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 <QMimeData>
  22 #include <QInputDialog>
  23 #include <QTimer>
  24 #include "QTreePushButton.h"
  25 #include <QUrl>
  26 #include <QSettings>
  27 #include <QShortcut>
  28 #include <QFileSystemWatcher>
  29
  30 // VV include
  31 #include "vvMainWindow.h"
  32 #include "vvHelpDialog.h"
  33 #include "vvRegisterForm.h"
  34 #include "vvDocumentation.h"
  35 #include "vvProgressDialog.h"
  36 #include "vvQDicomSeriesSelector.h"
  37 #include "vvSlicerManager.h"
  38 #include "clitkImageCommon.h"
  39 #include "vvSlicer.h"
  40 #include "vvInteractorStyleNavigator.h"
  41 #include "vvImageWriter.h"
  42 #include "vvSegmentationDialog.h"
  43 #include "vvSurfaceViewerDialog.h"
  44 #include "vvDeformationDialog.h"
  45 #include "vvImageWarp.h"
  46 #include "vvUtils.h"
  47 #include "vvMidPosition.h"
  48 #include "vvMesh.h"
  49 #include "vvStructSelector.h"
  50 #include "vvMeshReader.h"
  51 #include "vvSaveState.h"
  52 #include "vvReadState.h"
  53 #if CLITK_USE_PACS_CONNECTION
  54 #include "vvQPacsConnection.h"
  55 #endif
  56 #include "clitkConfiguration.h"
  57 #include "clitkMatrix.h"
  58 #ifdef Q_OS_OSX
  59 # include "vvOSXHelper.h"
  60 #endif
  61
  62 // ITK include
  63 #include <itkImage.h>
  64 #include <itkImageFileReader.h>
  65 #include <itkByteSwapper.h>
  66 #include <itkCommand.h>
  67 #include <itkNumericSeriesFileNames.h>
  68
  69 // VTK include
  70 #include <vtkImageMapper3D.h>
  71 #include <vtkInformation.h>
  72 #include <vtkVersion.h>
  73 #include <vtkImageData.h>
  74 #include <vtkImageActor.h>
  75 #include <vtkCornerAnnotation.h>
  76 #include <vtkRenderWindow.h>
  77 #include <vtkRenderWindowInteractor.h>
  78 #include <vtkRenderer.h>
  79 #include <vtkRendererCollection.h>
  80 #include <vtkWindowToImageFilter.h>
  81 #include <vtkBMPWriter.h>
  82 #include <vtkTIFFWriter.h>
  83 #include <vtkPNMWriter.h>
  84 #include <vtkPNGWriter.h>
  85 #include <vtkJPEGWriter.h>
  86 #include <vtkGenericMovieWriter.h>
  87 #include <vvAnimatedGIFWriter.h>
  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   setAcceptDrops(true); // enable to drop into the window
 138
 139   setDicomClient();
 140
 141   //Qt::WindowFlags flags = windowFlags();
 142   //setWindowFlags(flags | Qt::WindowStaysOnTopHint);
 143
 144   mInputPathName = "";
 145   mMenuTools = menuTools;
 146   //  mMenuSegmentation = menuSegmentation;
 147   mContextMenu = &contextMenu;
 148   mMenuExperimentalTools = menuExperimental;
 149   mMainWidget = this;
 150   mCurrentTime = -1;
 151   mCurrentSelectedImageId = "";
 152   mCurrentPickedImageId = "";
 153   mCurrentPickedImageIndex = 0;
 154
 155   //Init the contextMenu
 156   this->setContextMenuPolicy(Qt::CustomContextMenu);
 157   contextActions.resize(0);
 158   QAction* actionOpen_new_image = contextMenu.addAction(QIcon(QString::fromUtf8(":/common/icons/fileopen.png")),
 159     tr("O&pen new Image"));
 160   connect(actionOpen_new_image,SIGNAL(triggered()),this,SLOT(OpenImages()));
 161   contextActions.push_back(actionOpen_new_image);
 162   contextMenu.addSeparator();
 163
 164   QAction* actionClose_Image = contextMenu.addAction(QIcon(QString::fromUtf8(":/common/icons/exit.png")),
 165     tr("Close Current Image"));
 166   connect(actionClose_Image,SIGNAL(triggered()),this,SLOT(CloseImage()));
 167   contextActions.push_back(actionClose_Image);
 168
 169   QAction* actionReload_image = contextMenu.addAction(QIcon(QString::fromUtf8(":/common/icons/rotateright.png")),
 170     tr("Reload Current Image"));
 171   connect(actionReload_image,SIGNAL(triggered()),this,SLOT(ReloadImage()));
 172   contextActions.push_back(actionReload_image);
 173
 174   QAction* actionSave_image = contextMenu.addAction(QIcon(QString::fromUtf8(":/common/icons/filesave.png")),
 175     tr("Save Current Image"));
 176   connect(actionSave_image,SIGNAL(triggered()),this,SLOT(SaveAs()));
 177   contextActions.push_back(actionSave_image);
 178
 179   QAction* actionSave_state = contextMenu.addAction(QIcon(QString::fromUtf8(":/common/icons/filesave.png")),
 180     tr("Save Current State"));
 181   connect(actionSave_state,SIGNAL(triggered()),this,SLOT(SaveCurrentState()));
 182   contextActions.push_back(actionSave_state);
 183
 184   QAction* actionRead_state = contextMenu.addAction(QIcon(QString::fromUtf8(":/common/icons/filesave.png")),
 185     tr("Read Saved State"));
 186   connect(actionRead_state,SIGNAL(triggered()),this,SLOT(ReadSavedState()));
 187   contextActions.push_back(actionRead_state);
 188
 189   contextMenu.addSeparator();
 190
 191   contextMenu.addAction(actionAdd_VF_to_current_Image);
 192   contextActions.push_back(actionAdd_VF_to_current_Image);
 193
 194   //QAction* actionAdd_Overlay_to_current_Image = menuOverlay->addAction(QIcon(QString::fromUtf8(":/common/icons/GPSup.png")),
 195   //    tr("Add overlay image to current image"));
 196   contextMenu.addAction(actionAdd_overlay_image_to_current_image);
 197   contextActions.push_back(actionAdd_overlay_image_to_current_image);
 198
 199   contextMenu.addAction(actionAdd_fusion_image);
 200   contextActions.push_back(actionAdd_fusion_image);
 201
 202 #ifdef CLITK_EXPERIMENTAL
 203   contextMenu.addAction(actionAdd_USSequence_toCT);
 204   contextActions.push_back(actionAdd_USSequence_toCT);
 205 #endif
 206
 207
 208   contextMenu.addSeparator();
 209   QAction* actionResetMatrix = contextMenu.addAction(QIcon(QString::fromUtf8(":/common/icons/identity.png")),
 210     tr("Reset transformation to identity"));
 211   connect(actionResetMatrix, SIGNAL(triggered()), this,SLOT(ResetTransformationToIdentity()));
 212
 213   //init the DataTree
 214   mSlicerManagers.resize(0);
 215
 216   QStringList header;
 217   header.append("");
 218   header.append("TL");
 219   header.append("TR");
 220   header.append("BL");
 221   header.append("BR");
 222   header.append("");
 223   header.append("");
 224   header.append("Name");
 225
 226   DataTree->setHeaderLabels(header);
 227   DataTree->resizeColumnToContents(COLUMN_TREE);
 228   DataTree->resizeColumnToContents(COLUMN_UL_VIEW);
 229   DataTree->resizeColumnToContents(COLUMN_UR_VIEW);
 230   DataTree->resizeColumnToContents(COLUMN_DL_VIEW);
 231   DataTree->resizeColumnToContents(COLUMN_DR_VIEW);
 232   DataTree->resizeColumnToContents(COLUMN_CLOSE_IMAGE);
 233   DataTree->resizeColumnToContents(COLUMN_RELOAD_IMAGE);
 234   DataTree->resizeColumnToContents(COLUMN_IMAGE_NAME);
 235
 236   viewMode = 1;
 237   documentation = new vvDocumentation();
 238   help_dialog = new vvHelpDialog();
 239   dicomSeriesSelector = new vvDicomSeriesSelector();
 240 #if CLITK_USE_PACS_CONNECTION
 241      PacsConnection = new vvQPacsConnection();
 242 #endif
 243
 244   inverseButton->setEnabled(0);
 245   actionAdd_overlay_image_to_current_image->setEnabled(0);
 246   actionSave_As->setEnabled(0);
 247   actionAdd_VF_to_current_Image->setEnabled(0);
 248   actionAdd_fusion_image->setEnabled(0);
 249   actionAdd_USSequence_toCT->setEnabled(0);
 250
 251   //init the sliders
 252   verticalSliders.push_back(NOVerticalSlider);
 253   verticalSliders.push_back(NEVerticalSlider);
 254   verticalSliders.push_back(SOVerticalSlider);
 255   verticalSliders.push_back(SEVerticalSlider);
 256
 257   for (int i =0; i < 4; i++)
 258     verticalSliders[i]->hide();
 259
 260   horizontalSliders.push_back(NOHorizontalSlider);
 261   horizontalSliders.push_back(NEHorizontalSlider);
 262   horizontalSliders.push_back(SOHorizontalSlider);
 263   horizontalSliders.push_back(SEHorizontalSlider);
 264
 265   for (int i =0; i < 4; i++)
 266     horizontalSliders[i]->hide();
 267
 268
 269   connect(NOVerticalSlider,SIGNAL(valueChanged(int)),this,SLOT(NOVerticalSliderChanged()));
 270   connect(NEVerticalSlider,SIGNAL(valueChanged(int)),this,SLOT(NEVerticalSliderChanged()));
 271   connect(SOVerticalSlider,SIGNAL(valueChanged(int)),this,SLOT(SOVerticalSliderChanged()));
 272   connect(SEVerticalSlider,SIGNAL(valueChanged(int)),this,SLOT(SEVerticalSliderChanged()));
 273
 274   connect(NOHorizontalSlider,SIGNAL(valueChanged(int)),this,SLOT(NOHorizontalSliderMoved()));
 275   connect(NEHorizontalSlider,SIGNAL(valueChanged(int)),this,SLOT(NEHorizontalSliderMoved()));
 276   connect(SOHorizontalSlider,SIGNAL(valueChanged(int)),this,SLOT(SOHorizontalSliderMoved()));
 277   connect(SEHorizontalSlider,SIGNAL(valueChanged(int)),this,SLOT(SEHorizontalSliderMoved()));
 278
 279   //connect everything
 280   connect(actionCompute_mid_position_image,SIGNAL(triggered()),this,SLOT(ComputeMidPosition()));
 281   connect(actionDeformable_Registration,SIGNAL(triggered()),this,SLOT(ComputeDeformableRegistration()));
 282   connect(actionWarp_image_with_vector_field,SIGNAL(triggered()),this,SLOT(WarpImage()));
 283   connect(actionLoad_images,SIGNAL(triggered()),this,SLOT(OpenImages()));
 284   connect(actionOpen_Dicom,SIGNAL(triggered()),this,SLOT(OpenDicom()));
 285 #if CLITK_USE_PACS_CONNECTION
 286   connect(actionConnect_Pacs,SIGNAL(triggered()),this,SLOT(ConnectPacs()));
 287 #endif
 288   //  connect(actionOpen_Dicom_Struct,SIGNAL(triggered()),this,SLOT(OpenDCStructContour()));
 289   connect(actionOpen_VTK_contour,SIGNAL(triggered()),this,SLOT(OpenVTKContour()));
 290   connect(actionOpen_Multiple_Images_As_One,SIGNAL(triggered()),this,SLOT(MergeImages()));
 291   connect(actionSlice_Image_As_Multiple_Images,SIGNAL(triggered()),this,SLOT(SliceImages()));
 292   connect(actionOpen_Image_With_Time,SIGNAL(triggered()),this,SLOT(OpenImageWithTime()));
 293   connect(actionMerge_images_as_n_dim_t, SIGNAL(triggered()), this, SLOT(MergeImagesWithTime()));
 294   connect(actionSave_As,SIGNAL(triggered()),this,SLOT(SaveAs()));
 295   connect(actionSave_current_state,SIGNAL(triggered()),this,SLOT(SaveCurrentState()));
 296   connect(actionRead_saved_state,SIGNAL(triggered()),this,SLOT(ReadSavedState()));
 297   connect(actionExit,SIGNAL(triggered()),this,SLOT(close()));
 298   connect(actionAdd_VF_to_current_Image,SIGNAL(triggered()),this,SLOT(OpenField()));
 299   connect(actionAdd_fusion_image,SIGNAL(triggered()),this,SLOT(SelectFusionImage()));
 300   connect(actionAdd_overlay_image_to_current_image,SIGNAL(triggered()), this,SLOT(SelectOverlayImage()));
 301   connect(actionAdd_USSequence_toCT,SIGNAL(triggered()), this,SLOT(SelectFusionSequence()));
 302   connect(actionNavigation_Help,SIGNAL(triggered()),this,SLOT(ShowHelpDialog()));
 303
 304   QShortcut *shortcutHelp = new QShortcut(QKeySequence(QKeySequence::HelpContents),this);
 305   shortcutHelp->setContext(Qt::ApplicationShortcut);
 306   QObject::connect(shortcutHelp, SIGNAL(activated()), this, SLOT(ShowHelpDialog()));
 307
 308   connect(actionDocumentation,SIGNAL(triggered()),this,SLOT(ShowDocumentation()));
 309   connect(actionRegister_vv,SIGNAL(triggered()),this,SLOT(PopupRegisterForm()));
 310
 311   connect(overlayPanel, SIGNAL(FusionSequenceCorrespondancesButtonPressed()), this, SLOT(SelectFusionSequenceCorrespondances()));
 312
 313
 314   ///////////////////////////////////////////////
 315   connect(actionSegmentation,SIGNAL(triggered()),this,SLOT(SegmentationOnCurrentImage()));
 316   connect(actionSurface_Viewer,SIGNAL(triggered()),this,SLOT(SurfaceViewerLaunch()));
 317   ///////////////////////////////////////////////
 318
 319   actionNorth_East_Window->setEnabled(0);
 320   actionNorth_West_Window->setEnabled(0);
 321   actionSouth_East_Window->setEnabled(0);
 322   actionSouth_West_Window->setEnabled(0);
 323
 324   connect(actionNorth_East_Window,SIGNAL(triggered()),this,SLOT(SaveNEScreenshot()));
 325   connect(actionNorth_West_Window,SIGNAL(triggered()),this,SLOT(SaveNOScreenshot()));
 326   connect(actionSouth_East_Window,SIGNAL(triggered()),this,SLOT(SaveSEScreenshot()));
 327   connect(actionSouth_West_Window,SIGNAL(triggered()),this,SLOT(SaveSOScreenshot()));
 328   connect(actionSave_all_slices,SIGNAL(triggered()),this,SLOT(SaveScreenshotAllSlices()));
 329
 330   connect(DataTree,SIGNAL(itemSelectionChanged()),this,SLOT(ImageInfoChanged()));
 331   connect(DataTree,SIGNAL(itemClicked(QTreeWidgetItem*, int)),this,
 332     SLOT(DisplayChanged(QTreeWidgetItem*, int)));
 333
 334   connect(viewButton,SIGNAL(clicked()),this, SLOT(ChangeViewMode()) );
 335   connect(windowSpinBox,SIGNAL(editingFinished()),this,SLOT(WindowLevelEdited()));
 336   connect(levelSpinBox,SIGNAL(editingFinished()),this,SLOT(WindowLevelEdited()));
 337   connect(colorMapComboBox,SIGNAL(currentIndexChanged(int)),this,SLOT(UpdateColorMap()));
 338   connect(presetComboBox,SIGNAL(currentIndexChanged(int)),this,SLOT(UpdateWindowLevel()));
 339   connect(slicingPresetComboBox, SIGNAL(currentIndexChanged(int)),this,SLOT(UpdateSlicingPreset()));
 340   connect(inverseButton,SIGNAL(clicked()),this,SLOT(SwitchWindowLevel()));
 341   connect(applyWindowLevelToAllButton,SIGNAL(clicked()),this,SLOT(ApplyWindowLevelToAllImages()));
 342
 343   connect(this,SIGNAL(customContextMenuRequested(QPoint)),this,SLOT(ShowContextMenu(QPoint)));
 344
 345   connect(linkPanel,SIGNAL(addLink(QString,QString,bool)),this,SLOT(AddLink(QString,QString,bool)));
 346   connect(linkPanel,SIGNAL(removeLink(QString,QString)),this,SLOT(RemoveLink(QString,QString)));
 347   connect(overlayPanel,SIGNAL(VFPropertyUpdated(int,int,int,int,double,double,double)),this,SLOT(SetVFProperty(int,int,int,int,double,double,double)));
 348   connect(overlayPanel,SIGNAL(OverlayPropertyUpdated(int,int,double,double)),
 349     this,SLOT(SetOverlayProperty(int,int,double,double)));
 350   connect(overlayPanel,SIGNAL(FusionPropertyUpdated(int,int,int,double,double, bool)),
 351     this,SLOT(SetFusionProperty(int,int,int,double,double, bool)));
 352   connect(landmarksPanel,SIGNAL(UpdateRenderWindows()),this,SLOT(UpdateRenderWindows()));
 353   connect(landmarksPanel,SIGNAL(SelectedPointChanged()),this,SLOT(GoToLandmark()));
 354
 355   connect(overlayPanel,SIGNAL(FusionSequencePropertyUpdated(int, bool, unsigned int, bool)),
 356     this,SLOT(SetFusionSequenceProperty(int, bool,unsigned int, bool)));
 357
 358
 359   playMode = 0;//pause
 360   mFrameRate = 10;
 361   playButton->setEnabled(0);
 362   frameRateLabel->setEnabled(0);
 363   frameRateSpinBox->setEnabled(0);
 364   connect(playButton, SIGNAL(clicked()),this,SLOT(PlayPause()));
 365   connect(frameRateSpinBox, SIGNAL(valueChanged(int)),this,SLOT(ChangeFrameRate(int)));
 366
 367   goToCursorPushButton->setEnabled(0);
 368   connect(goToCursorPushButton, SIGNAL(clicked()),this,SLOT(GoToCursor()));
 369
 370   NOViewWidget->hide();
 371   NEViewWidget->hide();
 372   SOViewWidget->hide();
 373   SEViewWidget->hide();
 374
 375 #ifdef Q_OS_OSX
 376   disableGLHiDPI(NOViewWidget->winId());
 377   disableGLHiDPI(NEViewWidget->winId());
 378   disableGLHiDPI(SOViewWidget->winId());
 379   disableGLHiDPI(SEViewWidget->winId());
 380 #endif
 381
 382   //Recently opened files
 383   std::list<std::string> recent_files = GetRecentlyOpenedImages();
 384   recentlyOpenedFilesMenu=NULL;
 385   if ( !recent_files.empty() ) {
 386     createRecentlyOpenedFilesMenu();
 387     updateRecentlyOpenedFilesMenu(recent_files);
 388   }
 389
 390   //Update and get vv parameters
 391   setVVSettings();
 392
 393   // Adding all new tools (insertion in the menu)
 394   vvToolManager::GetInstance()->InsertToolsInMenu(this);
 395   vvToolManager::GetInstance()->EnableToolsInMenu(this, false);
 396
 397 //#ifndef CLITK_EXPERIMENTAL
 398 //#define CLITK_EXPERIMENTAL 0
 399 //#endif
 400 #ifdef CLITK_EXPERIMENTAL
 401   if (!CLITK_EXPERIMENTAL)
 402     menuExperimental->menuAction()->setVisible(false);
 403 #endif
 404
 405 #if !CLITK_USE_PACS_CONNECTION
 406     actionConnect_Pacs->setVisible(false);
 407 #endif
 408
 409   QTimer * timerMemory = new QTimer(this);
 410   //timerMemory->setInterval(5);
 411   connect(timerMemory, SIGNAL(timeout()), this, SLOT(UpdateMemoryUsage()));
 412   timerMemory->start(2000);
 413 }
 414
 415 //------------------------------------------------------------------------------
 416 void vvMainWindow::show()
 417 {
 418   vvMainWindowBase::show();
 419   PopupRegisterForm(true);
 420 }
 421 //------------------------------------------------------------------------------
 422 void vvMainWindow::UpdateMemoryUsage()
 423 {
 424   //  clitk::PrintMemory(true);
 425   if (clitk::GetMemoryUsageInMb() == 0) infoPanel->setMemoryInMb("NA");
 426   else infoPanel->setMemoryInMb(QString::number(clitk::GetMemoryUsageInMb())+" MB");
 427 }
 428 //------------------------------------------------------------------------------
 429
 430
 431 //------------------------------------------------------------------------------
 432 void vvMainWindow::createRecentlyOpenedFilesMenu()
 433 {
 434   recentlyOpenedFilesMenu = new QMenu("Recently opened files...");
 435   recentlyOpenedFilesMenu->setIcon(QIcon(QString::fromUtf8(":/common/icons/open.png")));
 436   menuFile->insertMenu(actionOpen_Image_With_Time,recentlyOpenedFilesMenu);
 437   menuFile->insertSeparator(actionOpen_Image_With_Time);
 438 }
 439 //------------------------------------------------------------------------------
 440
 441
 442 //------------------------------------------------------------------------------
 443
 444 void vvMainWindow::updateRecentlyOpenedFilesMenu(const std::list<std::string> &recent_files)
 445 {
 446   if(recentlyOpenedFilesMenu==NULL) {
 447     createRecentlyOpenedFilesMenu();
 448   } else {
 449     recentlyOpenedFilesMenu->clear();
 450   }
 451   for (std::list<std::string>::const_iterator i = recent_files.begin(); i!=recent_files.end(); i++) {
 452     QAction* current=new QAction(QIcon(QString::fromUtf8(":/common/icons/open.png")), i->c_str(),this);
 453     recentlyOpenedFilesMenu->addAction(current);
 454     connect(current,SIGNAL(triggered()),this,SLOT(OpenRecentImage()));
 455   }
 456 }
 457 //------------------------------------------------------------------------------
 458
 459
 460 //------------------------------------------------------------------------------
 461 void vvMainWindow::ComputeMidPosition()
 462 {
 463   bool ok;
 464   int index=GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
 465   int ref = QInputDialog::getInt(this,"Chose reference phase","Reference phase",0,0,\
 466 mSlicerManagers[index]->GetImage()->GetVTKImages().size()-1,1,&ok);
 467   if (ok) {
 468     vvMidPosition midp;
 469     midp.slicer_manager = mSlicerManagers[index];
 470     midp.reference_image_index = ref;
 471     QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
 472     midp.Update();
 473     if (midp.error)
 474       QMessageBox::warning(this, "Error computing midposition image",midp.error_message.c_str());
 475     else {
 476       QFileInfo info(midp.slicer_manager->GetFileName().c_str());
 477       AddImage(midp.output,info.path().toStdString()+"/"+info.completeBaseName().toStdString()+"_midposition.mhd");
 478     }
 479     QApplication::restoreOverrideCursor();
 480   }
 481 }
 482 //------------------------------------------------------------------------------
 483
 484
 485 //------------------------------------------------------------------------------
 486 void vvMainWindow::AddContour(int image_index, vvMesh::Pointer contour, bool propagation)
 487 {
 488   QTreeWidgetItem *item = new QTreeWidgetItem();
 489   item->setData(0,Qt::UserRole,"filename.vtk");
 490   item->setData(1,Qt::UserRole,tr("contour"));
 491   QBrush brush;
 492   brush.setColor(QColor(contour->r*255,contour->g*255,contour->b*255));
 493   brush.setStyle(Qt::SolidPattern);
 494   item->setData(COLUMN_IMAGE_NAME,Qt::BackgroundRole,brush);
 495   item->setData(COLUMN_IMAGE_NAME,Qt::DisplayRole,contour->structure_name.c_str());
 496
 497   for (int j = 1; j <= 4; j++)
 498     item->setData(j,Qt::CheckStateRole,DataTree->topLevelItem(image_index)->data(j,Qt::CheckStateRole));
 499
 500   QTreePushButton* cButton = new QTreePushButton;
 501   cButton->setItem(item);
 502   cButton->setColumn(COLUMN_CLOSE_IMAGE);
 503   cButton->setToolTip(tr("close image"));
 504   cButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/exit.png")));
 505   connect(cButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
 506     this,SLOT(CloseImage(QTreeWidgetItem*, int)));
 507
 508   QTreePushButton* rButton = new QTreePushButton;
