vv/vvMainWindow.cxx

   1 /*=========================================================================
   2 Program:   vv                     http://www.creatis.insa-lyon.fr/rio/vv
   3
   4 Authors belong to:
   5 - University of LYON              http://www.universite-lyon.fr/
   6 - Léon Bérard cancer center       http://www.centreleonberard.fr
   7 - CREATIS CNRS laboratory         http://www.creatis.insa-lyon.fr
   8
   9 This software is distributed WITHOUT ANY WARRANTY; without even
  10 the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
  11 PURPOSE.  See the copyright notices for more information.
  12
  13 It is distributed under dual licence
  14
  15 - BSD        See included LICENSE.txt file
  16 - CeCILL-B   http://www.cecill.info/licences/Licence_CeCILL-B_V1-en.html
  17 ===========================================================================**/
  18
  19 #include <algorithm>
  20 #include <QMessageBox>
  21 #include <QInputDialog>
  22 #include <QTimer>
  23 #include "QTreePushButton.h"
  24 #include <QUrl>
  25 #include <QSettings>
  26 #include <QShortcut>
  27
  28 // VV include
  29 #include "vvMainWindow.h"
  30 #include "vvHelpDialog.h"
  31 #include "vvRegisterForm.h"
  32 #include "vvDocumentation.h"
  33 #include "vvProgressDialog.h"
  34 #include "vvQDicomSeriesSelector.h"
  35 #include "vvSlicerManager.h"
  36 #include "clitkImageCommon.h"
  37 #include "vvSlicer.h"
  38 #include "vvInteractorStyleNavigator.h"
  39 #include "vvImageWriter.h"
  40 #include "vvSegmentationDialog.h"
  41 #include "vvSurfaceViewerDialog.h"
  42 #include "vvDeformationDialog.h"
  43 #include "vvImageWarp.h"
  44 #include "vvUtils.h"
  45 #include "vvMidPosition.h"
  46 #include "vvMesh.h"
  47 #include "vvStructSelector.h"
  48 #include "vvMeshReader.h"
  49 #include "vvSaveState.h"
  50 #include "vvReadState.h"
  51 #include "clitkConfiguration.h"
  52 #include "clitkMatrix.h"
  53 #ifdef Q_OS_OSX
  54 # include "vvOSXHelper.h"
  55 #endif
  56
  57 // ITK include
  58 #include <itkImage.h>
  59 #include <itkImageFileReader.h>
  60 #include <itkByteSwapper.h>
  61 #include <itkCommand.h>
  62 #include <itkNumericSeriesFileNames.h>
  63
  64 // VTK include
  65 #include <vtkImageMapper3D.h>
  66 #include <vtkInformation.h>
  67 #include <vtkVersion.h>
  68 #include <vtkImageData.h>
  69 #include <vtkImageActor.h>
  70 #include <vtkCornerAnnotation.h>
  71 #include <vtkRenderWindow.h>
  72 #include <vtkRenderWindowInteractor.h>
  73 #include <vtkRenderer.h>
  74 #include <vtkRendererCollection.h>
  75 #include <vtkWindowToImageFilter.h>
  76 #include <vtkBMPWriter.h>
  77 #include <vtkTIFFWriter.h>
  78 #include <vtkPNMWriter.h>
  79 #include <vtkPNGWriter.h>
  80 #include <vtkJPEGWriter.h>
  81 #include <vtkGenericMovieWriter.h>
  82 #ifdef CLITK_EXPERIMENTAL
  83 #  include <vvAnimatedGIFWriter.h>
  84 #endif
  85 #ifdef VTK_USE_VIDEO_FOR_WINDOWS
  86 #  include <vtkAVIWriter.h>
  87 #endif
  88 #ifdef VTK_USE_FFMPEG_ENCODER
  89 #  include <vtkFFMPEGWriter.h>
  90 #endif
  91 #ifdef VTK_USE_MPEG2_ENCODER
  92 #  include <vtkMPEG2Writer.h>
  93 #endif
  94 #include <vtkMatrix4x4.h>
  95 #include <vtkTransform.h>
  96
  97 // Standard includes
  98 #include <iostream>
  99 #include <fstream>
 100 #include <sstream>
 101 #include <iomanip>
 102
 103 #define COLUMN_TREE 0
 104 #define COLUMN_UL_VIEW 1
 105 #define COLUMN_UR_VIEW 2
 106 #define COLUMN_DL_VIEW 3
 107 #define COLUMN_DR_VIEW 4
 108 #define COLUMN_CLOSE_IMAGE 5
 109 #define COLUMN_RELOAD_IMAGE 6
 110 #define COLUMN_IMAGE_NAME 7
 111
 112 #ifdef CLITK_PRIVATE_FEATURES
 113 #define EXTENSIONS "Images ( *.bmp *.dcm *.png *.jpeg *.jpg *.tif *.mhd *.mha *.hdr *.vox *.his *.xdr *.SCAN *.nii *.nrrd *.nhdr *.refscan *.nii.gz *.usf *.svl)"
 114 #else
 115 #define EXTENSIONS "Images ( *.bmp *.dcm *.png *.jpeg *.jpg *.tif *.mhd *.mha *.hdr *.vox *.his *.xdr *.SCAN *.nii *.nrrd *.nhdr *.refscan *.nii.gz)"
 116 #endif
 117
 118
 119 /*Data Tree values
 120 0,Qt::UserRole full filename
 121 1,Qt::CheckStateRole checkbutton UL View
 122 1,Qt::UserRole overlay, fusion or vector
 123 2,Qt::CheckStateRole checkbutton UR View
 124 3,Qt::CheckStateRole checkbutton DL View
 125 4,Qt::CheckStateRole checkbutton DR View
 126 5,0  short filename
 127 5,Qt::UserRole mSlicerManager id*/
 128
 129 //------------------------------------------------------------------------------
 130 vvMainWindow::vvMainWindow():vvMainWindowBase()
 131 {
 132   setupUi(this); // this sets up the GUI
 133
 134   //Qt::WindowFlags flags = windowFlags();
 135   //setWindowFlags(flags | Qt::WindowStaysOnTopHint);
 136
 137   mInputPathName = "";
 138   mMenuTools = menuTools;
 139   //  mMenuSegmentation = menuSegmentation;
 140   mContextMenu = &contextMenu;
 141   mMenuExperimentalTools = menuExperimental;
 142   mMainWidget = this;
 143   mCurrentTime = -1;
 144   mCurrentSelectedImageId = "";
 145   mCurrentPickedImageId = "";
 146   mCurrentPickedImageIndex = 0;
 147
 148   //Init the contextMenu
 149   this->setContextMenuPolicy(Qt::CustomContextMenu);
 150   contextActions.resize(0);
 151   QAction* actionOpen_new_image = contextMenu.addAction(QIcon(QString::fromUtf8(":/common/icons/fileopen.png")),
 152     tr("O&pen new Image"));
 153   connect(actionOpen_new_image,SIGNAL(triggered()),this,SLOT(OpenImages()));
 154   contextActions.push_back(actionOpen_new_image);
 155   contextMenu.addSeparator();
 156
 157   QAction* actionClose_Image = contextMenu.addAction(QIcon(QString::fromUtf8(":/common/icons/exit.png")),
 158     tr("Close Current Image"));
 159   connect(actionClose_Image,SIGNAL(triggered()),this,SLOT(CloseImage()));
 160   contextActions.push_back(actionClose_Image);
 161
 162   QAction* actionReload_image = contextMenu.addAction(QIcon(QString::fromUtf8(":/common/icons/rotateright.png")),
 163     tr("Reload Current Image"));
 164   connect(actionReload_image,SIGNAL(triggered()),this,SLOT(ReloadImage()));
 165   contextActions.push_back(actionReload_image);
 166
 167   QAction* actionSave_image = contextMenu.addAction(QIcon(QString::fromUtf8(":/common/icons/filesave.png")),
 168     tr("Save Current Image"));
 169   connect(actionSave_image,SIGNAL(triggered()),this,SLOT(SaveAs()));
 170   contextActions.push_back(actionSave_image);
 171
 172   QAction* actionSave_state = contextMenu.addAction(QIcon(QString::fromUtf8(":/common/icons/filesave.png")),
 173     tr("Save Current State"));
 174   connect(actionSave_state,SIGNAL(triggered()),this,SLOT(SaveCurrentState()));
 175   contextActions.push_back(actionSave_state);
 176
 177   QAction* actionRead_state = contextMenu.addAction(QIcon(QString::fromUtf8(":/common/icons/filesave.png")),
 178     tr("Read Saved State"));
 179   connect(actionRead_state,SIGNAL(triggered()),this,SLOT(ReadSavedState()));
 180   contextActions.push_back(actionRead_state);
 181
 182   contextMenu.addSeparator();
 183
 184   contextMenu.addAction(actionAdd_VF_to_current_Image);
 185   contextActions.push_back(actionAdd_VF_to_current_Image);
 186
 187   //QAction* actionAdd_Overlay_to_current_Image = menuOverlay->addAction(QIcon(QString::fromUtf8(":/common/icons/GPSup.png")),
 188   //    tr("Add overlay image to current image"));
 189   contextMenu.addAction(actionAdd_overlay_image_to_current_image);
 190   contextActions.push_back(actionAdd_overlay_image_to_current_image);
 191
 192   contextMenu.addAction(actionAdd_fusion_image);
 193   contextActions.push_back(actionAdd_fusion_image);
 194
 195 #ifdef CLITK_EXPERIMENTAL
 196   contextMenu.addAction(actionAdd_USSequence_toCT);
 197   contextActions.push_back(actionAdd_USSequence_toCT);
 198 #endif
 199
 200
 201   contextMenu.addSeparator();
 202   QAction* actionResetMatrix = contextMenu.addAction(QIcon(QString::fromUtf8(":/common/icons/identity.png")),
 203     tr("Reset transformation to identity"));
 204   connect(actionResetMatrix, SIGNAL(triggered()), this,SLOT(ResetTransformationToIdentity()));
 205
 206   //init the DataTree
 207   mSlicerManagers.resize(0);
 208
 209   QStringList header;
 210   header.append("");
 211   header.append("TL");
 212   header.append("TR");
 213   header.append("BL");
 214   header.append("BR");
 215   header.append("");
 216   header.append("");
 217   header.append("Name");
 218
 219   DataTree->setHeaderLabels(header);
 220   DataTree->resizeColumnToContents(COLUMN_TREE);
 221   DataTree->resizeColumnToContents(COLUMN_UL_VIEW);
 222   DataTree->resizeColumnToContents(COLUMN_UR_VIEW);
 223   DataTree->resizeColumnToContents(COLUMN_DL_VIEW);
 224   DataTree->resizeColumnToContents(COLUMN_DR_VIEW);
 225   DataTree->resizeColumnToContents(COLUMN_CLOSE_IMAGE);
 226   DataTree->resizeColumnToContents(COLUMN_RELOAD_IMAGE);
 227   DataTree->resizeColumnToContents(COLUMN_IMAGE_NAME);
 228
 229   viewMode = 1;
 230   documentation = new vvDocumentation();
 231   help_dialog = new vvHelpDialog();
 232   dicomSeriesSelector = new vvDicomSeriesSelector();
 233
 234   inverseButton->setEnabled(0);
 235   actionAdd_overlay_image_to_current_image->setEnabled(0);
 236   actionSave_As->setEnabled(0);
 237   actionAdd_VF_to_current_Image->setEnabled(0);
 238   actionAdd_fusion_image->setEnabled(0);
 239   actionAdd_USSequence_toCT->setEnabled(0);
 240
 241   //init the sliders
 242   verticalSliders.push_back(NOVerticalSlider);
 243   verticalSliders.push_back(NEVerticalSlider);
 244   verticalSliders.push_back(SOVerticalSlider);
 245   verticalSliders.push_back(SEVerticalSlider);
 246
 247   for (int i =0; i < 4; i++)
 248     verticalSliders[i]->hide();
 249
 250   horizontalSliders.push_back(NOHorizontalSlider);
 251   horizontalSliders.push_back(NEHorizontalSlider);
 252   horizontalSliders.push_back(SOHorizontalSlider);
 253   horizontalSliders.push_back(SEHorizontalSlider);
 254
 255   for (int i =0; i < 4; i++)
 256     horizontalSliders[i]->hide();
 257
 258
 259   connect(NOVerticalSlider,SIGNAL(valueChanged(int)),this,SLOT(NOVerticalSliderChanged()));
 260   connect(NEVerticalSlider,SIGNAL(valueChanged(int)),this,SLOT(NEVerticalSliderChanged()));
 261   connect(SOVerticalSlider,SIGNAL(valueChanged(int)),this,SLOT(SOVerticalSliderChanged()));
 262   connect(SEVerticalSlider,SIGNAL(valueChanged(int)),this,SLOT(SEVerticalSliderChanged()));
 263
 264   connect(NOHorizontalSlider,SIGNAL(valueChanged(int)),this,SLOT(NOHorizontalSliderMoved()));
 265   connect(NEHorizontalSlider,SIGNAL(valueChanged(int)),this,SLOT(NEHorizontalSliderMoved()));
 266   connect(SOHorizontalSlider,SIGNAL(valueChanged(int)),this,SLOT(SOHorizontalSliderMoved()));
 267   connect(SEHorizontalSlider,SIGNAL(valueChanged(int)),this,SLOT(SEHorizontalSliderMoved()));
 268
 269   //connect everything
 270   connect(actionCompute_mid_position_image,SIGNAL(triggered()),this,SLOT(ComputeMidPosition()));
 271   connect(actionDeformable_Registration,SIGNAL(triggered()),this,SLOT(ComputeDeformableRegistration()));
 272   connect(actionWarp_image_with_vector_field,SIGNAL(triggered()),this,SLOT(WarpImage()));
 273   connect(actionLoad_images,SIGNAL(triggered()),this,SLOT(OpenImages()));
 274   connect(actionOpen_Dicom,SIGNAL(triggered()),this,SLOT(OpenDicom()));
 275   //  connect(actionOpen_Dicom_Struct,SIGNAL(triggered()),this,SLOT(OpenDCStructContour()));
 276   connect(actionOpen_VTK_contour,SIGNAL(triggered()),this,SLOT(OpenVTKContour()));
 277   connect(actionOpen_Multiple_Images_As_One,SIGNAL(triggered()),this,SLOT(MergeImages()));
 278   connect(actionSlice_Image_As_Multiple_Images,SIGNAL(triggered()),this,SLOT(SliceImages()));
 279   connect(actionOpen_Image_With_Time,SIGNAL(triggered()),this,SLOT(OpenImageWithTime()));
 280   connect(actionMerge_images_as_n_dim_t, SIGNAL(triggered()), this, SLOT(MergeImagesWithTime()));
 281   connect(actionSave_As,SIGNAL(triggered()),this,SLOT(SaveAs()));
 282   connect(actionSave_current_state,SIGNAL(triggered()),this,SLOT(SaveCurrentState()));
 283   connect(actionRead_saved_state,SIGNAL(triggered()),this,SLOT(ReadSavedState()));
 284   connect(actionExit,SIGNAL(triggered()),this,SLOT(close()));
 285   connect(actionAdd_VF_to_current_Image,SIGNAL(triggered()),this,SLOT(OpenField()));
 286   connect(actionAdd_fusion_image,SIGNAL(triggered()),this,SLOT(SelectFusionImage()));
 287   connect(actionAdd_overlay_image_to_current_image,SIGNAL(triggered()), this,SLOT(SelectOverlayImage()));
 288   connect(actionAdd_USSequence_toCT,SIGNAL(triggered()), this,SLOT(SelectFusionSequence()));
 289   connect(actionNavigation_Help,SIGNAL(triggered()),this,SLOT(ShowHelpDialog()));
 290
 291   QShortcut *shortcutHelp = new QShortcut(QKeySequence(QKeySequence::HelpContents),this);
 292   shortcutHelp->setContext(Qt::ApplicationShortcut);
