[index]->GetSlicer(i)->SetVFLog(1);
2430       else
2431         mSlicerManagers[index]->GetSlicer(i)->SetVFLog(0);
2432     }
2433   }
2434 }
2435 //------------------------------------------------------------------------------
2436
2437
2438 //------------------------------------------------------------------------------
2439 void vvMainWindow::SetOverlayProperty(int color, int linked, double window, double level)
2440 {
2441   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2442   if (mSlicerManagers[index]->GetSlicer(0)->GetOverlay()) {
2443     mSlicerManagers[index]->SetOverlayColor(color);
2444     mSlicerManagers[index]->SetColorMap(0);
2445     mSlicerManagers[index]->SetLinkOverlayWindowLevel(linked);
2446     mSlicerManagers[index]->SetOverlayColorWindow(window);
2447     mSlicerManagers[index]->SetOverlayColorLevel(level);
2448     mSlicerManagers[index]->Render();
2449   }
2450 }
2451 //------------------------------------------------------------------------------
2452
2453 //------------------------------------------------------------------------------
2454 void vvMainWindow::SetFusionProperty(int opacity, int thresOpacity, int colormap,double window, double level, bool showLegend)
2455 {
2456   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2457   if (mSlicerManagers[index]->GetSlicer(0)->GetFusion()) {
2458     mSlicerManagers[index]->SetFusionColorMap(colormap);
2459     mSlicerManagers[index]->SetFusionOpacity(opacity);
2460     mSlicerManagers[index]->SetFusionThresholdOpacity(thresOpacity);
2461     mSlicerManagers[index]->SetFusionWindow(window);
2462     mSlicerManagers[index]->SetFusionLevel(level);
2463     mSlicerManagers[index]->SetFusionShowLegend(showLegend);
2464     mSlicerManagers[index]->SetColorMap(0);
2465     mSlicerManagers[index]->Render();
2466   }
2467 }
2468 //------------------------------------------------------------------------------
2469
2470
2471 //------------------------------------------------------------------------------
2472 void vvMainWindow::SelectFusionSequence()
2473 {
2474   //get the index of the slicer manager of the main sequence (CT)
2475   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2476
2477   if (!(CheckAddedImage(index, "fusion")) || !(CheckAddedImage(index, "fusionSequence")))
2478     return;
2479
2480   QString Extensions = EXTENSIONS;
2481   Extensions += ";;All Files (*)";
2482   QStringList files = QFileDialog::getOpenFileNames(this,tr("Load Overlay image sequence"),mInputPathName,Extensions);
2483   if (files.isEmpty())
2484     return;
2485
2486   std::vector<std::string> vecFileNames;
2487   for (int i = 0; i < files.size(); i++) {
2488     vecFileNames.push_back(files[i].toStdString());
2489   }
2490
2491   //associate the secondary sequence (US) to the main one
2492   AddFusionSequence(index,vecFileNames,vvImageReader::MERGEDWITHTIME);
2493 }
2494 //------------------------------------------------------------------------------
2495
2496
2497 //------------------------------------------------------------------------------
2498 void vvMainWindow::SelectFusionSequenceCorrespondances()
2499 {
2500   //make sure the index is right?
2501   //in the end, I should attach the temporal data to the right sequence!
2502   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2503   //in case the other sequence got selected, make sure we select the primary sequence
2504   if ( (!mSlicerManagers[index]->GetSlicer(0)->GetFusion()) && mSlicerManagers[index]->GetFusionSequenceIndexOfLinkedManager()>=0 ) {
2505     index = mSlicerManagers[index]->GetFusionSequenceIndexOfLinkedManager();
2506   }
2507
2508   //open a dialog box to find a file
2509   //QString Extensions = EXTENSIONS;
2510   QString Extensions = ";;All Files (*)";
2511   QString fileName = QFileDialog::getOpenFileName(this,tr("Load respiratory signal for fused sequence"),mInputPathName,Extensions);
2512   if (fileName.isNull())
2513     return;
2514
2515   //read it as a vector of values
2516   vnl_vector<double> tmpVect;
2517
2518   std::ifstream file;
2519   file.open(fileName.toStdString().c_str());
2520   tmpVect.read_ascii(file);
2521   file.close();
2522
2523   //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
2524   bool signalOK = true;
2525   unsigned nbFrameMain = mSlicerManagers[index]->GetImage()->GetTransform().size();
2526   unsigned nbFrameSecondary = mSlicerManagers[index]->GetFusionSequenceNbFrames();
2527   std::cout<<"nbFrameMain = "<<nbFrameMain<<", nbFrameSecondary= "<<nbFrameSecondary<<", signal size: "<<tmpVect.size()<<std::endl;
2528   std::vector<unsigned> temporalCorrespondances;
2529   if ( tmpVect.size() == nbFrameMain + nbFrameSecondary ) {
2530     for (unsigned i=0 ; i<tmpVect.size() ; i++) {
2531       if (i<nbFrameMain) { //first part of the file: i -> index in secondary seq.
2532         if ( tmpVect(i)<nbFrameSecondary ) temporalCorrespondances.push_back(tmpVect(i));
2533         else { signalOK=false; break; } //pointing outside the secondary sequence...
2534       }
2535       else { //first part of the file -> index in secondary seq.
2536         if ( tmpVect(i)<nbFrameMain ) temporalCorrespondances.push_back(tmpVect(i));
2537         else { signalOK=false; break; } //pointing outside the secondary sequence...
2538       }
2539     }
2540   }
2541   else {signalOK=false;}
2542   if (!signalOK) {//else, send a message to signal the failure...
2543     QString error = "The provided temporal correspondances is invalid - check tooltip.\n";
2544     error += "Ignoring file: " + fileName;
2545     QMessageBox::information(this,tr("Problem adding temporal correspondances!"),error);
2546     return;
2547   }
2548   else {
2549     //for convenience, associate this sequence to both the current slicer manager, and to the linked one
2550     mSlicerManagers[index]->SetFusionSequenceCorrespondances(temporalCorrespondances);
2551     mSlicerManagers[ mSlicerManagers[index]->GetFusionSequenceIndexOfLinkedManager() ]->SetFusionSequenceCorrespondances(temporalCorrespondances);
2552     overlayPanel->enableFusionSequenceTemporalSync();
2553   }
2554
2555 }
2556 //------------------------------------------------------------------------------
2557
2558
2559 //------------------------------------------------------------------------------
2560 //when this function is called index is the slicer manager index corresponding to the main sequence (CT)
2561 //the files behind fileNames points to the data for the secondary sequence
2562 void vvMainWindow::AddFusionSequence(int index, std::vector<std::string> fileNames, vvImageReader::LoadedImageType type)
2563 {
2564   QString file(fileNames[0].c_str());
2565   if (QFile::exists(file))
2566   {
2567     mInputPathName = itksys::SystemTools::GetFilenamePath(file.toStdString()).c_str();
2568     itk::ImageIOBase::Pointer reader = itk::ImageIOFactory::CreateImageIO(
2569       file.toStdString().c_str(), itk::ImageIOFactory::ReadMode);
2570     std::sort (fileNames.begin(), fileNames.end());//make sure the files are sorted.