 509   rButton->setItem(item);
 510   rButton->setColumn(COLUMN_RELOAD_IMAGE);
 511   rButton->setToolTip(tr("reload image"));
 512   rButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/rotateright.png")));
 513   rButton->setEnabled(false);
 514   //Not implemented
 515   //connect(rButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
 516   //this,SLOT(ReloadImage(QTreeWidgetItem*, int)));
 517
 518   DataTree->topLevelItem(image_index)->setExpanded(1);
 519   DataTree->topLevelItem(image_index)->addChild(item);
 520   DataTree->setItemWidget(item, COLUMN_CLOSE_IMAGE, cButton);
 521   DataTree->setItemWidget(item, COLUMN_RELOAD_IMAGE, rButton);
 522   QString id = DataTree->topLevelItem(image_index)->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString();
 523   item->setData(COLUMN_IMAGE_NAME,Qt::UserRole,id.toStdString().c_str());
 524
 525   UpdateTree();
 526   mSlicerManagers[image_index]->AddContour(contour,propagation);
 527   mSlicerManagers[image_index]->Render();
 528 }
 529 //------------------------------------------------------------------------------
 530
 531
 532 //------------------------------------------------------------------------------
 533 void vvMainWindow::OpenVTKContour()
 534 {
 535   if (mSlicerManagers.size() > 0) {
 536     QString Extensions = "Images ( *.vtk *.obj)";
 537     Extensions += ";;All Files (*)";
 538     QString file = QFileDialog::getOpenFileName(this,tr("Open vtkPolyData"),mInputPathName,Extensions);
 539     if (file.isNull())
 540       return;
 541     QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
 542     int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
 543     vvMeshReader reader;
 544     reader.SetImage(mSlicerManagers[index]->GetImage());
 545     reader.SetModeToVTK();
 546     reader.SetFilename(file.toStdString());
 547     reader.Update();
 548     AddContour(index,reader.GetOutput()[0],false);
 549     QApplication::restoreOverrideCursor();
 550   }
 551 }
 552 //------------------------------------------------------------------------------
 553
 554
 555 //------------------------------------------------------------------------------
 556 void vvMainWindow::AddDCStructContour(int index, QString file)
 557 {
 558   vvMeshReader reader;
 559   reader.SetFilename(file.toStdString());
 560   vvStructSelector selector;
 561   selector.SetStructures(reader.GetROINames());
 562   if (!mSlicerManagers[index]->GetVF().IsNull())
 563     selector.EnablePropagationCheckBox();
 564   if (selector.exec()) {
 565     QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
 566     reader.SetSelectedItems(selector.getSelectedItems());
 567     reader.SetImage(mSlicerManagers[index]->GetImage());
 568     if (selector.PropagationEnabled())
 569       reader.SetPropagationVF(mSlicerManagers[index]->GetVF());
 570     reader.Update();
 571     std::vector<vvMesh::Pointer> contours=reader.GetOutput();
 572     for (std::vector<vvMesh::Pointer>::iterator i=contours.begin();
 573       i!=contours.end(); i++)
 574       AddContour(index,*i,selector.PropagationEnabled());
 575     QApplication::restoreOverrideCursor();
 576   }
 577 }
 578
 579 //------------------------------------------------------------------------------
 580 void vvMainWindow::OpenDCStructContour()
 581 {
 582   if (mSlicerManagers.size() > 0) {
 583     QString Extensions = "Dicom Files ( *.dcm RS*)";
 584     Extensions += ";;All Files (*)";
 585     QString file = QFileDialog::getOpenFileName(this,tr("Merge Images"),mInputPathName,Extensions);
 586     if (file.isNull())
 587       return;
 588     int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
 589     AddDCStructContour(index, file);
 590   }
 591 }
 592 //------------------------------------------------------------------------------
 593
 594
 595 //------------------------------------------------------------------------------
 596 void vvMainWindow::ComputeDeformableRegistration()
 597 {
 598   if (mSlicerManagers.size() > 0) {
 599     int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
 600     vvDeformationDialog dialog(index,mSlicerManagers);
 601     if (dialog.exec()) {
 602       std::string base_name=itksys::SystemTools::GetFilenameWithoutExtension(mSlicerManagers[dialog.GetInputFileIndex()]->GetFileName());
 603       AddField(dialog.GetOutput(),dialog.getFieldFile(),dialog.GetInputFileIndex());
 604       WarpImage(dialog.GetSelectedSlicer(),dialog.GetReferenceFrameIndex());
 605     } else
 606       std::cout << "Error or user cancellation while computing deformation field..." << std::endl;
 607   } else QMessageBox::information(this, "Need to open image","You must open an image first.");
 608 }
 609 //------------------------------------------------------------------------------
 610
 611
 612 //------------------------------------------------------------------------------
 613 void vvMainWindow::WarpImage()
 614 {
 615   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
 616   if (!mSlicerManagers[index]->GetVF().IsNull()) {
 617     bool ok;
 618     int ref = QInputDialog::getInt(this,"Chose reference phase","Reference phase",0,0,\
 619       mSlicerManagers[index]->GetImage()->GetVTKImages().size()-1,1,&ok);
 620     if (ok) {
 621       WarpImage(mSlicerManagers[index],ref);
 622     }
 623   } else
 624     QMessageBox::warning(this,tr("No vector field"),tr("Sorry, can't warp without a vector field"));
 625 }
 626 //------------------------------------------------------------------------------
 627
 628
 629 //------------------------------------------------------------------------------
 630 void vvMainWindow::WarpImage(vvSlicerManager* selected_slicer,int reference_phase)
 631 {
 632   if (!selected_slicer->GetVF().IsNull()) {
 633     QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
 634     QFileInfo info(selected_slicer->GetFileName().c_str());
 635     vvImageWarp warp(selected_slicer->GetImage(),selected_slicer->GetVF(),
 636       reference_phase,this);
 637     if (warp.ComputeWarpedImage()) {
 638       AddImage(warp.GetWarpedImage(),info.path().toStdString()+"/"+info.completeBaseName().toStdString()+"_warped.mhd");
 639       AddImage(warp.GetDiffImage()  ,info.path().toStdString()+"/"+info.completeBaseName().toStdString()+"_diff.mhd");
 640       AddImage(warp.GetJacobianImage()  ,info.path().toStdString()+"/"+info.completeBaseName().toStdString()+"_jacobian.mhd");
 641       QApplication::restoreOverrideCursor();
 642     } else {
 643       QApplication::restoreOverrideCursor();
 644       QMessageBox::warning(this,tr("Different spacings"),tr("The vector field and image spacings must be the same in order to warp."));
 645     }
 646   } else
 647     QMessageBox::warning(this,tr("No vector field"),tr("Sorry, can't warp without a vector field."));
 648 }
 649 //------------------------------------------------------------------------------
 650
 651
 652 //------------------------------------------------------------------------------
 653 vvMainWindow::~vvMainWindow()
 654 {
 655   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
 656     if (mSlicerManagers[i] != NULL)
 657       delete mSlicerManagers[i];
 658   }
 659   delete documentation;
 660   delete help_dialog;
 661   delete dicomSeriesSelector;
 662 }
 663 //------------------------------------------------------------------------------
 664
 665 //------------------------------------------------------------------------------
 666 QTabWidget * vvMainWindow::GetTab()
 667 {
 668   return tabWidget;
 669 }
 670 //------------------------------------------------------------------------------
 671
 672
 673 //------------------------------------------------------------------------------
 674 void vvMainWindow::MergeImages()
 675 {
 676   QString Extensions = EXTENSIONS;
 677   Extensions += ";;All Files (*)";
 678   QStringList files = QFileDialog::getOpenFileNames(this,tr("Merge Images"),mInputPathName,Extensions);
 679   if (files.isEmpty())
 680     return;
 681   mInputPathName = itksys::SystemTools::GetFilenamePath(files[0].toStdString()).c_str();
 682   std::vector<std::string> vector;
 683
 684   unsigned int currentDim = 0;
 685   std::vector<double> currentSpacing;
 686   std::vector<int> currentSize;
 687   std::vector<double> currentOrigin;
 688
 689   for (int i = 0; i < files.size(); i++) {
 690     itk::ImageIOBase::Pointer reader = itk::ImageIOFactory::CreateImageIO(
 691       files[i].toStdString().c_str(), itk::ImageIOFactory::ReadMode);
 692     reader->SetFileName(files[i].toStdString().c_str());
 693     reader->ReadImageInformation();
 694     if (reader)        {
 695       //NOViewWidget->hide();
 696       //NEViewWidget->hide();
 697       //SOViewWidget->hide();
 698       //SEViewWidget->hide();
 699       if (i == 0)
 700         currentDim = reader->GetNumberOfDimensions();
 701       bool IsOk = true;
 702       for (unsigned int j = 0; j < currentDim; j++) {
 703         if (i == 0) {
 704           if (j == 0) {
 705             currentSpacing.resize(currentDim);
 706             currentSize.resize(currentDim);
 707             currentOrigin.resize(currentDim);
 708           }
 709           currentOrigin[j] = reader->GetOrigin(j);
 710           currentSpacing[j] = reader->GetSpacing(j);
 711           currentSize[j] = reader->GetDimensions(j);
 712         } else if (currentDim != reader->GetNumberOfDimensions()
 713           || currentSpacing[j] != reader->GetSpacing(j)
 714           || currentSize[j] != (int)reader->GetDimensions(j)
 715           || currentOrigin[j] != reader->GetOrigin(j)) {
 716             QString error = "Cannot read file (too different from others ";
 717             error += files[i].toStdString().c_str();
 718             QMessageBox::information(this,tr("Reading problem"),error);
 719             IsOk = false;
 720             break;
 721         }
 722       }
 723       if (IsOk)
 724         vector.push_back(files[i].toStdString());
 725     }
 726   }
 727   if (vector.size() > 0)
 728     LoadImages(vector, vvImageReader::MERGED);
 729 }
 730 //------------------------------------------------------------------------------
 731
 732 //------------------------------------------------------------------------------
 733 void vvMainWindow::SliceImages()
 734 {
 735   QString Extensions = EXTENSIONS;
 736   Extensions += ";;All Files (*)";
 737
 738   QStringList files = QFileDialog::getOpenFileNames(this,tr("Slice Images"),mInputPathName,Extensions);
 739   if (files.isEmpty())
 740     return;
 741   mInputPathName = itksys::SystemTools::GetFilenamePath(files[0].toStdString()).c_str();
 742   std::vector<std::string> vector;
 743   for (int i = 0; i < files.size(); i++)
 744     vector.push_back(files[i].toStdString());
 745   LoadImages(vector, vvImageReader::SLICED);
 746 }
 747 //------------------------------------------------------------------------------
 748
 749 //------------------------------------------------------------------------------
 750 void vvMainWindow::MergeImagesWithTime()
 751 {
 752   QString Extensions = EXTENSIONS;
 753   Extensions += ";;All Files (*)";
 754   QStringList files = QFileDialog::getOpenFileNames(this,tr("Merge Images With Time"),mInputPathName,Extensions);
 755   if (files.isEmpty())
 756     return;
 757   mInputPathName = itksys::SystemTools::GetFilenamePath(files[0].toStdString()).c_str();
 758   std::vector<std::string> vector;
 759
 760   for (int i = 0; i < files.size(); i++)
 761     vector.push_back(files[i].toStdString());
 762   sort(vector.begin(),vector.end());
 763   if (vector.size() > 1)
 764     LoadImages(vector, vvImageReader::MERGEDWITHTIME);
 765   else
 766     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.");
 767 }
 768 //------------------------------------------------------------------------------
 769
 770
 771 //------------------------------------------------------------------------------
 772 void vvMainWindow::OpenDicom()
 773 {
 774   std::vector<std::string> files;
 775
 776   //std::cout << "dicomSeriesSelector " << std::endl;
 777   if (dicomSeriesSelector->exec() == QDialog::Accepted) {
 778     files = *(dicomSeriesSelector->GetFilenames());
 779     LoadImages(files, vvImageReader::DICOM);
 780   }
 781 }
 782 #if CLITK_USE_PACS_CONNECTION
 783 void vvMainWindow::ConnectPacs()
 784 {
 785   std::vector<std::string> files;
 786
 787   //std::cout << "dicomSeriesSelector " << std::endl;
 788 if (PacsConnection->exec() == QDialog::Accepted) {
 789         for (int i = 0; i < PacsConnection->getSeriesCount(); i++)
 790         {
 791                 files = PacsConnection->getFileNames(i);
 792                 LoadImages(files, vvImageReader::DICOM);
 793         }
 794         PacsConnection->clearMove();
 795   }
 796   }
 797
 798 #endif
 799 //------------------------------------------------------------------------------
 800
 801 //------------------------------------------------------------------------------
 802 void vvMainWindow::OpenImages()
 803 {
 804   QString Extensions = EXTENSIONS;
 805   Extensions += ";;All Files (*)";
 806
 807   QStringList files = QFileDialog::getOpenFileNames(this,tr("Load Images"),mInputPathName,Extensions);
 808   if (files.isEmpty())
 809     return;
 810   mInputPathName = itksys::SystemTools::GetFilenamePath(files[0].toStdString()).c_str();
 811   std::vector<std::string> vector;
 812   for (int i = 0; i < files.size(); i++)
 813     vector.push_back(files[i].toStdString());
 814   LoadImages(vector, vvImageReader::IMAGE);
 815 }
 816 //------------------------------------------------------------------------------
 817 void vvMainWindow::OpenRecentImage()
 818 {
 819   QAction * caller = qobject_cast<QAction*>(sender());
 820   std::vector<std::string> images;
 821   images.push_back(caller->text().toStdString());
 822   mInputPathName = itksys::SystemTools::GetFilenamePath(images[0]).c_str();
 823   LoadImages(images, vvImageReader::IMAGE);
 824 }
 825 //------------------------------------------------------------------------------
 826 void vvMainWindow::dragEnterEvent(QDragEnterEvent *event)
 827 {
 828   if (event->mimeData()->hasUrls()) {
 829     event->acceptProposedAction();
 830   }
 831 }
 832 //------------------------------------------------------------------------------
 833 void vvMainWindow::dropEvent(QDropEvent *event)
 834 {
 835   const QMimeData * mimeData = event->mimeData();
 836   if (!mimeData->hasUrls())
 837     return;
 838   std::vector<std::string> images;
 839   for (int i=0; i<mimeData->urls().size(); ++i) {
 840     images.push_back(mimeData->urls()[i].toLocalFile().toStdString());
 841   }
 842   LoadImages(images, vvImageReader::IMAGE);
 843 }
 844 //------------------------------------------------------------------------------
 845
 846
 847 //------------------------------------------------------------------------------
 848 void vvMainWindow::OpenImageWithTime()
 849 {
 850   QString Extensions = EXTENSIONS;
 851   Extensions += ";;All Files (*)";
 852
 853   QStringList files = QFileDialog::getOpenFileNames(this,tr("Load Images With Time"),mInputPathName,Extensions);
 854   if (files.isEmpty())
 855     return;
 856   mInputPathName = itksys::SystemTools::GetFilenamePath(files[0].toStdString()).c_str();
 857   std::vector<std::string> vector;
 858   for (int i = 0; i < files.size(); i++) {
 859     vector.push_back(files[i].toStdString());
 860   }
 861   LoadImages(vector, vvImageReader::IMAGEWITHTIME);
 862 }
 863 //------------------------------------------------------------------------------
 864
 865
 866 //------------------------------------------------------------------------------
 867 void vvMainWindow::LoadImages(std::vector<std::string> files, vvImageReader::LoadedImageType filetype)
 868 {
 869   //Separate the way to open images and dicoms
 870   int fileSize;
 871   if (filetype == vvImageReader::IMAGE || filetype == vvImageReader::IMAGEWITHTIME)
 872     fileSize = files.size();
 873   else
 874     fileSize = 1;
 875
 876   // For SLICED, we need the number of slices (ndim and #slices)
 877   std::vector<unsigned int> nSlices;
 878   nSlices.resize(files.size());
 879   std::fill(nSlices.begin(), nSlices.end(), 1);
 880   if (filetype == vvImageReader::SLICED) {
 881     for (int i = 0; i < fileSize; i++) {
 882       itk::ImageIOBase::Pointer header = clitk::readImageHeader(files[i]);
 883       QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
 884       if (!header) {
 885         nSlices[i] = 0;
 886         QString error = "Cannot open file \n";
 887         error += files[i].c_str();
 888         QMessageBox::information(this,tr("Reading problem"),error);
 889         return;
 890       }
 891       if (header->GetNumberOfDimensions() < 3) {
 892         nSlices[i] = 0;
 893         QString error = "Dimension problem. Cannot slice \n";
 894         error += files[i].c_str();
 895         QMessageBox::information(this,tr("Reading problem"),error);
 896         return;
 897       }
 898       nSlices[i] = header->GetDimensions( header->GetNumberOfDimensions()-1 );
 899     }
 900   }
 901
 902   //Only add to the list of recently opened files when a single file is opened,
 903   //to avoid polluting the list of recently opened files
 904   if (files.size() == 1) {
 905     QFileInfo finfo=tr(files[0].c_str());
 906     AddToRecentlyOpenedImages(finfo.absoluteFilePath().toStdString());
 907     updateRecentlyOpenedFilesMenu(GetRecentlyOpenedImages());
 908   }
 909   //init the progress events
 910   QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
 911   vvProgressDialog progress("Opening " + files[0],fileSize>1);
 912   qApp->processEvents();
 913
 914   int numberofsuccesulreads=0;
 915   //open images as 1 or multiples
 916   for (int i = 0; i < fileSize; i++) {
 917     progress.SetText("Opening " + files[i]);
 918     progress.SetProgress(i,fileSize);
 919     qApp->processEvents();
 920
 921     for (unsigned int j = 0; j < nSlices[i]; j++) {
 922       //read the image and put it in mSlicerManagers
 923       vvSlicerManager* imageManager = new vvSlicerManager(4);
 924       qApp->processEvents();
 925
 926       bool SetImageSucceed=false;
 927
 928       // Change filename if an image with the same already exist
 929       int number = GetImageDuplicateFilenameNumber(files[i] + std::string("_slice"));
 930
 931       if (filetype == vvImageReader::IMAGE || filetype == vvImageReader::IMAGEWITHTIME || filetype == vvImageReader::SLICED)
 932         SetImageSucceed = imageManager->SetImage(files[i],filetype, number, j);
 933       else if (filetype == vvImageReader::DICOM)
 934         SetImageSucceed = imageManager->SetImages(files,filetype, number, dicomSeriesSelector->IsPatientCoordianteSystemChecked());
 935       else
 936         SetImageSucceed = imageManager->SetImages(files,filetype, number);
 937
 938       if (!SetImageSucceed) {
 939         QApplication::restoreOverrideCursor();
 940         QString error = "Cannot open file \n";
 941         error += imageManager->GetLastError().c_str();
 942         QMessageBox::information(this,tr("Reading problem"),error);
 943         delete imageManager;
 944       } else {
 945
 946         mSlicerManagers.push_back(imageManager);
 947
 948         //create an item in the tree with good settings
 949         QTreeWidgetItem *item = new QTreeWidgetItem();
 950         item->setData(0,Qt::UserRole,files[i].c_str());
 951         QFileInfo fileinfo(imageManager->GetFileName().c_str()); //Do not show the path
 952         item->setData(COLUMN_IMAGE_NAME,Qt::DisplayRole,fileinfo.fileName());
 953         item->setData(1,Qt::UserRole,tr("image"));
 954         item->setToolTip(COLUMN_IMAGE_NAME, imageManager->GetListOfAbsoluteFilePathInOneString("image").c_str());
 955         qApp->processEvents();
 956
 957         //Create the buttons for reload and close
 958         qApp->processEvents();
 959         QTreePushButton* cButton = new QTreePushButton;
 960         cButton->setItem(item);
 961         cButton->setColumn(COLUMN_CLOSE_IMAGE);
 962         cButton->setToolTip(tr("close image"));
 963         cButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/exit.png")));
 964         connect(cButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