 293   QObject::connect(shortcutHelp, SIGNAL(activated()), this, SLOT(ShowHelpDialog()));
 294
 295   connect(actionDocumentation,SIGNAL(triggered()),this,SLOT(ShowDocumentation()));
 296   connect(actionRegister_vv,SIGNAL(triggered()),this,SLOT(PopupRegisterForm()));
 297
 298   connect(overlayPanel, SIGNAL(FusionSequenceCorrespondancesButtonPressed()), this, SLOT(SelectFusionSequenceCorrespondances()));
 299
 300
 301   ///////////////////////////////////////////////
 302   connect(actionSegmentation,SIGNAL(triggered()),this,SLOT(SegmentationOnCurrentImage()));
 303   connect(actionSurface_Viewer,SIGNAL(triggered()),this,SLOT(SurfaceViewerLaunch()));
 304   ///////////////////////////////////////////////
 305
 306   actionNorth_East_Window->setEnabled(0);
 307   actionNorth_West_Window->setEnabled(0);
 308   actionSouth_East_Window->setEnabled(0);
 309   actionSouth_West_Window->setEnabled(0);
 310
 311   connect(actionNorth_East_Window,SIGNAL(triggered()),this,SLOT(SaveNEScreenshot()));
 312   connect(actionNorth_West_Window,SIGNAL(triggered()),this,SLOT(SaveNOScreenshot()));
 313   connect(actionSouth_East_Window,SIGNAL(triggered()),this,SLOT(SaveSEScreenshot()));
 314   connect(actionSouth_West_Window,SIGNAL(triggered()),this,SLOT(SaveSOScreenshot()));
 315   connect(actionSave_all_slices,SIGNAL(triggered()),this,SLOT(SaveScreenshotAllSlices()));
 316
 317   connect(DataTree,SIGNAL(itemSelectionChanged()),this,SLOT(ImageInfoChanged()));
 318   connect(DataTree,SIGNAL(itemClicked(QTreeWidgetItem*, int)),this,
 319     SLOT(DisplayChanged(QTreeWidgetItem*, int)));
 320
 321   connect(viewButton,SIGNAL(clicked()),this, SLOT(ChangeViewMode()) );
 322   connect(windowSpinBox,SIGNAL(editingFinished()),this,SLOT(WindowLevelEdited()));
 323   connect(levelSpinBox,SIGNAL(editingFinished()),this,SLOT(WindowLevelEdited()));
 324   connect(colorMapComboBox,SIGNAL(currentIndexChanged(int)),this,SLOT(UpdateColorMap()));
 325   connect(presetComboBox,SIGNAL(currentIndexChanged(int)),this,SLOT(UpdateWindowLevel()));
 326   connect(slicingPresetComboBox, SIGNAL(currentIndexChanged(int)),this,SLOT(UpdateSlicingPreset()));
 327   connect(inverseButton,SIGNAL(clicked()),this,SLOT(SwitchWindowLevel()));
 328   connect(applyWindowLevelToAllButton,SIGNAL(clicked()),this,SLOT(ApplyWindowLevelToAllImages()));
 329
 330   connect(this,SIGNAL(customContextMenuRequested(QPoint)),this,SLOT(ShowContextMenu(QPoint)));
 331
 332   connect(linkPanel,SIGNAL(addLink(QString,QString,bool)),this,SLOT(AddLink(QString,QString,bool)));
 333   connect(linkPanel,SIGNAL(removeLink(QString,QString)),this,SLOT(RemoveLink(QString,QString)));
 334   connect(overlayPanel,SIGNAL(VFPropertyUpdated(int,int,int,int,double,double,double)),this,SLOT(SetVFProperty(int,int,int,int,double,double,double)));
 335   connect(overlayPanel,SIGNAL(OverlayPropertyUpdated(int,int,double,double)),
 336     this,SLOT(SetOverlayProperty(int,int,double,double)));
 337   connect(overlayPanel,SIGNAL(FusionPropertyUpdated(int,int,int,double,double, bool)),
 338     this,SLOT(SetFusionProperty(int,int,int,double,double, bool)));
 339   connect(landmarksPanel,SIGNAL(UpdateRenderWindows()),this,SLOT(UpdateRenderWindows()));
 340   connect(landmarksPanel,SIGNAL(SelectedPointChanged()),this,SLOT(GoToLandmark()));
 341
 342   connect(overlayPanel,SIGNAL(FusionSequencePropertyUpdated(int, bool, unsigned int, bool)),
 343     this,SLOT(SetFusionSequenceProperty(int, bool,unsigned int, bool)));
 344
 345
 346   playMode = 0;//pause
 347   mFrameRate = 10;
 348   playButton->setEnabled(0);
 349   frameRateLabel->setEnabled(0);
 350   frameRateSpinBox->setEnabled(0);
 351   connect(playButton, SIGNAL(clicked()),this,SLOT(PlayPause()));
 352   connect(frameRateSpinBox, SIGNAL(valueChanged(int)),this,SLOT(ChangeFrameRate(int)));
 353
 354   goToCursorPushButton->setEnabled(0);
 355   connect(goToCursorPushButton, SIGNAL(clicked()),this,SLOT(GoToCursor()));
 356
 357   NOViewWidget->hide();
 358   NEViewWidget->hide();
 359   SOViewWidget->hide();
 360   SEViewWidget->hide();
 361
 362 #ifdef Q_OS_OSX
 363   disableGLHiDPI(NOViewWidget->winId());
 364   disableGLHiDPI(NEViewWidget->winId());
 365   disableGLHiDPI(SOViewWidget->winId());
 366   disableGLHiDPI(SEViewWidget->winId());
 367 #endif
 368
 369   //Recently opened files
 370   std::list<std::string> recent_files = GetRecentlyOpenedImages();
 371   recentlyOpenedFilesMenu=NULL;
 372   if ( !recent_files.empty() ) {
 373     createRecentlyOpenedFilesMenu();
 374     updateRecentlyOpenedFilesMenu(recent_files);
 375   }
 376
 377   // Adding all new tools (insertion in the menu)
 378   vvToolManager::GetInstance()->InsertToolsInMenu(this);
 379   vvToolManager::GetInstance()->EnableToolsInMenu(this, false);
 380
 381 #ifndef CLITK_EXPERIMENTAL
 382 #define CLITK_EXPERIMENTAL 0
 383 #endif
 384   if (!CLITK_EXPERIMENTAL)
 385     menuExperimental->menuAction()->setVisible(false);
 386
 387
 388   QTimer * timerMemory = new QTimer(this);
 389   //timerMemory->setInterval(5);
 390   connect(timerMemory, SIGNAL(timeout()), this, SLOT(UpdateMemoryUsage()));
 391   timerMemory->start(2000);
 392 }
 393
 394 //------------------------------------------------------------------------------
 395 void vvMainWindow::show()
 396 {
 397   vvMainWindowBase::show();
 398   PopupRegisterForm(true);
 399 }
 400 //------------------------------------------------------------------------------
 401 void vvMainWindow::UpdateMemoryUsage()
 402 {
 403   //  clitk::PrintMemory(true);
 404   if (clitk::GetMemoryUsageInMb() == 0) infoPanel->setMemoryInMb("NA");
 405   else infoPanel->setMemoryInMb(QString::number(clitk::GetMemoryUsageInMb())+" MiB");
 406 }
 407 //------------------------------------------------------------------------------
 408
 409
 410 //------------------------------------------------------------------------------
 411 void vvMainWindow::createRecentlyOpenedFilesMenu()
 412 {
 413   recentlyOpenedFilesMenu = new QMenu("Recently opened files...");
 414   recentlyOpenedFilesMenu->setIcon(QIcon(QString::fromUtf8(":/common/icons/open.png")));
 415   menuFile->insertMenu(actionOpen_Image_With_Time,recentlyOpenedFilesMenu);
 416   menuFile->insertSeparator(actionOpen_Image_With_Time);
 417 }
 418 //------------------------------------------------------------------------------
 419
 420
 421 //------------------------------------------------------------------------------
 422
 423 void vvMainWindow::updateRecentlyOpenedFilesMenu(const std::list<std::string> &recent_files)
 424 {
 425   if(recentlyOpenedFilesMenu==NULL) {
 426     createRecentlyOpenedFilesMenu();
 427   } else {
 428     recentlyOpenedFilesMenu->clear();
 429   }
 430   for (std::list<std::string>::const_iterator i = recent_files.begin(); i!=recent_files.end(); i++) {
 431     QAction* current=new QAction(QIcon(QString::fromUtf8(":/common/icons/open.png")), i->c_str(),this);
 432     recentlyOpenedFilesMenu->addAction(current);
 433     connect(current,SIGNAL(triggered()),this,SLOT(OpenRecentImage()));
 434   }
 435 }
 436 //------------------------------------------------------------------------------
 437
 438
 439 //------------------------------------------------------------------------------
 440 void vvMainWindow::ComputeMidPosition()
 441 {
 442   bool ok;
 443   int index=GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
 444   int ref = QInputDialog::getInt(this,"Chose reference phase","Reference phase",0,0,\
 445 mSlicerManagers[index]->GetImage()->GetVTKImages().size()-1,1,&ok);
 446   if (ok) {
 447     vvMidPosition midp;
 448     midp.slicer_manager = mSlicerManagers[index];
 449     midp.reference_image_index = ref;
 450     QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
 451     midp.Update();
 452     if (midp.error)
 453       QMessageBox::warning(this, "Error computing midposition image",midp.error_message.c_str());
 454     else {
 455       QFileInfo info(midp.slicer_manager->GetFileName().c_str());
 456       AddImage(midp.output,info.path().toStdString()+"/"+info.completeBaseName().toStdString()+"_midposition.mhd");
 457     }
 458     QApplication::restoreOverrideCursor();
 459   }
 460 }
 461 //------------------------------------------------------------------------------
 462
 463
 464 //------------------------------------------------------------------------------
 465 void vvMainWindow::AddContour(int image_index, vvMesh::Pointer contour, bool propagation)
 466 {
 467   QTreeWidgetItem *item = new QTreeWidgetItem();
 468   item->setData(0,Qt::UserRole,"filename.vtk");
 469   item->setData(1,Qt::UserRole,tr("contour"));
 470   QBrush brush;
 471   brush.setColor(QColor(contour->r*255,contour->g*255,contour->b*255));
 472   brush.setStyle(Qt::SolidPattern);
 473   item->setData(COLUMN_IMAGE_NAME,Qt::BackgroundRole,brush);
 474   item->setData(COLUMN_IMAGE_NAME,Qt::DisplayRole,contour->structure_name.c_str());
 475
 476   for (int j = 1; j <= 4; j++)
 477     item->setData(j,Qt::CheckStateRole,DataTree->topLevelItem(image_index)->data(j,Qt::CheckStateRole));
 478
 479   QTreePushButton* cButton = new QTreePushButton;
 480   cButton->setItem(item);
 481   cButton->setColumn(COLUMN_CLOSE_IMAGE);
 482   cButton->setToolTip(tr("close image"));
 483   cButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/exit.png")));
 484   connect(cButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
 485     this,SLOT(CloseImage(QTreeWidgetItem*, int)));
 486
 487   QTreePushButton* rButton = new QTreePushButton;
 488   rButton->setItem(item);
 489   rButton->setColumn(COLUMN_RELOAD_IMAGE);
 490   rButton->setToolTip(tr("reload image"));
 491   rButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/rotateright.png")));
 492   rButton->setEnabled(false);
 493   //Not implemented
 494   //connect(rButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
 495   //this,SLOT(ReloadImage(QTreeWidgetItem*, int)));
 496
 497   DataTree->topLevelItem(image_index)->setExpanded(1);
 498   DataTree->topLevelItem(image_index)->addChild(item);
 499   DataTree->setItemWidget(item, COLUMN_CLOSE_IMAGE, cButton);
 500   DataTree->setItemWidget(item, COLUMN_RELOAD_IMAGE, rButton);
 501   QString id = DataTree->topLevelItem(image_index)->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString();
 502   item->setData(COLUMN_IMAGE_NAME,Qt::UserRole,id.toStdString().c_str());
 503
 504   UpdateTree();
 505   mSlicerManagers[image_index]->AddContour(contour,propagation);
 506   mSlicerManagers[image_index]->Render();
 507 }
 508 //------------------------------------------------------------------------------
 509
 510
 511 //------------------------------------------------------------------------------
 512 void vvMainWindow::OpenVTKContour()
 513 {
 514   if (mSlicerManagers.size() > 0) {
 515     QString Extensions = "Images ( *.vtk *.obj)";
 516     Extensions += ";;All Files (*)";
 517     QString file = QFileDialog::getOpenFileName(this,tr("Open vtkPolyData"),mInputPathName,Extensions);
 518     if (file.isNull())
 519       return;
 520     QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
 521     int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
 522     vvMeshReader reader;
 523     reader.SetImage(mSlicerManagers[index]->GetImage());
 524     reader.SetModeToVTK();
 525     reader.SetFilename(file.toStdString());
 526     reader.Update();
 527     AddContour(index,reader.GetOutput()[0],false);
 528     QApplication::restoreOverrideCursor();
 529   }
 530 }
 531 //------------------------------------------------------------------------------
 532
 533
 534 //------------------------------------------------------------------------------
 535 void vvMainWindow::AddDCStructContour(int index, QString file)
 536 {
 537   vvMeshReader reader;
 538   reader.SetFilename(file.toStdString());
 539   vvStructSelector selector;
 540   selector.SetStructures(reader.GetROINames());
 541   if (!mSlicerManagers[index]->GetVF().IsNull())
 542     selector.EnablePropagationCheckBox();
 543   if (selector.exec()) {
 544     QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
 545     reader.SetSelectedItems(selector.getSelectedItems());
 546     reader.SetImage(mSlicerManagers[index]->GetImage());
 547     if (selector.PropagationEnabled())
 548       reader.SetPropagationVF(mSlicerManagers[index]->GetVF());
 549     reader.Update();
 550     std::vector<vvMesh::Pointer> contours=reader.GetOutput();
 551     for (std::vector<vvMesh::Pointer>::iterator i=contours.begin();
 552       i!=contours.end(); i++)
 553       AddContour(index,*i,selector.PropagationEnabled());
 554     QApplication::restoreOverrideCursor();
 555   }
 556 }
 557