2571     reader->SetFileName(fileNames[0].c_str());
2572     reader->ReadImageInformation();
2573     std::string component = reader->GetComponentTypeAsString(reader->GetComponentType());
2574     int dimension = reader->GetNumberOfDimensions();
2575     QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
2576     vvProgressDialog progress("Opening " + file.toStdString());
2577     qApp->processEvents();
2578
2579     std::string filename = itksys::SystemTools::GetFilenameWithoutExtension(file.toStdString()).c_str();
2580
2581     if (mSlicerManagers[index]->SetFusionSequence(fileNames,dimension, component,type)) {
2582       //create an item in the tree with good settings
2583       QTreeWidgetItem *item = new QTreeWidgetItem();
2584       item->setData(0,Qt::UserRole,file.toStdString().c_str());
2585       item->setData(1,Qt::UserRole,tr("fusionSequence"));
2586
2587       QFileInfo fileinfo(file); //Do not show the path
2588       item->setData(COLUMN_IMAGE_NAME,Qt::DisplayRole,fileinfo.fileName());
2589       item->setToolTip(COLUMN_IMAGE_NAME, mSlicerManagers[index]->GetListOfAbsoluteFilePathInOneString("fusionSequence").c_str());
2590       qApp->processEvents();
2591 #if VTK_MAJOR_VERSION > 5
2592       for ( unsigned int i = 0; i < mSlicerManagers[index]->GetNumberOfSlicers(); i++)
2593         mSlicerManagers[index]->GetSlicer(i)->ForceUpdateDisplayExtent();
2594 #endif
2595       for (int j = 1; j <= 4; j++) {
2596         item->setData(j,Qt::CheckStateRole,DataTree->topLevelItem(index)->data(j,Qt::CheckStateRole));
2597       }
2598
2599       //Create the buttons for reload and close
2600       qApp->processEvents();
2601       QTreePushButton* cButton = new QTreePushButton;
2602       cButton->setItem(item);
2603       cButton->setColumn(COLUMN_CLOSE_IMAGE);
2604       cButton->setToolTip(tr("close image"));
2605       cButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/exit.png")));
2606       connect(cButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
2607         this,SLOT(CloseImage(QTreeWidgetItem*, int)));
2608
2609       QTreePushButton* rButton = new QTreePushButton;
2610       rButton->setItem(item);
2611       rButton->setColumn(COLUMN_RELOAD_IMAGE);
2612       rButton->setToolTip(tr("reload image"));
2613       rButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/rotateright.png")));
2614       connect(rButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
2615         this,SLOT(ReloadImage(QTreeWidgetItem*, int)));
2616
2617       DataTree->topLevelItem(index)->setExpanded(1);
2618       DataTree->topLevelItem(index)->addChild(item);
2619       DataTree->setItemWidget(item, COLUMN_CLOSE_IMAGE, cButton);
2620       DataTree->setItemWidget(item, COLUMN_RELOAD_IMAGE, rButton);
2621
2622       //store the original transform matrix
2623       int indexParent = GetSlicerIndexFromItem( DataTree->topLevelItem(index) );
2624       mSlicerManagers[indexParent]->SetFusionSequenceMainTransformMatrix( mSlicerManagers[indexParent]->GetSlicer(0)->GetImage()->GetTransform()[0]->GetMatrix() );
2625
2626       //set the id of the image
2627       QString id = DataTree->topLevelItem(index)->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString();
2628       item->setData(COLUMN_IMAGE_NAME,Qt::UserRole,id.toStdString().c_str());
2629       UpdateTree();
2630       qApp->processEvents();
2631
2632       //ImageInfoChanged();
2633
2634       QApplication::restoreOverrideCursor();
2635       // Update the display to update, e.g., the sliders
2636       for(int i=0; i<4; i++)
2637         DisplaySliders(index, i);
2638
2639
2640       //This loads the secondary sequence (US) as an independent sequence
2641       LoadImages(fileNames, type);
2642       //reset the transforms to identity
2643       //FIX -- and set the thickness of the US slices to a large value (necessary for visualization purposes...)
2644       double sp_x, sp_y, sp_z;
2645       mSlicerManagers[indexParent]->GetImage()->GetVTKImages()[0]->GetSpacing(sp_x, sp_y, sp_z);
2646       sp_z = std::max(sp_x, std::max(sp_y, sp_z)) + 0.5; //
2647       for (unsigned i=0 ; i<mSlicerManagers.back()->GetImage()->GetTransform().size() ; i++) {
2648         sp_x = mSlicerManagers.back()->GetImage()->GetVTKImages()[i]->GetSpacing()[0];
2649         sp_y = mSlicerManagers.back()->GetImage()->GetVTKImages()[i]->GetSpacing()[1];
2650         mSlicerManagers.back()->GetImage()->GetVTKImages()[i]->SetSpacing( sp_x, sp_y, sp_z);
2651         mSlicerManagers.back()->GetImage()->GetTransform()[i]->Identity();
2652         mSlicerManagers.back()->GetImage()->GetTransform()[i]->Update();
2653       }
2654
2655       //automatically link both images...
2656       AddLink(mSlicerManagers[indexParent]->GetId().c_str(), mSlicerManagers.back()->GetId().c_str(), false);
2657
2658       //tie the main and secondary sequences by raising flags and informing each another of their respective SlicerManager indices
2659       mSlicerManagers[indexParent]->SetFusionSequenceIndexOfLinkedManager(mSlicerManagers.size()-1);
2660       mSlicerManagers[indexParent]->SetFusionSequenceInvolvmentCode(0); //main sequence
2661       mSlicerManagers.back()->SetFusionSequenceIndexOfLinkedManager(indexParent);
2662       mSlicerManagers.back()->SetFusionSequenceInvolvmentCode(1); //secondary sequence
2663       for (unsigned i=0 ; i<4 ; i++) {
2664         mSlicerManagers.back()->GetSlicer(i)->SetFusionSequenceCode(1); //flag the slicers of the secondary sequence
2665       }
2666
2667     } else {
2668       QApplication::restoreOverrideCursor();
2669       QString error = "Cannot import the new image.\n";
2670       error += mSlicerManagers[index]->GetLastError().c_str();
2671       QMessageBox::information(this,tr("Problem reading image !"),error);
2672     }
2673     WindowLevelChanged();
2674     ImageInfoChanged(); //this internally calls WindowLevelChanged...
2675   }
2676   else {
2677     QMessageBox::information(this,tr("Problem reading fusion sequence !"),"File doesn't exist!");
2678     return;
2679   }
2680
2681 }
2682 //------------------------------------------------------------------------------
2683
2684
2685 //------------------------------------------------------------------------------
2686 //fusionSequenceFrameIndex and fusionSequenceNbFrames are relative to the secondary sequence (US)
2687 void vvMainWindow::SetFusionSequenceProperty(int fusionSequenceFrameIndex, bool spatialSyncFlag, unsigned int fusionSequenceNbFrames, bool temporalSyncFlag)
2688 {
2689   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2690
2691   if (!mSlicerManagers[index]->IsInvolvedInFusionSequence()) return;
2692
2693   //check if the focus moved to the linked sequence, and in this case, select the master sequence instead
2694   if (!mSlicerManagers[index]->IsMainSequenceOfFusionSequence()) {
2695     index = mSlicerManagers[index]->GetFusionSequenceIndexOfLinkedManager();
2696   }
2697   int secondaryIndex = mSlicerManagers[index]->GetFusionSequenceIndexOfLinkedManager();
2698   if (secondaryIndex==-1) return; //this should never happen
2699   if ( (!mSlicerManagers[index]->IsMainSequenceOfFusionSequence()) ||
2700     (!mSlicerManagers[secondaryIndex]->IsSecondarySequenceOfFusionSequence()) )
2701   {return;} //this should never happen, raise an exception?