 965           this,SLOT(CloseImage(QTreeWidgetItem*, int)));
 966
 967         QTreePushButton* rButton = new QTreePushButton;
 968         rButton->setItem(item);
 969         rButton->setColumn(COLUMN_RELOAD_IMAGE);
 970         rButton->setToolTip(tr("reload image"));
 971         rButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/rotateright.png")));
 972         connect(rButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
 973           this,SLOT(ReloadImage(QTreeWidgetItem*, int)));
 974
 975         DataTree->addTopLevelItem(item);
 976         DataTree->setItemWidget(item, COLUMN_CLOSE_IMAGE, cButton);
 977         DataTree->setItemWidget(item, COLUMN_RELOAD_IMAGE, rButton);
 978
 979         //set the id of the image
 980         QString id = QDir::current().absoluteFilePath(files[i].c_str()) + QString::number(mSlicerManagers.size()-1);
 981         item->setData(COLUMN_IMAGE_NAME,Qt::UserRole,id.toStdString().c_str());
 982         mSlicerManagers.back()->SetId(id.toStdString());
 983
 984         linkPanel->addImage(imageManager->GetFileName(), id.toStdString());
 985
 986         //Create a watcher to see if the image file is modified. In such a case, reload it automatically
 987         QFileSystemWatcher* watcher = new QFileSystemWatcher;
 988         watcher->addPath(files[i].c_str());
 989         connect(watcher, SIGNAL(fileChanged(const QString&)), this, SLOT(SlotFileChanged(const QString&)));
 990
 991
 992         connect(mSlicerManagers.back(), SIGNAL(currentImageChanged(std::string)),
 993           this,SLOT(CurrentImageChanged(std::string)));
 994         connect(mSlicerManagers.back(), SIGNAL(currentPickedImageChanged(std::string)),
 995           this, SLOT(CurrentPickedImageChanged(std::string)));
 996         connect(mSlicerManagers.back(), SIGNAL(UpdatePosition(int, double, double, double, double, double, double, double)),
 997           this,SLOT(MousePositionChanged(int,double, double, double, double, double, double, double)));
 998         connect(mSlicerManagers.back(), SIGNAL(UpdateVector(int, double, double, double, double)),
 999           this, SLOT(VectorChanged(int,double,double,double, double)));
1000         connect(mSlicerManagers.back(), SIGNAL(UpdateOverlay(int, double, double)),
1001           this, SLOT(OverlayChanged(int,double,double)));
1002         connect(mSlicerManagers.back(), SIGNAL(UpdateFusion(int, double)),
1003           this, SLOT(FusionChanged(int,double)));
1004         connect(mSlicerManagers.back(), SIGNAL(WindowLevelChanged()),
1005           this,SLOT(WindowLevelChanged()));
1006         connect(mSlicerManagers.back(), SIGNAL(UpdateSlice(int,int)),
1007           this,SLOT(UpdateSlice(int,int)));
1008         connect(mSlicerManagers.back(), SIGNAL(UpdateTSlice(int, int, int)),
1009           this,SLOT(UpdateTSlice(int, int, int)));
1010         connect(mSlicerManagers.back(), SIGNAL(UpdateTSlice(int, int, int)),
1011           this,SLOT(ImageInfoChanged()));
1012         connect(mSlicerManagers.back(), SIGNAL(UpdateSliceRange(int,int,int,int,int)),
1013           this,SLOT(UpdateSliceRange(int,int,int,int,int)));
1014         connect(mSlicerManagers.back(), SIGNAL(UpdateLinkManager(std::string,int,double,double,double,int)),
1015           this,SLOT(UpdateLinkManager(std::string,int,double,double,double,int)));
1016         connect(mSlicerManagers.back(), SIGNAL(UpdateLinkedNavigation(std::string,vvSlicerManager*,vvSlicer*)),
1017           this,SLOT(UpdateLinkedNavigation(std::string,vvSlicerManager*,vvSlicer*)));
1018         connect(mSlicerManagers.back(), SIGNAL(ChangeImageWithIndexOffset(vvSlicerManager*,int,int)),
1019           this,SLOT(ChangeImageWithIndexOffset(vvSlicerManager*,int,int)));
1020         connect(mSlicerManagers.back(),SIGNAL(LandmarkAdded()),landmarksPanel,SLOT(AddPoint()));
1021         connect(landmarksPanel,SIGNAL(UpdateLandmarkTransform()), mSlicerManagers.back(), SLOT(UpdateLandmark()));
1022         InitSlicers();
1023         numberofsuccesulreads++;
1024       }
1025     }
1026   }
1027
1028   if (numberofsuccesulreads) {
1029     NOViewWidget->show();
1030     NEViewWidget->show();
1031     SOViewWidget->show();
1032     SEViewWidget->show();
1033     UpdateTree();
1034     InitDisplay();
1035     ShowLastImage();
1036
1037     // Try to guess default WindowLevel
1038     double range[2];
1039     mSlicerManagers.back()->GetImage()->GetFirstVTKImageData()->GetScalarRange(range);
1040     if ((range[0] == 0) && (range[1] == 1)) {
1041       presetComboBox->setCurrentIndex(WL_BINARY);// binary
1042     } else {
1043       // TODO
1044     }
1045   }
1046   QApplication::restoreOverrideCursor();
1047 }
1048 //------------------------------------------------------------------------------
1049
1050 //------------------------------------------------------------------------------
1051 void vvMainWindow::UpdateTree()
1052 {
1053   DataTree->resizeColumnToContents(COLUMN_TREE);
1054   DataTree->resizeColumnToContents(COLUMN_UL_VIEW);
1055   DataTree->resizeColumnToContents(COLUMN_UR_VIEW);
1056   DataTree->resizeColumnToContents(COLUMN_DL_VIEW);
1057   DataTree->resizeColumnToContents(COLUMN_DR_VIEW);
1058   DataTree->resizeColumnToContents(COLUMN_IMAGE_NAME);
1059   DataTree->resizeColumnToContents(COLUMN_CLOSE_IMAGE);
1060   DataTree->resizeColumnToContents(COLUMN_RELOAD_IMAGE);
1061 }
1062 //------------------------------------------------------------------------------
1063
1064 //------------------------------------------------------------------------------
1065 void vvMainWindow::CurrentImageChanged(std::string id)
1066 {
1067   if (id == mCurrentSelectedImageId) return; // Do nothing
1068   int selected = 0;
1069   for (int i = 0; i < DataTree->topLevelItemCount(); i++) {
1070     if (DataTree->topLevelItem(i)->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString().toStdString() == id) {
1071       selected = i;
1072     } else {
1073       DataTree->topLevelItem(i)->setSelected(0);
1074     }
1075     for (int child = 0; child < DataTree->topLevelItem(i)->childCount(); child++)
1076       DataTree->topLevelItem(i)->child(child)->setSelected(0);
1077
1078   }
1079   DataTree->topLevelItem(selected)->setSelected(1);
1080   mCurrentSelectedImageId = id;
1081
1082   landmarksPanel->SetCurrentLandmarks(mSlicerManagers[selected]->GetLandmarks(),
1083                                       mSlicerManagers[selected]->GetTSlice());
1084   landmarksPanel->SetCurrentPath(mInputPathName.toStdString());
1085   landmarksPanel->SetCurrentImage(mSlicerManagers[selected]->GetFileName().c_str());
1086
1087   emit SelectedImageHasChanged(mSlicerManagers[selected]);
1088 }
1089 //------------------------------------------------------------------------------
1090
1091 //------------------------------------------------------------------------------
1092 void vvMainWindow::CurrentPickedImageChanged(std::string id)
1093 {
1094   if (id == mCurrentPickedImageId) return; // Do nothing
1095   int selected = 0;
1096   for (int i = 0; i < DataTree->topLevelItemCount(); i++) {
1097     if (DataTree->topLevelItem(i)->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString().toStdString() == id) {
1098       selected = i;
1099     } else {
1100       DataTree->topLevelItem(i)->setSelected(0);
1101     }
1102     for (int child = 0; child < DataTree->topLevelItem(i)->childCount(); child++)
1103       DataTree->topLevelItem(i)->child(child)->setSelected(0);
1104
1105   }
1106   DataTree->topLevelItem(selected)->setSelected(1);
1107   mCurrentPickedImageId = id;
1108   mCurrentPickedImageIndex = selected;
1109 }
1110 //------------------------------------------------------------------------------
1111
1112 //------------------------------------------------------------------------------
1113 void vvMainWindow::ImageInfoChanged()
1114 {
1115   contextActions[6]->setEnabled(1);
1116   contextActions[5]->setEnabled(1);
1117   actionSave_As->setEnabled(1);
1118   actionAdd_VF_to_current_Image->setEnabled(1);
1119   actionAdd_fusion_image->setEnabled(1);
1120   actionAdd_overlay_image_to_current_image->setEnabled(1);
1121   actionAdd_USSequence_toCT->setEnabled(1);
1122   actionNorth_East_Window->setEnabled(1);
1123   actionNorth_West_Window->setEnabled(1);
1124   actionSouth_East_Window->setEnabled(1);
1125   actionSouth_West_Window->setEnabled(1);
1126   vvToolManager::GetInstance()->EnableToolsInMenu(this, true);
1127   inverseButton->setEnabled(1);
1128
1129   goToCursorPushButton->setEnabled(1);
1130
1131   if (DataTree->selectedItems().size()) {
1132     int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1133
1134     colorMapComboBox->setEnabled(1);
1135     for (int i = 0; i < DataTree->topLevelItem(index)->childCount(); i++) {
1136       if (DataTree->topLevelItem(index)->child(i)->data(1,Qt::UserRole).toString() == "overlay" ||
1137         DataTree->topLevelItem(index)->child(i)->data(1,Qt::UserRole).toString() == "fusion" ||
1138         DataTree->topLevelItem(index)->child(i)->data(1,Qt::UserRole).toString() == "fusionSequence") {
1139           colorMapComboBox->setEnabled(0);
1140           break;
1141       }
1142     }
1143
1144     std::vector<double> origin;
1145     std::vector<double> inputSpacing;
1146     std::vector<int> inputSize;
1147     std::vector<double> sizeMM;
1148     vtkSmartPointer<vtkMatrix4x4> transformation;
1149     int dimension=0;
1150     QString pixelType;
1151     QString inputSizeInBytes;
1152     QString image = DataTree->selectedItems()[0]->data(COLUMN_IMAGE_NAME,Qt::DisplayRole).toString();
1153
1154     int nframes = mSlicerManagers[index]->GetSlicer(0)->GetTMax();
1155
1156     if (nframes > 1 || playMode == 1) {
1157       playButton->setEnabled(1);
1158       frameRateLabel->setEnabled(1);
1159       frameRateSpinBox->setEnabled(1);
1160     } else {
1161       playButton->setEnabled(0);
1162       frameRateLabel->setEnabled(0);
1163       frameRateSpinBox->setEnabled(0);
1164     }
1165
1166     //read image header
1167     int NPixel = 1;
1168
1169     int tSlice = 0;
1170     vvImage::Pointer imageSelected;
1171     if (DataTree->topLevelItem(index) == DataTree->selectedItems()[0]) {
1172       imageSelected = mSlicerManagers[index]->GetSlicer(0)->GetImage();
1173       tSlice = mSlicerManagers[index]->GetSlicer(0)->GetTSlice();
1174     } else if (DataTree->selectedItems()[0]->data(1,Qt::UserRole).toString() == "vector") {
1175       imageSelected = mSlicerManagers[index]->GetSlicer(0)->GetVF();
1176       tSlice = mSlicerManagers[index]->GetSlicer(0)->GetOverlayTSlice();
1177     } else if (DataTree->selectedItems()[0]->data(1,Qt::UserRole).toString() == "overlay") {
1178       imageSelected = mSlicerManagers[index]->GetSlicer(0)->GetOverlay();
1179       tSlice = mSlicerManagers[index]->GetSlicer(0)->GetOverlayTSlice();
1180     } else if (DataTree->selectedItems()[0]->data(1,Qt::UserRole).toString() == "fusion") {
1181       imageSelected = mSlicerManagers[index]->GetSlicer(0)->GetFusion();
1182       tSlice = mSlicerManagers[index]->GetSlicer(0)->GetFusionTSlice();
1183     }
1184     else if (DataTree->selectedItems()[0]->data(1,Qt::UserRole).toString() == "fusionSequence") {
1185       imageSelected = mSlicerManagers[index]->GetSlicer(0)->GetFusion();
1186       tSlice = mSlicerManagers[index]->GetSlicer(0)->GetFusionTSlice();
1187     }
1188     else if (DataTree->selectedItems()[0]->data(1,Qt::UserRole).toString() == "contour") {
1189       imageSelected = mSlicerManagers[index]->GetSlicer(0)->GetImage();
1190       tSlice = mSlicerManagers[index]->GetSlicer(0)->GetTSlice();
1191     }
1192     else {
1193       imageSelected = mSlicerManagers[index]->GetSlicer(0)->GetImage();
1194       tSlice = mSlicerManagers[index]->GetSlicer(0)->GetTSlice();
1195     }
1196
1197     dimension = imageSelected->GetNumberOfDimensions();
1198     origin.resize(dimension);
1199     inputSpacing.resize(dimension);
1200     inputSize.resize(dimension);
1201     sizeMM.resize(dimension);
1202     pixelType = mSlicerManagers[index]->GetImage()->GetScalarTypeAsITKString().c_str();
1203     for (int i = 0; i < dimension; i++) {
1204       origin[i] = imageSelected->GetOrigin()[i];
1205       inputSpacing[i] = imageSelected->GetSpacing()[i];
1206       inputSize[i] = imageSelected->GetSize()[i];
1207       sizeMM[i] = inputSize[i]*inputSpacing[i];
1208       NPixel *= inputSize[i];
1209     }
1210     inputSizeInBytes = GetSizeInBytes(imageSelected->GetActualMemorySize());
1211
1212     QString dim = QString::number(dimension) + " (";
1213     dim += pixelType + ")";
1214
1215     infoPanel->setFileName(image);
1216     std::string creationImageTimeValue("No creation time");
1217     itk::ExposeMetaData< std::string > (*imageSelected->GetFirstMetaDataDictionary(), "creationImageTime", creationImageTimeValue);
1218     infoPanel->setImageCreationTime(QString(creationImageTimeValue.c_str()));
1219     infoPanel->setDimension(dim);
1220     infoPanel->setSizePixel(GetVectorIntAsString(inputSize));
1221     infoPanel->setSizeMM(GetVectorDoubleAsString(sizeMM));
1222     infoPanel->setOrigin(GetVectorDoubleAsString(origin));
1223     infoPanel->setSpacing(GetVectorDoubleAsString(inputSpacing));
1224     infoPanel->setNPixel(QString::number(NPixel)+" ("+inputSizeInBytes+")");
1225
1226     transformation = imageSelected->GetTransform()[tSlice]->GetMatrix();
1227     infoPanel->setTransformation(clitk::Get4x4MatrixDoubleAsString(transformation).c_str());
1228
1229     landmarksPanel->SetCurrentLandmarks(mSlicerManagers[index]->GetLandmarks(),
1230                                         mSlicerManagers[index]->GetTSlice());
1231     landmarksPanel->SetCurrentPath(mInputPathName.toStdString());
1232     landmarksPanel->SetCurrentImage(mSlicerManagers[index]->GetFileName().c_str());
1233
1234     overlayPanel->getCurrentImageName(mSlicerManagers[index]->GetFileName().c_str());
1235     for (int i = 0; i < 4; i++) {
1236       if (DataTree->selectedItems()[0]->data(i+1,Qt::CheckStateRole).toInt() > 0 || i == 3) {
1237         mSlicerManagers[index]->UpdateInfoOnCursorPosition(i);
1238         break;
1239       }
1240     }
1241
1242 //     infoPanel->setFileName(image);
1243 //     infoPanel->setDimension(dim);
1244 //     infoPanel->setSizePixel(GetVectorIntAsString(inputSize));
1245 //     infoPanel->setSizeMM(GetVectorDoubleAsString(sizeMM));
1246 //     infoPanel->setOrigin(GetVectorDoubleAsString(origin));
1247 //     infoPanel->setSpacing(GetVectorDoubleAsString(inputSpacing));
1248 //     infoPanel->setNPixel(QString::number(NPixel)+" ("+inputSizeInBytes+")");
1249 //
1250 //     landmarksPanel->SetCurrentLandmarks(mSlicerManagers[index]->GetLandmarks(),
1251 //                                         mSlicerManagers[index]->GetTSlice());
1252 //     landmarksPanel->SetCurrentPath(mInputPathName.toStdString());
1253 //     landmarksPanel->SetCurrentImage(mSlicerManagers[index]->GetFileName().c_str());
1254 //
1255 //     overlayPanel->getCurrentImageName(mSlicerManagers[index]->GetFileName().c_str());
1256 //     for (int i = 0; i < 4; i++) {
1257 //       if (DataTree->selectedItems()[0]->data(i+1,Qt::CheckStateRole).toInt() > 0 || i == 3) {
1258 //         mSlicerManagers[index]->UpdateInfoOnCursorPosition(i);
1259 //         break;
1260 //       }
1261 //     }
1262     WindowLevelChanged();
1263
1264     slicingPresetComboBox->setCurrentIndex(mSlicerManagers[index]->GetSlicingPreset());
1265
1266     if (mSlicerManagers[index]->GetSlicer(0)->GetVF()) {
1267       overlayPanel->getVFName(mSlicerManagers[index]->GetVFName().c_str());
1268       overlayPanel->getVFProperty(mSlicerManagers[index]->GetSlicer(0)->GetVFSubSampling(),
1269         mSlicerManagers[index]->GetSlicer(0)->GetVFScale(),
1270         mSlicerManagers[index]->GetSlicer(0)->GetVFLog());
1271     } else {
1272       overlayPanel->getVFName(mSlicerManagers[index]->GetVFName().c_str());
1273       overlayPanel->getVFProperty(-1,-1,-1);
1274     }
1275     if (mSlicerManagers[index]->GetSlicer(0)->GetOverlay()) {
1276       overlayPanel->getOverlayName(mSlicerManagers[index]->GetOverlayName().c_str());
1277     } else {
1278       overlayPanel->getOverlayName(mSlicerManagers[index]->GetOverlayName().c_str());
1279     }
1280
1281     if (mSlicerManagers[index]->GetSlicer(0)->GetFusion()) {
1282       overlayPanel->getFusionName(mSlicerManagers[index]->GetFusionName().c_str());
1283     } else {
1284       overlayPanel->getFusionName(mSlicerManagers[index]->GetFusionName().c_str());
1285     }
1286   }
1287 }
1288 //------------------------------------------------------------------------------
1289
1290 //------------------------------------------------------------------------------
1291 void vvMainWindow::ShowDocumentation()
1292 {
1293   documentation->show();
1294 }
1295 //------------------------------------------------------------------------------
1296
1297 //------------------------------------------------------------------------------
1298 void vvMainWindow::PopupRegisterForm(bool checkCanPush)
1299 {
1300   vvRegisterForm* registerForm = new vvRegisterForm(QUrl("http://www.creatis.insa-lyon.fr/~dsarrut/vvregister/write.php"), getVVSettingsPath(), getSettingsOptionFormat());
1301   if(!checkCanPush) {
1302     registerForm->show();
1303   } else {
1304     if(registerForm->canPush()) {
1305       registerForm->show();
1306       registerForm->acquitPushed();//too bad if there is not internet connection anymore.
1307     }
1308   }
1309 }
1310 //------------------------------------------------------------------------------
1311
1312 //------------------------------------------------------------------------------
1313 void vvMainWindow::ShowHelpDialog()
1314 {
1315   help_dialog->show();
1316 }
1317 //------------------------------------------------------------------------------
1318
1319 //------------------------------------------------------------------------------
1320 void vvMainWindow::ChangeViewMode()
1321 {
1322   typedef struct _SIZE{
1323     QSplitter* splitter;
1324     QList<int> size1, size2;
1325     int cols[3];
1326   }SplitterSize;
1327   SplitterSize sizes[4];
1328   sizes[0].splitter = OSplitter;
1329   sizes[0].size1.push_back(1);
1330   sizes[0].size1.push_back(0);
1331   sizes[0].size2.push_back(1);
1332   sizes[0].size2.push_back(0);
1333   sizes[0].cols[0] = 2;
1334   sizes[0].cols[1] = 3;
1335   sizes[0].cols[2] = 4;
1336
1337   sizes[1].splitter = ESplitter;
1338   sizes[1].size1.push_back(0);
1339   sizes[1].size1.push_back(1);
1340   sizes[1].size2.push_back(1);
1341   sizes[1].size2.push_back(0);
1342   sizes[1].cols[0] = 1;
1343   sizes[1].cols[1] = 3;
1344   sizes[1].cols[2] = 4;
1345
1346   sizes[2].splitter = OSplitter;
1347   sizes[2].size1.push_back(1);
1348   sizes[2].size1.push_back(0);
1349   sizes[2].size2.push_back(0);
1350   sizes[2].size2.push_back(1);
1351   sizes[2].cols[0] = 1;
1352   sizes[2].cols[1] = 2;
1353   sizes[2].cols[2] = 4;
1354
1355   sizes[3].splitter = ESplitter;
1356   sizes[3].size1.push_back(0);
1357   sizes[3].size1.push_back(1);
1358   sizes[3].size2.push_back(0);
1359   sizes[3].size2.push_back(1);
1360   sizes[3].cols[0] = 1;
1361   sizes[3].cols[1] = 2;
1362   sizes[3].cols[2] = 3;
1363
1364   int slicer = mSlicerManagers[mCurrentPickedImageIndex]->GetSelectedSlicer();
1365   if (viewMode == 1) {
1366     if (slicer >= 0) {
1367       viewMode = 0;
1368       splitter_3->setSizes(sizes[slicer].size1);
1369       sizes[slicer].splitter->setSizes(sizes[slicer].size2);
1370       DataTree->setColumnHidden(sizes[slicer].cols[0],1);
1371       DataTree->setColumnHidden(sizes[slicer].cols[1],1);
1372       DataTree->setColumnHidden(sizes[slicer].cols[2],1);
1373     }
1374   } else {
1375     QList<int> size;
1376     if (slicer >= 0) {
1377       viewMode = 1;
1378       size.push_back(1);
1379       size.push_back(1);
1380       splitter_3->setSizes(size);
1381       sizes[slicer].splitter->setSizes(size);
1382       DataTree->setColumnHidden(sizes[slicer].cols[0],0);
1383       DataTree->setColumnHidden(sizes[slicer].cols[1],0);
1384       DataTree->setColumnHidden(sizes[slicer].cols[2],0);
1385     }
1386   }
1387   UpdateRenderWindows();
1388   /*
1389   ** I don't know why but for both resized QVTKWidget we also need to render
1390   ** the associated Slicer to redraw crosses.