 558 //------------------------------------------------------------------------------
 559 void vvMainWindow::OpenDCStructContour()
 560 {
 561   if (mSlicerManagers.size() > 0) {
 562     QString Extensions = "Dicom Files ( *.dcm RS*)";
 563     Extensions += ";;All Files (*)";
 564     QString file = QFileDialog::getOpenFileName(this,tr("Merge Images"),mInputPathName,Extensions);
 565     if (file.isNull())
 566       return;
 567     int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
 568     AddDCStructContour(index, file);
 569   }
 570 }
 571 //------------------------------------------------------------------------------
 572
 573
 574 //------------------------------------------------------------------------------
 575 void vvMainWindow::ComputeDeformableRegistration()
 576 {
 577   if (mSlicerManagers.size() > 0) {
 578     int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
 579     vvDeformationDialog dialog(index,mSlicerManagers);
 580     if (dialog.exec()) {
 581       std::string base_name=itksys::SystemTools::GetFilenameWithoutExtension(mSlicerManagers[dialog.GetInputFileIndex()]->GetFileName());
 582       AddField(dialog.GetOutput(),dialog.getFieldFile(),dialog.GetInputFileIndex());
 583       WarpImage(dialog.GetSelectedSlicer(),dialog.GetReferenceFrameIndex());
 584     } else
 585       std::cout << "Error or user cancellation while computing deformation field..." << std::endl;
 586   } else QMessageBox::information(this, "Need to open image","You must open an image first.");
 587 }
 588 //------------------------------------------------------------------------------
 589
 590
 591 //------------------------------------------------------------------------------
 592 void vvMainWindow::WarpImage()
 593 {
 594   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
 595   if (!mSlicerManagers[index]->GetVF().IsNull()) {
 596     bool ok;
 597     int ref = QInputDialog::getInt(this,"Chose reference phase","Reference phase",0,0,\
 598       mSlicerManagers[index]->GetImage()->GetVTKImages().size()-1,1,&ok);
 599     if (ok) {
 600       WarpImage(mSlicerManagers[index],ref);
 601     }
 602   } else
 603     QMessageBox::warning(this,tr("No vector field"),tr("Sorry, can't warp without a vector field"));
 604 }
 605 //------------------------------------------------------------------------------
 606
 607
 608 //------------------------------------------------------------------------------
 609 void vvMainWindow::WarpImage(vvSlicerManager* selected_slicer,int reference_phase)
 610 {
 611   if (!selected_slicer->GetVF().IsNull()) {
 612     QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
 613     QFileInfo info(selected_slicer->GetFileName().c_str());
 614     vvImageWarp warp(selected_slicer->GetImage(),selected_slicer->GetVF(),
 615       reference_phase,this);
 616     if (warp.ComputeWarpedImage()) {
 617       AddImage(warp.GetWarpedImage(),info.path().toStdString()+"/"+info.completeBaseName().toStdString()+"_warped.mhd");
 618       AddImage(warp.GetDiffImage()  ,info.path().toStdString()+"/"+info.completeBaseName().toStdString()+"_diff.mhd");
 619       AddImage(warp.GetJacobianImage()  ,info.path().toStdString()+"/"+info.completeBaseName().toStdString()+"_jacobian.mhd");
 620       QApplication::restoreOverrideCursor();
 621     } else {
 622       QApplication::restoreOverrideCursor();
 623       QMessageBox::warning(this,tr("Different spacings"),tr("The vector field and image spacings must be the same in order to warp."));
 624     }
 625   } else
 626     QMessageBox::warning(this,tr("No vector field"),tr("Sorry, can't warp without a vector field."));
 627 }
 628 //------------------------------------------------------------------------------
 629
 630
 631 //------------------------------------------------------------------------------
 632 vvMainWindow::~vvMainWindow()
 633 {
 634   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
 635     if (mSlicerManagers[i] != NULL)
 636       delete mSlicerManagers[i];
 637   }
 638   delete documentation;
 639   delete help_dialog;
 640   delete dicomSeriesSelector;
 641 }
 642 //------------------------------------------------------------------------------
 643
 644 //------------------------------------------------------------------------------
 645 QTabWidget * vvMainWindow::GetTab()
 646 {
 647   return tabWidget;
 648 }
 649 //------------------------------------------------------------------------------
 650
 651
 652 //------------------------------------------------------------------------------
 653 void vvMainWindow::MergeImages()
 654 {
 655   QString Extensions = EXTENSIONS;
 656   Extensions += ";;All Files (*)";
 657   QStringList files = QFileDialog::getOpenFileNames(this,tr("Merge Images"),mInputPathName,Extensions);
 658   if (files.isEmpty())
 659     return;
 660   mInputPathName = itksys::SystemTools::GetFilenamePath(files[0].toStdString()).c_str();
 661   std::vector<std::string> vector;
 662
 663   unsigned int currentDim = 0;
 664   std::vector<double> currentSpacing;
 665   std::vector<int> currentSize;
 666   std::vector<double> currentOrigin;
 667
 668   for (int i = 0; i < files.size(); i++) {
 669     itk::ImageIOBase::Pointer reader = itk::ImageIOFactory::CreateImageIO(
 670       files[i].toStdString().c_str(), itk::ImageIOFactory::ReadMode);
 671     reader->SetFileName(files[i].toStdString().c_str());
 672     reader->ReadImageInformation();
 673     if (reader)        {
 674       //NOViewWidget->hide();
 675       //NEViewWidget->hide();
 676       //SOViewWidget->hide();
 677       //SEViewWidget->hide();
 678       if (i == 0)
 679         currentDim = reader->GetNumberOfDimensions();
 680       bool IsOk = true;
 681       for (unsigned int j = 0; j < currentDim; j++) {
 682         if (i == 0) {
 683           if (j == 0) {
 684             currentSpacing.resize(currentDim);
 685             currentSize.resize(currentDim);
 686             currentOrigin.resize(currentDim);
 687           }
 688           currentOrigin[j] = reader->GetOrigin(j);
 689           currentSpacing[j] = reader->GetSpacing(j);
 690           currentSize[j] = reader->GetDimensions(j);
 691         } else if (currentDim != reader->GetNumberOfDimensions()
 692           || currentSpacing[j] != reader->GetSpacing(j)
 693           || currentSize[j] != (int)reader->GetDimensions(j)
 694           || currentOrigin[j] != reader->GetOrigin(j)) {
 695             QString error = "Cannot read file (too different from others ";
 696             error += files[i].toStdString().c_str();
 697             QMessageBox::information(this,tr("Reading problem"),error);
 698             IsOk = false;
 699             break;
 700         }
 701       }
 702       if (IsOk)
 703         vector.push_back(files[i].toStdString());
 704     }
 705   }
 706   if (vector.size() > 0)
 707     LoadImages(vector, vvImageReader::MERGED);
 708 }
 709 //------------------------------------------------------------------------------
 710
 711 //------------------------------------------------------------------------------
 712 void vvMainWindow::SliceImages()
 713 {
 714   QString Extensions = EXTENSIONS;
 715   Extensions += ";;All Files (*)";
 716
 717   QStringList files = QFileDialog::getOpenFileNames(this,tr("Slice Images"),mInputPathName,Extensions);
 718   if (files.isEmpty())
 719     return;
 720   mInputPathName = itksys::SystemTools::GetFilenamePath(files[0].toStdString()).c_str();
 721   std::vector<std::string> vector;
 722   for (int i = 0; i < files.size(); i++)
 723     vector.push_back(files[i].toStdString());
 724   LoadImages(vector, vvImageReader::SLICED);
 725 }
 726 //------------------------------------------------------------------------------
 727
 728 //------------------------------------------------------------------------------
 729 void vvMainWindow::MergeImagesWithTime()
 730 {
 731   QString Extensions = EXTENSIONS;
 732   Extensions += ";;All Files (*)";
 733   QStringList files = QFileDialog::getOpenFileNames(this,tr("Merge Images With Time"),mInputPathName,Extensions);
 734   if (files.isEmpty())
 735     return;
 736   mInputPathName = itksys::SystemTools::GetFilenamePath(files[0].toStdString()).c_str();
 737   std::vector<std::string> vector;
 738
 739   for (int i = 0; i < files.size(); i++)
 740     vector.push_back(files[i].toStdString());
 741   sort(vector.begin(),vector.end());
 742   if (vector.size() > 1)
 743     LoadImages(vector, vvImageReader::MERGEDWITHTIME);
 744   else
 745     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.");
 746 }
 747 //------------------------------------------------------------------------------
 748
 749
 750 //------------------------------------------------------------------------------
 751 void vvMainWindow::OpenDicom()
 752 {
 753   std::vector<std::string> files;
 754
 755   //std::cout << "dicomSeriesSelector " << std::endl;
 756   if (dicomSeriesSelector->exec() == QDialog::Accepted) {
 757     files = *(dicomSeriesSelector->GetFilenames());
 758     LoadImages(files, vvImageReader::DICOM);
 759   }
 760 }
 761 //------------------------------------------------------------------------------
 762
 763 //------------------------------------------------------------------------------
 764 void vvMainWindow::OpenImages()
 765 {
 766   QString Extensions = EXTENSIONS;
 767   Extensions += ";;All Files (*)";
 768
 769   QStringList files = QFileDialog::getOpenFileNames(this,tr("Load Images"),mInputPathName,Extensions);
 770   if (files.isEmpty())
 771     return;
 772   mInputPathName = itksys::SystemTools::GetFilenamePath(files[0].toStdString()).c_str();
 773   std::vector<std::string> vector;
 774   for (int i = 0; i < files.size(); i++)
 775     vector.push_back(files[i].toStdString());
 776   LoadImages(vector, vvImageReader::IMAGE);
 777 }
 778 //------------------------------------------------------------------------------
 779 void vvMainWindow::OpenRecentImage()
 780 {
 781   QAction * caller = qobject_cast<QAction*>(sender());
 782   std::vector<std::string> images;
 783   images.push_back(caller->text().toStdString());
 784   mInputPathName = itksys::SystemTools::GetFilenamePath(images[0]).c_str();
 785   LoadImages(images, vvImageReader::IMAGE);
 786 }
 787 //------------------------------------------------------------------------------
 788
 789
 790 //------------------------------------------------------------------------------
 791 void vvMainWindow::OpenImageWithTime()
 792 {
 793   QString Extensions = EXTENSIONS;
 794   Extensions += ";;All Files (*)";
 795
 796   QStringList files = QFileDialog::getOpenFileNames(this,tr("Load Images With Time"),mInputPathName,Extensions);
 797   if (files.isEmpty())
 798     return;
 799   mInputPathName = itksys::SystemTools::GetFilenamePath(files[0].toStdString()).c_str();
 800   std::vector<std::string> vector;
 801   for (int i = 0; i < files.size(); i++) {
 802     vector.push_back(files[i].toStdString());
 803   }
 804   LoadImages(vector, vvImageReader::IMAGEWITHTIME);
 805 }
 806 //------------------------------------------------------------------------------
 807
 808
 809 //------------------------------------------------------------------------------
 810 void vvMainWindow::LoadImages(std::vector<std::string> files, vvImageReader::LoadedImageType filetype)
 811 {
 812   //Separate the way to open images and dicoms
 813   int fileSize;
 814   if (filetype == vvImageReader::IMAGE || filetype == vvImageReader::IMAGEWITHTIME)
 815     fileSize = files.size();
 816   else
 817     fileSize = 1;
 818
 819   // For SLICED, we need the number of slices (ndim and #slices)
 820   std::vector<unsigned int> nSlices;
 821   nSlices.resize(files.size());
 822   std::fill(nSlices.begin(), nSlices.end(), 1);
 823   if (filetype == vvImageReader::SLICED) {
 824     for (int i = 0; i < fileSize; i++) {
 825       itk::ImageIOBase::Pointer header = clitk::readImageHeader(files[i]);
 826       QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
 827       if (!header) {
 828         nSlices[i] = 0;
 829         QString error = "Cannot open file \n";
 830         error += files[i].c_str();
 831         QMessageBox::information(this,tr("Reading problem"),error);
 832         return;
 833       }
 834       if (header->GetNumberOfDimensions() < 3) {
 835         nSlices[i] = 0;
 836         QString error = "Dimension problem. Cannot slice \n";
 837         error += files[i].c_str();
 838         QMessageBox::information(this,tr("Reading problem"),error);
 839         return;
 840       }
 841       nSlices[i] = header->GetDimensions( header->GetNumberOfDimensions()-1 );
 842     }
 843   }