2702
2703   if (mSlicerManagers[index]->GetSlicer(0)->GetFusion()) {
2704
2705     //First, if the spatialSync button is unchecked, then reposition the parent sequence (CT) in its original coordinate frame
2706     if ( (!spatialSyncFlag) && (mSlicerManagers[index]->GetFusionSequenceSpatialSyncFlag()) ) {
2707       for ( unsigned i=0 ; i<mSlicerManagers[index]->GetSlicer(0)->GetImage()->GetTransform().size() ; i++ ) {
2708         mSlicerManagers[index]->GetSlicer(0)->GetImage()->GetTransform()[i]->SetMatrix( mSlicerManagers[index]->GetFusionSequenceMainTransformMatrix() );
2709         mSlicerManagers[index]->GetSlicer(0)->GetImage()->GetTransform()[i]->Update();
2710       }
2711
2712       for (int i=0; i<mSlicerManagers[index]->GetNumberOfSlicers(); i++) {
2713         mSlicerManagers[index]->GetSlicer(i)->ForceUpdateDisplayExtent();
2714         mSlicerManagers[index]->GetSlicer(i)->Render();
2715       }
2716     }
2717
2718     //then, update the property values in the slicer manager
2719     mSlicerManagers[index]->SetFusionSequenceLength(fusionSequenceNbFrames);
2720     mSlicerManagers[index]->SetFusionSequenceSpatialSyncFlag(spatialSyncFlag);
2721     mSlicerManagers[index]->SetFusionSequenceTemporalSyncFlag(temporalSyncFlag);
2722     mSlicerManagers[index]->SetFusionSequenceFrameIndex(fusionSequenceFrameIndex);
2723
2724     //select the right frame of the US sequence
2725     mSlicerManagers[index]->SetFusionSequenceTSlice(fusionSequenceFrameIndex); //here, I should only update the overlayed sequence
2726     mSlicerManagers[secondaryIndex]->SetTSlice(fusionSequenceFrameIndex, false); //this should update the secondary sequence (individual version)
2727
2728     //update the horizontal sliders of the main window
2729     overlayPanel->updateFusionSequenceSliderValueFromWindow(fusionSequenceFrameIndex, false);
2730
2731     if (spatialSyncFlag) { //reslice the CT
2732
2733       if (temporalSyncFlag) { //do the temporal synchronisation
2734         int mainSequenceFrameIndex=0;
2735         //estimate the TSlice to set to the CT
2736         unsigned nbFramesMain = mSlicerManagers[index]->GetImage()->GetTransform().size();
2737         mainSequenceFrameIndex = mSlicerManagers[index]->GetFusionSequenceCorrespondances()[ nbFramesMain + fusionSequenceFrameIndex];
2738         //and set it!
2739         mSlicerManagers[index]->SetTSlice(mainSequenceFrameIndex, false);
2740         //warning, there is a loopback, and modification of the TSlice in main sequence forces an update of the TSlice in secondary, etc...
2741       }
2742
2743
2744       //Set the transform matrix of the parent sequence (typically CT / 4DCT)
2745       vtkSmartPointer<vtkMatrix4x4> tmpMat = vtkSmartPointer<vtkMatrix4x4>::New();
2746       vtkMatrix4x4::Invert( mSlicerManagers[index]->GetFusionSequenceInitialTransformMatrixAtFrame(fusionSequenceFrameIndex), tmpMat );
2747       for ( unsigned i=0 ; i<mSlicerManagers[index]->GetSlicer(0)->GetImage()->GetTransform().size() ; i++ ) {
2748         mSlicerManagers[index]->GetSlicer(0)->GetImage()->GetTransform()[i]->SetMatrix( mSlicerManagers[index]->GetFusionSequenceMainTransformMatrix() );
2749         mSlicerManagers[index]->GetSlicer(0)->GetImage()->GetTransform()[i]->PreMultiply();
2750         mSlicerManagers[index]->GetSlicer(0)->GetImage()->GetTransform()[i]->Concatenate( tmpMat );
2751         mSlicerManagers[index]->GetSlicer(0)->GetImage()->GetTransform()[i]->Update();
2752       }
2753
2754       for (int i=0; i<mSlicerManagers[index]->GetNumberOfSlicers(); i++) {
2755         mSlicerManagers[index]->GetSlicer(i)->ForceUpdateDisplayExtent();
2756         mSlicerManagers[index]->GetSlicer(i)->Render();
2757       }
2758
2759     }
2760
2761   }
2762 }
2763 //------------------------------------------------------------------------------
2764
2765
2766 //------------------------------------------------------------------------------
2767 void vvMainWindow::SaveAs()
2768 {
2769   if (DataTree->selectedItems()[0]->data(1,Qt::UserRole).toString() == "vector") {
2770     QMessageBox::warning(this,tr("Unsupported type"),tr("Sorry, saving a vector field is unsupported for the moment"));
2771     return;
2772   }
2773
2774   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2775   int dimension = mSlicerManagers[index]->GetDimension();
2776   QStringList OutputListeFormat;
2777   OutputListeFormat.clear();
2778   if (dimension == 1) {
2779     OutputListeFormat.push_back(".mhd");
2780     OutputListeFormat.push_back(".mha");
2781   }
2782   if (dimension == 2) {
2783     OutputListeFormat.push_back(".bmp");
2784     OutputListeFormat.push_back(".png");
2785     OutputListeFormat.push_back(".jpeg");
2786     OutputListeFormat.push_back(".tif");
2787     OutputListeFormat.push_back(".mhd");
2788     OutputListeFormat.push_back(".mha");
2789     OutputListeFormat.push_back(".hdr");
2790     OutputListeFormat.push_back(".vox");
2791   } else if (dimension == 3) {
2792     OutputListeFormat.push_back(".mhd");
2793     OutputListeFormat.push_back(".mha");
2794     OutputListeFormat.push_back(".nii");
2795     OutputListeFormat.push_back(".nrrd");
2796     OutputListeFormat.push_back(".nhdr");
2797     OutputListeFormat.push_back(".hdr");
2798     OutputListeFormat.push_back(".vox");
2799   } else if (dimension == 4) {
2800     OutputListeFormat.push_back(".mhd");
2801     OutputListeFormat.push_back(".mha");
2802     OutputListeFormat.push_back(".nii");
2803     OutputListeFormat.push_back(".nrrd");
2804     OutputListeFormat.push_back(".nhdr");
2805   }
2806   QString Extensions = "AllFiles(*.*)";
2807   for (int i = 0; i < OutputListeFormat.count(); i++) {
2808     Extensions += ";;Images ( *";
2809     Extensions += OutputListeFormat[i];
2810     Extensions += ")";
2811   }
2812   QString fileName = QFileDialog::getSaveFileName(this,
2813     tr("Save As"),
2814     mSlicerManagers[index]->GetFileName().c_str(),
2815     Extensions);
2816   if (!fileName.isEmpty()) {
2817     std::string fileformat = itksys::SystemTools::GetFilenameLastExtension(fileName.toStdString());
2818     if (OutputListeFormat.contains(
2819       fileformat.c_str())) {
2820         QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
2821         std::string action = "Saving";
2822         vvProgressDialog progress("Saving "+fileName.toStdString());
2823         qApp->processEvents();
2824         vvImageWriter::Pointer writer = vvImageWriter::New();
2825         writer->SetOutputFileName(fileName.toStdString());
2826         writer->SetInput(mSlicerManagers[index]->GetImage());
2827
2828         // Check on transform and prompt user
2829         writer->SetSaveTransform(false);
2830         bool bId = true;
2831         for(int i=0; i<4; i++)
2832           for(int j=0; j<4; j++) {
2833             // TODO SR and BP: check on the list of transforms and not the first only
2834             double elt = mSlicerManagers[index]->GetImage()->GetTransform()[0]->GetMatrix()->GetElement(i,j);
2835             if(i==j && elt!=1.)
2836               bId = false;
2837             if(i!=j && elt!=0.)