1391   */
1392   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
1393     //     if (DataTree->topLevelItem(i)->data(COLUMN_UL_VIEW,Qt::CheckStateRole).toInt() > 1)
1394     mSlicerManagers[i]->GetSlicer(0)->Render();
1395     mSlicerManagers[i]->GetSlicer(1)->Render();
1396     //     if (DataTree->topLevelItem(i)->data(COLUMN_DL_VIEW,Qt::CheckStateRole).toInt() > 1)
1397     mSlicerManagers[i]->GetSlicer(2)->Render();
1398     mSlicerManagers[i]->GetSlicer(3)->Render();
1399   }
1400 }
1401 //------------------------------------------------------------------------------
1402
1403 //------------------------------------------------------------------------------
1404 QString vvMainWindow::GetSizeInBytes(unsigned long size)
1405 {
1406   QString result = "";// QString::number(size);
1407   //result += " bytes (";
1408   if (size > 1000000000) {
1409     size /= 1000000000;
1410     result += QString::number(size);
1411     result += "GB";//)";
1412   } else if (size > 1000000) {
1413     size /= 1000000;
1414     result += QString::number(size);
1415     result += "MB";//)";
1416   } else if (size > 1000) {
1417     size /= 1000;
1418     result += QString::number(size);
1419     result += "kB";//)";
1420   }
1421   return result;
1422 }
1423 //------------------------------------------------------------------------------
1424
1425 //------------------------------------------------------------------------------
1426 QString vvMainWindow::GetVectorDoubleAsString(std::vector<double> vectorDouble)
1427 {
1428   QString result;
1429   for (unsigned int i= 0; i < vectorDouble.size(); i++) {
1430     if (i != 0)
1431       result += " ";
1432     result += QString::number(vectorDouble[i]);
1433   }
1434   return result;
1435 }
1436 //------------------------------------------------------------------------------
1437
1438 //------------------------------------------------------------------------------
1439 QString vvMainWindow::GetVectorIntAsString(std::vector<int> vectorInt)
1440 {
1441   QString result;
1442   for (unsigned int i= 0; i < vectorInt.size(); i++) {
1443     if (i != 0)
1444       result += " ";
1445     result += QString::number(vectorInt[i]);
1446   }
1447   return result;
1448 }
1449 //------------------------------------------------------------------------------
1450
1451 //------------------------------------------------------------------------------
1452 void vvMainWindow::SlotFileChanged(const QString& pathname)
1453 {
1454   std::vector<QTreeWidgetItem*> items = GetItemFromPathname(pathname);
1455   for (unsigned int i=0; i< items.size(); ++i)
1456     ReloadImage(items[i], 0);
1457 }
1458 //------------------------------------------------------------------------------
1459
1460 //------------------------------------------------------------------------------
1461 std::vector<QTreeWidgetItem*> vvMainWindow::GetItemFromPathname(const QString& pathname)
1462 {
1463   std::vector<QTreeWidgetItem*> items;
1464   for (int i = 0; i < DataTree->topLevelItemCount(); ++i) {
1465     QString tempItemPathname(DataTree->topLevelItem(i)->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString());
1466     tempItemPathname = tempItemPathname.left(tempItemPathname.length() - 1);
1467     if (tempItemPathname == pathname)
1468       items.push_back(DataTree->topLevelItem(i));
1469   }
1470   return items;
1471 }
1472 //------------------------------------------------------------------------------
1473
1474 //------------------------------------------------------------------------------
1475 //this actually returns the SlicerManager index!
1476 int vvMainWindow::GetSlicerIndexFromItem(QTreeWidgetItem* item)
1477 {
1478   QString id = item->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString();
1479   for (int i = 0; i < DataTree->topLevelItemCount(); i++) {
1480     if (DataTree->topLevelItem(i)->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString() == id)
1481       return i;
1482   }
1483   return -1;
1484 }
1485 //------------------------------------------------------------------------------
1486
1487 //------------------------------------------------------------------------------
1488 QTreeWidgetItem* vvMainWindow::GetItemFromSlicerManager(vvSlicerManager* sm)
1489 {
1490   QString id = sm->GetId().c_str();
1491   for (int i = 0; i < DataTree->topLevelItemCount(); i++) {
1492     if (DataTree->topLevelItem(i)->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString() == id)
1493       return DataTree->topLevelItem(i);
1494   }
1495   return NULL;
1496 }
1497 //------------------------------------------------------------------------------
1498
1499 //------------------------------------------------------------------------------
1500 void vvMainWindow::DisplayChanged(QTreeWidgetItem *clickedItem, int column)
1501 {
1502   if ( column >= COLUMN_CLOSE_IMAGE || column <= 0)
1503     return;
1504
1505   // Get parent information (might be the same item)
1506   int slicerManagerIndex = GetSlicerIndexFromItem(clickedItem);
1507   QTreeWidgetItem* clickedParentItem = DataTree->topLevelItem(slicerManagerIndex);
1508   vvSlicer* clickedSlicer = mSlicerManagers[slicerManagerIndex]->GetSlicer(column-1);
1509
1510   // Go over the complete item tree (only 2 levels, parents and children)
1511   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
1512     // Trick to avoid redoing twice the job for a key (sr)
1513     mSlicerManagers[i]->GetSlicer(column-1)->GetRenderWindow()->GetInteractor()->SetKeySym("Crap");
1514
1515     QTreeWidgetItem* currentParentItem = DataTree->topLevelItem(i);
1516     if(currentParentItem != clickedParentItem) {
1517       // Not the branch of the clicked item, uncheck all
1518
1519       // Parent
1520       currentParentItem->setData(column,Qt::CheckStateRole, 0);
1521       mSlicerManagers[i]->UpdateSlicer(column-1, false);
1522
1523       // Children
1524       for (int iChild = 0; iChild < currentParentItem->childCount(); iChild++) {
1525         currentParentItem->child(iChild)->setData(column,Qt::CheckStateRole, 0);
1526       }
1527     }
1528     else {
1529       // Branch of the clicked one: get check status from actor visibility in slicer
1530       // and toggle the clicked one
1531
1532       // Parent
1533       bool vis = clickedSlicer->GetActorVisibility("image", 0);
1534       bool draw = clickedSlicer->GetRenderer()->GetDraw();
1535
1536       // Update slicer (after getting visibility)
1537       mSlicerManagers[slicerManagerIndex]->UpdateSlicer(column-1, true);
1538       mSlicerManagers[slicerManagerIndex]->UpdateInfoOnCursorPosition(column-1);
1539       DisplaySliders(slicerManagerIndex, column-1);
1540       if(clickedParentItem == clickedItem) {
1541         // Toggle
1542         vis = !draw || !vis;
1543       }
1544       clickedSlicer->SetActorVisibility("image", 0, vis);
1545       clickedParentItem->setData(column, Qt::CheckStateRole, vis?2:0);
1546
1547       // Children
1548       std::map<std::string, int> actorTypeCounts;
1549       for (int iChild = 0; iChild < clickedParentItem->childCount(); iChild++) {
1550         QTreeWidgetItem* currentChildItem = clickedParentItem->child(iChild);
1551         std::string actorType = currentChildItem->data(1,Qt::UserRole).toString().toStdString();
1552         vis = clickedSlicer->GetActorVisibility(actorType, actorTypeCounts[actorType]);
1553         if(currentChildItem == clickedItem) {
1554           // Toggle or force visibility if it was not on this branch so far
1555           vis = !draw || !vis;
1556           clickedSlicer->SetActorVisibility(actorType, actorTypeCounts[actorType], vis);
1557         }
1558         currentChildItem->setData(column, Qt::CheckStateRole, vis?2:0);
1559         actorTypeCounts[actorType]++;
1560       }
1561     }
1562   }
1563
1564   clickedSlicer->Render();
1565 }
1566 //------------------------------------------------------------------------------
1567
1568 void vvMainWindow::InitSlicers()
1569 {
1570   if (mSlicerManagers.size()) {
1571     mSlicerManagers.back()->GenerateDefaultLookupTable();
1572     mSlicerManagers.back()->SetSlicerWindow(0,NOViewWidget->GetRenderWindow());
1573     mSlicerManagers.back()->SetSlicerWindow(1,NEViewWidget->GetRenderWindow());
1574     mSlicerManagers.back()->SetSlicerWindow(2,SOViewWidget->GetRenderWindow());
1575     mSlicerManagers.back()->SetSlicerWindow(3,SEViewWidget->GetRenderWindow());
1576 #if VTK_MAJOR_VERSION <= 5
1577     mSlicerManagers.back()->Render(); // SR: displayed #slice is wrong without this / TB: With VTK6 and multiple images, all slicers are updated, not only the first
1578 #endif
1579   }
1580 }
1581
1582 //------------------------------------------------------------------------------
1583 void vvMainWindow::InitDisplay()
1584 {
1585   if (mSlicerManagers.size()) {
1586     //BE CAREFUL : this is absolutely necessary to set the interactor style
1587     //in order to have the same style instanciation for all SlicerManagers in
1588     // a same window
1589     for (int j = 0; j < 4; j++) {
1590       vvInteractorStyleNavigator* style = vvInteractorStyleNavigator::New();
1591       style->SetAutoAdjustCameraClippingRange(1);
1592       bool AlreadySelected = false;
1593       for (int i = 0; i < DataTree->topLevelItemCount(); i++) {
1594         mSlicerManagers[i]->SetInteractorStyleNavigator(j,style);
1595         //select the image only if previous are not selected
1596         if (DataTree->topLevelItem(i)->data(j+1,Qt::CheckStateRole).toInt() > 1) {
1597           mSlicerManagers[i]->UpdateSlicer(j,1);
1598           AlreadySelected = true;
1599         } else if (i == DataTree->topLevelItemCount()-1 && !AlreadySelected) {
1600           if (DataTree->selectedItems().size() == 0) {
1601             DataTree->topLevelItem(i)->setSelected(1);
1602           }
1603           DataTree->topLevelItem(i)->setData(j+1,Qt::CheckStateRole,2);
1604           mSlicerManagers[i]->UpdateSlicer(j,1);
1605           DisplaySliders(i,j);
1606         } else {
1607           DataTree->topLevelItem(i)->setData(j+1,Qt::CheckStateRole,0);
1608           mSlicerManagers[i]->UpdateSlicer(j,0);
1609         }
1610       }
1611       style->Delete();
1612     }
1613   }
1614 }
1615 //------------------------------------------------------------------------------
1616
1617 //------------------------------------------------------------------------------
1618 void vvMainWindow::DisplaySliders(int slicer, int window)
1619 {
1620   if(!mSlicerManagers[slicer]->GetSlicer(window)->GetRenderer()->GetDraw())
1621     return;
1622
1623   int range[2];
1624   mSlicerManagers[slicer]->GetSlicer(window)->GetSliceRange(range);
1625   int position = mSlicerManagers[slicer]->GetSlicer(window)->GetSlice();
1626   if (range[1]>0)
1627     verticalSliders[window]->show();
1628   else
1629     verticalSliders[window]->hide();
1630   verticalSliders[window]->setRange(range[0],range[1]);
1631   verticalSliders[window]->setValue(position);
1632
1633   int tRange[2];
1634   tRange[0] = 0;
1635   tRange[1] = mSlicerManagers[slicer]->GetSlicer(window)->GetTMax();
1636   if (tRange[1]>0)
1637     horizontalSliders[window]->show();
1638   else
1639     horizontalSliders[window]->hide();
1640   horizontalSliders[window]->setRange(tRange[0],tRange[1]);
1641   int tPosition = mSlicerManagers[slicer]->GetSlicer(window)->GetMaxCurrentTSlice();
1642   horizontalSliders[window]->setValue(tPosition);
1643 }
1644 //------------------------------------------------------------------------------
1645
1646 //------------------------------------------------------------------------------
1647 void vvMainWindow::CloseImage(QTreeWidgetItem* item, int column)
1648 {
1649   int index = GetSlicerIndexFromItem(item);
1650
1651   if (DataTree->topLevelItem(index) != item) {
1652     QString warning = "Do you really want to close the overlay : ";
1653     warning += item->data(COLUMN_IMAGE_NAME,Qt::DisplayRole).toString();
1654     QMessageBox msgBox(QMessageBox::Warning, tr("Close Overlay"),
1655       warning, 0, this);
1656     msgBox.addButton(tr("Close"), QMessageBox::AcceptRole);
1657     msgBox.addButton(tr("Cancel"), QMessageBox::RejectRole);
1658     if (msgBox.exec() == QMessageBox::AcceptRole) {
1659       std::string overlay_type=item->data(1,Qt::UserRole).toString().toStdString();
1660       int overlay_index=0;
1661       for (int child = 0; child < DataTree->topLevelItem(index)->childCount(); child++) {
1662         if (DataTree->topLevelItem(index)->\
1663           child(child)->data(1,Qt::UserRole).toString().toStdString() == overlay_type)
1664           overlay_index++;
1665         if (DataTree->topLevelItem(index)->child(child) == item) break;
1666       }
1667       if (overlay_type=="fusionSequence") {
1668         //removing the overlay sequence in a fusion sequence visualization mode
1669         //reset the transforms
1670         overlayPanel->getFusionSequenceProperty(-1, false, 0, false);
1671
1672         //unlink and untie the slicer managers
1673         RemoveLink(mSlicerManagers[index]->GetId().c_str(), mSlicerManagers[mSlicerManagers[index]->GetFusionSequenceIndexOfLinkedManager()]->GetId().c_str());
1674         mSlicerManagers[index]->SetFusionSequenceInvolvmentCode(-1);
1675         mSlicerManagers[mSlicerManagers[index]->GetFusionSequenceIndexOfLinkedManager()]->SetFusionSequenceInvolvmentCode(-1);
1676         for (unsigned i=0 ; i<4 ; i++) {
1677             mSlicerManagers[index]->GetSlicer(i)->SetFusionSequenceCode(-1);
1678             mSlicerManagers[mSlicerManagers[index]->GetFusionSequenceIndexOfLinkedManager()]->GetSlicer(i)->SetFusionSequenceCode(-1);
1679         }
1680
1681       }
1682       mSlicerManagers[index]->RemoveActor(overlay_type, overlay_index-1);
1683       mSlicerManagers[index]->SetColorMap(0);
1684       DataTree->topLevelItem(index)->takeChild(DataTree->topLevelItem(index)->indexOfChild(item));
1685       mSlicerManagers[index]->Render();
1686     }
1687   } else if (DataTree->topLevelItemCount() <= 1) {
1688     QString warning = "Do you really want to close the image : ";
1689     warning += item->data(COLUMN_IMAGE_NAME,Qt::DisplayRole).toString();
1690     warning += "\nThis is the last image, you're about to close vv !!!";
1691     QMessageBox msgBox(QMessageBox::Warning, tr("Close Image"),
1692       warning, 0, this);
1693     msgBox.addButton(tr("Close vv"), QMessageBox::AcceptRole);
1694     msgBox.addButton(tr("Cancel"), QMessageBox::RejectRole);
1695     if (msgBox.exec() == QMessageBox::AcceptRole) {
1696       this->close();
1697     }
1698   } else {
1699     QString warning = "Do you really want to close the image : ";
1700     warning += item->data(COLUMN_IMAGE_NAME,Qt::DisplayRole).toString();
1701     QMessageBox msgBox(QMessageBox::Warning, tr("Close Image"),
1702       warning, 0, this);
1703     msgBox.addButton(tr("Close"), QMessageBox::AcceptRole);
1704     msgBox.addButton(tr("Cancel"), QMessageBox::RejectRole);
1705     if (msgBox.exec() == QMessageBox::AcceptRole) {
1706
1707       // Tell tools that we close an image
1708       emit AnImageIsBeingClosed(mSlicerManagers[index]);
1709
1710       std::vector<vvSlicerManager*>::iterator Manageriter = mSlicerManagers.begin();
1711       DataTree->takeTopLevelItem(index);
1712       for (int i = 0; i < index; i++) {
1713         Manageriter++;
1714       }
1715       //if the slicer manager was involved in a fusion sequence visualization...
1716       if ( mSlicerManagers[index]->IsInvolvedInFusionSequence() ) {
1717         //in both cases, close the overlay: find it... and close it
1718         //ideally, I should duplicate the code, and avoid calling CloseImage, since this pops up another interactive box
1719         QTreeWidgetItem* overlayItem;
1720         if (mSlicerManagers[index]->IsMainSequenceOfFusionSequence()) {
1721           for (unsigned i=0 ; i<item->childCount() ; i++) {
1722             overlayItem = item->child(i);
1723             this->CloseImage( overlayItem, 0 );
1724           }
1725         }
1726         else {
1727           QTreeWidgetItem* linkedItem = this->GetItemFromSlicerManager( mSlicerManagers[mSlicerManagers[index]->GetFusionSequenceIndexOfLinkedManager()] );
1728           for (unsigned i=0 ; i<linkedItem->childCount() ; i++) {
1729             overlayItem = linkedItem->child(i);
1730             this->CloseImage( overlayItem, 0 );
1731           }
1732         }
1733
1734         /* -- this is normally already done when closing the overlay.
1735         //reset the transforms
1736         overlayPanel->getFusionSequenceProperty(-1, false, 0, false);
1737
1738         //unlink and untie the slicer managers
1739         RemoveLink(mSlicerManagers[index]->GetId().c_str(), mSlicerManagers[mSlicerManagers[index]->GetFusionSequenceIndexOfLinkedManager()]->GetId().c_str());
1740         mSlicerManagers[index]->SetFusionSequenceInvolvmentCode(-1);
1741         mSlicerManagers[mSlicerManagers[index]->GetFusionSequenceIndexOfLinkedManager()]->SetFusionSequenceInvolvmentCode(-1);
1742         for (unsigned i=0 ; i<4 ; i++) {
1743             mSlicerManagers[index]->GetSlicer(i)->SetFusionSequenceCode(-1);
1744             mSlicerManagers[mSlicerManagers[index]->GetFusionSequenceIndexOfLinkedManager()]->GetSlicer(i)->SetFusionSequenceCode(-1);
1745         }
1746         */
1747       }
1748
1749       linkPanel->removeImage(index);
1750       mSlicerManagers[index]->RemoveActors();
1751
1752       //remove the slicer manager
1753       delete mSlicerManagers[index];
1754       mSlicerManagers.erase(Manageriter);
1755
1756       //
1757       InitDisplay();
1758     }
1759   }
1760   ImageInfoChanged();
1761 }
1762 //------------------------------------------------------------------------------
1763
1764 //------------------------------------------------------------------------------
1765 void vvMainWindow::ReloadImage(QTreeWidgetItem* item, int column)
1766 {
1767   // int index = GetSlicerIndexFromItem(item);
1768   //   QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
1769   //   if (item->data(1,Qt::UserRole).toString() == "vector")
1770   //     mSlicerManagers[index]->ReloadVF();
1771   //   else
1772   //     mSlicerManagers[index]->Reload();
1773
1774   //   QApplication::restoreOverrideCursor();
1775   int index = GetSlicerIndexFromItem(item);
1776   QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
1777   QString role=item->data(1,Qt::UserRole).toString();
1778   if ( role == "vector") {
1779     mSlicerManagers[index]->ReloadVF();
1780   }
1781   else if (role == "overlay") {
1782     mSlicerManagers[index]->ReloadOverlay();
1783   }
1784   else if (role == "fusion") {
1785     mSlicerManagers[index]->ReloadFusion();
1786   }
1787   else if (role == "fusionSequence") {
1788     //both versions of the secondary sequence must be updated.
1789     mSlicerManagers[index]->ReloadFusionSequence();
1790     mSlicerManagers[mSlicerManagers[index]->GetFusionSequenceIndexOfLinkedManager()]->Reload();
1791   }
1792   else {
1793     mSlicerManagers[index]->Reload();
1794     //if we update the secondary sequence, then the overlay of the main sequence should also be updated
1795     if (mSlicerManagers[index]->IsSecondarySequenceOfFusionSequence()) mSlicerManagers[mSlicerManagers[index]->GetFusionSequenceIndexOfLinkedManager()]->ReloadFusionSequence();
1796   }
1797   // Update view and info
1798   ImageInfoChanged();
1799   mSlicerManagers[index]->Render();
1800   QApplication::restoreOverrideCursor();
1801 }
1802 //------------------------------------------------------------------------------
1803
1804 //------------------------------------------------------------------------------
1805 void vvMainWindow::MousePositionChanged(int visibility,double x, double y, double z, double X, double Y, double Z , double value)
1806 {
1807   infoPanel->setCurrentInfo(visibility,x,y,z,X,Y,Z,value);
1808 }
1809 //------------------------------------------------------------------------------
1810
1811 //------------------------------------------------------------------------------
1812 void vvMainWindow::VectorChanged(int visibility,double x, double y, double z, double value)
1813 {
1814   overlayPanel->getCurrentVectorInfo(visibility,x,y,z,value);
1815 }
1816 //------------------------------------------------------------------------------
1817
1818 //------------------------------------------------------------------------------
1819 void vvMainWindow::OverlayChanged(int visibility, double valueOver, double valueRef)
1820 {
1821   overlayPanel->getCurrentOverlayInfo(visibility,valueOver, valueRef);
1822 }
1823 //------------------------------------------------------------------------------
1824
1825 //------------------------------------------------------------------------------
1826 void vvMainWindow::FusionChanged(int visibility, double value)
1827 {
1828   overlayPanel->getCurrentFusionInfo(visibility,value);
1829 }
1830 //------------------------------------------------------------------------------
1831
1832 //------------------------------------------------------------------------------
1833 //called when AddOverlayImage, AddFusionSequence
1834 //or when UpdateWindowLevel() is called ; when slicerManager emits WindowLevelChanged
1835 //when ImageInfoChanged() is called
1836 void vvMainWindow::WindowLevelChanged()
1837 {
1838   // Base image
1839   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1840   if(index==-1) return;
1841   windowSpinBox->setValue(mSlicerManagers[index]->GetColorWindow());
1842   levelSpinBox->setValue(mSlicerManagers[index]->GetColorLevel());
1843   colorMapComboBox->setCurrentIndex(mSlicerManagers[index]->GetColorMap());
1844   presetComboBox->setCurrentIndex(mSlicerManagers[index]->GetPreset());
1845
1846   // Overlay image
1847   if (mSlicerManagers[index]->GetSlicer(0)->GetOverlay())
1848     overlayPanel->getOverlayProperty(mSlicerManagers[index]->GetOverlayColor(),
1849     mSlicerManagers[index]->GetLinkOverlayWindowLevel(),
1850     mSlicerManagers[index]->GetOverlayColorWindow(),
1851     mSlicerManagers[index]->GetOverlayColorLevel());
1852   else
1853     overlayPanel->getOverlayProperty(-1,0,0.,0.);
1854
1855   // Fusion & SequenceFusion image
1856   if (mSlicerManagers[index]->GetSlicer(0)->GetFusion()) {
1857     overlayPanel->getFusionProperty(mSlicerManagers[index]->GetFusionOpacity(),
1858       mSlicerManagers[index]->GetFusionThresholdOpacity(),
1859       mSlicerManagers[index]->GetFusionColorMap(),
1860       mSlicerManagers[index]->GetFusionWindow(),
1861       mSlicerManagers[index]->GetFusionLevel());
1862     if (mSlicerManagers[index]->IsMainSequenceOfFusionSequence()) {
1863       overlayPanel->getFusionSequenceProperty(mSlicerManagers[index]->GetFusionSequenceFrameIndex(),
1864         mSlicerManagers[index]->GetFusionSequenceSpatialSyncFlag(),
1865         mSlicerManagers[index]->GetFusionSequenceNbFrames(),
1866         mSlicerManagers[index]->GetFusionSequenceTemporalSyncFlag());
1867     }
1868   }
1869   else if ( mSlicerManagers[index]->IsSecondarySequenceOfFusionSequence() ) {
1870     //if the image is involved in a fusion sequence, preserve the overlay panel!