 844
 845   //Only add to the list of recently opened files when a single file is opened,
 846   //to avoid polluting the list of recently opened files
 847   if (files.size() == 1) {
 848     QFileInfo finfo=tr(files[0].c_str());
 849     AddToRecentlyOpenedImages(finfo.absoluteFilePath().toStdString());
 850     updateRecentlyOpenedFilesMenu(GetRecentlyOpenedImages());
 851   }
 852   //init the progress events
 853   QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
 854   vvProgressDialog progress("Opening " + files[0],fileSize>1);
 855   qApp->processEvents();
 856
 857   int numberofsuccesulreads=0;
 858   //open images as 1 or multiples
 859   for (int i = 0; i < fileSize; i++) {
 860     progress.SetText("Opening " + files[i]);
 861     progress.SetProgress(i,fileSize);
 862     qApp->processEvents();
 863
 864     for (unsigned int j = 0; j < nSlices[i]; j++) {
 865       //read the image and put it in mSlicerManagers
 866       vvSlicerManager* imageManager = new vvSlicerManager(4);
 867       qApp->processEvents();
 868
 869       bool SetImageSucceed=false;
 870
 871       // Change filename if an image with the same already exist
 872       int number = GetImageDuplicateFilenameNumber(files[i] + std::string("_slice"));
 873
 874       if (filetype == vvImageReader::IMAGE || filetype == vvImageReader::IMAGEWITHTIME || filetype == vvImageReader::SLICED) {
 875         SetImageSucceed = imageManager->SetImage(files[i],filetype, number, j);
 876       } else {
 877         SetImageSucceed = imageManager->SetImages(files,filetype, number);
 878       }
 879       if (!SetImageSucceed) {
 880         QApplication::restoreOverrideCursor();
 881         QString error = "Cannot open file \n";
 882         error += imageManager->GetLastError().c_str();
 883         QMessageBox::information(this,tr("Reading problem"),error);
 884         delete imageManager;
 885       } else {
 886
 887         mSlicerManagers.push_back(imageManager);
 888
 889         //create an item in the tree with good settings
 890         QTreeWidgetItem *item = new QTreeWidgetItem();
 891         item->setData(0,Qt::UserRole,files[i].c_str());
 892         QFileInfo fileinfo(imageManager->GetFileName().c_str()); //Do not show the path
 893         item->setData(COLUMN_IMAGE_NAME,Qt::DisplayRole,fileinfo.fileName());
 894         item->setData(1,Qt::UserRole,tr("image"));
 895         item->setToolTip(COLUMN_IMAGE_NAME, imageManager->GetListOfAbsoluteFilePathInOneString("image").c_str());
 896         qApp->processEvents();
 897
 898         //Create the buttons for reload and close
 899         qApp->processEvents();
 900         QTreePushButton* cButton = new QTreePushButton;
 901         cButton->setItem(item);
 902         cButton->setColumn(COLUMN_CLOSE_IMAGE);
 903         cButton->setToolTip(tr("close image"));
 904         cButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/exit.png")));
 905         connect(cButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
 906           this,SLOT(CloseImage(QTreeWidgetItem*, int)));
 907
 908         QTreePushButton* rButton = new QTreePushButton;
 909         rButton->setItem(item);
 910         rButton->setColumn(COLUMN_RELOAD_IMAGE);
 911         rButton->setToolTip(tr("reload image"));
 912         rButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/rotateright.png")));
 913         connect(rButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
 914           this,SLOT(ReloadImage(QTreeWidgetItem*, int)));
 915
 916         DataTree->addTopLevelItem(item);
 917         DataTree->setItemWidget(item, COLUMN_CLOSE_IMAGE, cButton);
 918         DataTree->setItemWidget(item, COLUMN_RELOAD_IMAGE, rButton);
 919
 920         //set the id of the image
 921         QString id = QDir::current().absoluteFilePath(files[i].c_str()) + QString::number(mSlicerManagers.size()-1);
 922         item->setData(COLUMN_IMAGE_NAME,Qt::UserRole,id.toStdString().c_str());
 923         mSlicerManagers.back()->SetId(id.toStdString());
 924
 925         linkPanel->addImage(imageManager->GetFileName(), id.toStdString());
 926
 927         connect(mSlicerManagers.back(), SIGNAL(currentImageChanged(std::string)),
 928           this,SLOT(CurrentImageChanged(std::string)));
 929         connect(mSlicerManagers.back(), SIGNAL(currentPickedImageChanged(std::string)),
 930           this, SLOT(CurrentPickedImageChanged(std::string)));
 931         connect(mSlicerManagers.back(), SIGNAL(UpdatePosition(int, double, double, double, double, double, double, double)),
 932           this,SLOT(MousePositionChanged(int,double, double, double, double, double, double, double)));
 933         connect(mSlicerManagers.back(), SIGNAL(UpdateVector(int, double, double, double, double)),
 934           this, SLOT(VectorChanged(int,double,double,double, double)));
 935         connect(mSlicerManagers.back(), SIGNAL(UpdateOverlay(int, double, double)),
 936           this, SLOT(OverlayChanged(int,double,double)));
 937         connect(mSlicerManagers.back(), SIGNAL(UpdateFusion(int, double)),
 938           this, SLOT(FusionChanged(int,double)));
 939         connect(mSlicerManagers.back(), SIGNAL(WindowLevelChanged()),
 940           this,SLOT(WindowLevelChanged()));
 941         connect(mSlicerManagers.back(), SIGNAL(UpdateSlice(int,int)),
 942           this,SLOT(UpdateSlice(int,int)));
 943         connect(mSlicerManagers.back(), SIGNAL(UpdateTSlice(int, int, int)),
 944           this,SLOT(UpdateTSlice(int, int, int)));
 945         connect(mSlicerManagers.back(), SIGNAL(UpdateTSlice(int, int, int)),
 946           this,SLOT(ImageInfoChanged()));
 947         connect(mSlicerManagers.back(), SIGNAL(UpdateSliceRange(int,int,int,int,int)),
 948           this,SLOT(UpdateSliceRange(int,int,int,int,int)));
 949         connect(mSlicerManagers.back(), SIGNAL(UpdateLinkManager(std::string,int,double,double,double,int)),
 950           this,SLOT(UpdateLinkManager(std::string,int,double,double,double,int)));
 951         connect(mSlicerManagers.back(), SIGNAL(UpdateLinkedNavigation(std::string,vvSlicerManager*,vvSlicer*)),
 952           this,SLOT(UpdateLinkedNavigation(std::string,vvSlicerManager*,vvSlicer*)));
 953         connect(mSlicerManagers.back(), SIGNAL(ChangeImageWithIndexOffset(vvSlicerManager*,int,int)),
 954           this,SLOT(ChangeImageWithIndexOffset(vvSlicerManager*,int,int)));
 955         connect(mSlicerManagers.back(),SIGNAL(LandmarkAdded()),landmarksPanel,SLOT(AddPoint()));
 956         InitSlicers();
 957         numberofsuccesulreads++;
 958       }
 959     }
 960   }
 961
 962   if (numberofsuccesulreads) {
 963     NOViewWidget->show();
 964     NEViewWidget->show();
 965     SOViewWidget->show();
 966     SEViewWidget->show();
 967     UpdateTree();
 968     InitDisplay();
 969     ShowLastImage();
 970
 971     // Try to guess default WindowLevel
 972     double range[2];
 973     mSlicerManagers.back()->GetImage()->GetFirstVTKImageData()->GetScalarRange(range);
 974     if ((range[0] == 0) && (range[1] == 1)) {
 975       presetComboBox->setCurrentIndex(WL_BINARY);// binary
 976     } else {
 977       // TODO
 978     }
 979   }
 980   QApplication::restoreOverrideCursor();
 981 }
 982 //------------------------------------------------------------------------------
 983
 984 //------------------------------------------------------------------------------
 985 void vvMainWindow::UpdateTree()
 986 {
 987   DataTree->resizeColumnToContents(COLUMN_TREE);
 988   DataTree->resizeColumnToContents(COLUMN_UL_VIEW);
 989   DataTree->resizeColumnToContents(COLUMN_UR_VIEW);
 990   DataTree->resizeColumnToContents(COLUMN_DL_VIEW);
 991   DataTree->resizeColumnToContents(COLUMN_DR_VIEW);
 992   DataTree->resizeColumnToContents(COLUMN_IMAGE_NAME);
 993   DataTree->resizeColumnToContents(COLUMN_CLOSE_IMAGE);
 994   DataTree->resizeColumnToContents(COLUMN_RELOAD_IMAGE);
 995 }
 996 //------------------------------------------------------------------------------
 997
 998 //------------------------------------------------------------------------------
 999 void vvMainWindow::CurrentImageChanged(std::string id)
1000 {
1001   if (id == mCurrentSelectedImageId) return; // Do nothing
1002   int selected = 0;
1003   for (int i = 0; i < DataTree->topLevelItemCount(); i++) {
1004     if (DataTree->topLevelItem(i)->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString().toStdString() == id) {
1005       selected = i;
1006     } else {
1007       DataTree->topLevelItem(i)->setSelected(0);
1008     }
1009     for (int child = 0; child < DataTree->topLevelItem(i)->childCount(); child++)
1010       DataTree->topLevelItem(i)->child(child)->setSelected(0);
1011
1012   }
1013   DataTree->topLevelItem(selected)->setSelected(1);
1014   mCurrentSelectedImageId = id;
1015
1016   landmarksPanel->SetCurrentLandmarks(mSlicerManagers[selected]->GetLandmarks(),
1017                                       mSlicerManagers[selected]->GetTSlice());
1018   landmarksPanel->SetCurrentPath(mInputPathName.toStdString());
1019   landmarksPanel->SetCurrentImage(mSlicerManagers[selected]->GetFileName().c_str());
1020
1021   emit SelectedImageHasChanged(mSlicerManagers[selected]);
1022 }
1023 //------------------------------------------------------------------------------
1024
1025 //------------------------------------------------------------------------------
1026 void vvMainWindow::CurrentPickedImageChanged(std::string id)
1027 {
1028   if (id == mCurrentPickedImageId) return; // Do nothing
1029   int selected = 0;
1030   for (int i = 0; i < DataTree->topLevelItemCount(); i++) {
1031     if (DataTree->topLevelItem(i)->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString().toStdString() == id) {
1032       selected = i;
1033     } else {
1034       DataTree->topLevelItem(i)->setSelected(0);
1035     }
1036     for (int child = 0; child < DataTree->topLevelItem(i)->childCount(); child++)
1037       DataTree->topLevelItem(i)->child(child)->setSelected(0);
1038
1039   }
1040   DataTree->topLevelItem(selected)->setSelected(1);
1041   mCurrentPickedImageId = id;
1042   mCurrentPickedImageIndex = selected;
1043 }
1044 //------------------------------------------------------------------------------
1045
1046 //------------------------------------------------------------------------------
1047 void vvMainWindow::ImageInfoChanged()
1048 {
1049   contextActions[6]->setEnabled(1);
1050   contextActions[5]->setEnabled(1);
1051   actionSave_As->setEnabled(1);
1052   actionAdd_VF_to_current_Image->setEnabled(1);
1053   actionAdd_fusion_image->setEnabled(1);
1054   actionAdd_overlay_image_to_current_image->setEnabled(1);
1055   actionAdd_USSequence_toCT->setEnabled(1);
1056   actionNorth_East_Window->setEnabled(1);
1057   actionNorth_West_Window->setEnabled(1);
1058   actionSouth_East_Window->setEnabled(1);
1059   actionSouth_West_Window->setEnabled(1);
1060   vvToolManager::GetInstance()->EnableToolsInMenu(this, true);
1061   inverseButton->setEnabled(1);
1062
1063   goToCursorPushButton->setEnabled(1);
1064
1065   if (DataTree->selectedItems().size()) {
1066     int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1067
1068     colorMapComboBox->setEnabled(1);
1069     for (int i = 0; i < DataTree->topLevelItem(index)->childCount(); i++) {
1070       if (DataTree->topLevelItem(index)->child(i)->data(1,Qt::UserRole).toString() == "overlay" ||
1071         DataTree->topLevelItem(index)->child(i)->data(1,Qt::UserRole).toString() == "fusion" ||
1072         DataTree->topLevelItem(index)->child(i)->data(1,Qt::UserRole).toString() == "fusionSequence") {
1073           colorMapComboBox->setEnabled(0);
1074           break;
1075       }
1076     }
1077
1078     std::vector<double> origin;
1079     std::vector<double> inputSpacing;
1080     std::vector<int> inputSize;
1081     std::vector<double> sizeMM;
1082     vtkSmartPointer<vtkMatrix4x4> transformation;
1083     int dimension=0;
1084     QString pixelType;
1085     QString inputSizeInBytes;
1086     QString image = DataTree->selectedItems()[0]->data(COLUMN_IMAGE_NAME,Qt::DisplayRole).toString();
1087
1088     int nframes = mSlicerManagers[index]->GetSlicer(0)->GetTMax();
1089
1090     if (nframes > 1 || playMode == 1) {
1091       playButton->setEnabled(1);
1092       frameRateLabel->setEnabled(1);
1093       frameRateSpinBox->setEnabled(1);
1094     } else {
1095       playButton->setEnabled(0);
1096       frameRateLabel->setEnabled(0);
1097       frameRateSpinBox->setEnabled(0);
1098     }
1099
1100     //read image header
1101     int NPixel = 1;
1102
1103     int tSlice = 0;
1104     vvImage::Pointer imageSelected;
1105     if (DataTree->topLevelItem(index) == DataTree->selectedItems()[0]) {