2838               bId = false;
2839           }
2840           if( !bId ) {
2841             QString warning = "The image has an associated linear transform. Do you want to save it along?";
2842             QMessageBox msgBox(QMessageBox::Warning, tr("Save transform"), warning, 0, this);
2843             msgBox.addButton(tr("Yes"), QMessageBox::AcceptRole);
2844             msgBox.addButton(tr("No"), QMessageBox::RejectRole);
2845             if (msgBox.exec() == QMessageBox::AcceptRole)
2846               writer->SetSaveTransform(true);
2847           }
2848
2849           writer->Update();
2850           QApplication::restoreOverrideCursor();
2851           if (writer->GetLastError().size()) {
2852             QString error = "Saving did not succeed\n";
2853             error += writer->GetLastError().c_str();
2854             QMessageBox::information(this,tr("Saving Problem"),error);
2855             SaveAs();
2856           }
2857     } else {
2858       QString error = fileformat.c_str();
2859       if (error.isEmpty())
2860         error += "no file format specified !";
2861       else
2862         error += " format unknown !!!\n";
2863       QMessageBox::information(this,tr("Saving Problem"),error);
2864       SaveAs();
2865     }
2866   }
2867 }
2868 //------------------------------------------------------------------------------
2869
2870 //------------------------------------------------------------------------------
2871 void vvMainWindow::SaveCurrentState()
2872 {
2873   QString Extensions = "XML Files(*.xml)";
2874   QString fileName = QFileDialog::getSaveFileName(this,
2875     tr("Save Current Window State"),
2876     "",
2877     Extensions);
2878
2879   SaveCurrentStateAs(fileName.toStdString());
2880 }
2881 //------------------------------------------------------------------------------
2882
2883 //------------------------------------------------------------------------------
2884 void vvMainWindow::SaveCurrentStateAs(const std::string& stateFile)
2885 {
2886   vvSaveState save_state;
2887   save_state.Run(this, stateFile);
2888 }
2889
2890 //------------------------------------------------------------------------------
2891 void vvMainWindow::ReadSavedState()
2892 {
2893   QString Extensions = "XML Files(*.xml)";
2894   QString fileName = QFileDialog::getOpenFileName(this,
2895     tr("Load Window State"),
2896     "",
2897     Extensions);
2898
2899   ReadSavedStateFile(fileName.toStdString());
2900 }
2901 //------------------------------------------------------------------------------
2902
2903 //------------------------------------------------------------------------------
2904 void vvMainWindow::ReadSavedStateFile(const std::string& stateFile)
2905 {
2906   vvReadState read_state;
2907   read_state.Run(this, stateFile);
2908 }
2909 //------------------------------------------------------------------------------
2910
2911 //------------------------------------------------------------------------------
2912 void vvMainWindow::LinkAllImages()
2913 {
2914   linkPanel->linkAll();
2915 }
2916
2917 //------------------------------------------------------------------------------
2918 void vvMainWindow::AddLink(QString image1,QString image2,bool fromPanel)
2919 {
2920   if (!fromPanel) {
2921     // delegate to linkPanel if call came from elsewhere...
2922     linkPanel->addLinkFromIds(image1, image2);
2923     return;
2924   }
2925
2926   unsigned int sm1 = 0;
2927   unsigned int sm2 = 0;
2928
2929   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
2930     if (image1.toStdString() == mSlicerManagers[i]->GetId()) {
2931       mSlicerManagers[i]->AddLink(image2.toStdString());
2932       sm1 = i;
2933     }
2934     if (image2.toStdString() == mSlicerManagers[i]->GetId()) {
2935       mSlicerManagers[i]->AddLink(image1.toStdString());
2936       sm2 = i;
2937     }
2938   }
2939
2940   if (linkPanel->isLinkAll())   {
2941     emit UpdateLinkedNavigation(mSlicerManagers[sm1]->GetId(), mSlicerManagers[mCurrentPickedImageIndex], mSlicerManagers[mCurrentPickedImageIndex]->GetSlicer(0));
2942     emit UpdateLinkedNavigation(mSlicerManagers[sm2]->GetId(), mSlicerManagers[mCurrentPickedImageIndex], mSlicerManagers[mCurrentPickedImageIndex]->GetSlicer(0));
2943   } else {
2944     emit UpdateLinkedNavigation(mSlicerManagers[sm2]->GetId(), mSlicerManagers[sm1], mSlicerManagers[sm1]->GetSlicer(0));
2945   }
2946 }
2947
2948 //------------------------------------------------------------------------------
2949
2950
2951 //------------------------------------------------------------------------------
2952 void vvMainWindow::RemoveLink(QString image1,QString image2)
2953 {
2954   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
2955     if (image1.toStdString() == mSlicerManagers[i]->GetId()) {
2956       mSlicerManagers[i]->RemoveLink(image2.toStdString());
2957     }
2958     if (image2.toStdString() == mSlicerManagers[i]->GetId()) {
2959       mSlicerManagers[i]->RemoveLink(image1.toStdString());
2960     }
2961   }
2962 }
2963 //------------------------------------------------------------------------------
2964
2965 //------------------------------------------------------------------------------
2966 void vvMainWindow::ChangeImageWithIndexOffset(vvSlicerManager *sm, int slicer, int offset)
2967 {
2968   if(mSlicerManagers.size()==1)
2969     return;
2970
2971   int index = 0;
2972   while(sm != mSlicerManagers[index])
2973     index++;
2974   index = (index+offset+mSlicerManagers.size()) % mSlicerManagers.size();
2975
2976   QTreeWidgetItem* item = GetItemFromSlicerManager(mSlicerManagers[index]);
2977   item->setData(slicer+1,Qt::CheckStateRole,2);         //change checkbox
2978   CurrentImageChanged(mSlicerManagers[index]->GetId()); //select new image
2979   DisplayChanged(item,slicer+1);
2980 }
2981 //------------------------------------------------------------------------------
2982 void vvMainWindow::HorizontalSliderMoved(int value,int column, int slicer_index)
2983 {
2984   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
2985     if (DataTree->topLevelItem(i)->data(column,Qt::CheckStateRole).toInt() > 1) {
2986       //i is the SlicerManager that is in charge of this slicer.
2987       if (mSlicerManagers[i]->IsInvolvedInFusionSequence()) {
2988         //if the slicerManager is involved in a fusionSequence as the secondary sequence, then update the slider position in the overlay panel and everything accordingly
2989         if (mSlicerManagers[i]->IsSecondarySequenceOfFusionSequence()) {
2990           overlayPanel->updateFusionSequenceSliderValueFromWindow(value, true);
2991         }
2992         else { //if this is the primary sequence that has been modified
2993           if (mSlicerManagers[i]->GetFusionSequenceTemporalSyncFlag()) {
2994             //WARNING: for some obscure reason, there are problems when accessing mSlicerManagers[mSlicerManagers[i]->GetFusionSequenceIndexOfLinkedManager()]->GetFusionSequenceFrameIndex();
2995
2996             int estimatedValue=0;
2997             //estimate a corresponding time index for the secondary (US) sequence, and update it accordingly.
2998             estimatedValue = mSlicerManagers[i]->GetFusionSequenceCorrespondances()[ value ];
2999             //TODO: at the moment, there is a loop in TSlice modifications
3000             //modifying sequence 1 causes seq 2 to update, which in turns update seq1...
3001             //I disable control on seq1 at the moment.
3002             //overlayPanel->updateFusionSequenceSliderValueFromWindow(estimatedValue, true);
3003           }
3004         }
3005       }
3006
3007       for (int j = 0; j < 4; j++) {
3008         mSlicerManagers[i]->SetTSliceInSlicer(value,j);
3009       }
3010       mSlicerManagers[i]->GetSlicer(slicer_index)->Render();
3011       break;
3012     }
3013   }
3014 }
3015 //------------------------------------------------------------------------------
3016
3017
3018 //------------------------------------------------------------------------------
3019 void vvMainWindow::NOHorizontalSliderMoved()
3020 {
3021   // if (mCurrentTime == NOHorizontalSlider->value()) return;
3022   HorizontalSliderMoved(NOHorizontalSlider->value(),COLUMN_UL_VIEW,0);
3023   //  mCurrentTime = NOHorizontalSlider->value();
3024 }
3025 //------------------------------------------------------------------------------
3026
3027
3028 //------------------------------------------------------------------------------
3029 void vvMainWindow::NEHorizontalSliderMoved()
3030 {
3031   // if (mCurrentTime == NEHorizontalSlider->value()) return;
3032   HorizontalSliderMoved(NEHorizontalSlider->value(),COLUMN_UR_VIEW,1);
3033   //  mCurrentTime = NEHorizontalSlider->value();
3034 }
3035 //------------------------------------------------------------------------------
3036
3037
3038 //------------------------------------------------------------------------------
3039 void vvMainWindow::SOHorizontalSliderMoved()
3040 {
3041   // if (mCurrentTime == SOHorizontalSlider->value()) return;
3042   HorizontalSliderMoved(SOHorizontalSlider->value(),COLUMN_DL_VIEW,2);
3043   // mCurrentTime = SOHorizontalSlider->value();
3044 }
3045 //------------------------------------------------------------------------------
3046
3047
3048 //------------------------------------------------------------------------------
3049 void vvMainWindow::SEHorizontalSliderMoved()
3050 {
3051   // if (mCurrentTime == SEHorizontalSlider->value()) return;
3052   HorizontalSliderMoved(SEHorizontalSlider->value(),COLUMN_DR_VIEW,3);
3053   // mCurrentTime = SEHorizontalSlider->value();
3054 }
3055 //------------------------------------------------------------------------------
3056
3057 //------------------------------------------------------------------------------
3058 void vvMainWindow::NOVerticalSliderChanged()
3059 {
3060   static int value=-1;
3061   if (value == NOVerticalSlider->value()) return;
3062   else value = NOVerticalSlider->value();
3063   //  int value = NOVerticalSlider->value();
3064   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
3065     if (DataTree->topLevelItem(i)->data(COLUMN_UL_VIEW,Qt::CheckStateRole).toInt() > 1) {
3066       if (mSlicerManagers[i]->GetSlicer(0)->GetSlice() != value) {
3067         mSlicerManagers[i]->GetSlicer(0)->SetSlice(value);
3068         mSlicerManagers[i]->VerticalSliderHasChanged(0, value);
3069
3070         // If nor Update/Render -> slider not work
3071         // only render = ok navigation, but for contour Update needed but slower ?