1871     int ind = mSlicerManagers[index]->GetFusionSequenceIndexOfLinkedManager();
1872     overlayPanel->getFusionProperty(mSlicerManagers[ind]->GetFusionOpacity(),
1873       mSlicerManagers[ind]->GetFusionThresholdOpacity(),
1874       mSlicerManagers[ind]->GetFusionColorMap(),
1875       mSlicerManagers[ind]->GetFusionWindow(),
1876       mSlicerManagers[ind]->GetFusionLevel());
1877     overlayPanel->getFusionSequenceProperty(mSlicerManagers[ind]->GetFusionSequenceFrameIndex(),
1878       mSlicerManagers[ind]->GetFusionSequenceSpatialSyncFlag(),
1879       mSlicerManagers[ind]->GetFusionSequenceNbFrames(),
1880       mSlicerManagers[ind]->GetFusionSequenceTemporalSyncFlag());
1881   }
1882   else
1883   {
1884     overlayPanel->getFusionProperty(-1, -1, -1, -1, -1);
1885     overlayPanel->getFusionSequenceProperty(-1, false, 0, false);
1886   }
1887 }
1888 //------------------------------------------------------------------------------
1889
1890 //------------------------------------------------------------------------------
1891 void vvMainWindow::WindowLevelEdited()
1892 {
1893   presetComboBox->setCurrentIndex(WL_USER);
1894   UpdateWindowLevel();
1895 }
1896 //------------------------------------------------------------------------------
1897
1898 //------------------------------------------------------------------------------
1899 void vvMainWindow::SetWindowLevel(double w, double l)
1900 {
1901   windowSpinBox->setValue(w);
1902   levelSpinBox->setValue(l);
1903   presetComboBox->setCurrentIndex(WL_USER);
1904   colorMapComboBox->setCurrentIndex(0);
1905   UpdateWindowLevel();
1906 }
1907 //------------------------------------------------------------------------------
1908
1909 //------------------------------------------------------------------------------
1910 void vvMainWindow::UpdateWindowLevel()
1911 {
1912   if (DataTree->selectedItems().size()) {
1913     if (presetComboBox->currentIndex() == WL_VENTILATION) //For ventilation
1914       colorMapComboBox->setCurrentIndex(5);
1915     int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1916     mSlicerManagers[index]->SetColorWindow(windowSpinBox->value());
1917     mSlicerManagers[index]->SetColorLevel(levelSpinBox->value());
1918     mSlicerManagers[index]->SetPreset(presetComboBox->currentIndex());
1919     mSlicerManagers[index]->Render();
1920     WindowLevelChanged();
1921   }
1922 }
1923 //------------------------------------------------------------------------------
1924
1925 //------------------------------------------------------------------------------
1926 void vvMainWindow::UpdateSlicingPreset()
1927 {
1928   if (DataTree->selectedItems().size()) {
1929     int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1930     mSlicerManagers[index]->SetSlicingPreset(vvSlicerManager::SlicingPresetType(slicingPresetComboBox->currentIndex()));
1931   }
1932 }
1933 //------------------------------------------------------------------------------
1934
1935 //------------------------------------------------------------------------------
1936 void vvMainWindow::UpdateColorMap()
1937 {
1938   if (DataTree->selectedItems().size()) {
1939     int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1940     mSlicerManagers[index]->SetColorMap(colorMapComboBox->currentIndex());
1941     mSlicerManagers[index]->Render();
1942   }
1943 }
1944 //------------------------------------------------------------------------------
1945 void vvMainWindow::SwitchWindowLevel()
1946 {
1947   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1948   int window = mSlicerManagers[index]->GetColorWindow();
1949   presetComboBox->setCurrentIndex(WL_USER);
1950   windowSpinBox->setValue(-window);
1951   UpdateWindowLevel();
1952 }
1953 //------------------------------------------------------------------------------
1954
1955 //------------------------------------------------------------------------------
1956 void vvMainWindow::ApplyWindowLevelToAllImages()
1957 {
1958   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1959   if(index==-1) return;
1960   double window = mSlicerManagers[index]->GetColorWindow();
1961   double level = mSlicerManagers[index]->GetColorLevel();
1962
1963   double fusWindow = mSlicerManagers[index]->GetFusionWindow();
1964   double fusLevel = mSlicerManagers[index]->GetFusionLevel();
1965
1966   double overWindow = mSlicerManagers[index]->GetOverlayColorWindow();
1967   double overLevel = mSlicerManagers[index]->GetOverlayColorLevel();
1968
1969   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
1970     if (mSlicerManagers[i] == NULL)
1971       continue;
1972     mSlicerManagers[i]->SetColorWindow(window);
1973     mSlicerManagers[i]->SetColorLevel(level);
1974     mSlicerManagers[i]->SetPreset(WL_USER);
1975     mSlicerManagers[i]->SetFusionWindow(fusWindow);
1976     mSlicerManagers[i]->SetFusionLevel(fusLevel);
1977     mSlicerManagers[i]->SetOverlayColorWindow(overWindow);
1978     mSlicerManagers[i]->SetOverlayColorLevel(overLevel);
1979     mSlicerManagers[i]->Render();
1980   }
1981 }
1982 //------------------------------------------------------------------------------
1983
1984 //------------------------------------------------------------------------------
1985 void vvMainWindow::ApplyWindowToSetOfImages(double window, unsigned int indexMin, unsigned int indexMax)
1986 {
1987   for (unsigned int i = indexMin; i <= indexMax && i < mSlicerManagers.size(); i++) {
1988     if (mSlicerManagers[i] == NULL)
1989       continue;
1990     SetWindowLevel(window, mSlicerManagers[i]->GetColorLevel());
1991     mSlicerManagers[i]->SetColorWindow(window);
1992     mSlicerManagers[i]->SetPreset(WL_USER);
1993     mSlicerManagers[i]->Render();
1994   }
1995 }
1996 //------------------------------------------------------------------------------
1997
1998 //------------------------------------------------------------------------------
1999 void vvMainWindow::ApplyLevelToSetOfImages(double level, unsigned int indexMin, unsigned int indexMax)
2000 {
2001   for (unsigned int i = indexMin; i <= indexMax && i < mSlicerManagers.size(); i++) {
2002     if (mSlicerManagers[i] == NULL)
2003       continue;
2004     SetWindowLevel(mSlicerManagers[i]->GetColorWindow(), level);
2005     mSlicerManagers[i]->SetColorLevel(level);
2006     mSlicerManagers[i]->SetPreset(WL_USER);
2007     mSlicerManagers[i]->Render();
2008   }
2009 }
2010 //------------------------------------------------------------------------------
2011
2012 //------------------------------------------------------------------------------
2013 void vvMainWindow::UpdateLinkManager(std::string id, int slicer, double x, double y, double z, int temps)
2014 {
2015   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
2016     if (mSlicerManagers[i]->GetId() == id) {
2017       mSlicerManagers[i]->GetSlicer(slicer)->SetCurrentPosition(x,y,z,temps);
2018       mSlicerManagers[i]->UpdateViews(0,slicer);
2019       break;
2020     }
2021   }
2022 }
2023 //------------------------------------------------------------------------------
2024
2025 //------------------------------------------------------------------------------
2026 void vvMainWindow::UpdateLinkedNavigation(std::string id, vvSlicerManager * sm, vvSlicer* refSlicer)
2027 {
2028   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
2029     if (id == mSlicerManagers[i]->GetId()) {
2030       mSlicerManagers[i]->UpdateLinkedNavigation(refSlicer);
2031     }
2032   }
2033 }
2034 //------------------------------------------------------------------------------
2035
2036 //------------------------------------------------------------------------------
2037 void vvMainWindow::ShowContextMenu(QPoint point)
2038 {
2039   if (!DataTree->selectedItems().size()) {
2040     contextActions[1]->setEnabled(0);
2041     contextActions[2]->setEnabled(0);
2042     contextActions[3]->setEnabled(0);
2043     contextActions[4]->setEnabled(0);
2044     contextActions[5]->setEnabled(0);
2045     contextActions[6]->setEnabled(0);
2046   } else {
2047     int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2048     contextActions[1]->setEnabled(1);
2049     contextActions[2]->setEnabled(
2050       DataTree->itemWidget(DataTree->selectedItems()[0],
2051       COLUMN_RELOAD_IMAGE)->isEnabled());
2052     contextActions[3]->setEnabled(1);
2053     contextActions[5]->setEnabled(1);
2054     contextActions[6]->setEnabled(1);
2055
2056     if (mSlicerManagers[index]->GetDimension() < 3)
2057       contextActions[4]->setEnabled(0);
2058     else
2059       contextActions[4]->setEnabled(1);
2060   }
2061   contextMenu.exec(QCursor::pos());
2062 }
2063 //------------------------------------------------------------------------------
2064
2065 //------------------------------------------------------------------------------
2066 void vvMainWindow::CloseImage()
2067 {
2068   CloseImage(DataTree->selectedItems()[0],0);
2069 }
2070 //------------------------------------------------------------------------------
2071
2072 //------------------------------------------------------------------------------
2073 void vvMainWindow::ReloadImage()
2074 {
2075   ReloadImage(DataTree->selectedItems()[0],0);
2076 }
2077 //------------------------------------------------------------------------------
2078
2079 //------------------------------------------------------------------------------
2080 void vvMainWindow::SelectOverlayImage()
2081 {
2082   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2083
2084   if (!(CheckAddedImage(index, "overlay")))
2085     return;
2086
2087   QString Extensions = EXTENSIONS;
2088   Extensions += ";;All Files (*)";
2089   QStringList files = QFileDialog::getOpenFileNames(this,tr("Load Overlay image"),mInputPathName,Extensions);
2090   if (files.isEmpty())
2091     return;
2092
2093   std::vector<std::string> vecFileNames;
2094   for (int i = 0; i < files.size(); i++) {
2095     vecFileNames.push_back(files[i].toStdString());
2096   }
2097
2098   AddOverlayImage(index,vecFileNames,vvImageReader::IMAGE);
2099 }
2100 //------------------------------------------------------------------------------
2101
2102 //------------------------------------------------------------------------------
2103 bool vvMainWindow::CheckAddedImage(int index, QString imageType)
2104 {
2105   //check if one overlay image is added
2106   for (int child = 0; child < DataTree->topLevelItem(index)->childCount(); child++)
2107     if (DataTree->topLevelItem(index)->child(child)->data(1,Qt::UserRole).toString().compare(imageType) == 0) {
2108       QString error = "Cannot add more than one compared image\n";
2109       error += "Please remove first ";
2110       error += DataTree->topLevelItem(index)->child(child)->data(COLUMN_IMAGE_NAME,Qt::DisplayRole).toString();
2111       QMessageBox::information(this,tr("Problem adding compared image !"),error);
2112       return false;
2113     }
2114     return true;
2115 }
2116 //------------------------------------------------------------------------------
2117
2118 //------------------------------------------------------------------------------
2119 void vvMainWindow::AddOverlayImage(int index, std::vector<std::string> fileNames, vvImageReader::LoadedImageType type)
2120 {
2121   QString file(fileNames[0].c_str());
2122   if (QFile::exists(file))
2123   {
2124     mInputPathName = itksys::SystemTools::GetFilenamePath(file.toStdString()).c_str();
2125     itk::ImageIOBase::Pointer reader = itk::ImageIOFactory::CreateImageIO(
2126       file.toStdString().c_str(), itk::ImageIOFactory::ReadMode);
2127     reader->SetFileName(fileNames[0].c_str());
2128     reader->ReadImageInformation();
2129     std::string component = reader->GetComponentTypeAsString(reader->GetComponentType());
2130     int dimension = reader->GetNumberOfDimensions();
2131     QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
2132     vvProgressDialog progress("Opening " + file.toStdString());
2133     qApp->processEvents();
2134
2135     std::string filename = itksys::SystemTools::GetFilenameWithoutExtension(file.toStdString()).c_str();
2136     if (mSlicerManagers[index]->SetOverlay(fileNames,dimension, component,type)) {
2137       //create an item in the tree with good settings
2138       QTreeWidgetItem *item = new QTreeWidgetItem();
2139       item->setData(0,Qt::UserRole,file.toStdString().c_str());
2140       item->setData(1,Qt::UserRole,tr("overlay"));
2141       QFileInfo fileinfo(file); //Do not show the path
2142       item->setData(COLUMN_IMAGE_NAME,Qt::DisplayRole,fileinfo.fileName());
2143       item->setToolTip(COLUMN_IMAGE_NAME, mSlicerManagers[index]->GetListOfAbsoluteFilePathInOneString("overlay").c_str());
2144       qApp->processEvents();
2145 #if VTK_MAJOR_VERSION > 5
2146       for ( unsigned int i = 0; i < mSlicerManagers[index]->GetNumberOfSlicers(); i++)
2147         mSlicerManagers[index]->GetSlicer(i)->ForceUpdateDisplayExtent();
2148 #endif
2149
2150       for (int j = 1; j <= 4; j++) {
2151         item->setData(j,Qt::CheckStateRole,DataTree->topLevelItem(index)->data(j,Qt::CheckStateRole));
2152       }
2153
2154       //Create the buttons for reload and close
2155       qApp->processEvents();
2156       QTreePushButton* cButton = new QTreePushButton;
2157       cButton->setItem(item);
2158       cButton->setColumn(COLUMN_CLOSE_IMAGE);
2159       cButton->setToolTip(tr("close image"));
2160       cButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/exit.png")));
2161       connect(cButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
2162         this,SLOT(CloseImage(QTreeWidgetItem*, int)));
2163
2164       QTreePushButton* rButton = new QTreePushButton;
2165       rButton->setItem(item);
2166       rButton->setColumn(COLUMN_RELOAD_IMAGE);
2167       rButton->setToolTip(tr("reload image"));
2168       rButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/rotateright.png")));
2169       connect(rButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
2170         this,SLOT(ReloadImage(QTreeWidgetItem*, int)));
2171
2172       DataTree->topLevelItem(index)->setExpanded(1);
2173       DataTree->topLevelItem(index)->addChild(item);
2174       DataTree->setItemWidget(item, COLUMN_CLOSE_IMAGE, cButton);
2175       DataTree->setItemWidget(item, COLUMN_RELOAD_IMAGE, rButton);
2176
2177       //set the id of the image
2178       QString id = DataTree->topLevelItem(index)->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString();
2179       item->setData(COLUMN_IMAGE_NAME,Qt::UserRole,id.toStdString().c_str());
2180       UpdateTree();
2181       qApp->processEvents();
2182       ImageInfoChanged();
2183       QApplication::restoreOverrideCursor();
2184
2185       // Update the display to update, e.g., the sliders
2186       for(int i=0; i<4; i++)
2187         DisplaySliders(index, i);
2188     } else {
2189       QApplication::restoreOverrideCursor();
2190       QString error = "Cannot import the new image.\n";
2191       error += mSlicerManagers[index]->GetLastError().c_str();
2192       QMessageBox::information(this,tr("Problem reading image !"),error);
2193     }
2194     WindowLevelChanged();
2195   }
2196   else
2197     QMessageBox::information(this,tr("Problem reading Overlay !"),"File doesn't exist!");
2198 }
2199 //------------------------------------------------------------------------------
2200
2201
2202 //------------------------------------------------------------------------------
2203 void vvMainWindow::AddROI(int index, QString file)
2204 {
2205   /*
2206   // Get slice manager
2207
2208   // Load image
2209
2210   vvImageReader * mReader = new vvImageReader;
2211   mReader->SetInputFilename(filename.toStdString());
2212   mReader->Update(IMAGE);
2213   if (mReader->GetLastError().size() != 0) {
2214   std::cerr << "Error while reading " << filename.toStdString() << std::endl;
2215   QString error = "Cannot open file \n";
2216   error += mReader->GetLastError().c_str();
2217   QMessageBox::information(this,tr("Reading problem"),error);
2218   delete mReader;
2219   return;
2220   }
2221   vvImage::Pointer roi = mReader->GetOutput();
2222
2223   // Create roi in new tool
2224   vvToolStructureSetManager::AddImage(mCurrentSlicerManager, roi);
2225   */
2226 }
2227 //------------------------------------------------------------------------------
2228
2229 //------------------------------------------------------------------------------
2230 void vvMainWindow::SelectFusionImage()
2231 {
2232   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2233
2234   if (!(CheckAddedImage(index, "fusion")) || !(CheckAddedImage(index, "fusionSequence")))
2235     return;
2236
2237   QString Extensions = EXTENSIONS;
2238   Extensions += ";;All Files (*)";
2239   QStringList files = QFileDialog::getOpenFileNames(this,tr("Load Fusion image"),mInputPathName,Extensions);
2240   if (files.isEmpty())
2241     return;
2242
2243   std::vector<std::string> vecFileNames;
2244   for (int i = 0; i < files.size(); i++) {
2245     vecFileNames.push_back(files[i].toStdString());
2246   }
2247   AddFusionImage(index,vecFileNames,vvImageReader::IMAGE);
2248 }
2249 //------------------------------------------------------------------------------
2250
2251 //------------------------------------------------------------------------------
2252 void vvMainWindow::ResetTransformationToIdentity()
2253 {
2254   std::string actorType = DataTree->selectedItems()[0]->data(1,Qt::UserRole).toString().toStdString();
2255   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2256   mSlicerManagers[index]->ResetTransformationToIdentity(actorType);
2257   ImageInfoChanged();
2258 }
2259 //------------------------------------------------------------------------------
2260
2261 //------------------------------------------------------------------------------
2262 void vvMainWindow::AddFusionImage(int index, std::vector<std::string> fileNames, vvImageReader::LoadedImageType type)
2263 {
2264   QString file(fileNames[0].c_str());
2265   if (QFile::exists(file))
2266   {
2267     mInputPathName = itksys::SystemTools::GetFilenamePath(file.toStdString()).c_str();
2268     itk::ImageIOBase::Pointer reader = itk::ImageIOFactory::CreateImageIO(
2269       file.toStdString().c_str(), itk::ImageIOFactory::ReadMode);
2270     reader->SetFileName(fileNames[0].c_str());
2271     reader->ReadImageInformation();
2272     std::string component = reader->GetComponentTypeAsString(reader->GetComponentType());
2273     int dimension = reader->GetNumberOfDimensions();
2274     QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
2275     vvProgressDialog progress("Opening fusion");
2276     qApp->processEvents();
2277
2278     std::string filename = itksys::SystemTools::GetFilenameWithoutExtension(file.toStdString()).c_str();
2279     if (mSlicerManagers[index]->SetFusion(fileNames,dimension, component,type)) {
2280       //create an item in the tree with good settings
2281       QTreeWidgetItem *item = new QTreeWidgetItem();
2282       item->setData(0,Qt::UserRole,file.toStdString().c_str());
2283       item->setData(1,Qt::UserRole,tr("fusion"));
2284       QFileInfo fileinfo(file); //Do not show the path
2285           item->setData(COLUMN_IMAGE_NAME,Qt::DisplayRole,fileinfo.fileName());
2286           item->setToolTip(COLUMN_IMAGE_NAME, mSlicerManagers[index]->GetListOfAbsoluteFilePathInOneString("fusion").c_str());
2287           qApp->processEvents();
2288 #if VTK_MAJOR_VERSION > 5
2289       for ( unsigned int i = 0; i < mSlicerManagers[index]->GetNumberOfSlicers(); i++)
2290         mSlicerManagers[index]->GetSlicer(i)->ForceUpdateDisplayExtent();
2291 #endif
2292       for (int j = 1; j <= 4; j++) {
2293         item->setData(j,Qt::CheckStateRole,DataTree->topLevelItem(index)->data(j,Qt::CheckStateRole));
2294       }
2295
2296       //Create the buttons for reload and close
2297       qApp->processEvents();
2298       QTreePushButton* cButton = new QTreePushButton;
2299       cButton->setItem(item);
2300       cButton->setColumn(COLUMN_CLOSE_IMAGE);
2301       cButton->setToolTip(tr("close image"));
2302       cButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/exit.png")));
2303       connect(cButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
2304         this,SLOT(CloseImage(QTreeWidgetItem*, int)));
2305
2306       QTreePushButton* rButton = new QTreePushButton;
2307       rButton->setItem(item);
2308       rButton->setColumn(COLUMN_RELOAD_IMAGE);
2309       rButton->setToolTip(tr("reload image"));
2310       rButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/rotateright.png")));
2311       connect(rButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
2312         this,SLOT(ReloadImage(QTreeWidgetItem*, int)));
2313
2314       DataTree->topLevelItem(index)->setExpanded(1);
2315       DataTree->topLevelItem(index)->addChild(item);
2316       DataTree->setItemWidget(item, COLUMN_CLOSE_IMAGE, cButton);
2317       DataTree->setItemWidget(item, COLUMN_RELOAD_IMAGE, rButton);
2318
2319       //set the id of the image
2320       QString id = DataTree->topLevelItem(index)->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString();
2321       item->setData(COLUMN_IMAGE_NAME,Qt::UserRole,id.toStdString().c_str());
2322       UpdateTree();
2323       qApp->processEvents();
2324       ImageInfoChanged();
2325       QApplication::restoreOverrideCursor();
2326
2327       // Update the display to update, e.g., the sliders
2328       for(int i=0; i<4; i++)
2329         DisplaySliders(index, i);
2330     } else {
2331       QApplication::restoreOverrideCursor();
2332       QString error = "Cannot import the new image.\n";
2333       error += mSlicerManagers[index]->GetLastError().c_str();
2334       QMessageBox::information(this,tr("Problem reading image !"),error);
2335     }
2336     WindowLevelChanged();
2337   }
2338   else
2339     QMessageBox::information(this,tr("Problem reading Fusion !"),"File doesn't exist!");
2340 }
2341 //------------------------------------------------------------------------------
2342 //------------------------------------------------------------------------------
2343 void vvMainWindow::AddLandmarks(int index, std::vector<std::string> files)
2344 {
2345     if (!landmarksPanel->LoadFromFile(files))
2346       QMessageBox::information(this,tr("Problem reading Landmarks !"),"File doesn't exist!");
2347
2348     landmarksPanel->SetCurrentPath(mInputPathName.toStdString());
2349     landmarksPanel->SetCurrentImage(mSlicerManagers[index]->GetFileName().c_str());
2350 }
2351
2352 //------------------------------------------------------------------------------
2353 void vvMainWindow::OpenField()
2354 {
2355   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2356
2357   if (!(CheckAddedImage(index, "vector")))
2358     return;
2359
2360   QString Extensions = "Images ( *.mhd *.mha *.vf *.nii *.nrrd *.nhdr)";
2361   // Extensions += ";;Images ( *.mha)";
2362   // Extensions += ";;VF Images ( *.vf)";