1106       imageSelected = mSlicerManagers[index]->GetSlicer(0)->GetImage();
1107       tSlice = mSlicerManagers[index]->GetSlicer(0)->GetTSlice();
1108     } else if (DataTree->selectedItems()[0]->data(1,Qt::UserRole).toString() == "vector") {
1109       imageSelected = mSlicerManagers[index]->GetSlicer(0)->GetVF();
1110       tSlice = mSlicerManagers[index]->GetSlicer(0)->GetOverlayTSlice();
1111     } else if (DataTree->selectedItems()[0]->data(1,Qt::UserRole).toString() == "overlay") {
1112       imageSelected = mSlicerManagers[index]->GetSlicer(0)->GetOverlay();
1113       tSlice = mSlicerManagers[index]->GetSlicer(0)->GetOverlayTSlice();
1114     } else if (DataTree->selectedItems()[0]->data(1,Qt::UserRole).toString() == "fusion") {
1115       imageSelected = mSlicerManagers[index]->GetSlicer(0)->GetFusion();
1116       tSlice = mSlicerManagers[index]->GetSlicer(0)->GetFusionTSlice();
1117     }
1118     else if (DataTree->selectedItems()[0]->data(1,Qt::UserRole).toString() == "fusionSequence") {
1119       imageSelected = mSlicerManagers[index]->GetSlicer(0)->GetFusion();
1120       tSlice = mSlicerManagers[index]->GetSlicer(0)->GetFusionTSlice();
1121     }
1122     else if (DataTree->selectedItems()[0]->data(1,Qt::UserRole).toString() == "contour") {
1123       imageSelected = mSlicerManagers[index]->GetSlicer(0)->GetImage();
1124       tSlice = mSlicerManagers[index]->GetSlicer(0)->GetTSlice();
1125     }
1126     else {
1127       imageSelected = mSlicerManagers[index]->GetSlicer(0)->GetImage();
1128       tSlice = mSlicerManagers[index]->GetSlicer(0)->GetTSlice();
1129     }
1130
1131     dimension = imageSelected->GetNumberOfDimensions();
1132     origin.resize(dimension);
1133     inputSpacing.resize(dimension);
1134     inputSize.resize(dimension);
1135     sizeMM.resize(dimension);
1136     pixelType = mSlicerManagers[index]->GetImage()->GetScalarTypeAsITKString().c_str();
1137     for (int i = 0; i < dimension; i++) {
1138       origin[i] = imageSelected->GetOrigin()[i];
1139       inputSpacing[i] = imageSelected->GetSpacing()[i];
1140       inputSize[i] = imageSelected->GetSize()[i];
1141       sizeMM[i] = inputSize[i]*inputSpacing[i];
1142       NPixel *= inputSize[i];
1143     }
1144     inputSizeInBytes = GetSizeInBytes(imageSelected->GetActualMemorySize()*1000);
1145
1146     QString dim = QString::number(dimension) + " (";
1147     dim += pixelType + ")";
1148
1149     infoPanel->setFileName(image);
1150     std::string creationImageTimeValue("No creation time");
1151     itk::ExposeMetaData< std::string > (*imageSelected->GetFirstMetaDataDictionary(), "creationImageTime", creationImageTimeValue);
1152     infoPanel->setImageCreationTime(QString(creationImageTimeValue.c_str()));
1153     infoPanel->setDimension(dim);
1154     infoPanel->setSizePixel(GetVectorIntAsString(inputSize));
1155     infoPanel->setSizeMM(GetVectorDoubleAsString(sizeMM));
1156     infoPanel->setOrigin(GetVectorDoubleAsString(origin));
1157     infoPanel->setSpacing(GetVectorDoubleAsString(inputSpacing));
1158     infoPanel->setNPixel(QString::number(NPixel)+" ("+inputSizeInBytes+")");
1159
1160     transformation = imageSelected->GetTransform()[tSlice]->GetMatrix();
1161     infoPanel->setTransformation(clitk::Get4x4MatrixDoubleAsString(transformation).c_str());
1162
1163     landmarksPanel->SetCurrentLandmarks(mSlicerManagers[index]->GetLandmarks(),
1164                                         mSlicerManagers[index]->GetTSlice());
1165     landmarksPanel->SetCurrentPath(mInputPathName.toStdString());
1166     landmarksPanel->SetCurrentImage(mSlicerManagers[index]->GetFileName().c_str());
1167
1168     overlayPanel->getCurrentImageName(mSlicerManagers[index]->GetFileName().c_str());
1169     for (int i = 0; i < 4; i++) {
1170       if (DataTree->selectedItems()[0]->data(i+1,Qt::CheckStateRole).toInt() > 0 || i == 3) {
1171         mSlicerManagers[index]->UpdateInfoOnCursorPosition(i);
1172         break;
1173       }
1174     }
1175
1176 //     infoPanel->setFileName(image);
1177 //     infoPanel->setDimension(dim);
1178 //     infoPanel->setSizePixel(GetVectorIntAsString(inputSize));
1179 //     infoPanel->setSizeMM(GetVectorDoubleAsString(sizeMM));
1180 //     infoPanel->setOrigin(GetVectorDoubleAsString(origin));
1181 //     infoPanel->setSpacing(GetVectorDoubleAsString(inputSpacing));
1182 //     infoPanel->setNPixel(QString::number(NPixel)+" ("+inputSizeInBytes+")");
1183 //
1184 //     landmarksPanel->SetCurrentLandmarks(mSlicerManagers[index]->GetLandmarks(),
1185 //                                         mSlicerManagers[index]->GetTSlice());
1186 //     landmarksPanel->SetCurrentPath(mInputPathName.toStdString());
1187 //     landmarksPanel->SetCurrentImage(mSlicerManagers[index]->GetFileName().c_str());
1188 //
1189 //     overlayPanel->getCurrentImageName(mSlicerManagers[index]->GetFileName().c_str());
1190 //     for (int i = 0; i < 4; i++) {
1191 //       if (DataTree->selectedItems()[0]->data(i+1,Qt::CheckStateRole).toInt() > 0 || i == 3) {
1192 //         mSlicerManagers[index]->UpdateInfoOnCursorPosition(i);
1193 //         break;
1194 //       }
1195 //     }
1196     WindowLevelChanged();
1197
1198     slicingPresetComboBox->setCurrentIndex(mSlicerManagers[index]->GetSlicingPreset());
1199
1200     if (mSlicerManagers[index]->GetSlicer(0)->GetVF()) {
1201       overlayPanel->getVFName(mSlicerManagers[index]->GetVFName().c_str());
1202       overlayPanel->getVFProperty(mSlicerManagers[index]->GetSlicer(0)->GetVFSubSampling(),
1203         mSlicerManagers[index]->GetSlicer(0)->GetVFScale(),
1204         mSlicerManagers[index]->GetSlicer(0)->GetVFLog());
1205     } else {
1206       overlayPanel->getVFName(mSlicerManagers[index]->GetVFName().c_str());
1207       overlayPanel->getVFProperty(-1,-1,-1);
1208     }
1209     if (mSlicerManagers[index]->GetSlicer(0)->GetOverlay()) {
1210       overlayPanel->getOverlayName(mSlicerManagers[index]->GetOverlayName().c_str());
1211     } else {
1212       overlayPanel->getOverlayName(mSlicerManagers[index]->GetOverlayName().c_str());
1213     }
1214
1215     if (mSlicerManagers[index]->GetSlicer(0)->GetFusion()) {
1216       overlayPanel->getFusionName(mSlicerManagers[index]->GetFusionName().c_str());
1217     } else {
1218       overlayPanel->getFusionName(mSlicerManagers[index]->GetFusionName().c_str());
1219     }
1220   }
1221 }
1222 //------------------------------------------------------------------------------
1223
1224 //------------------------------------------------------------------------------
1225 void vvMainWindow::ShowDocumentation()
1226 {
1227   documentation->show();
1228 }
1229 //------------------------------------------------------------------------------
1230
1231 //------------------------------------------------------------------------------
1232 void vvMainWindow::PopupRegisterForm(bool checkCanPush)
1233 {
1234   vvRegisterForm* registerForm = new vvRegisterForm(QUrl("http://www.creatis.insa-lyon.fr/~dsarrut/vvregister/write.php"), getVVSettingsPath(), getSettingsOptionFormat());
1235   if(!checkCanPush) {
1236     registerForm->show();
1237   } else {
1238     if(registerForm->canPush()) {
1239       registerForm->show();
1240       registerForm->acquitPushed();//too bad if there is not internet connection anymore.
1241     }
1242   }
1243 }
1244 //------------------------------------------------------------------------------
1245
1246 //------------------------------------------------------------------------------
1247 void vvMainWindow::ShowHelpDialog()
1248 {
1249   help_dialog->show();
1250 }
1251 //------------------------------------------------------------------------------
1252
1253 //------------------------------------------------------------------------------
1254 void vvMainWindow::ChangeViewMode()
1255 {
1256   typedef struct _SIZE{
1257     QSplitter* splitter;
1258     QList<int> size1, size2;
1259     int cols[3];
1260   }SplitterSize;
1261   SplitterSize sizes[4];
1262   sizes[0].splitter = OSplitter;
1263   sizes[0].size1.push_back(1);
1264   sizes[0].size1.push_back(0);
1265   sizes[0].size2.push_back(1);
1266   sizes[0].size2.push_back(0);
1267   sizes[0].cols[0] = 2;
1268   sizes[0].cols[1] = 3;
1269   sizes[0].cols[2] = 4;
1270
1271   sizes[1].splitter = ESplitter;
1272   sizes[1].size1.push_back(0);
1273   sizes[1].size1.push_back(1);
1274   sizes[1].size2.push_back(1);
1275   sizes[1].size2.push_back(0);
1276   sizes[1].cols[0] = 1;
1277   sizes[1].cols[1] = 3;
1278   sizes[1].cols[2] = 4;
1279
1280   sizes[2].splitter = OSplitter;
1281   sizes[2].size1.push_back(1);
1282   sizes[2].size1.push_back(0);
1283   sizes[2].size2.push_back(0);
1284   sizes[2].size2.push_back(1);
1285   sizes[2].cols[0] = 1;
1286   sizes[2].cols[1] = 2;
1287   sizes[2].cols[2] = 4;
1288
1289   sizes[3].splitter = ESplitter;
1290   sizes[3].size1.push_back(0);
1291   sizes[3].size1.push_back(1);
1292   sizes[3].size2.push_back(0);
1293   sizes[3].size2.push_back(1);
1294   sizes[3].cols[0] = 1;
1295   sizes[3].cols[1] = 2;
1296   sizes[3].cols[2] = 3;
1297
1298   int slicer = mSlicerManagers[mCurrentPickedImageIndex]->GetSelectedSlicer();
1299   if (viewMode == 1) {
1300     if (slicer >= 0) {
1301       viewMode = 0;
1302       splitter_3->setSizes(sizes[slicer].size1);
1303       sizes[slicer].splitter->setSizes(sizes[slicer].size2);
1304       DataTree->setColumnHidden(sizes[slicer].cols[0],1);
1305       DataTree->setColumnHidden(sizes[slicer].cols[1],1);
1306       DataTree->setColumnHidden(sizes[slicer].cols[2],1);
1307     }
1308   } else {
1309     QList<int> size;
1310     if (slicer >= 0) {
1311       viewMode = 1;
1312       size.push_back(1);
1313       size.push_back(1);
1314       splitter_3->setSizes(size);
1315       sizes[slicer].splitter->setSizes(size);
1316       DataTree->setColumnHidden(sizes[slicer].cols[0],0);
1317       DataTree->setColumnHidden(sizes[slicer].cols[1],0);
1318       DataTree->setColumnHidden(sizes[slicer].cols[2],0);
1319     }
1320   }
1321   UpdateRenderWindows();
1322   /*
1323   ** I don't know why but for both resized QVTKWidget we also need to render
1324   ** the associated Slicer to redraw crosses.
1325   */
1326   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
1327     //     if (DataTree->topLevelItem(i)->data(COLUMN_UL_VIEW,Qt::CheckStateRole).toInt() > 1)
1328     mSlicerManagers[i]->GetSlicer(0)->Render();
1329     mSlicerManagers[i]->GetSlicer(1)->Render();
1330     //     if (DataTree->topLevelItem(i)->data(COLUMN_DL_VIEW,Qt::CheckStateRole).toInt() > 1)
1331     mSlicerManagers[i]->GetSlicer(2)->Render();
1332     mSlicerManagers[i]->GetSlicer(3)->Render();
1333   }
1334 }
1335 //------------------------------------------------------------------------------
1336
1337 //------------------------------------------------------------------------------
1338 QString vvMainWindow::GetSizeInBytes(unsigned long size)
1339 {
1340   QString result = "";// QString::number(size);
1341   //result += " bytes (";
1342   if (size > 1000000000) {
1343     size /= 1000000000;
1344     result += QString::number(size);
1345     result += "Gb";//)";
1346   } else if (size > 1000000) {
1347     size /= 1000000;
1348     result += QString::number(size);
1349     result += "Mb";//)";
1350   } else if (size > 1000) {
1351     size /= 1000;
1352     result += QString::number(size);
1353     result += "kb";//)";
1354   }
1355   return result;
1356 }
1357 //------------------------------------------------------------------------------
1358
1359 //------------------------------------------------------------------------------
1360 QString vvMainWindow::GetVectorDoubleAsString(std::vector<double> vectorDouble)
1361 {
1362   QString result;
1363   for (unsigned int i= 0; i < vectorDouble.size(); i++) {
1364     if (i != 0)
1365       result += " ";
1366     result += QString::number(vectorDouble[i]);
1367   }
1368   return result;
1369 }
1370 //------------------------------------------------------------------------------
1371
1372 //------------------------------------------------------------------------------
1373 QString vvMainWindow::GetVectorIntAsString(std::vector<int> vectorInt)
1374 {
1375   QString result;
1376   for (unsigned int i= 0; i < vectorInt.size(); i++) {
1377     if (i != 0)
1378       result += " ";
1379     result += QString::number(vectorInt[i]);
1380   }
1381   return result;
1382 }
1383 //------------------------------------------------------------------------------
1384
1385 //------------------------------------------------------------------------------
1386 //this actually returns the SlicerManager index!