3072
3073         mSlicerManagers[i]->UpdateSlice(0);  // <-- DS add this. Not too much update ? YES. but needed for ImageContour ...
3074         //mSlicerManagers[i]->GetSlicer(0)->Render(); // <-- DS add this, needed for contour, seems ok ? not too slow ?
3075       }
3076       break;
3077     }
3078   }
3079 }
3080 //------------------------------------------------------------------------------
3081
3082
3083 //------------------------------------------------------------------------------
3084 void vvMainWindow::NEVerticalSliderChanged()
3085 {
3086   static int value=-1;
3087   if (value == NEVerticalSlider->value()) return;
3088   else value = NEVerticalSlider->value();
3089   //  int value = NEVerticalSlider->value();
3090   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
3091     if (DataTree->topLevelItem(i)->data(COLUMN_UR_VIEW,Qt::CheckStateRole).toInt() > 1) {
3092       if (mSlicerManagers[i]->GetSlicer(1)->GetSlice() != value) {
3093         mSlicerManagers[i]->GetSlicer(1)->SetSlice(value);
3094         mSlicerManagers[i]->VerticalSliderHasChanged(1, value);
3095         mSlicerManagers[i]->UpdateSlice(1);
3096         //mSlicerManagers[i]->GetSlicer(1)->Render(); // <-- DS add this, needed for contour, seems ok ? not too slow ?
3097       }
3098       break;
3099     }
3100   }
3101 }
3102 //------------------------------------------------------------------------------
3103
3104
3105 //------------------------------------------------------------------------------
3106 void vvMainWindow::SOVerticalSliderChanged()
3107 {
3108   static int value=-1;
3109   if (value == SOVerticalSlider->value()) return;
3110   else value = SOVerticalSlider->value();
3111   //int value = SOVerticalSlider->value();
3112   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
3113     if (DataTree->topLevelItem(i)->data(COLUMN_DL_VIEW,Qt::CheckStateRole).toInt() > 1) {
3114       if (mSlicerManagers[i]->GetSlicer(2)->GetSlice() != value) {
3115         mSlicerManagers[i]->GetSlicer(2)->SetSlice(value);
3116         mSlicerManagers[i]->VerticalSliderHasChanged(2, value);
3117         mSlicerManagers[i]->UpdateSlice(2);
3118         //mSlicerManagers[i]->GetSlicer(2)->Render(); // <-- DS add this, needed for contour, seems ok ? not too slow ?
3119       }
3120       // else { DD("avoid SOVerticalSlider slicer update"); }
3121       break;
3122     }
3123   }
3124 }
3125 //------------------------------------------------------------------------------
3126
3127
3128 //------------------------------------------------------------------------------
3129 void vvMainWindow::SEVerticalSliderChanged()
3130 {
3131   static int value=-1;
3132   if (value == SEVerticalSlider->value()) return;
3133   else value = SEVerticalSlider->value();
3134   // int value = SEVerticalSlider->value();
3135   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
3136     if (DataTree->topLevelItem(i)->data(COLUMN_DR_VIEW,Qt::CheckStateRole).toInt() > 1) {
3137       if (mSlicerManagers[i]->GetSlicer(3)->GetSlice() != value) {
3138         mSlicerManagers[i]->GetSlicer(3)->SetSlice(value);
3139         mSlicerManagers[i]->VerticalSliderHasChanged(3, value);
3140         mSlicerManagers[i]->UpdateSlice(3);
3141         //mSlicerManagers[i]->GetSlicer(3)->Render(); // <-- DS add this, needed for contour, seems ok ? not too slow ?
3142       }
3143       break;
3144     }
3145   }
3146 }
3147 //------------------------------------------------------------------------------
3148
3149
3150 //------------------------------------------------------------------------------
3151 void vvMainWindow::UpdateSlice(int slicer, int slice)
3152 {
3153   // DD("vvMainWindow::UpdateSlice");
3154   //   DD(slicer);
3155   //   DD(slice);
3156   if (slicer == 0) {
3157     //    if (slice != NOVerticalSlider->value())
3158     NOVerticalSlider->setValue(slice);
3159   } else {
3160     if (slicer == 1)
3161       NEVerticalSlider->setValue(slice);
3162     else {
3163       if (slicer == 2)
3164         SOVerticalSlider->setValue(slice);
3165       else {
3166         if (slicer == 3)
3167           SEVerticalSlider->setValue(slice);
3168       }
3169     }
3170   }
3171   // DD("vvMainWindow:UpdateSlice END");
3172 }
3173 //------------------------------------------------------------------------------
3174
3175
3176 //------------------------------------------------------------------------------
3177 void vvMainWindow::UpdateTSlice(int slicer, int slice, int code)
3178 {
3179   //FusionSequence: the slider value should be updated for slicers which show the same sequence as requested
3180   bool doUpdate=false;
3181   if (code==-1) doUpdate=true;
3182   else {
3183     for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
3184       if (DataTree->topLevelItem(i)->data(slicer+1,Qt::CheckStateRole).toInt() > 1) {
3185         //i is the active SlicerManager
3186         if (mSlicerManagers[i]->GetFusionSequenceInvolvmentCode()==code) doUpdate=true;
3187         break;
3188       }
3189     }
3190   }
3191   if (!doUpdate) return;
3192
3193   switch (slicer) {
3194   case 0:
3195     if (NOHorizontalSlider->value()==slice) return;
3196     NOHorizontalSlider->setValue(slice);
3197     break;
3198   case 1:
3199     if (NEHorizontalSlider->value()==slice) return;
3200     NEHorizontalSlider->setValue(slice);
3201     break;
3202   case 2:
3203     if (SOHorizontalSlider->value()==slice) return;
3204     SOHorizontalSlider->setValue(slice);
3205     break;
3206   case 3:
3207     if (SEHorizontalSlider->value()==slice) return;
3208     SEHorizontalSlider->setValue(slice);
3209     break;
3210   }
3211 }
3212 //------------------------------------------------------------------------------
3213
3214
3215 //------------------------------------------------------------------------------
3216 void vvMainWindow::UpdateSliceRange(int slicer, int min, int max, int tmin, int tmax)
3217 {
3218   //int position = int((min+max)/2);
3219   int position = mSlicerManagers[mCurrentPickedImageIndex]->GetSlicer(slicer)->GetSlice();
3220   if (slicer == 0) {
3221     NOVerticalSlider->setRange(min,max);
3222     NOHorizontalSlider->setRange(tmin,tmax);
3223     NOVerticalSlider->setValue(position);
3224   } else if (slicer == 1) {
3225     NEVerticalSlider->setRange(min,max);
3226     NEHorizontalSlider->setRange(tmin,tmax);
3227     NEVerticalSlider->setValue(position);
3228   } else if (slicer == 2) {
3229     SOVerticalSlider->setRange(min,max);
3230     SOHorizontalSlider->setRange(tmin,tmax);
3231     SOVerticalSlider->setValue(position);
3232   } else if (slicer == 3) {
3233     SEVerticalSlider->setRange(min,max);
3234     SEHorizontalSlider->setRange(tmin,tmax);
3235     SEVerticalSlider->setValue(position);
3236   }
3237 }
3238 //------------------------------------------------------------------------------
3239
3240
3241 //------------------------------------------------------------------------------
3242 void vvMainWindow::SaveNOScreenshot()