2363   // Extensions += ";;nii Images ( *.nii)";
2364   // Extensions += ";;nrrd Images ( *.nrrd)";
2365   // Extensions += ";;nhdr Images ( *.nhdr)";
2366   Extensions += ";;All Files (*)";
2367   QString file = QFileDialog::getOpenFileName(this,tr("Load deformation field"),mInputPathName,Extensions);
2368   if (!file.isEmpty())
2369     AddField(file,index);
2370 }
2371 //------------------------------------------------------------------------------
2372
2373
2374 //------------------------------------------------------------------------------
2375 void vvMainWindow::AddFieldEntry(QString filename,int index,bool from_disk)
2376 {
2377   //create an item in the tree with good settings
2378   QTreeWidgetItem *item = new QTreeWidgetItem();
2379   item->setData(0,Qt::UserRole,filename.toStdString().c_str());
2380   item->setData(1,Qt::UserRole,tr("vector"));
2381   QFileInfo fileinfo(filename); //Do not show the path
2382   item->setData(COLUMN_IMAGE_NAME,Qt::DisplayRole,fileinfo.fileName());
2383   item->setToolTip(COLUMN_IMAGE_NAME, mSlicerManagers[index]->GetListOfAbsoluteFilePathInOneString("vector").c_str());
2384   qApp->processEvents();
2385
2386   for (int j = 1; j <= 4; j++) {
2387     item->setData(j,Qt::CheckStateRole,DataTree->topLevelItem(index)->data(j,Qt::CheckStateRole));
2388   }
2389
2390   //Create the buttons for reload and close
2391   qApp->processEvents();
2392   QTreePushButton* cButton = new QTreePushButton;
2393   cButton->setItem(item);
2394   cButton->setColumn(COLUMN_CLOSE_IMAGE);
2395   cButton->setToolTip(tr("close vector field"));
2396   cButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/exit.png")));
2397   connect(cButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
2398     this,SLOT(CloseImage(QTreeWidgetItem*, int)));
2399
2400   QTreePushButton* rButton = new QTreePushButton;
2401   rButton->setItem(item);
2402   rButton->setColumn(COLUMN_RELOAD_IMAGE);
2403   rButton->setToolTip(tr("reload vector field"));
2404   rButton->setEnabled(from_disk);
2405   rButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/rotateright.png")));
2406   connect(rButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
2407     this,SLOT(ReloadImage(QTreeWidgetItem*, int)));
2408
2409   DataTree->topLevelItem(index)->setExpanded(1);
2410   DataTree->topLevelItem(index)->addChild(item);
2411   DataTree->setItemWidget(item, COLUMN_RELOAD_IMAGE, rButton);
2412   DataTree->setItemWidget(item, COLUMN_CLOSE_IMAGE, cButton);
2413
2414   //set the id of the image
2415   QString id = DataTree->topLevelItem(index)->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString();
2416   item->setData(COLUMN_IMAGE_NAME,Qt::UserRole,id.toStdString().c_str());
2417   UpdateTree();
2418   qApp->processEvents();
2419   ImageInfoChanged();
2420   QApplication::restoreOverrideCursor();
2421 }
2422 //------------------------------------------------------------------------------
2423
2424
2425 //------------------------------------------------------------------------------
2426 void vvMainWindow::AddField(vvImage::Pointer vf,QString file,int index)
2427 {
2428   QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
2429   vvSlicerManager* imageManager = mSlicerManagers[index];
2430   if (imageManager->SetVF(vf,file.toStdString())) {
2431     AddFieldEntry(file,index,false);
2432 #if VTK_MAJOR_VERSION > 5
2433       for ( unsigned int i = 0; i < mSlicerManagers[index]->GetNumberOfSlicers(); i++)
2434         mSlicerManagers[index]->GetSlicer(i)->ForceUpdateDisplayExtent();
2435 #endif
2436   } else {
2437     QString error = "Cannot import the vector field for this image.\n";
2438     error += imageManager->GetLastError().c_str();
2439     QMessageBox::information(this,tr("Problem reading VF !"),error);
2440   }
2441   QApplication::restoreOverrideCursor();
2442 }
2443 //------------------------------------------------------------------------------
2444
2445
2446 //------------------------------------------------------------------------------
2447 void vvMainWindow::AddField(QString file,int index)
2448 {
2449   if (QFile::exists(file)) {
2450     mInputPathName = itksys::SystemTools::GetFilenamePath(file.toStdString()).c_str();
2451
2452     //init the progress events
2453     QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
2454     vvProgressDialog progress("Opening " + file.toStdString());
2455     qApp->processEvents();
2456
2457     //read the vector and put it in the current mSlicerManager
2458     vvSlicerManager* imageManager = mSlicerManagers[index];
2459     qApp->processEvents();
2460
2461     std::string filename = itksys::SystemTools::GetFilenameWithoutExtension(file.toStdString()).c_str();
2462     if (imageManager->SetVF(file.toStdString())) {
2463       imageManager->Render();
2464       AddFieldEntry(file,index,true);
2465     } else {
2466       QApplication::restoreOverrideCursor();
2467       QString error = "Cannot import the vector field for this image.\n";
2468       error += imageManager->GetLastError().c_str();
2469       QMessageBox::information(this,tr("Problem reading VF !"),error);
2470     }
2471   } else
2472     QMessageBox::information(this,tr("Problem reading VF !"),"File doesn't exist!");
2473
2474 }
2475 //------------------------------------------------------------------------------
2476
2477
2478 //------------------------------------------------------------------------------
2479 void vvMainWindow::SetVFProperty(int subsampling, int scale, int log, int width, double r, double g, double b)
2480 {
2481   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2482   if (mSlicerManagers[index]->GetSlicer(0)->GetVF()) {
2483     for (int i = 0; i < 4; i++) {
2484       mSlicerManagers[index]->GetSlicer(i)->SetVFSubSampling(subsampling);
2485       mSlicerManagers[index]->GetSlicer(i)->SetVFScale(scale);
2486       mSlicerManagers[index]->GetSlicer(i)->SetVFWidth(width);
2487       mSlicerManagers[index]->GetSlicer(i)->SetVFColor(r,g,b);
2488       if (log > 0)
2489         mSlicerManagers[index]->GetSlicer(i)->SetVFLog(1);
2490       else
2491         mSlicerManagers[index]->GetSlicer(i)->SetVFLog(0);
2492     }
2493   }
2494 }
2495 //------------------------------------------------------------------------------
2496
2497
2498 //------------------------------------------------------------------------------
2499 void vvMainWindow::SetOverlayProperty(int color, int linked, double window, double level)
2500 {
2501   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2502   if (mSlicerManagers[index]->GetSlicer(0)->GetOverlay()) {
2503     mSlicerManagers[index]->SetOverlayColor(color);
2504     mSlicerManagers[index]->SetColorMap(0);
2505     mSlicerManagers[index]->SetLinkOverlayWindowLevel(linked);
2506     mSlicerManagers[index]->SetOverlayColorWindow(window);
2507     mSlicerManagers[index]->SetOverlayColorLevel(level);
2508     mSlicerManagers[index]->Render();
2509   }
2510 }
2511 //------------------------------------------------------------------------------
2512
2513 //------------------------------------------------------------------------------
2514 void vvMainWindow::SetFusionProperty(int opacity, int thresOpacity, int colormap,double window, double level, bool showLegend)
2515 {
2516   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2517   if (mSlicerManagers[index]->GetSlicer(0)->GetFusion()) {
2518     mSlicerManagers[index]->SetFusionColorMap(colormap);
2519     mSlicerManagers[index]->SetFusionOpacity(opacity);
2520     mSlicerManagers[index]->SetFusionThresholdOpacity(thresOpacity);
2521     mSlicerManagers[index]->SetFusionWindow(window);
2522     mSlicerManagers[index]->SetFusionLevel(level);
2523     mSlicerManagers[index]->SetFusionShowLegend(showLegend);
2524     mSlicerManagers[index]->SetColorMap(0);
2525     mSlicerManagers[index]->Render();
2526   }
2527 }
2528 //------------------------------------------------------------------------------
2529
2530
2531 //------------------------------------------------------------------------------
2532 void vvMainWindow::SelectFusionSequence()
2533 {
2534   //get the index of the slicer manager of the main sequence (CT)
2535   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2536
2537   if (!(CheckAddedImage(index, "fusion")) || !(CheckAddedImage(index, "fusionSequence")))
2538     return;
2539
2540   QString Extensions = EXTENSIONS;
2541   Extensions += ";;All Files (*)";
2542   QStringList files = QFileDialog::getOpenFileNames(this,tr("Load Overlay image sequence"),mInputPathName,Extensions);
2543   if (files.isEmpty())
2544     return;
2545
2546   std::vector<std::string> vecFileNames;
2547   for (int i = 0; i < files.size(); i++) {
2548     vecFileNames.push_back(files[i].toStdString());
2549   }
2550
2551   //associate the secondary sequence (US) to the main one
2552   AddFusionSequence(index,vecFileNames,vvImageReader::MERGEDWITHTIME);
2553 }
2554 //------------------------------------------------------------------------------
2555
2556
2557 //------------------------------------------------------------------------------
2558 void vvMainWindow::SelectFusionSequenceCorrespondances()
2559 {
2560   //make sure the index is right?
2561   //in the end, I should attach the temporal data to the right sequence!
2562   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2563   //in case the other sequence got selected, make sure we select the primary sequence
2564   if ( (!mSlicerManagers[index]->GetSlicer(0)->GetFusion()) && mSlicerManagers[index]->GetFusionSequenceIndexOfLinkedManager()>=0 ) {
2565     index = mSlicerManagers[index]->GetFusionSequenceIndexOfLinkedManager();
2566   }
2567
2568   //open a dialog box to find a file
2569   //QString Extensions = EXTENSIONS;
2570   QString Extensions = ";;All Files (*)";
2571   QString fileName = QFileDialog::getOpenFileName(this,tr("Load respiratory signal for fused sequence"),mInputPathName,Extensions);
2572   if (fileName.isNull())
2573     return;
2574
2575   //read it as a vector of values
2576   vnl_vector<double> tmpVect;
2577
2578   std::ifstream file;
2579   file.open(fileName.toStdString().c_str());
2580   tmpVect.read_ascii(file);
2581   file.close();
2582
2583   //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
2584   bool signalOK = true;
2585   unsigned nbFrameMain = mSlicerManagers[index]->GetImage()->GetTransform().size();
2586   unsigned nbFrameSecondary = mSlicerManagers[index]->GetFusionSequenceNbFrames();
2587   std::cout<<"nbFrameMain = "<<nbFrameMain<<", nbFrameSecondary= "<<nbFrameSecondary<<", signal size: "<<tmpVect.size()<<std::endl;
2588   std::vector<unsigned> temporalCorrespondances;
2589   if ( tmpVect.size() == nbFrameMain + nbFrameSecondary ) {
2590     for (unsigned i=0 ; i<tmpVect.size() ; i++) {
2591       if (i<nbFrameMain) { //first part of the file: i -> index in secondary seq.
2592         if ( tmpVect(i)<nbFrameSecondary ) temporalCorrespondances.push_back(tmpVect(i));
2593         else { signalOK=false; break; } //pointing outside the secondary sequence...
2594       }
2595       else { //first part of the file -> index in secondary seq.
2596         if ( tmpVect(i)<nbFrameMain ) temporalCorrespondances.push_back(tmpVect(i));
2597         else { signalOK=false; break; } //pointing outside the secondary sequence...
2598       }
2599     }
2600   }
2601   else {signalOK=false;}
2602   if (!signalOK) {//else, send a message to signal the failure...
2603     QString error = "The provided temporal correspondances is invalid - check tooltip.\n";
2604     error += "Ignoring file: " + fileName;
2605     QMessageBox::information(this,tr("Problem adding temporal correspondances!"),error);
2606     return;
2607   }
2608   else {
2609     //for convenience, associate this sequence to both the current slicer manager, and to the linked one
2610     mSlicerManagers[index]->SetFusionSequenceCorrespondances(temporalCorrespondances);
2611     mSlicerManagers[ mSlicerManagers[index]->GetFusionSequenceIndexOfLinkedManager() ]->SetFusionSequenceCorrespondances(temporalCorrespondances);
2612     overlayPanel->enableFusionSequenceTemporalSync();
2613   }
2614
2615 }
2616 //------------------------------------------------------------------------------
2617
2618
2619 //------------------------------------------------------------------------------
2620 //when this function is called index is the slicer manager index corresponding to the main sequence (CT)
2621 //the files behind fileNames points to the data for the secondary sequence
2622 void vvMainWindow::AddFusionSequence(int index, std::vector<std::string> fileNames, vvImageReader::LoadedImageType type)
2623 {
2624   QString file(fileNames[0].c_str());
2625   if (QFile::exists(file))
2626   {
2627     mInputPathName = itksys::SystemTools::GetFilenamePath(file.toStdString()).c_str();
2628     itk::ImageIOBase::Pointer reader = itk::ImageIOFactory::CreateImageIO(
2629       file.toStdString().c_str(), itk::ImageIOFactory::ReadMode);
2630     std::sort (fileNames.begin(), fileNames.end());//make sure the files are sorted.
2631     reader->SetFileName(fileNames[0].c_str());
2632     reader->ReadImageInformation();
2633     std::string component = reader->GetComponentTypeAsString(reader->GetComponentType());
2634     int dimension = reader->GetNumberOfDimensions();
2635     QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
2636     vvProgressDialog progress("Opening " + file.toStdString());
2637     qApp->processEvents();
2638
2639     std::string filename = itksys::SystemTools::GetFilenameWithoutExtension(file.toStdString()).c_str();
2640
2641     if (mSlicerManagers[index]->SetFusionSequence(fileNames,dimension, component,type)) {
2642       //create an item in the tree with good settings
2643       QTreeWidgetItem *item = new QTreeWidgetItem();
2644       item->setData(0,Qt::UserRole,file.toStdString().c_str());
2645       item->setData(1,Qt::UserRole,tr("fusionSequence"));
2646
2647       QFileInfo fileinfo(file); //Do not show the path
2648       item->setData(COLUMN_IMAGE_NAME,Qt::DisplayRole,fileinfo.fileName());
2649       item->setToolTip(COLUMN_IMAGE_NAME, mSlicerManagers[index]->GetListOfAbsoluteFilePathInOneString("fusionSequence").c_str());
2650       qApp->processEvents();
2651 #if VTK_MAJOR_VERSION > 5
2652       for ( unsigned int i = 0; i < mSlicerManagers[index]->GetNumberOfSlicers(); i++)
2653         mSlicerManagers[index]->GetSlicer(i)->ForceUpdateDisplayExtent();
2654 #endif
2655       for (int j = 1; j <= 4; j++) {
2656         item->setData(j,Qt::CheckStateRole,DataTree->topLevelItem(index)->data(j,Qt::CheckStateRole));
2657       }
2658
2659       //Create the buttons for reload and close
2660       qApp->processEvents();
2661       QTreePushButton* cButton = new QTreePushButton;
2662       cButton->setItem(item);
2663       cButton->setColumn(COLUMN_CLOSE_IMAGE);
2664       cButton->setToolTip(tr("close image"));
2665       cButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/exit.png")));
2666       connect(cButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
2667         this,SLOT(CloseImage(QTreeWidgetItem*, int)));
2668
2669       QTreePushButton* rButton = new QTreePushButton;
2670       rButton->setItem(item);
2671       rButton->setColumn(COLUMN_RELOAD_IMAGE);
2672       rButton->setToolTip(tr("reload image"));
2673       rButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/rotateright.png")));
2674       connect(rButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
2675         this,SLOT(ReloadImage(QTreeWidgetItem*, int)));
2676
2677       DataTree->topLevelItem(index)->setExpanded(1);
2678       DataTree->topLevelItem(index)->addChild(item);
2679       DataTree->setItemWidget(item, COLUMN_CLOSE_IMAGE, cButton);
2680       DataTree->setItemWidget(item, COLUMN_RELOAD_IMAGE, rButton);
2681
2682       //store the original transform matrix
2683       int indexParent = GetSlicerIndexFromItem( DataTree->topLevelItem(index) );
2684       mSlicerManagers[indexParent]->SetFusionSequenceMainTransformMatrix( mSlicerManagers[indexParent]->GetSlicer(0)->GetImage()->GetTransform()[0]->GetMatrix() );
2685
2686       //set the id of the image
2687       QString id = DataTree->topLevelItem(index)->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString();
2688       item->setData(COLUMN_IMAGE_NAME,Qt::UserRole,id.toStdString().c_str());
2689       UpdateTree();
2690       qApp->processEvents();
2691
2692       //ImageInfoChanged();
2693
2694       QApplication::restoreOverrideCursor();
2695       // Update the display to update, e.g., the sliders
2696       for(int i=0; i<4; i++)
2697         DisplaySliders(index, i);
2698
2699
2700       //This loads the secondary sequence (US) as an independent sequence
2701       LoadImages(fileNames, type);
2702       //reset the transforms to identity
2703       //FIX -- and set the thickness of the US slices to a large value (necessary for visualization purposes...)
2704       double sp_x, sp_y, sp_z;
2705       mSlicerManagers[indexParent]->GetImage()->GetVTKImages()[0]->GetSpacing(sp_x, sp_y, sp_z);
2706       sp_z = std::max(sp_x, std::max(sp_y, sp_z)) + 0.5; //
2707       for (unsigned i=0 ; i<mSlicerManagers.back()->GetImage()->GetTransform().size() ; i++) {
2708         sp_x = mSlicerManagers.back()->GetImage()->GetVTKImages()[i]->GetSpacing()[0];
2709         sp_y = mSlicerManagers.back()->GetImage()->GetVTKImages()[i]->GetSpacing()[1];
2710         mSlicerManagers.back()->GetImage()->GetVTKImages()[i]->SetSpacing( sp_x, sp_y, sp_z);
2711         mSlicerManagers.back()->GetImage()->GetTransform()[i]->Identity();
2712         mSlicerManagers.back()->GetImage()->GetTransform()[i]->Update();
2713       }
2714
2715       //automatically link both images...
2716       AddLink(mSlicerManagers[indexParent]->GetId().c_str(), mSlicerManagers.back()->GetId().c_str(), false);
2717
2718       //tie the main and secondary sequences by raising flags and informing each another of their respective SlicerManager indices
2719       mSlicerManagers[indexParent]->SetFusionSequenceIndexOfLinkedManager(mSlicerManagers.size()-1);
2720       mSlicerManagers[indexParent]->SetFusionSequenceInvolvmentCode(0); //main sequence
2721       mSlicerManagers.back()->SetFusionSequenceIndexOfLinkedManager(indexParent);
2722       mSlicerManagers.back()->SetFusionSequenceInvolvmentCode(1); //secondary sequence
2723       for (unsigned i=0 ; i<4 ; i++) {
2724         mSlicerManagers.back()->GetSlicer(i)->SetFusionSequenceCode(1); //flag the slicers of the secondary sequence
2725       }
2726
2727     } else {
2728       QApplication::restoreOverrideCursor();
2729       QString error = "Cannot import the new image.\n";
2730       error += mSlicerManagers[index]->GetLastError().c_str();
2731       QMessageBox::information(this,tr("Problem reading image !"),error);
2732     }
2733     WindowLevelChanged();
2734     ImageInfoChanged(); //this internally calls WindowLevelChanged...
2735   }
2736   else {
2737     QMessageBox::information(this,tr("Problem reading fusion sequence !"),"File doesn't exist!");
2738     return;
2739   }
2740
2741 }
2742 //------------------------------------------------------------------------------
2743
2744
2745 //------------------------------------------------------------------------------
2746 //fusionSequenceFrameIndex and fusionSequenceNbFrames are relative to the secondary sequence (US)
2747 void vvMainWindow::SetFusionSequenceProperty(int fusionSequenceFrameIndex, bool spatialSyncFlag, unsigned int fusionSequenceNbFrames, bool temporalSyncFlag)
2748 {
2749   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2750
2751   if (!mSlicerManagers[index]->IsInvolvedInFusionSequence()) return;
2752
2753   //check if the focus moved to the linked sequence, and in this case, select the master sequence instead
2754   if (!mSlicerManagers[index]->IsMainSequenceOfFusionSequence()) {
2755     index = mSlicerManagers[index]->GetFusionSequenceIndexOfLinkedManager();
2756   }
2757   int secondaryIndex = mSlicerManagers[index]->GetFusionSequenceIndexOfLinkedManager();
2758   if (secondaryIndex==-1) return; //this should never happen
2759   if ( (!mSlicerManagers[index]->IsMainSequenceOfFusionSequence()) ||
2760     (!mSlicerManagers[secondaryIndex]->IsSecondarySequenceOfFusionSequence()) )
2761   {return;} //this should never happen, raise an exception?
2762
2763   if (mSlicerManagers[index]->GetSlicer(0)->GetFusion()) {
2764
2765     //First, if the spatialSync button is unchecked, then reposition the parent sequence (CT) in its original coordinate frame
2766     if ( (!spatialSyncFlag) && (mSlicerManagers[index]->GetFusionSequenceSpatialSyncFlag()) ) {
2767       for ( unsigned i=0 ; i<mSlicerManagers[index]->GetSlicer(0)->GetImage()->GetTransform().size() ; i++ ) {
2768         mSlicerManagers[index]->GetSlicer(0)->GetImage()->GetTransform()[i]->SetMatrix( mSlicerManagers[index]->GetFusionSequenceMainTransformMatrix() );
2769         mSlicerManagers[index]->GetSlicer(0)->GetImage()->GetTransform()[i]->Update();
2770       }
2771
2772       for (int i=0; i<mSlicerManagers[index]->GetNumberOfSlicers(); i++) {
2773         mSlicerManagers[index]->GetSlicer(i)->ForceUpdateDisplayExtent();
2774         mSlicerManagers[index]->GetSlicer(i)->Render();
2775       }
2776     }
2777
2778     //then, update the property values in the slicer manager
2779     mSlicerManagers[index]->SetFusionSequenceLength(fusionSequenceNbFrames);
2780     mSlicerManagers[index]->SetFusionSequenceSpatialSyncFlag(spatialSyncFlag);
2781     mSlicerManagers[index]->SetFusionSequenceTemporalSyncFlag(temporalSyncFlag);
2782     mSlicerManagers[index]->SetFusionSequenceFrameIndex(fusionSequenceFrameIndex);
2783
2784     //select the right frame of the US sequence
2785     mSlicerManagers[index]->SetFusionSequenceTSlice(fusionSequenceFrameIndex); //here, I should only update the overlayed sequence
2786     mSlicerManagers[secondaryIndex]->SetTSlice(fusionSequenceFrameIndex, false); //this should update the secondary sequence (individual version)
2787
2788     //update the horizontal sliders of the main window
2789     overlayPanel->updateFusionSequenceSliderValueFromWindow(fusionSequenceFrameIndex, false);
2790
2791     if (spatialSyncFlag) { //reslice the CT
2792
2793       if (temporalSyncFlag) { //do the temporal synchronisation
2794         int mainSequenceFrameIndex=0;
2795         //estimate the TSlice to set to the CT
2796         unsigned nbFramesMain = mSlicerManagers[index]->GetImage()->GetTransform().size();
2797         mainSequenceFrameIndex = mSlicerManagers[index]->GetFusionSequenceCorrespondances()[ nbFramesMain + fusionSequenceFrameIndex];
2798         //and set it!
2799         mSlicerManagers[index]->SetTSlice(mainSequenceFrameIndex, false);
2800         //warning, there is a loopback, and modification of the TSlice in main sequence forces an update of the TSlice in secondary, etc...