1387 int vvMainWindow::GetSlicerIndexFromItem(QTreeWidgetItem* item)
1388 {
1389   QString id = item->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString();
1390   for (int i = 0; i < DataTree->topLevelItemCount(); i++) {
1391     if (DataTree->topLevelItem(i)->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString() == id)
1392       return i;
1393   }
1394   return -1;
1395 }
1396 //------------------------------------------------------------------------------
1397
1398 //------------------------------------------------------------------------------
1399 QTreeWidgetItem* vvMainWindow::GetItemFromSlicerManager(vvSlicerManager* sm)
1400 {
1401   QString id = sm->GetId().c_str();
1402   for (int i = 0; i < DataTree->topLevelItemCount(); i++) {
1403     if (DataTree->topLevelItem(i)->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString() == id)
1404       return DataTree->topLevelItem(i);
1405   }
1406   return NULL;
1407 }
1408 //------------------------------------------------------------------------------
1409
1410 //------------------------------------------------------------------------------
1411 void vvMainWindow::DisplayChanged(QTreeWidgetItem *clickedItem, int column)
1412 {
1413   if ( column >= COLUMN_CLOSE_IMAGE || column <= 0)
1414     return;
1415
1416   // Get parent information (might be the same item)
1417   int slicerManagerIndex = GetSlicerIndexFromItem(clickedItem);
1418   QTreeWidgetItem* clickedParentItem = DataTree->topLevelItem(slicerManagerIndex);
1419   vvSlicer* clickedSlicer = mSlicerManagers[slicerManagerIndex]->GetSlicer(column-1);
1420
1421   // Go over the complete item tree (only 2 levels, parents and children)
1422   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
1423     // Trick to avoid redoing twice the job for a key (sr)
1424     mSlicerManagers[i]->GetSlicer(column-1)->GetRenderWindow()->GetInteractor()->SetKeySym("Crap");
1425
1426     QTreeWidgetItem* currentParentItem = DataTree->topLevelItem(i);
1427     if(currentParentItem != clickedParentItem) {
1428       // Not the branch of the clicked item, uncheck all
1429
1430       // Parent
1431       currentParentItem->setData(column,Qt::CheckStateRole, 0);
1432       mSlicerManagers[i]->UpdateSlicer(column-1, false);
1433
1434       // Children
1435       for (int iChild = 0; iChild < currentParentItem->childCount(); iChild++) {
1436         currentParentItem->child(iChild)->setData(column,Qt::CheckStateRole, 0);
1437       }
1438     }
1439     else {
1440       // Branch of the clicked one: get check status from actor visibility in slicer
1441       // and toggle the clicked one
1442
1443       // Parent
1444       bool vis = clickedSlicer->GetActorVisibility("image", 0);
1445       bool draw = clickedSlicer->GetRenderer()->GetDraw();
1446
1447       // Update slicer (after getting visibility)
1448       mSlicerManagers[slicerManagerIndex]->UpdateSlicer(column-1, true);
1449       mSlicerManagers[slicerManagerIndex]->UpdateInfoOnCursorPosition(column-1);
1450       DisplaySliders(slicerManagerIndex, column-1);
1451       if(clickedParentItem == clickedItem) {
1452         // Toggle
1453         vis = !draw || !vis;
1454       }
1455       clickedSlicer->SetActorVisibility("image", 0, vis);
1456       clickedParentItem->setData(column, Qt::CheckStateRole, vis?2:0);
1457
1458       // Children
1459       std::map<std::string, int> actorTypeCounts;
1460       for (int iChild = 0; iChild < clickedParentItem->childCount(); iChild++) {
1461         QTreeWidgetItem* currentChildItem = clickedParentItem->child(iChild);
1462         std::string actorType = currentChildItem->data(1,Qt::UserRole).toString().toStdString();
1463         vis = clickedSlicer->GetActorVisibility(actorType, actorTypeCounts[actorType]);
1464         if(currentChildItem == clickedItem) {
1465           // Toggle or force visibility if it was not on this branch so far
1466           vis = !draw || !vis;
1467           clickedSlicer->SetActorVisibility(actorType, actorTypeCounts[actorType], vis);
1468         }
1469         currentChildItem->setData(column, Qt::CheckStateRole, vis?2:0);
1470         actorTypeCounts[actorType]++;
1471       }
1472     }
1473   }
1474
1475   clickedSlicer->Render();
1476 }
1477 //------------------------------------------------------------------------------
1478
1479 void vvMainWindow::InitSlicers()
1480 {
1481   if (mSlicerManagers.size()) {
1482     mSlicerManagers.back()->GenerateDefaultLookupTable();
1483     mSlicerManagers.back()->SetSlicerWindow(0,NOViewWidget->GetRenderWindow());
1484     mSlicerManagers.back()->SetSlicerWindow(1,NEViewWidget->GetRenderWindow());
1485     mSlicerManagers.back()->SetSlicerWindow(2,SOViewWidget->GetRenderWindow());
1486     mSlicerManagers.back()->SetSlicerWindow(3,SEViewWidget->GetRenderWindow());
1487 #if VTK_MAJOR_VERSION <= 5
1488     mSlicerManagers.back()->Render(); // SR: displayed #slice is wrong without this / TB: With VTK6 and multiple images, all slicers are updated, not only the first
1489 #endif
1490   }
1491 }
1492
1493 //------------------------------------------------------------------------------
1494 void vvMainWindow::InitDisplay()
1495 {
1496   if (mSlicerManagers.size()) {
1497     //BE CAREFUL : this is absolutely necessary to set the interactor style
1498     //in order to have the same style instanciation for all SlicerManagers in
1499     // a same window
1500     for (int j = 0; j < 4; j++) {
1501       vvInteractorStyleNavigator* style = vvInteractorStyleNavigator::New();
1502       style->SetAutoAdjustCameraClippingRange(1);
1503       bool AlreadySelected = false;
1504       for (int i = 0; i < DataTree->topLevelItemCount(); i++) {
1505         mSlicerManagers[i]->SetInteractorStyleNavigator(j,style);
1506         //select the image only if previous are not selected
1507         if (DataTree->topLevelItem(i)->data(j+1,Qt::CheckStateRole).toInt() > 1) {
1508           mSlicerManagers[i]->UpdateSlicer(j,1);
1509           AlreadySelected = true;
1510         } else if (i == DataTree->topLevelItemCount()-1 && !AlreadySelected) {
1511           if (DataTree->selectedItems().size() == 0) {
1512             DataTree->topLevelItem(i)->setSelected(1);
1513           }
1514           DataTree->topLevelItem(i)->setData(j+1,Qt::CheckStateRole,2);
1515           mSlicerManagers[i]->UpdateSlicer(j,1);
1516           DisplaySliders(i,j);
1517         } else {
1518           DataTree->topLevelItem(i)->setData(j+1,Qt::CheckStateRole,0);
1519           mSlicerManagers[i]->UpdateSlicer(j,0);
1520         }
1521       }
1522       style->Delete();
1523     }
1524   }
1525 }
1526 //------------------------------------------------------------------------------
1527
1528 //------------------------------------------------------------------------------
1529 void vvMainWindow::DisplaySliders(int slicer, int window)
1530 {
1531   if(!mSlicerManagers[slicer]->GetSlicer(window)->GetRenderer()->GetDraw())
1532     return;
1533
1534   int range[2];
1535   mSlicerManagers[slicer]->GetSlicer(window)->GetSliceRange(range);
1536   int position = mSlicerManagers[slicer]->GetSlicer(window)->GetSlice();
1537   if (range[1]>0)
1538     verticalSliders[window]->show();
1539   else
1540     verticalSliders[window]->hide();
1541   verticalSliders[window]->setRange(range[0],range[1]);
1542   verticalSliders[window]->setValue(position);
1543
1544   int tRange[2];
1545   tRange[0] = 0;
1546   tRange[1] = mSlicerManagers[slicer]->GetSlicer(window)->GetTMax();
1547   if (tRange[1]>0)
1548     horizontalSliders[window]->show();
1549   else
1550     horizontalSliders[window]->hide();
1551   horizontalSliders[window]->setRange(tRange[0],tRange[1]);
1552   int tPosition = mSlicerManagers[slicer]->GetSlicer(window)->GetMaxCurrentTSlice();
1553   horizontalSliders[window]->setValue(tPosition);
1554 }
1555 //------------------------------------------------------------------------------
1556
1557 //------------------------------------------------------------------------------
1558 void vvMainWindow::CloseImage(QTreeWidgetItem* item, int column)
1559 {
1560   int index = GetSlicerIndexFromItem(item);
1561
1562   if (DataTree->topLevelItem(index) != item) {
1563     QString warning = "Do you really want to close the overlay : ";
1564     warning += item->data(COLUMN_IMAGE_NAME,Qt::DisplayRole).toString();
1565     QMessageBox msgBox(QMessageBox::Warning, tr("Close Overlay"),
1566       warning, 0, this);
1567     msgBox.addButton(tr("Close"), QMessageBox::AcceptRole);
1568     msgBox.addButton(tr("Cancel"), QMessageBox::RejectRole);
1569     if (msgBox.exec() == QMessageBox::AcceptRole) {
1570       std::string overlay_type=item->data(1,Qt::UserRole).toString().toStdString();
1571       int overlay_index=0;
1572       for (int child = 0; child < DataTree->topLevelItem(index)->childCount(); child++) {
1573         if (DataTree->topLevelItem(index)->\
1574           child(child)->data(1,Qt::UserRole).toString().toStdString() == overlay_type)
1575           overlay_index++;
1576         if (DataTree->topLevelItem(index)->child(child) == item) break;
1577       }
1578       if (overlay_type=="fusionSequence") {
1579         //removing the overlay sequence in a fusion sequence visualization mode
1580         //reset the transforms
1581         overlayPanel->getFusionSequenceProperty(-1, false, 0, false);
1582
1583         //unlink and untie the slicer managers
1584         RemoveLink(mSlicerManagers[index]->GetId().c_str(), mSlicerManagers[mSlicerManagers[index]->GetFusionSequenceIndexOfLinkedManager()]->GetId().c_str());
1585         mSlicerManagers[index]->SetFusionSequenceInvolvmentCode(-1);
1586         mSlicerManagers[mSlicerManagers[index]->GetFusionSequenceIndexOfLinkedManager()]->SetFusionSequenceInvolvmentCode(-1);
1587         for (unsigned i=0 ; i<4 ; i++) {
1588             mSlicerManagers[index]->GetSlicer(i)->SetFusionSequenceCode(-1);
1589             mSlicerManagers[mSlicerManagers[index]->GetFusionSequenceIndexOfLinkedManager()]->GetSlicer(i)->SetFusionSequenceCode(-1);
1590         }
1591
1592       }
1593       mSlicerManagers[index]->RemoveActor(overlay_type, overlay_index-1);
1594       mSlicerManagers[index]->SetColorMap(0);
1595       DataTree->topLevelItem(index)->takeChild(DataTree->topLevelItem(index)->indexOfChild(item));
1596       mSlicerManagers[index]->Render();
1597     }
1598   } else if (DataTree->topLevelItemCount() <= 1) {
1599     QString warning = "Do you really want to close the image : ";
1600     warning += item->data(COLUMN_IMAGE_NAME,Qt::DisplayRole).toString();
1601     warning += "\nThis is the last image, you're about to close vv !!!";
1602     QMessageBox msgBox(QMessageBox::Warning, tr("Close Image"),
1603       warning, 0, this);
1604     msgBox.addButton(tr("Close vv"), QMessageBox::AcceptRole);
1605     msgBox.addButton(tr("Cancel"), QMessageBox::RejectRole);
1606     if (msgBox.exec() == QMessageBox::AcceptRole) {
1607       this->close();
1608     }
1609   } else {
1610     QString warning = "Do you really want to close the image : ";
1611     warning += item->data(COLUMN_IMAGE_NAME,Qt::DisplayRole).toString();
1612     QMessageBox msgBox(QMessageBox::Warning, tr("Close Image"),
1613       warning, 0, this);
1614     msgBox.addButton(tr("Close"), QMessageBox::AcceptRole);
1615     msgBox.addButton(tr("Cancel"), QMessageBox::RejectRole);
1616     if (msgBox.exec() == QMessageBox::AcceptRole) {
1617
1618       // Tell tools that we close an image
1619       emit AnImageIsBeingClosed(mSlicerManagers[index]);
1620
1621       std::vector<vvSlicerManager*>::iterator Manageriter = mSlicerManagers.begin();
1622       DataTree->takeTopLevelItem(index);
1623       for (int i = 0; i < index; i++) {
1624         Manageriter++;
1625       }
1626       //if the slicer manager was involved in a fusion sequence visualization...