3243 {
3244   SaveScreenshot(NOViewWidget);
3245 }
3246 //------------------------------------------------------------------------------
3247
3248
3249 //------------------------------------------------------------------------------
3250 void vvMainWindow::SaveNEScreenshot()
3251 {
3252   SaveScreenshot(NEViewWidget);
3253 }
3254 //------------------------------------------------------------------------------
3255
3256
3257 //------------------------------------------------------------------------------
3258 void vvMainWindow::SaveSOScreenshot()
3259 {
3260   SaveScreenshot(SOViewWidget);
3261 }
3262 //------------------------------------------------------------------------------
3263
3264
3265 //------------------------------------------------------------------------------
3266 void vvMainWindow::SaveSEScreenshot()
3267 {
3268   SaveScreenshot(SEViewWidget);
3269 }
3270 //------------------------------------------------------------------------------
3271
3272
3273 //------------------------------------------------------------------------------
3274 void vvMainWindow::SaveScreenshotAllSlices()
3275 {
3276   QVTKWidget *widget = NOViewWidget;
3277
3278   int index = 0;// GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
3279   vvSlicerManager * SM = mSlicerManagers[index];
3280   vvImage * image = SM->GetImage();
3281   vvSlicer * slicer = SM->GetSlicer(0);
3282   int orientation = slicer->GetOrientation();
3283   int nbSlices = image->GetSize()[orientation];
3284   vtkSmartPointer<vtkRenderWindow>  renderWindow = widget->GetRenderWindow();
3285
3286   // Select filename base
3287   QString filename = QFileDialog::getSaveFileName(this,
3288     tr("Save As (filename will be completed by slice number)"),
3289     itksys::SystemTools::GetFilenamePath(mSlicerManagers[index]->GetFileName()).c_str(),
3290     "Images( *.png);;Images( *.jpg)");
3291
3292   // Loop on slices
3293   for(int i=0; i<nbSlices; i++) {
3294     // Change the slice
3295     slicer->SetSlice(i); // -> change the slice of the current slicer
3296     SM->UpdateSlice(0); // --> this one emit UpdateSlice
3297     QCoreApplication::flush(); // -> needed to force display of contours
3298
3299     // Screenshot
3300     vtkSmartPointer<vtkWindowToImageFilter> windowToImageFilter = vtkSmartPointer<vtkWindowToImageFilter>::New();
3301     windowToImageFilter->SetInput(renderWindow);
3302     windowToImageFilter->SetMagnification(1);
3303     windowToImageFilter->SetInputBufferTypeToRGBA(); //also record the alpha (transparency) channel
3304     windowToImageFilter->Update();
3305
3306     vtkSmartPointer<vtkPNGWriter> writer = vtkSmartPointer<vtkPNGWriter>::New();
3307     std::string fn = itksys::SystemTools::GetFilenameWithoutLastExtension(filename.toStdString());
3308     std::string num = clitk::toString(i);
3309     if (i<10) num = "0"+num;
3310     if (i<100) num = "0"+num;
3311     if (i<1000) num = "0"+num;
3312
3313     fn = itksys::SystemTools::GetFilenamePath(filename.toStdString()) + "/"+ fn
3314       + "_" + num + itksys::SystemTools::GetFilenameLastExtension(filename.toStdString());
3315     writer->SetFileName(fn.c_str());
3316 #if VTK_MAJOR_VERSION <= 5
3317     writer->SetInput(windowToImageFilter->GetOutput());
3318 #else
3319     writer->SetInputConnection(windowToImageFilter->GetOutputPort());
3320 #endif
3321     writer->Write();
3322   }
3323 }
3324 //------------------------------------------------------------------------------
3325
3326
3327 //------------------------------------------------------------------------------
3328 void vvMainWindow::SaveScreenshot(QVTKWidget *widget)
3329 {
3330   QString Extensions = "Images( *.png);;";
3331   Extensions += "Images( *.jpg);;";
3332   Extensions += "Images( *.bmp);;";
3333   Extensions += "Images( *.tif);;";
3334   Extensions += "Images( *.ppm)";
3335 #if defined(VTK_USE_FFMPEG_ENCODER) || defined(VTK_USE_VIDEO_FOR_WINDOWS)
3336   Extensions += ";;Video( *.avi)";
3337 #endif
3338 #ifdef VTK_USE_MPEG2_ENCODER
3339   Extensions += ";;Video( *.mpg)";
3340 #endif
3341 #ifdef CLITK_EXPERIMENTAL
3342   Extensions += ";;Video( *.gif)";
3343 #endif
3344
3345   int smIndex=GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
3346   QString fileName = QFileDialog::getSaveFileName(this,
3347     tr("Save As"),
3348     itksys::SystemTools::GetFilenamePath(mSlicerManagers[smIndex]->GetFileName()).c_str(),
3349     Extensions);
3350
3351   if (!fileName.isEmpty()) {
3352     vtkSmartPointer<vtkWindowToImageFilter> w2i = vtkSmartPointer<vtkWindowToImageFilter>::New();
3353     w2i->SetInput(widget->GetRenderWindow());
3354     w2i->SetMagnification(1);
3355     w2i->SetInputBufferTypeToRGBA(); //also record the alpha (transparency) channel
3356     w2i->Update();
3357     vtkImageData *image = w2i->GetOutput();
3358
3359     std::string ext(itksys::SystemTools::GetFilenameLastExtension(fileName.toStdString()));
3360
3361     // Image
3362     vtkImageWriter *imgwriter = NULL;
3363     if (ext==".bmp")
3364       imgwriter = vtkBMPWriter::New();
3365     else if (ext==".tif")
3366       imgwriter = vtkTIFFWriter::New();
3367     else if (ext==".ppm")
3368       imgwriter = vtkPNMWriter::New();
3369     else if (ext==".png")
3370       imgwriter = vtkPNGWriter::New();
3371     else if (ext==".jpg")
3372       imgwriter = vtkJPEGWriter::New();
3373
3374     // Snapshot image if not null
3375     if(imgwriter!=NULL) {
3376 #if VTK_MAJOR_VERSION <= 5
3377       imgwriter->SetInput(image);
3378 #else
3379       imgwriter->SetInputConnection(w2i->GetOutputPort());
3380 #endif
3381       imgwriter->SetFileName(fileName.toStdString().c_str());
3382       imgwriter->Write();
3383       return;
3384     }
3385
3386     // Video
3387     vtkGenericMovieWriter *vidwriter = NULL;
3388 #if CLITK_EXPERIMENTAL == 1
3389     if (ext==".gif") {
3390       vvAnimatedGIFWriter *gif = vvAnimatedGIFWriter::New();
3391       vidwriter = gif;
3392
3393       // FPS
3394       bool ok;
3395       int fps = QInputDialog::getInt(this, tr("Number of frames per second"),
3396         tr("FPS:"), 5, 0, 1000, 1, &ok);
3397       if(ok)
3398         gif->SetRate(fps);
3399
3400       // Loops
3401       int loops = QInputDialog::getInt(this, tr("Loops"),
3402         tr("Number of loops (0 means infinite):"), 0, 0, 1000000000, 1, &ok);
3403       if(ok)
3404         gif->SetLoops(loops);
3405
3406       // Dithering
3407       QString msg = "Would you like to activate dithering?";
3408       QMessageBox msgBox(QMessageBox::Question, tr("Dithering"),msg, 0, this);
3409       msgBox.addButton(tr("Yes"), QMessageBox::AcceptRole);
3410       msgBox.addButton(tr("No"), QMessageBox::RejectRole);
3411       gif->SetDither(msgBox.exec() == QMessageBox::AcceptRole);
3412     }
3413 #endif
3414 #ifdef VTK_USE_VIDEO_FOR_WINDOWS
3415     if (ext==".avi") {
3416       vtkAVIWriter *mpg = vtkAVIWriter::New();
3417       vidwriter = mpg;
3418       mpg->SetQuality(2);