2801       }
2802
2803
2804       //Set the transform matrix of the parent sequence (typically CT / 4DCT)
2805       vtkSmartPointer<vtkMatrix4x4> tmpMat = vtkSmartPointer<vtkMatrix4x4>::New();
2806       vtkMatrix4x4::Invert( mSlicerManagers[index]->GetFusionSequenceInitialTransformMatrixAtFrame(fusionSequenceFrameIndex), tmpMat );
2807       for ( unsigned i=0 ; i<mSlicerManagers[index]->GetSlicer(0)->GetImage()->GetTransform().size() ; i++ ) {
2808         mSlicerManagers[index]->GetSlicer(0)->GetImage()->GetTransform()[i]->SetMatrix( mSlicerManagers[index]->GetFusionSequenceMainTransformMatrix() );
2809         mSlicerManagers[index]->GetSlicer(0)->GetImage()->GetTransform()[i]->PreMultiply();
2810         mSlicerManagers[index]->GetSlicer(0)->GetImage()->GetTransform()[i]->Concatenate( tmpMat );
2811         mSlicerManagers[index]->GetSlicer(0)->GetImage()->GetTransform()[i]->Update();
2812       }
2813
2814       for (int i=0; i<mSlicerManagers[index]->GetNumberOfSlicers(); i++) {
2815         mSlicerManagers[index]->GetSlicer(i)->ForceUpdateDisplayExtent();
2816         mSlicerManagers[index]->GetSlicer(i)->Render();
2817       }
2818
2819     }
2820
2821   }
2822 }
2823 //------------------------------------------------------------------------------
2824
2825
2826 //------------------------------------------------------------------------------
2827 void vvMainWindow::SaveAs()
2828 {
2829   if (DataTree->selectedItems()[0]->data(1,Qt::UserRole).toString() == "vector") {
2830     QMessageBox::warning(this,tr("Unsupported type"),tr("Sorry, saving a vector field is unsupported for the moment"));
2831     return;
2832   }
2833
2834   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2835   int dimension = mSlicerManagers[index]->GetDimension();
2836   QStringList OutputListeFormat;
2837   OutputListeFormat.clear();
2838   if (dimension == 1) {
2839     OutputListeFormat.push_back(".mhd");
2840     OutputListeFormat.push_back(".mha");
2841   }
2842   if (dimension == 2) {
2843     OutputListeFormat.push_back(".bmp");
2844     OutputListeFormat.push_back(".png");
2845     OutputListeFormat.push_back(".jpeg");
2846     OutputListeFormat.push_back(".tif");
2847     OutputListeFormat.push_back(".mhd");
2848     OutputListeFormat.push_back(".mha");
2849     OutputListeFormat.push_back(".hdr");
2850     OutputListeFormat.push_back(".vox");
2851   } else if (dimension == 3) {
2852     OutputListeFormat.push_back(".mhd");
2853     OutputListeFormat.push_back(".mha");
2854     OutputListeFormat.push_back(".nii");
2855     OutputListeFormat.push_back(".nrrd");
2856     OutputListeFormat.push_back(".nhdr");
2857     OutputListeFormat.push_back(".hdr");
2858     OutputListeFormat.push_back(".vox");
2859   } else if (dimension == 4) {
2860     OutputListeFormat.push_back(".mhd");
2861     OutputListeFormat.push_back(".mha");
2862     OutputListeFormat.push_back(".nii");
2863     OutputListeFormat.push_back(".nrrd");
2864     OutputListeFormat.push_back(".nhdr");
2865   }
2866   QString Extensions = "AllFiles(*.*)";
2867   for (int i = 0; i < OutputListeFormat.count(); i++) {
2868     Extensions += ";;Images ( *";
2869     Extensions += OutputListeFormat[i];
2870     Extensions += ")";
2871   }
2872   QString fileName = QFileDialog::getSaveFileName(this,
2873     tr("Save As"),
2874     mSlicerManagers[index]->GetFileName().c_str(),
2875     Extensions);
2876   if (!fileName.isEmpty()) {
2877     std::string fileformat = itksys::SystemTools::GetFilenameLastExtension(fileName.toStdString());
2878     if (OutputListeFormat.contains(
2879       fileformat.c_str())) {
2880         QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
2881         std::string action = "Saving";
2882         vvProgressDialog progress("Saving "+fileName.toStdString());
2883         qApp->processEvents();
2884         vvImageWriter::Pointer writer = vvImageWriter::New();
2885         writer->SetOutputFileName(fileName.toStdString());
2886         writer->SetInput(mSlicerManagers[index]->GetImage());
2887
2888         // Check on transform and prompt user
2889         writer->SetSaveTransform(false);
2890         bool bId = true;
2891         for(int i=0; i<4; i++)
2892           for(int j=0; j<4; j++) {
2893             // TODO SR and BP: check on the list of transforms and not the first only
2894             double elt = mSlicerManagers[index]->GetImage()->GetTransform()[0]->GetMatrix()->GetElement(i,j);
2895             if(i==j && elt!=1.)
2896               bId = false;
2897             if(i!=j && elt!=0.)
2898               bId = false;
2899           }
2900           if( !bId ) {
2901             QString warning = "The image has an associated linear transform. Do you want to save it along?";
2902             QMessageBox msgBox(QMessageBox::Warning, tr("Save transform"), warning, 0, this);
2903             msgBox.addButton(tr("Yes"), QMessageBox::AcceptRole);
2904             msgBox.addButton(tr("No"), QMessageBox::RejectRole);
2905             if (msgBox.exec() == QMessageBox::AcceptRole)
2906               writer->SetSaveTransform(true);
2907           }
2908
2909           writer->Update();
2910           QApplication::restoreOverrideCursor();
2911           if (writer->GetLastError().size()) {
2912             QString error = "Saving did not succeed\n";
2913             error += writer->GetLastError().c_str();
2914             QMessageBox::information(this,tr("Saving Problem"),error);
2915             SaveAs();
2916           }
2917     } else {
2918       QString error = fileformat.c_str();
2919       if (error.isEmpty())
2920         error += "no file format specified !";
2921       else
2922         error += " format unknown !!!\n";
2923       QMessageBox::information(this,tr("Saving Problem"),error);
2924       SaveAs();
2925     }
2926   }
2927 }
2928 //------------------------------------------------------------------------------
2929
2930 //------------------------------------------------------------------------------
2931 void vvMainWindow::SaveCurrentState()
2932 {
2933   QString Extensions = "XML Files(*.xml)";
2934   QString fileName = QFileDialog::getSaveFileName(this,
2935     tr("Save Current Window State"),
2936     "",
2937     Extensions);
2938
2939   SaveCurrentStateAs(fileName.toStdString());
2940 }
2941 //------------------------------------------------------------------------------
2942
2943 //------------------------------------------------------------------------------
2944 void vvMainWindow::SaveCurrentStateAs(const std::string& stateFile)
2945 {
2946   vvSaveState save_state;
2947   save_state.Run(this, stateFile);
2948 }
2949
2950 //------------------------------------------------------------------------------
2951 void vvMainWindow::ReadSavedState()
2952 {
2953   QString Extensions = "XML Files(*.xml)";
2954   QString fileName = QFileDialog::getOpenFileName(this,
2955     tr("Load Window State"),
2956     "",
2957     Extensions);
2958
2959   ReadSavedStateFile(fileName.toStdString());
2960 }
2961 //------------------------------------------------------------------------------
2962
2963 //------------------------------------------------------------------------------
2964 void vvMainWindow::ReadSavedStateFile(const std::string& stateFile)
2965 {
2966   vvReadState read_state;
2967   read_state.Run(this, stateFile);
2968 }
2969 //------------------------------------------------------------------------------
2970
2971 //------------------------------------------------------------------------------
2972 void vvMainWindow::LinkAllImages()
2973 {
2974   linkPanel->linkAll();
2975 }
2976
2977 //------------------------------------------------------------------------------
2978 void vvMainWindow::AddLink(QString image1,QString image2,bool fromPanel)
2979 {
2980   if (!fromPanel) {
2981     // delegate to linkPanel if call came from elsewhere...
2982     linkPanel->addLinkFromIds(image1, image2);
2983     return;
2984   }
2985
2986   unsigned int sm1 = 0;
2987   unsigned int sm2 = 0;
2988
2989   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
2990     if (image1.toStdString() == mSlicerManagers[i]->GetId()) {
2991       mSlicerManagers[i]->AddLink(image2.toStdString());
2992       sm1 = i;
2993     }
2994     if (image2.toStdString() == mSlicerManagers[i]->GetId()) {
2995       mSlicerManagers[i]->AddLink(image1.toStdString());
2996       sm2 = i;
2997     }
2998   }
2999
3000   if (linkPanel->isLinkAll())   {
3001     emit UpdateLinkedNavigation(mSlicerManagers[sm1]->GetId(), mSlicerManagers[mCurrentPickedImageIndex], mSlicerManagers[mCurrentPickedImageIndex]->GetSlicer(0));
3002     emit UpdateLinkedNavigation(mSlicerManagers[sm2]->GetId(), mSlicerManagers[mCurrentPickedImageIndex], mSlicerManagers[mCurrentPickedImageIndex]->GetSlicer(0));
3003   } else {
3004     emit UpdateLinkedNavigation(mSlicerManagers[sm2]->GetId(), mSlicerManagers[sm1], mSlicerManagers[sm1]->GetSlicer(0));
3005   }
3006 }
3007
3008 //------------------------------------------------------------------------------
3009
3010
3011 //------------------------------------------------------------------------------
3012 void vvMainWindow::RemoveLink(QString image1,QString image2)
3013 {
3014   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
3015     if (image1.toStdString() == mSlicerManagers[i]->GetId()) {
3016       mSlicerManagers[i]->RemoveLink(image2.toStdString());
3017     }
3018     if (image2.toStdString() == mSlicerManagers[i]->GetId()) {
3019       mSlicerManagers[i]->RemoveLink(image1.toStdString());
3020     }
3021   }
3022 }
3023 //------------------------------------------------------------------------------
3024
3025 //------------------------------------------------------------------------------
3026 void vvMainWindow::ChangeImageWithIndexOffset(vvSlicerManager *sm, int slicer, int offset)
3027 {
3028   if(mSlicerManagers.size()==1)
3029     return;
3030
3031   int index = 0;
3032   while(sm != mSlicerManagers[index])
3033     index++;
3034   index = (index+offset+mSlicerManagers.size()) % mSlicerManagers.size();
3035
3036   QTreeWidgetItem* item = GetItemFromSlicerManager(mSlicerManagers[index]);
3037   item->setData(slicer+1,Qt::CheckStateRole,2);         //change checkbox
3038   CurrentImageChanged(mSlicerManagers[index]->GetId()); //select new image
3039   DisplayChanged(item,slicer+1);
3040 }
3041 //------------------------------------------------------------------------------
3042 void vvMainWindow::HorizontalSliderMoved(int value,int column, int slicer_index)
3043 {
3044   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
3045     if (DataTree->topLevelItem(i)->data(column,Qt::CheckStateRole).toInt() > 1) {
3046       //i is the SlicerManager that is in charge of this slicer.
3047       if (mSlicerManagers[i]->IsInvolvedInFusionSequence()) {
3048         //if the slicerManager is involved in a fusionSequence as the secondary sequence, then update the slider position in the overlay panel and everything accordingly
3049         if (mSlicerManagers[i]->IsSecondarySequenceOfFusionSequence()) {
3050           overlayPanel->updateFusionSequenceSliderValueFromWindow(value, true);
3051         }
3052         else { //if this is the primary sequence that has been modified
3053           if (mSlicerManagers[i]->GetFusionSequenceTemporalSyncFlag()) {
3054             //WARNING: for some obscure reason, there are problems when accessing mSlicerManagers[mSlicerManagers[i]->GetFusionSequenceIndexOfLinkedManager()]->GetFusionSequenceFrameIndex();
3055
3056             int estimatedValue=0;
3057             //estimate a corresponding time index for the secondary (US) sequence, and update it accordingly.
3058             estimatedValue = mSlicerManagers[i]->GetFusionSequenceCorrespondances()[ value ];
3059             //TODO: at the moment, there is a loop in TSlice modifications
3060             //modifying sequence 1 causes seq 2 to update, which in turns update seq1...
3061             //I disable control on seq1 at the moment.
3062             //overlayPanel->updateFusionSequenceSliderValueFromWindow(estimatedValue, true);
3063           }
3064         }
3065       }
3066
3067       for (int j = 0; j < 4; j++) {
3068         mSlicerManagers[i]->SetTSliceInSlicer(value,j);
3069       }
3070       mSlicerManagers[i]->GetSlicer(slicer_index)->Render();
3071       break;
3072     }
3073   }
3074 }
3075 //------------------------------------------------------------------------------
3076
3077
3078 //------------------------------------------------------------------------------
3079 void vvMainWindow::NOHorizontalSliderMoved()
3080 {
3081   // if (mCurrentTime == NOHorizontalSlider->value()) return;
3082   HorizontalSliderMoved(NOHorizontalSlider->value(),COLUMN_UL_VIEW,0);
3083   //  mCurrentTime = NOHorizontalSlider->value();
3084 }
3085 //------------------------------------------------------------------------------
3086
3087
3088 //------------------------------------------------------------------------------
3089 void vvMainWindow::NEHorizontalSliderMoved()
3090 {
3091   // if (mCurrentTime == NEHorizontalSlider->value()) return;
3092   HorizontalSliderMoved(NEHorizontalSlider->value(),COLUMN_UR_VIEW,1);
3093   //  mCurrentTime = NEHorizontalSlider->value();
3094 }
3095 //------------------------------------------------------------------------------
3096
3097
3098 //------------------------------------------------------------------------------
3099 void vvMainWindow::SOHorizontalSliderMoved()
3100 {
3101   // if (mCurrentTime == SOHorizontalSlider->value()) return;
3102   HorizontalSliderMoved(SOHorizontalSlider->value(),COLUMN_DL_VIEW,2);
3103   // mCurrentTime = SOHorizontalSlider->value();
3104 }
3105 //------------------------------------------------------------------------------
3106
3107
3108 //------------------------------------------------------------------------------
3109 void vvMainWindow::SEHorizontalSliderMoved()
3110 {
3111   // if (mCurrentTime == SEHorizontalSlider->value()) return;
3112   HorizontalSliderMoved(SEHorizontalSlider->value(),COLUMN_DR_VIEW,3);
3113   // mCurrentTime = SEHorizontalSlider->value();
3114 }
3115 //------------------------------------------------------------------------------
3116
3117 //------------------------------------------------------------------------------
3118 void vvMainWindow::NOVerticalSliderChanged()
3119 {
3120   static int value=-1;
3121   if (value == NOVerticalSlider->value()) return;
3122   else value = NOVerticalSlider->value();
3123   //  int value = NOVerticalSlider->value();
3124   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
3125     if (DataTree->topLevelItem(i)->data(COLUMN_UL_VIEW,Qt::CheckStateRole).toInt() > 1) {
3126       if (mSlicerManagers[i]->GetSlicer(0)->GetSlice() != value) {
3127         mSlicerManagers[i]->GetSlicer(0)->SetSlice(value);
3128         mSlicerManagers[i]->VerticalSliderHasChanged(0, value);
3129
3130         // If nor Update/Render -> slider not work
3131         // only render = ok navigation, but for contour Update needed but slower ?
3132
3133         mSlicerManagers[i]->UpdateSlice(0);  // <-- DS add this. Not too much update ? YES. but needed for ImageContour ...
3134         //mSlicerManagers[i]->GetSlicer(0)->Render(); // <-- DS add this, needed for contour, seems ok ? not too slow ?
3135       }
3136       break;
3137     }
3138   }
3139 }
3140 //------------------------------------------------------------------------------
3141
3142
3143 //------------------------------------------------------------------------------
3144 void vvMainWindow::NEVerticalSliderChanged()
3145 {
3146   static int value=-1;
3147   if (value == NEVerticalSlider->value()) return;
3148   else value = NEVerticalSlider->value();
3149   //  int value = NEVerticalSlider->value();
3150   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
3151     if (DataTree->topLevelItem(i)->data(COLUMN_UR_VIEW,Qt::CheckStateRole).toInt() > 1) {
3152       if (mSlicerManagers[i]->GetSlicer(1)->GetSlice() != value) {
3153         mSlicerManagers[i]->GetSlicer(1)->SetSlice(value);
3154         mSlicerManagers[i]->VerticalSliderHasChanged(1, value);
3155         mSlicerManagers[i]->UpdateSlice(1);
3156         //mSlicerManagers[i]->GetSlicer(1)->Render(); // <-- DS add this, needed for contour, seems ok ? not too slow ?
3157       }
3158       break;
3159     }
3160   }
3161 }
3162 //------------------------------------------------------------------------------
3163
3164
3165 //------------------------------------------------------------------------------
3166 void vvMainWindow::SOVerticalSliderChanged()
3167 {
3168   static int value=-1;
3169   if (value == SOVerticalSlider->value()) return;
3170   else value = SOVerticalSlider->value();
3171   //int value = SOVerticalSlider->value();
3172   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
3173     if (DataTree->topLevelItem(i)->data(COLUMN_DL_VIEW,Qt::CheckStateRole).toInt() > 1) {
3174       if (mSlicerManagers[i]->GetSlicer(2)->GetSlice() != value) {
3175         mSlicerManagers[i]->GetSlicer(2)->SetSlice(value);
3176         mSlicerManagers[i]->VerticalSliderHasChanged(2, value);
3177         mSlicerManagers[i]->UpdateSlice(2);
3178         //mSlicerManagers[i]->GetSlicer(2)->Render(); // <-- DS add this, needed for contour, seems ok ? not too slow ?
3179       }
3180       // else { DD("avoid SOVerticalSlider slicer update"); }
3181       break;
3182     }
3183   }
3184 }
3185 //------------------------------------------------------------------------------
3186
3187
3188 //------------------------------------------------------------------------------
3189 void vvMainWindow::SEVerticalSliderChanged()
3190 {
3191   static int value=-1;
3192   if (value == SEVerticalSlider->value()) return;
3193   else value = SEVerticalSlider->value();
3194   // int value = SEVerticalSlider->value();
3195   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
3196     if (DataTree->topLevelItem(i)->data(COLUMN_DR_VIEW,Qt::CheckStateRole).toInt() > 1) {
3197       if (mSlicerManagers[i]->GetSlicer(3)->GetSlice() != value) {
3198         mSlicerManagers[i]->GetSlicer(3)->SetSlice(value);
3199         mSlicerManagers[i]->VerticalSliderHasChanged(3, value);
3200         mSlicerManagers[i]->UpdateSlice(3);
3201         //mSlicerManagers[i]->GetSlicer(3)->Render(); // <-- DS add this, needed for contour, seems ok ? not too slow ?