1627       if ( mSlicerManagers[index]->IsInvolvedInFusionSequence() ) {
1628         //in both cases, close the overlay: find it... and close it
1629         //ideally, I should duplicate the code, and avoid calling CloseImage, since this pops up another interactive box
1630         QTreeWidgetItem* overlayItem;
1631         if (mSlicerManagers[index]->IsMainSequenceOfFusionSequence()) {
1632           for (unsigned i=0 ; i<item->childCount() ; i++) {
1633             overlayItem = item->child(i);
1634             this->CloseImage( overlayItem, 0 );
1635           }
1636         }
1637         else {
1638           QTreeWidgetItem* linkedItem = this->GetItemFromSlicerManager( mSlicerManagers[mSlicerManagers[index]->GetFusionSequenceIndexOfLinkedManager()] );
1639           for (unsigned i=0 ; i<linkedItem->childCount() ; i++) {
1640             overlayItem = linkedItem->child(i);
1641             this->CloseImage( overlayItem, 0 );
1642           }
1643         }
1644
1645         /* -- this is normally already done when closing the overlay.
1646         //reset the transforms
1647         overlayPanel->getFusionSequenceProperty(-1, false, 0, false);
1648
1649         //unlink and untie the slicer managers
1650         RemoveLink(mSlicerManagers[index]->GetId().c_str(), mSlicerManagers[mSlicerManagers[index]->GetFusionSequenceIndexOfLinkedManager()]->GetId().c_str());
1651         mSlicerManagers[index]->SetFusionSequenceInvolvmentCode(-1);
1652         mSlicerManagers[mSlicerManagers[index]->GetFusionSequenceIndexOfLinkedManager()]->SetFusionSequenceInvolvmentCode(-1);
1653         for (unsigned i=0 ; i<4 ; i++) {
1654             mSlicerManagers[index]->GetSlicer(i)->SetFusionSequenceCode(-1);
1655             mSlicerManagers[mSlicerManagers[index]->GetFusionSequenceIndexOfLinkedManager()]->GetSlicer(i)->SetFusionSequenceCode(-1);
1656         }
1657         */
1658       }
1659
1660       linkPanel->removeImage(index);
1661       mSlicerManagers[index]->RemoveActors();
1662
1663       //remove the slicer manager
1664       delete mSlicerManagers[index];
1665       mSlicerManagers.erase(Manageriter);
1666
1667       //
1668       InitDisplay();
1669     }
1670   }
1671   ImageInfoChanged();
1672 }
1673 //------------------------------------------------------------------------------
1674
1675 //------------------------------------------------------------------------------
1676 void vvMainWindow::ReloadImage(QTreeWidgetItem* item, int column)
1677 {
1678   // int index = GetSlicerIndexFromItem(item);
1679   //   QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
1680   //   if (item->data(1,Qt::UserRole).toString() == "vector")
1681   //     mSlicerManagers[index]->ReloadVF();
1682   //   else
1683   //     mSlicerManagers[index]->Reload();
1684
1685   //   QApplication::restoreOverrideCursor();
1686   int index = GetSlicerIndexFromItem(item);
1687   QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
1688   QString role=item->data(1,Qt::UserRole).toString();
1689   if ( role == "vector") {
1690     mSlicerManagers[index]->ReloadVF();
1691   }
1692   else if (role == "overlay") {
1693     mSlicerManagers[index]->ReloadOverlay();
1694   }
1695   else if (role == "fusion") {
1696     mSlicerManagers[index]->ReloadFusion();
1697   }
1698   else if (role == "fusionSequence") {
1699     //both versions of the secondary sequence must be updated.
1700     mSlicerManagers[index]->ReloadFusionSequence();
1701     mSlicerManagers[mSlicerManagers[index]->GetFusionSequenceIndexOfLinkedManager()]->Reload();
1702   }
1703   else {
1704     mSlicerManagers[index]->Reload();
1705     //if we update the secondary sequence, then the overlay of the main sequence should also be updated
1706     if (mSlicerManagers[index]->IsSecondarySequenceOfFusionSequence()) mSlicerManagers[mSlicerManagers[index]->GetFusionSequenceIndexOfLinkedManager()]->ReloadFusionSequence();
1707   }
1708   // Update view and info
1709   ImageInfoChanged();
1710   mSlicerManagers[index]->Render();
1711   QApplication::restoreOverrideCursor();
1712 }
1713 //------------------------------------------------------------------------------
1714
1715 //------------------------------------------------------------------------------
1716 void vvMainWindow::MousePositionChanged(int visibility,double x, double y, double z, double X, double Y, double Z , double value)
1717 {
1718   infoPanel->setCurrentInfo(visibility,x,y,z,X,Y,Z,value);
1719 }
1720 //------------------------------------------------------------------------------
1721
1722 //------------------------------------------------------------------------------
1723 void vvMainWindow::VectorChanged(int visibility,double x, double y, double z, double value)
1724 {
1725   overlayPanel->getCurrentVectorInfo(visibility,x,y,z,value);
1726 }
1727 //------------------------------------------------------------------------------
1728
1729 //------------------------------------------------------------------------------
1730 void vvMainWindow::OverlayChanged(int visibility, double valueOver, double valueRef)
1731 {
1732   overlayPanel->getCurrentOverlayInfo(visibility,valueOver, valueRef);
1733 }
1734 //------------------------------------------------------------------------------
1735
1736 //------------------------------------------------------------------------------
1737 void vvMainWindow::FusionChanged(int visibility, double value)
1738 {
1739   overlayPanel->getCurrentFusionInfo(visibility,value);
1740 }
1741 //------------------------------------------------------------------------------
1742
1743 //------------------------------------------------------------------------------
1744 //called when AddOverlayImage, AddFusionSequence
1745 //or when UpdateWindowLevel() is called ; when slicerManager emits WindowLevelChanged
1746 //when ImageInfoChanged() is called
1747 void vvMainWindow::WindowLevelChanged()
1748 {
1749   // Base image
1750   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1751   if(index==-1) return;
1752   windowSpinBox->setValue(mSlicerManagers[index]->GetColorWindow());
1753   levelSpinBox->setValue(mSlicerManagers[index]->GetColorLevel());
1754   colorMapComboBox->setCurrentIndex(mSlicerManagers[index]->GetColorMap());
1755   presetComboBox->setCurrentIndex(mSlicerManagers[index]->GetPreset());
1756
1757   // Overlay image
1758   if (mSlicerManagers[index]->GetSlicer(0)->GetOverlay())
1759     overlayPanel->getOverlayProperty(mSlicerManagers[index]->GetOverlayColor(),
1760     mSlicerManagers[index]->GetLinkOverlayWindowLevel(),
1761     mSlicerManagers[index]->GetOverlayColorWindow(),
1762     mSlicerManagers[index]->GetOverlayColorLevel());
1763   else
1764     overlayPanel->getOverlayProperty(-1,0,0.,0.);
1765
1766   // Fusion & SequenceFusion image
1767   if (mSlicerManagers[index]->GetSlicer(0)->GetFusion()) {
1768     overlayPanel->getFusionProperty(mSlicerManagers[index]->GetFusionOpacity(),
1769       mSlicerManagers[index]->GetFusionThresholdOpacity(),
1770       mSlicerManagers[index]->GetFusionColorMap(),
1771       mSlicerManagers[index]->GetFusionWindow(),
1772       mSlicerManagers[index]->GetFusionLevel());
1773     if (mSlicerManagers[index]->IsMainSequenceOfFusionSequence()) {
1774       overlayPanel->getFusionSequenceProperty(mSlicerManagers[index]->GetFusionSequenceFrameIndex(),
1775         mSlicerManagers[index]->GetFusionSequenceSpatialSyncFlag(),
1776         mSlicerManagers[index]->GetFusionSequenceNbFrames(),
1777         mSlicerManagers[index]->GetFusionSequenceTemporalSyncFlag());
1778     }
1779   }
1780   else if ( mSlicerManagers[index]->IsSecondarySequenceOfFusionSequence() ) {
1781     //if the image is involved in a fusion sequence, preserve the overlay panel!
1782     int ind = mSlicerManagers[index]->GetFusionSequenceIndexOfLinkedManager();
1783     overlayPanel->getFusionProperty(mSlicerManagers[ind]->GetFusionOpacity(),
1784       mSlicerManagers[ind]->GetFusionThresholdOpacity(),
1785       mSlicerManagers[ind]->GetFusionColorMap(),
1786       mSlicerManagers[ind]->GetFusionWindow(),
1787       mSlicerManagers[ind]->GetFusionLevel());
1788     overlayPanel->getFusionSequenceProperty(mSlicerManagers[ind]->GetFusionSequenceFrameIndex(),
1789       mSlicerManagers[ind]->GetFusionSequenceSpatialSyncFlag(),
1790       mSlicerManagers[ind]->GetFusionSequenceNbFrames(),
1791       mSlicerManagers[ind]->GetFusionSequenceTemporalSyncFlag());
1792   }
1793   else
1794   {
1795     overlayPanel->getFusionProperty(-1, -1, -1, -1, -1);
1796     overlayPanel->getFusionSequenceProperty(-1, false, 0, false);
1797   }
1798 }
1799 //------------------------------------------------------------------------------
1800
1801 //------------------------------------------------------------------------------
1802 void vvMainWindow::WindowLevelEdited()
1803 {
1804   presetComboBox->setCurrentIndex(WL_USER);
1805   UpdateWindowLevel();
1806 }
1807 //------------------------------------------------------------------------------
1808
1809 //------------------------------------------------------------------------------
1810 void vvMainWindow::SetWindowLevel(double w, double l)
1811 {
1812   windowSpinBox->setValue(w);
1813   levelSpinBox->setValue(l);
1814   presetComboBox->setCurrentIndex(WL_USER);
1815   colorMapComboBox->setCurrentIndex(0);
1816   UpdateWindowLevel();
1817 }
1818 //------------------------------------------------------------------------------
1819
1820 //------------------------------------------------------------------------------
1821 void vvMainWindow::UpdateWindowLevel()
1822 {
1823   if (DataTree->selectedItems().size()) {
1824     if (presetComboBox->currentIndex() == WL_VENTILATION) //For ventilation
1825       colorMapComboBox->setCurrentIndex(5);
1826     int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1827     mSlicerManagers[index]->SetColorWindow(windowSpinBox->value());
1828     mSlicerManagers[index]->SetColorLevel(levelSpinBox->value());
1829     mSlicerManagers[index]->SetPreset(presetComboBox->currentIndex());
1830     mSlicerManagers[index]->Render();
1831     WindowLevelChanged();
1832   }
1833 }
1834 //------------------------------------------------------------------------------
1835
1836 //------------------------------------------------------------------------------
1837 void vvMainWindow::UpdateSlicingPreset()
1838 {
1839   if (DataTree->selectedItems().size()) {
1840     int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1841     mSlicerManagers[index]->SetSlicingPreset(vvSlicerManager::SlicingPresetType(slicingPresetComboBox->currentIndex()));
1842   }
1843 }
1844 //------------------------------------------------------------------------------
1845
1846 //------------------------------------------------------------------------------
1847 void vvMainWindow::UpdateColorMap()
1848 {
1849   if (DataTree->selectedItems().size()) {
1850     int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1851     mSlicerManagers[index]->SetColorMap(colorMapComboBox->currentIndex());
1852     mSlicerManagers[index]->Render();
1853   }
1854 }
1855 //------------------------------------------------------------------------------
1856 void vvMainWindow::SwitchWindowLevel()
1857 {
1858   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1859   int window = mSlicerManagers[index]->GetColorWindow();
1860   presetComboBox->setCurrentIndex(WL_USER);
1861   windowSpinBox->setValue(-window);
1862   UpdateWindowLevel();
1863 }
1864 //------------------------------------------------------------------------------
1865
1866 //------------------------------------------------------------------------------
1867 void vvMainWindow::ApplyWindowLevelToAllImages()
1868 {
1869   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1870   if(index==-1) return;
1871   double window = mSlicerManagers[index]->GetColorWindow();
1872   double level = mSlicerManagers[index]->GetColorLevel();
1873
1874   double fusWindow = mSlicerManagers[index]->GetFusionWindow();
1875   double fusLevel = mSlicerManagers[index]->GetFusionLevel();
1876
1877   double overWindow = mSlicerManagers[index]->GetOverlayColorWindow();
1878   double overLevel = mSlicerManagers[index]->GetOverlayColorLevel();
1879
1880   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
1881     if (mSlicerManagers[i] == NULL)
1882       continue;
1883     mSlicerManagers[i]->SetColorWindow(window);
1884     mSlicerManagers[i]->SetColorLevel(level);
1885     mSlicerManagers[i]->SetPreset(WL_USER);
1886     mSlicerManagers[i]->SetFusionWindow(fusWindow);
1887     mSlicerManagers[i]->SetFusionLevel(fusLevel);
1888     mSlicerManagers[i]->SetOverlayColorWindow(overWindow);
1889     mSlicerManagers[i]->SetOverlayColorLevel(overLevel);
1890     mSlicerManagers[i]->Render();
1891   }
1892 }
1893 //------------------------------------------------------------------------------
1894
1895 //------------------------------------------------------------------------------
1896 void vvMainWindow::ApplyWindowToSetOfImages(double window, unsigned int indexMin, unsigned int indexMax)
1897 {
1898   for (unsigned int i = indexMin; i <= indexMax && i < mSlicerManagers.size(); i++) {
1899     if (mSlicerManagers[i] == NULL)
1900       continue;
1901     SetWindowLevel(window, mSlicerManagers[i]->GetColorLevel());
1902     mSlicerManagers[i]->SetColorWindow(window);
1903     mSlicerManagers[i]->SetPreset(WL_USER);
1904     mSlicerManagers[i]->Render();
1905   }
1906 }
1907 //------------------------------------------------------------------------------
1908
1909 //------------------------------------------------------------------------------
1910 void vvMainWindow::ApplyLevelToSetOfImages(double level, unsigned int indexMin, unsigned int indexMax)
1911 {
1912   for (unsigned int i = indexMin; i <= indexMax && i < mSlicerManagers.size(); i++) {