3419       bool ok;
3420       int fps = QInputDialog::getInt(this, tr("Number of frames per second"),
3421         tr("FPS:"), 5, 0, 1024, 1, &ok);
3422       if(!ok)
3423         fps = 5;
3424       mpg->SetRate(fps);
3425     }
3426 #endif
3427 #ifdef VTK_USE_FFMPEG_ENCODER
3428     if (ext==".avi") {
3429       vtkFFMPEGWriter *mpg = vtkFFMPEGWriter::New();
3430       vidwriter = mpg;
3431       mpg->SetQuality(2);
3432       bool ok;
3433       int fps = QInputDialog::getInt(this, tr("Number of frames per second"),
3434         tr("FPS:"), 5, 0, 1024, 1, &ok);
3435       if(!ok)
3436         fps = 5;
3437       mpg->SetRate(fps);
3438       mpg->SetBitRateTolerance(int(ceil(12.0*1024*1024/fps)));
3439     }
3440 #endif
3441 #ifdef VTK_USE_MPEG2_ENCODER
3442     if (ext==".mpg") {
3443       vtkMPEG2Writer *mpg = vtkMPEG2Writer::New();
3444       vidwriter = mpg;
3445     }
3446 #endif
3447
3448     // Take video if not null
3449     if(vidwriter!=NULL){
3450 #if VTK_MAJOR_VERSION <= 5
3451       vidwriter->SetInput(image);
3452 #else
3453       vidwriter->SetInputConnection(w2i->GetOutputPort());
3454 #endif
3455       vidwriter->SetFileName(fileName.toStdString().c_str());
3456       vidwriter->Start();
3457       int nSlice = mSlicerManagers[smIndex]->GetSlicer(0)->GetTMax();
3458       for(int i=0; i<=nSlice; i++) {
3459         mSlicerManagers[smIndex]->SetNextTSlice(0);
3460         vtkSmartPointer<vtkWindowToImageFilter> w2i = vtkSmartPointer<vtkWindowToImageFilter>::New();
3461         w2i->SetInput(widget->GetRenderWindow());
3462         w2i->Update();
3463 #if VTK_MAJOR_VERSION <= 5
3464         vidwriter->SetInput(w2i->GetOutput());
3465 #else
3466         vidwriter->SetInputConnection(w2i->GetOutputPort());
3467 #endif
3468         vidwriter->Write();
3469       }
3470       vidwriter->End();
3471       vidwriter->Delete();
3472       return;
3473     }
3474
3475     QMessageBox::information(this,tr("Problem saving screenshot !"),tr("Cannot save image.\nPlease set a file extension !!!"));
3476   }
3477 }
3478 //------------------------------------------------------------------------------
3479
3480
3481 //------------------------------------------------------------------------------
3482 void vvMainWindow::GoToCursor()
3483 {
3484   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
3485   for (int column = 1; column < 5; column++) {
3486     if (DataTree->selectedItems()[0]->data(column,Qt::CheckStateRole).toInt() > 1) {
3487       double* cursorPos = mSlicerManagers[index]->GetSlicer(column-1)->GetCursorPosition();
3488       mSlicerManagers[index]->GetSlicer(column-1)->SetCurrentPosition(
3489         cursorPos[0],cursorPos[1],cursorPos[2],cursorPos[3]);
3490       mSlicerManagers[index]->UpdateViews(1,column-1);
3491       mSlicerManagers[index]->UpdateLinked(column-1);
3492       break;
3493     }
3494   }
3495 }
3496 //------------------------------------------------------------------------------
3497
3498 //------------------------------------------------------------------------------
3499 void vvMainWindow::GoToLandmark()
3500 {
3501   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
3502   for (int column = 1; column < 5; column++) {
3503     if (DataTree->selectedItems()[0]->data(column,Qt::CheckStateRole).toInt() > 1) {
3504       double* cursorPos = landmarksPanel->GetSelectedPoint();
3505       mSlicerManagers[index]->GetSlicer(column-1)->SetCurrentPosition(
3506         cursorPos[0],cursorPos[1],cursorPos[2],cursorPos[3]);
3507       mSlicerManagers[index]->UpdateViews(1,column-1);
3508       mSlicerManagers[index]->UpdateLinked(column-1);
3509       break;
3510     }
3511   }
3512 }
3513 //------------------------------------------------------------------------------
3514
3515 //------------------------------------------------------------------------------
3516 void vvMainWindow::PlayPause()
3517 {
3518   if (playMode) {
3519     playMode = 0;
3520     playButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/player_play.png")));
3521     ImageInfoChanged();
3522     return;
3523   } else {
3524     int image_number=DataTree->topLevelItemCount();
3525     bool has_temporal;
3526     for (int i=0; i<image_number; i++)
3527       if (mSlicerManagers[i]->GetSlicer(0)->GetTMax() > 0) {
3528         has_temporal=true;
3529         break;
3530       }
3531       if (has_temporal) {
3532         playMode = 1;
3533         playButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/player_pause.png")));
3534         QTimer::singleShot(1000/mFrameRate, this, SLOT(PlayNext()));
3535       }
3536   }
3537 }
3538 //------------------------------------------------------------------------------
3539
3540 //------------------------------------------------------------------------------
3541 void vvMainWindow::PlayNext()
3542 {
3543   if (playMode && !this->isHidden()) {
3544     int image_number=DataTree->topLevelItemCount();
3545     ///Only play one slicer per SM, and only if the SM is being displayed
3546     for (int i=0; i<image_number; i++)
3547       for (int j=0; j<4; j++)
3548         if (mSlicerManagers[i]->GetSlicer(0)->GetTMax() > 0 &&
3549           DataTree->topLevelItem(i)->data(j+1,Qt::CheckStateRole).toInt() > 0) {
3550             mSlicerManagers[i]->SetNextTSlice(j);
3551             break;
3552         }
3553         QTimer::singleShot(1000/mFrameRate, this, SLOT(PlayNext()));
3554   }
3555 }
3556 //------------------------------------------------------------------------------
3557
3558 void vvMainWindow::ShowLastImage()
3559 {
3560   if (mSlicerManagers.size() > 1) {
3561     QTreeWidgetItem * item=DataTree->topLevelItem(DataTree->topLevelItemCount()-1);
3562     CurrentImageChanged(mSlicerManagers.back()->GetId()); //select new image
3563     item->setData(1,Qt::CheckStateRole,2); //show the new image in the first panel
3564     //mSlicerManagers[GetSlicerIndexFromItem(item)]->GetSlicer(0)->SetActorVisibility("image", 0, 1); //Set the Last Image visibles
3565     DisplayChanged(item,1);
3566   }
3567 }
3568
3569 //------------------------------------------------------------------------------
3570 void vvMainWindow::UpdateRenderWindows()
3571 {
3572   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
3573       for (unsigned int j = 0; j < 4; ++j) {
3574         mSlicerManagers[i]->GetSlicer(j)->RemoveLandmarks();
3575         mSlicerManagers[i]->GetSlicer(j)->DisplayLandmarks();
3576       }
3577   }
3578   if (NOViewWidget->GetRenderWindow()) NOViewWidget->GetRenderWindow()->Render();
3579   if (NEViewWidget->GetRenderWindow()) NEViewWidget->GetRenderWindow()->Render();
3580   if (SOViewWidget->GetRenderWindow()) SOViewWidget->GetRenderWindow()->Render();
3581   if (SEViewWidget->GetRenderWindow()) SEViewWidget->GetRenderWindow()->Render();
3582 }
3583 //------------------------------------------------------------------------------
3584
3585 //------------------------------------------------------------------------------