3202       }
3203       break;
3204     }
3205   }
3206 }
3207 //------------------------------------------------------------------------------
3208
3209
3210 //------------------------------------------------------------------------------
3211 void vvMainWindow::UpdateSlice(int slicer, int slice)
3212 {
3213   // DD("vvMainWindow::UpdateSlice");
3214   //   DD(slicer);
3215   //   DD(slice);
3216   if (slicer == 0) {
3217     //    if (slice != NOVerticalSlider->value())
3218     NOVerticalSlider->setValue(slice);
3219   } else {
3220     if (slicer == 1)
3221       NEVerticalSlider->setValue(slice);
3222     else {
3223       if (slicer == 2)
3224         SOVerticalSlider->setValue(slice);
3225       else {
3226         if (slicer == 3)
3227           SEVerticalSlider->setValue(slice);
3228       }
3229     }
3230   }
3231   // DD("vvMainWindow:UpdateSlice END");
3232 }
3233 //------------------------------------------------------------------------------
3234
3235
3236 //------------------------------------------------------------------------------
3237 void vvMainWindow::UpdateTSlice(int slicer, int slice, int code)
3238 {
3239   //FusionSequence: the slider value should be updated for slicers which show the same sequence as requested
3240   bool doUpdate=false;
3241   if (code==-1) doUpdate=true;
3242   else {
3243     for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
3244       if (DataTree->topLevelItem(i)->data(slicer+1,Qt::CheckStateRole).toInt() > 1) {
3245         //i is the active SlicerManager
3246         if (mSlicerManagers[i]->GetFusionSequenceInvolvmentCode()==code) doUpdate=true;
3247         break;
3248       }
3249     }
3250   }
3251   if (!doUpdate) return;
3252
3253   switch (slicer) {
3254   case 0:
3255     if (NOHorizontalSlider->value()==slice) return;
3256     NOHorizontalSlider->setValue(slice);
3257     break;
3258   case 1:
3259     if (NEHorizontalSlider->value()==slice) return;
3260     NEHorizontalSlider->setValue(slice);
3261     break;
3262   case 2:
3263     if (SOHorizontalSlider->value()==slice) return;
3264     SOHorizontalSlider->setValue(slice);
3265     break;
3266   case 3:
3267     if (SEHorizontalSlider->value()==slice) return;
3268     SEHorizontalSlider->setValue(slice);
3269     break;
3270   }
3271 }
3272 //------------------------------------------------------------------------------
3273
3274
3275 //------------------------------------------------------------------------------
3276 void vvMainWindow::UpdateSliceRange(int slicer, int min, int max, int tmin, int tmax)
3277 {
3278   //int position = int((min+max)/2);
3279   int position = mSlicerManagers[mCurrentPickedImageIndex]->GetSlicer(slicer)->GetSlice();
3280   if (slicer == 0) {
3281     NOVerticalSlider->setRange(min,max);
3282     NOHorizontalSlider->setRange(tmin,tmax);
3283     NOVerticalSlider->setValue(position);
3284   } else if (slicer == 1) {
3285     NEVerticalSlider->setRange(min,max);
3286     NEHorizontalSlider->setRange(tmin,tmax);
3287     NEVerticalSlider->setValue(position);
3288   } else if (slicer == 2) {
3289     SOVerticalSlider->setRange(min,max);
3290     SOHorizontalSlider->setRange(tmin,tmax);
3291     SOVerticalSlider->setValue(position);
3292   } else if (slicer == 3) {
3293     SEVerticalSlider->setRange(min,max);
3294     SEHorizontalSlider->setRange(tmin,tmax);
3295     SEVerticalSlider->setValue(position);
3296   }
3297 }
3298 //------------------------------------------------------------------------------
3299
3300
3301 //------------------------------------------------------------------------------
3302 void vvMainWindow::SaveNOScreenshot()
3303 {
3304   SaveScreenshot(NOViewWidget);
3305 }
3306 //------------------------------------------------------------------------------
3307
3308
3309 //------------------------------------------------------------------------------
3310 void vvMainWindow::SaveNEScreenshot()
3311 {
3312   SaveScreenshot(NEViewWidget);
3313 }
3314 //------------------------------------------------------------------------------
3315
3316
3317 //------------------------------------------------------------------------------
3318 void vvMainWindow::SaveSOScreenshot()
3319 {
3320   SaveScreenshot(SOViewWidget);
3321 }
3322 //------------------------------------------------------------------------------
3323
3324
3325 //------------------------------------------------------------------------------
3326 void vvMainWindow::SaveSEScreenshot()
3327 {
3328   SaveScreenshot(SEViewWidget);
3329 }
3330 //------------------------------------------------------------------------------
3331
3332
3333 //------------------------------------------------------------------------------
3334 void vvMainWindow::SaveScreenshotAllSlices()
3335 {
3336 #if (VTK_MAJOR_VERSION == 8 && VTK_MINOR_VERSION >= 2) || VTK_MAJOR_VERSION >= 9
3337   QVTKOpenGLNativeWidget *widget = NOViewWidget;
3338 #else
3339   QVTKWidget *widget = NOViewWidget;
3340 #endif
3341
3342   int index = 0;// GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
3343   vvSlicerManager * SM = mSlicerManagers[index];
3344   vvImage * image = SM->GetImage();
3345   vvSlicer * slicer = SM->GetSlicer(0);
3346   int orientation = slicer->GetOrientation();
3347   int nbSlices = image->GetSize()[orientation];
3348   vtkSmartPointer<vtkRenderWindow>  renderWindow = widget->GetRenderWindow();
3349
3350   // Select filename base
3351   QString filename = QFileDialog::getSaveFileName(this,
3352     tr("Save As (filename will be completed by slice number)"),
3353     itksys::SystemTools::GetFilenamePath(mSlicerManagers[index]->GetFileName()).c_str(),
3354     "Images( *.png);;Images( *.jpg)");
3355
3356   // Loop on slices
3357   for(int i=0; i<nbSlices; i++) {
3358     // Change the slice
3359     slicer->SetSlice(i); // -> change the slice of the current slicer
3360     SM->UpdateSlice(0); // --> this one emit UpdateSlice
3361     QCoreApplication::flush(); // -> needed to force display of contours
3362
3363     // Screenshot
3364     vtkSmartPointer<vtkWindowToImageFilter> windowToImageFilter = vtkSmartPointer<vtkWindowToImageFilter>::New();
3365     windowToImageFilter->SetInput(renderWindow);
3366 #if (VTK_MAJOR_VERSION >= 8 && VTK_MINOR_VERSION >= 2) || VTK_MAJOR_VERSION >= 9
3367     windowToImageFilter->SetScale(1);
3368 #else
3369     windowToImageFilter->SetMagnification(1);
3370 #endif
3371     windowToImageFilter->SetInputBufferTypeToRGBA(); //also record the alpha (transparency) channel
3372     windowToImageFilter->Update();
3373
3374     vtkSmartPointer<vtkPNGWriter> writer = vtkSmartPointer<vtkPNGWriter>::New();
3375     std::string fn = itksys::SystemTools::GetFilenameWithoutLastExtension(filename.toStdString());
3376     std::string num = clitk::toString(i);
3377     if (i<10) num = "0"+num;
3378     if (i<100) num = "0"+num;
3379     if (i<1000) num = "0"+num;
3380
3381     fn = itksys::SystemTools::GetFilenamePath(filename.toStdString()) + "/"+ fn
3382       + "_" + num + itksys::SystemTools::GetFilenameLastExtension(filename.toStdString());
3383     writer->SetFileName(fn.c_str());
3384 #if VTK_MAJOR_VERSION <= 5
3385     writer->SetInput(windowToImageFilter->GetOutput());
3386 #else
3387     writer->SetInputConnection(windowToImageFilter->GetOutputPort());
3388 #endif
3389     writer->Write();
3390   }
3391 }
3392 //------------------------------------------------------------------------------
3393
3394
3395 //------------------------------------------------------------------------------
3396 #if (VTK_MAJOR_VERSION == 8 && VTK_MINOR_VERSION >= 2) || VTK_MAJOR_VERSION >= 9
3397 void vvMainWindow::SaveScreenshot(QVTKOpenGLNativeWidget *widget)
3398 #else
3399 void vvMainWindow::SaveScreenshot(QVTKWidget *widget)
3400 #endif
3401 {
3402   QString Extensions = "*.png;;";
3403   Extensions += "*.jpg;;";
3404   Extensions += "*.bmp;;";
3405   Extensions += "*.tif;;";
3406   Extensions += "*.ppm";
3407 #if defined(VTK_USE_FFMPEG_ENCODER) || defined(VTK_USE_VIDEO_FOR_WINDOWS)
3408   Extensions += ";;*.avi Video";
3409 #endif
3410 #ifdef VTK_USE_MPEG2_ENCODER
3411   Extensions += ";;*.mpg Video";
3412 #endif
3413   Extensions += ";;*.gif Video";
3414
3415   int smIndex=GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
3416   QString fileName = QFileDialog::getSaveFileName(this,
3417     tr("Save As"),
3418     itksys::SystemTools::GetFilenamePath(mSlicerManagers[smIndex]->GetFileName()).c_str(),
3419     Extensions);
3420
3421   if (!fileName.isEmpty()) {
3422     vtkSmartPointer<vtkWindowToImageFilter> w2i = vtkSmartPointer<vtkWindowToImageFilter>::New();
3423     w2i->SetInput(widget->GetRenderWindow());
3424 #if (VTK_MAJOR_VERSION >= 8 && VTK_MINOR_VERSION >= 2) || VTK_MAJOR_VERSION >= 9
3425     w2i->SetScale(1);
3426 #else
3427     w2i->SetMagnification(1);
3428 #endif
3429     //w2i->SetInputBufferTypeToRGBA(); //also record the alpha (transparency) channel
3430     w2i->Update();
3431     vtkImageData *image = w2i->GetOutput();
3432
3433     std::string ext(itksys::SystemTools::GetFilenameLastExtension(fileName.toStdString()));
3434
3435     // Image
3436     vtkImageWriter *imgwriter = NULL;
3437     if (ext==".bmp")
3438       imgwriter = vtkBMPWriter::New();
3439     else if (ext==".tif")
3440       imgwriter = vtkTIFFWriter::New();
3441     else if (ext==".ppm")
3442       imgwriter = vtkPNMWriter::New();
3443     else if (ext==".png")
3444       imgwriter = vtkPNGWriter::New();
3445     else if (ext==".jpg")
3446       imgwriter = vtkJPEGWriter::New();
3447
3448     // Snapshot image if not null
3449     if(imgwriter!=NULL) {
3450 #if VTK_MAJOR_VERSION <= 5
3451       imgwriter->SetInput(image);
3452 #else
3453       imgwriter->SetInputConnection(w2i->GetOutputPort());
3454 #endif
3455       imgwriter->SetFileName(fileName.toStdString().c_str());
3456       imgwriter->Write();
3457       return;
3458     }
3459
3460     // Video
3461     vtkGenericMovieWriter *vidwriter = NULL;
3462     if (ext==".gif") {
3463       vvAnimatedGIFWriter *gif = vvAnimatedGIFWriter::New();
3464       vidwriter = gif;
3465
3466       // FPS
3467       bool ok;
3468       int fps = QInputDialog::getInt(this, tr("Number of frames per second"),
3469         tr("FPS:"), 5, 0, 1000, 1, &ok);
3470       if(ok)
3471         gif->SetRate(fps);
3472
3473       // Loops
3474       int loops = QInputDialog::getInt(this, tr("Loops"),
3475         tr("Number of loops (0 means infinite):"), 0, 0, 1000000000, 1, &ok);
3476       if(ok)
3477         gif->SetLoops(loops);
3478
3479       // Dithering
3480       QString msg = "Would you like to activate dithering?";
3481       QMessageBox msgBox(QMessageBox::Question, tr("Dithering"),msg, 0, this);
3482       msgBox.addButton(tr("Yes"), QMessageBox::AcceptRole);
3483       msgBox.addButton(tr("No"), QMessageBox::RejectRole);
3484       gif->SetDither(msgBox.exec() == QMessageBox::AcceptRole);
3485     }
3486 #ifdef VTK_USE_VIDEO_FOR_WINDOWS
3487     if (ext==".avi") {
3488       vtkAVIWriter *mpg = vtkAVIWriter::New();
3489       vidwriter = mpg;
3490       mpg->SetQuality(2);
3491       bool ok;
3492       int fps = QInputDialog::getInt(this, tr("Number of frames per second"),
3493         tr("FPS:"), 5, 0, 1024, 1, &ok);
3494       if(!ok)
3495         fps = 5;
3496       mpg->SetRate(fps);
3497     }
3498 #endif
3499 #ifdef VTK_USE_FFMPEG_ENCODER
3500     if (ext==".avi") {
3501       vtkFFMPEGWriter *mpg = vtkFFMPEGWriter::New();
3502       vidwriter = mpg;
3503       mpg->SetQuality(2);
3504       bool ok;
3505       int fps = QInputDialog::getInt(this, tr("Number of frames per second"),
3506         tr("FPS:"), 5, 0, 1024, 1, &ok);
3507       if(!ok)
3508         fps = 5;
3509       mpg->SetRate(fps);
3510       mpg->SetBitRateTolerance(int(ceil(12.0*1024*1024/fps)));
3511     }
3512 #endif
3513 #ifdef VTK_USE_MPEG2_ENCODER
3514     if (ext==".mpg") {
3515       vtkMPEG2Writer *mpg = vtkMPEG2Writer::New();
3516       vidwriter = mpg;
3517     }
3518 #endif
3519
3520     // Take video if not null
3521     if(vidwriter!=NULL){
3522 #if VTK_MAJOR_VERSION <= 5
3523       vidwriter->SetInput(image);
3524 #else
3525       vidwriter->SetInputConnection(w2i->GetOutputPort());
3526 #endif
3527       vidwriter->SetFileName(fileName.toStdString().c_str());
3528       vidwriter->Start();
3529       int nSlice = mSlicerManagers[smIndex]->GetSlicer(0)->GetTMax();
3530       for(int i=0; i<=nSlice; i++) {
3531         mSlicerManagers[smIndex]->SetNextTSlice(0);
3532         vtkSmartPointer<vtkWindowToImageFilter> w2i = vtkSmartPointer<vtkWindowToImageFilter>::New();
3533         w2i->SetInput(widget->GetRenderWindow());
3534         w2i->Update();
3535 #if VTK_MAJOR_VERSION <= 5
3536         vidwriter->SetInput(w2i->GetOutput());
3537 #else
3538         vidwriter->SetInputConnection(w2i->GetOutputPort());
3539 #endif
3540         vidwriter->Write();
3541       }
3542       vidwriter->End();
3543       vidwriter->Delete();
3544       return;
3545     }
3546
3547     QMessageBox::information(this,tr("Problem saving screenshot !"),tr("Cannot save image.\nPlease set a file extension !!!"));
3548   }
3549 }
3550 //------------------------------------------------------------------------------
3551
3552
3553 //------------------------------------------------------------------------------
3554 void vvMainWindow::GoToCursor()
3555 {
3556   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
3557   for (int column = 1; column < 5; column++) {
3558     if (DataTree->selectedItems()[0]->data(column,Qt::CheckStateRole).toInt() > 1) {
3559       double* cursorPos = mSlicerManagers[index]->GetSlicer(column-1)->GetCursorPosition();
3560       mSlicerManagers[index]->GetSlicer(column-1)->SetCurrentPosition(
3561         cursorPos[0],cursorPos[1],cursorPos[2],cursorPos[3]);
3562       mSlicerManagers[index]->UpdateViews(1,column-1);
3563       mSlicerManagers[index]->UpdateLinked(column-1);
3564       break;
3565     }
3566   }
3567 }
3568 //------------------------------------------------------------------------------
3569
3570 //------------------------------------------------------------------------------
3571 void vvMainWindow::GoToLandmark()
3572 {
3573   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
3574   for (int column = 1; column < 5; column++) {
3575     if (DataTree->selectedItems()[0]->data(column,Qt::CheckStateRole).toInt() > 1) {
3576       double* cursorPos = landmarksPanel->GetSelectedPoint();
3577       mSlicerManagers[index]->GetSlicer(column-1)->SetCurrentPosition(
3578         cursorPos[0],cursorPos[1],cursorPos[2],cursorPos[3]);
3579       mSlicerManagers[index]->UpdateViews(1,column-1);
3580       mSlicerManagers[index]->UpdateLinked(column-1);
3581       break;
3582     }
3583   }
3584 }
3585 //------------------------------------------------------------------------------
3586
3587 //------------------------------------------------------------------------------
3588 void vvMainWindow::PlayPause()
3589 {
3590   if (playMode) {
3591     playMode = 0;
3592     playButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/player_play.png")));
3593     ImageInfoChanged();
3594     return;
3595   } else {
3596     int image_number=DataTree->topLevelItemCount();
3597     bool has_temporal;
3598     for (int i=0; i<image_number; i++)
3599       if (mSlicerManagers[i]->GetSlicer(0)->GetTMax() > 0) {
3600         has_temporal=true;
3601         break;
3602       }
3603       if (has_temporal) {
3604         playMode = 1;
3605         playButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/player_pause.png")));
3606         QTimer::singleShot(1000/mFrameRate, this, SLOT(PlayNext()));
3607       }
3608   }
3609 }
3610 //------------------------------------------------------------------------------
3611
3612 //------------------------------------------------------------------------------
3613 void vvMainWindow::PlayNext()
3614 {
3615   if (playMode && !this->isHidden()) {
3616     int image_number=DataTree->topLevelItemCount();
3617     ///Only play one slicer per SM, and only if the SM is being displayed
3618     for (int i=0; i<image_number; i++)
3619       for (int j=0; j<4; j++)
3620         if (mSlicerManagers[i]->GetSlicer(0)->GetTMax() > 0 &&
3621           DataTree->topLevelItem(i)->data(j+1,Qt::CheckStateRole).toInt() > 0) {
3622             mSlicerManagers[i]->SetNextTSlice(j);
3623             break;
3624         }
3625         QTimer::singleShot(1000/mFrameRate, this, SLOT(PlayNext()));
3626   }
3627 }
3628 //------------------------------------------------------------------------------
3629
3630 void vvMainWindow::ShowLastImage()
3631 {
3632   if (mSlicerManagers.size() > 1) {
3633     QTreeWidgetItem * item=DataTree->topLevelItem(DataTree->topLevelItemCount()-1);
3634     CurrentImageChanged(mSlicerManagers.back()->GetId()); //select new image
3635     item->setData(1,Qt::CheckStateRole,2); //show the new image in the first panel
3636     //mSlicerManagers[GetSlicerIndexFromItem(item)]->GetSlicer(0)->SetActorVisibility("image", 0, 1); //Set the Last Image visibles
3637     DisplayChanged(item,1);
3638   }
3639 }
3640
3641 //------------------------------------------------------------------------------
3642 void vvMainWindow::UpdateRenderWindows()
3643 {
3644   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
3645       for (unsigned int j = 0; j < 4; ++j) {
3646         mSlicerManagers[i]->GetSlicer(j)->RemoveLandmarks();
3647         mSlicerManagers[i]->GetSlicer(j)->DisplayLandmarks();
3648       }
3649   }
3650   if (NOViewWidget->GetRenderWindow()) NOViewWidget->GetRenderWindow()->Render();
3651   if (NEViewWidget->GetRenderWindow()) NEViewWidget->GetRenderWindow()->Render();
3652   if (SOViewWidget->GetRenderWindow()) SOViewWidget->GetRenderWindow()->Render();
3653   if (SEViewWidget->GetRenderWindow()) SEViewWidget->GetRenderWindow()->Render();
3654 }
3655 //------------------------------------------------------------------------------
3656
3657 //------------------------------------------------------------------------------
3658 void vvMainWindow::SegmentationOnCurrentImage()
3659 {
3660   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
3661
3662   vvSegmentationDialog segmentation;
3663   segmentation.SetImage(mSlicerManagers[index]->GetSlicer(0)->GetImage());
3664   segmentation.exec();
3665 }
3666 //------------------------------------------------------------------------------
3667
3668 void vvMainWindow::SurfaceViewerLaunch()
3669 {
3670   vvSurfaceViewerDialog surfaceViewer;
3671   surfaceViewer.exec();
3672 }
3673 //------------------------------------------------------------------------------
3674
3675
3676 //------------------------------------------------------------------------------
3677 int vvMainWindow::GetImageDuplicateFilenameNumber(std::string filename)
3678 {
3679   int number=0;
3680   for(unsigned int l=0; l<mSlicerManagers.size(); l++) {
3681     vvSlicerManager * v = mSlicerManagers[l];
3682     if (v->GetBaseFileName() ==
3683       vtksys::SystemTools::GetFilenameName(vtksys::SystemTools::GetFilenameWithoutLastExtension(filename))) {
3684         number = std::max(number, v->GetBaseFileNameNumber()+1);
3685     }
3686   }
3687   return number;
3688 }
3689 //------------------------------------------------------------------------------
3690
3691
3692 //------------------------------------------------------------------------------
3693 vvSlicerManager* vvMainWindow::AddImage(vvImage::Pointer image,std::string filename)
3694 {
3695   // Change filename if another image exist with the same name
3696   int number = GetImageDuplicateFilenameNumber(filename);
3697
3698   // Create new SliceManager
3699   vvSlicerManager* slicer_manager = new vvSlicerManager(4);
3700   slicer_manager->SetImage(image);//, IMAGE, number);
3701   //  filename = filename+"_"+clitk::toString(number);
3702   slicer_manager->SetFilename(filename, number);
3703   mSlicerManagers.push_back(slicer_manager);
3704
3705   //create an item in the tree with good settings
3706   QTreeWidgetItem *item = new QTreeWidgetItem();
3707   item->setData(0,Qt::UserRole,slicer_manager->GetFileName().c_str());//files[i].c_str());
3708   item->setData(1,Qt::UserRole,tr("image"));
3709   item->setData(COLUMN_IMAGE_NAME,Qt::DisplayRole,slicer_manager->GetFileName().c_str());//filename.c_str());
3710   qApp->processEvents();
3711
3712   for (int j = 1; j <= 4; j++) item->setData(j,Qt::CheckStateRole,1);
3713
3714   //Create the buttons for reload and close
3715   qApp->processEvents();
3716   QTreePushButton* cButton = new QTreePushButton;
3717   cButton->setItem(item);
3718   cButton->setColumn(COLUMN_CLOSE_IMAGE);
3719   cButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/exit.png")));
3720   connect(cButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
3721     this,SLOT(CloseImage(QTreeWidgetItem*, int)));
3722
3723   QTreePushButton* rButton = new QTreePushButton;
3724   rButton->setItem(item);
3725   rButton->setColumn(COLUMN_RELOAD_IMAGE);
3726   rButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/rotateright.png")));
3727   rButton->setEnabled(0);
3728   connect(rButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
3729     this,SLOT(ReloadImage(QTreeWidgetItem*, int)));
3730
3731   DataTree->addTopLevelItem(item);
3732   DataTree->setItemWidget(item, COLUMN_CLOSE_IMAGE, cButton);
3733   DataTree->setItemWidget(item, COLUMN_RELOAD_IMAGE, rButton);
3734
3735   //set the id of the image
3736   QString id = QDir::current().absoluteFilePath(slicer_manager->GetFileName().c_str()) + QString::number(mSlicerManagers.size()-1);
3737   item->setData(COLUMN_IMAGE_NAME,Qt::UserRole,id.toStdString().c_str());
3738   mSlicerManagers.back()->SetId(id.toStdString());
3739
3740   linkPanel->addImage(slicer_manager->GetFileName().c_str()// filename
3741     , id.toStdString());
3742
3743   connect(mSlicerManagers.back(), SIGNAL(currentImageChanged(std::string)),
3744     this, SLOT(CurrentImageChanged(std::string)));
3745   connect(mSlicerManagers.back(), SIGNAL(currentPickedImageChanged(std::string)),
3746     this, SLOT(CurrentPickedImageChanged(std::string)));
3747   connect(mSlicerManagers.back(), SIGNAL(UpdatePosition(int, double, double, double, double, double, double, double)),
3748     this, SLOT(MousePositionChanged(int,double, double, double, double, double, double, double)));
3749   connect(mSlicerManagers.back(), SIGNAL(UpdateVector(int, double, double, double, double)),
3750     this, SLOT(VectorChanged(int,double,double,double, double)));
3751   connect(mSlicerManagers.back(), SIGNAL(UpdateOverlay(int, double, double)),
3752     this, SLOT(OverlayChanged(int,double,double)));
3753   connect(mSlicerManagers.back(), SIGNAL(UpdateFusion(int, double)),
3754     this, SLOT(FusionChanged(int,double)));
3755   //connect(mSlicerManagers.back(), SIGNAL(UpdateFusionSequence(int, bool, unsigned int)),
3756   //  this, SLOT(FusionSequenceChanged(int, bool, unsigned int)));
3757   connect(mSlicerManagers.back(), SIGNAL(WindowLevelChanged()),
3758     this,SLOT(WindowLevelChanged()));
3759   connect(mSlicerManagers.back(), SIGNAL(UpdateSlice(int,int)),
3760     this,SLOT(UpdateSlice(int,int)));
3761   connect(mSlicerManagers.back(), SIGNAL(UpdateTSlice(int, int, int)),
3762     this,SLOT(UpdateTSlice(int, int, int)));
3763   connect(mSlicerManagers.back(), SIGNAL(UpdateTSlice(int, int, int)),
3764     this,SLOT(ImageInfoChanged()));
3765   connect(mSlicerManagers.back(), SIGNAL(UpdateSliceRange(int,int,int,int,int)),
3766     this,SLOT(UpdateSliceRange(int,int,int,int,int)));
3767   connect(mSlicerManagers.back(), SIGNAL(UpdateLinkManager(std::string,int,double,double,double,int)),
3768     this,SLOT(UpdateLinkManager(std::string,int,double,double,double,int)));
3769   connect(mSlicerManagers.back(), SIGNAL(UpdateLinkedNavigation(std::string,vvSlicerManager*,vvSlicer*)),
3770     this,SLOT(UpdateLinkedNavigation(std::string,vvSlicerManager*,vvSlicer*)));
3771   connect(mSlicerManagers.back(), SIGNAL(ChangeImageWithIndexOffset(vvSlicerManager*,int,int)),
3772     this,SLOT(ChangeImageWithIndexOffset(vvSlicerManager*,int,int)));
3773   connect(mSlicerManagers.back(), SIGNAL(LandmarkAdded()),landmarksPanel,SLOT(AddPoint()));
3774   connect(landmarksPanel,SIGNAL(UpdateLandmarkTransform()), mSlicerManagers.back(), SLOT(UpdateLandmark()));
3775
3776
3777
3778   InitSlicers();
3779   UpdateTree();
3780   qApp->processEvents();
3781   InitDisplay();
3782   ShowLastImage();
3783   qApp->processEvents();
3784   // End
3785   ImageInfoChanged();
3786   return slicer_manager;
3787 }
3788 //------------------------------------------------------------------------------
3789
3790
3791 //------------------------------------------------------------------------------
3792 void vvMainWindow::UpdateCurrentSlicer()
3793 {
3794   int index = -1;
3795   if (DataTree->selectedItems().size() > 0) {
3796     index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
3797   }
3798   mSlicerManagerCurrentIndex = index;
3799 }
3800 //------------------------------------------------------------------------------