3586 void vvMainWindow::SegmentationOnCurrentImage()
3587 {
3588   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
3589
3590   vvSegmentationDialog segmentation;
3591   segmentation.SetImage(mSlicerManagers[index]->GetSlicer(0)->GetImage());
3592   segmentation.exec();
3593 }
3594 //------------------------------------------------------------------------------
3595
3596 void vvMainWindow::SurfaceViewerLaunch()
3597 {
3598   vvSurfaceViewerDialog surfaceViewer;
3599   surfaceViewer.exec();
3600 }
3601 //------------------------------------------------------------------------------
3602
3603
3604 //------------------------------------------------------------------------------
3605 int vvMainWindow::GetImageDuplicateFilenameNumber(std::string filename)
3606 {
3607   int number=0;
3608   for(unsigned int l=0; l<mSlicerManagers.size(); l++) {
3609     vvSlicerManager * v = mSlicerManagers[l];
3610     if (v->GetBaseFileName() ==
3611       vtksys::SystemTools::GetFilenameName(vtksys::SystemTools::GetFilenameWithoutLastExtension(filename))) {
3612         number = std::max(number, v->GetBaseFileNameNumber()+1);
3613     }
3614   }
3615   return number;
3616 }
3617 //------------------------------------------------------------------------------
3618
3619
3620 //------------------------------------------------------------------------------
3621 vvSlicerManager* vvMainWindow::AddImage(vvImage::Pointer image,std::string filename)
3622 {
3623   // Change filename if another image exist with the same name
3624   int number = GetImageDuplicateFilenameNumber(filename);
3625
3626   // Create new SliceManager
3627   vvSlicerManager* slicer_manager = new vvSlicerManager(4);
3628   slicer_manager->SetImage(image);//, IMAGE, number);
3629   //  filename = filename+"_"+clitk::toString(number);
3630   slicer_manager->SetFilename(filename, number);
3631   mSlicerManagers.push_back(slicer_manager);
3632
3633   //create an item in the tree with good settings
3634   QTreeWidgetItem *item = new QTreeWidgetItem();
3635   item->setData(0,Qt::UserRole,slicer_manager->GetFileName().c_str());//files[i].c_str());
3636   item->setData(1,Qt::UserRole,tr("image"));
3637   item->setData(COLUMN_IMAGE_NAME,Qt::DisplayRole,slicer_manager->GetFileName().c_str());//filename.c_str());
3638   qApp->processEvents();
3639
3640   for (int j = 1; j <= 4; j++) item->setData(j,Qt::CheckStateRole,1);
3641
3642   //Create the buttons for reload and close
3643   qApp->processEvents();
3644   QTreePushButton* cButton = new QTreePushButton;
3645   cButton->setItem(item);
3646   cButton->setColumn(COLUMN_CLOSE_IMAGE);
3647   cButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/exit.png")));
3648   connect(cButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
3649     this,SLOT(CloseImage(QTreeWidgetItem*, int)));
3650
3651   QTreePushButton* rButton = new QTreePushButton;
3652   rButton->setItem(item);
3653   rButton->setColumn(COLUMN_RELOAD_IMAGE);
3654   rButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/rotateright.png")));
3655   rButton->setEnabled(0);
3656   connect(rButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
3657     this,SLOT(ReloadImage(QTreeWidgetItem*, int)));
3658
3659   DataTree->addTopLevelItem(item);
3660   DataTree->setItemWidget(item, COLUMN_CLOSE_IMAGE, cButton);
3661   DataTree->setItemWidget(item, COLUMN_RELOAD_IMAGE, rButton);
3662
3663   //set the id of the image
3664   QString id = QDir::current().absoluteFilePath(slicer_manager->GetFileName().c_str()) + QString::number(mSlicerManagers.size()-1);
3665   item->setData(COLUMN_IMAGE_NAME,Qt::UserRole,id.toStdString().c_str());
3666   mSlicerManagers.back()->SetId(id.toStdString());
3667
3668   linkPanel->addImage(slicer_manager->GetFileName().c_str()// filename
3669     , id.toStdString());
3670
3671   connect(mSlicerManagers.back(), SIGNAL(currentImageChanged(std::string)),
3672     this, SLOT(CurrentImageChanged(std::string)));
3673   connect(mSlicerManagers.back(), SIGNAL(currentPickedImageChanged(std::string)),
3674     this, SLOT(CurrentPickedImageChanged(std::string)));
3675   connect(mSlicerManagers.back(), SIGNAL(UpdatePosition(int, double, double, double, double, double, double, double)),
3676     this, SLOT(MousePositionChanged(int,double, double, double, double, double, double, double)));
3677   connect(mSlicerManagers.back(), SIGNAL(UpdateVector(int, double, double, double, double)),
3678     this, SLOT(VectorChanged(int,double,double,double, double)));
3679   connect(mSlicerManagers.back(), SIGNAL(UpdateOverlay(int, double, double)),
3680     this, SLOT(OverlayChanged(int,double,double)));
3681   connect(mSlicerManagers.back(), SIGNAL(UpdateFusion(int, double)),
3682     this, SLOT(FusionChanged(int,double)));
3683   //connect(mSlicerManagers.back(), SIGNAL(UpdateFusionSequence(int, bool, unsigned int)),
3684   //  this, SLOT(FusionSequenceChanged(int, bool, unsigned int)));
3685   connect(mSlicerManagers.back(), SIGNAL(WindowLevelChanged()),
3686     this,SLOT(WindowLevelChanged()));
3687   connect(mSlicerManagers.back(), SIGNAL(UpdateSlice(int,int)),
3688     this,SLOT(UpdateSlice(int,int)));
3689   connect(mSlicerManagers.back(), SIGNAL(UpdateTSlice(int, int, int)),
3690     this,SLOT(UpdateTSlice(int, int, int)));
3691   connect(mSlicerManagers.back(), SIGNAL(UpdateTSlice(int, int, int)),
3692     this,SLOT(ImageInfoChanged()));
3693   connect(mSlicerManagers.back(), SIGNAL(UpdateSliceRange(int,int,int,int,int)),
3694     this,SLOT(UpdateSliceRange(int,int,int,int,int)));
3695   connect(mSlicerManagers.back(), SIGNAL(UpdateLinkManager(std::string,int,double,double,double,int)),
3696     this,SLOT(UpdateLinkManager(std::string,int,double,double,double,int)));
3697   connect(mSlicerManagers.back(), SIGNAL(UpdateLinkedNavigation(std::string,vvSlicerManager*,vvSlicer*)),
3698     this,SLOT(UpdateLinkedNavigation(std::string,vvSlicerManager*,vvSlicer*)));
3699   connect(mSlicerManagers.back(), SIGNAL(ChangeImageWithIndexOffset(vvSlicerManager*,int,int)),
3700     this,SLOT(ChangeImageWithIndexOffset(vvSlicerManager*,int,int)));
3701   connect(mSlicerManagers.back(), SIGNAL(LandmarkAdded()),landmarksPanel,SLOT(AddPoint()));
3702
3703
3704
3705   InitSlicers();
3706   UpdateTree();
3707   qApp->processEvents();
3708   InitDisplay();
3709   ShowLastImage();
3710   qApp->processEvents();
3711   // End
3712   ImageInfoChanged();
3713   return slicer_manager;
3714 }
3715 //------------------------------------------------------------------------------
3716
3717
3718 //------------------------------------------------------------------------------
3719 void vvMainWindow::UpdateCurrentSlicer()
3720 {
3721   int index = -1;
3722   if (DataTree->selectedItems().size() > 0) {
3723     index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
3724   }
3725   mSlicerManagerCurrentIndex = index;
3726 }
3727 //------------------------------------------------------------------------------