1913     if (mSlicerManagers[i] == NULL)
1914       continue;
1915     SetWindowLevel(mSlicerManagers[i]->GetColorWindow(), level);
1916     mSlicerManagers[i]->SetColorLevel(level);
1917     mSlicerManagers[i]->SetPreset(WL_USER);
1918     mSlicerManagers[i]->Render();
1919   }
1920 }
1921 //------------------------------------------------------------------------------
1922
1923 //------------------------------------------------------------------------------
1924 void vvMainWindow::UpdateLinkManager(std::string id, int slicer, double x, double y, double z, int temps)
1925 {
1926   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
1927     if (mSlicerManagers[i]->GetId() == id) {
1928       mSlicerManagers[i]->GetSlicer(slicer)->SetCurrentPosition(x,y,z,temps);
1929       mSlicerManagers[i]->UpdateViews(0,slicer);
1930       break;
1931     }
1932   }
1933 }
1934 //------------------------------------------------------------------------------
1935
1936 //------------------------------------------------------------------------------
1937 void vvMainWindow::UpdateLinkedNavigation(std::string id, vvSlicerManager * sm, vvSlicer* refSlicer)
1938 {
1939   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
1940     if (id == mSlicerManagers[i]->GetId()) {
1941       mSlicerManagers[i]->UpdateLinkedNavigation(refSlicer);
1942     }
1943   }
1944 }
1945 //------------------------------------------------------------------------------
1946
1947 //------------------------------------------------------------------------------
1948 void vvMainWindow::ShowContextMenu(QPoint point)
1949 {
1950   if (!DataTree->selectedItems().size()) {
1951     contextActions[1]->setEnabled(0);
1952     contextActions[2]->setEnabled(0);
1953     contextActions[3]->setEnabled(0);
1954     contextActions[4]->setEnabled(0);
1955     contextActions[5]->setEnabled(0);
1956     contextActions[6]->setEnabled(0);
1957   } else {
1958     int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1959     contextActions[1]->setEnabled(1);
1960     contextActions[2]->setEnabled(
1961       DataTree->itemWidget(DataTree->selectedItems()[0],
1962       COLUMN_RELOAD_IMAGE)->isEnabled());
1963     contextActions[3]->setEnabled(1);
1964     contextActions[5]->setEnabled(1);
1965     contextActions[6]->setEnabled(1);
1966
1967     if (mSlicerManagers[index]->GetDimension() < 3)
1968       contextActions[4]->setEnabled(0);
1969     else
1970       contextActions[4]->setEnabled(1);
1971   }
1972   contextMenu.exec(QCursor::pos());
1973 }
1974 //------------------------------------------------------------------------------
1975
1976 //------------------------------------------------------------------------------
1977 void vvMainWindow::CloseImage()
1978 {
1979   CloseImage(DataTree->selectedItems()[0],0);
1980 }
1981 //------------------------------------------------------------------------------
1982
1983 //------------------------------------------------------------------------------
1984 void vvMainWindow::ReloadImage()
1985 {
1986   ReloadImage(DataTree->selectedItems()[0],0);
1987 }
1988 //------------------------------------------------------------------------------
1989
1990 //------------------------------------------------------------------------------
1991 void vvMainWindow::SelectOverlayImage()
1992 {
1993   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1994
1995   if (!(CheckAddedImage(index, "overlay")))
1996     return;
1997
1998   QString Extensions = EXTENSIONS;
1999   Extensions += ";;All Files (*)";
2000   QStringList files = QFileDialog::getOpenFileNames(this,tr("Load Overlay image"),mInputPathName,Extensions);
2001   if (files.isEmpty())
2002     return;
2003
2004   std::vector<std::string> vecFileNames;
2005   for (int i = 0; i < files.size(); i++) {
2006     vecFileNames.push_back(files[i].toStdString());
2007   }
2008
2009   AddOverlayImage(index,vecFileNames,vvImageReader::IMAGE);
2010 }
2011 //------------------------------------------------------------------------------
2012
2013 //------------------------------------------------------------------------------
2014 bool vvMainWindow::CheckAddedImage(int index, QString imageType)
2015 {
2016   //check if one overlay image is added
2017   for (int child = 0; child < DataTree->topLevelItem(index)->childCount(); child++)
2018     if (DataTree->topLevelItem(index)->child(child)->data(1,Qt::UserRole).toString().compare(imageType) == 0) {
2019       QString error = "Cannot add more than one compared image\n";
2020       error += "Please remove first ";
2021       error += DataTree->topLevelItem(index)->child(child)->data(COLUMN_IMAGE_NAME,Qt::DisplayRole).toString();
2022       QMessageBox::information(this,tr("Problem adding compared image !"),error);
2023       return false;
2024     }
2025     return true;
2026 }
2027 //------------------------------------------------------------------------------
2028
2029 //------------------------------------------------------------------------------
2030 void vvMainWindow::AddOverlayImage(int index, std::vector<std::string> fileNames, vvImageReader::LoadedImageType type)
2031 {
2032   QString file(fileNames[0].c_str());
2033   if (QFile::exists(file))
2034   {
2035     mInputPathName = itksys::SystemTools::GetFilenamePath(file.toStdString()).c_str();
2036     itk::ImageIOBase::Pointer reader = itk::ImageIOFactory::CreateImageIO(
2037       file.toStdString().c_str(), itk::ImageIOFactory::ReadMode);
2038     reader->SetFileName(fileNames[0].c_str());
2039     reader->ReadImageInformation();
2040     std::string component = reader->GetComponentTypeAsString(reader->GetComponentType());
2041     int dimension = reader->GetNumberOfDimensions();
2042     QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
2043     vvProgressDialog progress("Opening " + file.toStdString());
2044     qApp->processEvents();
2045
2046     std::string filename = itksys::SystemTools::GetFilenameWithoutExtension(file.toStdString()).c_str();
2047     if (mSlicerManagers[index]->SetOverlay(fileNames,dimension, component,type)) {
2048       //create an item in the tree with good settings
2049       QTreeWidgetItem *item = new QTreeWidgetItem();
2050       item->setData(0,Qt::UserRole,file.toStdString().c_str());
2051       item->setData(1,Qt::UserRole,tr("overlay"));
2052       QFileInfo fileinfo(file); //Do not show the path
2053       item->setData(COLUMN_IMAGE_NAME,Qt::DisplayRole,fileinfo.fileName());
2054       item->setToolTip(COLUMN_IMAGE_NAME, mSlicerManagers[index]->GetListOfAbsoluteFilePathInOneString("overlay").c_str());
2055       qApp->processEvents();
2056 #if VTK_MAJOR_VERSION > 5
2057       for ( unsigned int i = 0; i < mSlicerManagers[index]->GetNumberOfSlicers(); i++)
2058         mSlicerManagers[index]->GetSlicer(i)->ForceUpdateDisplayExtent();
2059 #endif
2060
2061       for (int j = 1; j <= 4; j++) {
2062         item->setData(j,Qt::CheckStateRole,DataTree->topLevelItem(index)->data(j,Qt::CheckStateRole));
2063       }
2064
2065       //Create the buttons for reload and close
2066       qApp->processEvents();
2067       QTreePushButton* cButton = new QTreePushButton;
2068       cButton->setItem(item);
2069       cButton->setColumn(COLUMN_CLOSE_IMAGE);
2070       cButton->setToolTip(tr("close image"));
2071       cButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/exit.png")));
2072       connect(cButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
2073         this,SLOT(CloseImage(QTreeWidgetItem*, int)));
2074
2075       QTreePushButton* rButton = new QTreePushButton;
2076       rButton->setItem(item);
2077       rButton->setColumn(COLUMN_RELOAD_IMAGE);
2078       rButton->setToolTip(tr("reload image"));
2079       rButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/rotateright.png")));
2080       connect(rButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
2081         this,SLOT(ReloadImage(QTreeWidgetItem*, int)));
2082
2083       DataTree->topLevelItem(index)->setExpanded(1);
2084       DataTree->topLevelItem(index)->addChild(item);
2085       DataTree->setItemWidget(item, COLUMN_CLOSE_IMAGE, cButton);
2086       DataTree->setItemWidget(item, COLUMN_RELOAD_IMAGE, rButton);
2087
2088       //set the id of the image
2089       QString id = DataTree->topLevelItem(index)->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString();
2090       item->setData(COLUMN_IMAGE_NAME,Qt::UserRole,id.toStdString().c_str());
2091       UpdateTree();
2092       qApp->processEvents();
2093       ImageInfoChanged();
2094       QApplication::restoreOverrideCursor();
2095
2096       // Update the display to update, e.g., the sliders
2097       for(int i=0; i<4; i++)
2098         DisplaySliders(index, i);
2099     } else {
2100       QApplication::restoreOverrideCursor();
2101       QString error = "Cannot import the new image.\n";
2102       error += mSlicerManagers[index]->GetLastError().c_str();
2103       QMessageBox::information(this,tr("Problem reading image !"),error);
2104     }
2105     WindowLevelChanged();
2106   }
2107   else
2108     QMessageBox::information(this,tr("Problem reading Overlay !"),"File doesn't exist!");
2109 }
2110 //------------------------------------------------------------------------------
2111
2112
2113 //------------------------------------------------------------------------------
2114 void vvMainWindow::AddROI(int index, QString file)
2115 {
2116   /*
2117   // Get slice manager
2118
2119   // Load image
2120
2121   vvImageReader * mReader = new vvImageReader;
2122   mReader->SetInputFilename(filename.toStdString());
2123   mReader->Update(IMAGE);
2124   if (mReader->GetLastError().size() != 0) {
2125   std::cerr << "Error while reading " << filename.toStdString() << std::endl;
2126   QString error = "Cannot open file \n";
2127   error += mReader->GetLastError().c_str();
2128   QMessageBox::information(this,tr("Reading problem"),error);
2129   delete mReader;
2130   return;
2131   }
2132   vvImage::Pointer roi = mReader->GetOutput();
2133
2134   // Create roi in new tool
2135   vvToolStructureSetManager::AddImage(mCurrentSlicerManager, roi);
2136   */
2137 }
2138 //------------------------------------------------------------------------------
2139
2140 //------------------------------------------------------------------------------
2141 void vvMainWindow::SelectFusionImage()
2142 {
2143   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2144
2145   if (!(CheckAddedImage(index, "fusion")) || !(CheckAddedImage(index, "fusionSequence")))
2146     return;
2147
2148   QString Extensions = EXTENSIONS;
2149   Extensions += ";;All Files (*)";
2150   QStringList files = QFileDialog::getOpenFileNames(this,tr("Load Fusion image"),mInputPathName,Extensions);
2151   if (files.isEmpty())
2152     return;
2153
2154   std::vector<std::string> vecFileNames;
2155   for (int i = 0; i < files.size(); i++) {
2156     vecFileNames.push_back(files[i].toStdString());
2157   }
2158   AddFusionImage(index,vecFileNames,vvImageReader::IMAGE);
2159 }
2160 //------------------------------------------------------------------------------
2161
2162 //------------------------------------------------------------------------------
2163 void vvMainWindow::ResetTransformationToIdentity()
2164 {
2165   std::string actorType = DataTree->selectedItems()[0]->data(1,Qt::UserRole).toString().toStdString();
2166   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2167   mSlicerManagers[index]->ResetTransformationToIdentity(actorType);
2168   ImageInfoChanged();
2169 }
2170 //------------------------------------------------------------------------------
2171
2172 //------------------------------------------------------------------------------
2173 void vvMainWindow::AddFusionImage(int index, std::vector<std::string> fileNames, vvImageReader::LoadedImageType type)
2174 {
2175   QString file(fileNames[0].c_str());
2176   if (QFile::exists(file))
2177   {
2178     mInputPathName = itksys::SystemTools::GetFilenamePath(file.toStdString()).c_str();
2179     itk::ImageIOBase::Pointer reader = itk::ImageIOFactory::CreateImageIO(
2180       file.toStdString().c_str(), itk::ImageIOFactory::ReadMode);
2181     reader->SetFileName(fileNames[0].c_str());
2182     reader->ReadImageInformation();
2183     std::string component = reader->GetComponentTypeAsString(reader->GetComponentType());
2184     int dimension = reader->GetNumberOfDimensions();
2185     QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
2186     vvProgressDialog progress("Opening fusion");
2187     qApp->processEvents();
2188
2189     std::string filename = itksys::SystemTools::GetFilenameWithoutExtension(file.toStdString()).c_str();
2190     if (mSlicerManagers[index]->SetFusion(fileNames,dimension, component,type)) {
2191       //create an item in the tree with good settings
2192       QTreeWidgetItem *item = new QTreeWidgetItem();
2193       item->setData(0,Qt::UserRole,file.toStdString().c_str());
2194       item->setData(1,Qt::UserRole,tr("fusion"));
2195       QFileInfo fileinfo(file); //Do not show the path
2196           item->setData(COLUMN_IMAGE_NAME,Qt::DisplayRole,fileinfo.fileName());
2197           item->setToolTip(COLUMN_IMAGE_NAME, mSlicerManagers[index]->GetListOfAbsoluteFilePathInOneString("fusion").c_str());
2198           qApp->processEvents();
2199 #if VTK_MAJOR_VERSION > 5
2200       for ( unsigned int i = 0; i < mSlicerManagers[index]->GetNumberOfSlicers(); i++)
2201         mSlicerManagers[index]->GetSlicer(i)->ForceUpdateDisplayExtent();
2202 #endif
2203       for (int j = 1; j <= 4; j++) {
2204         item->setData(j,Qt::CheckStateRole,DataTree->topLevelItem(index)->data(j,Qt::CheckStateRole));
2205       }
2206
2207       //Create the buttons for reload and close
2208       qApp->processEvents();
2209       QTreePushButton* cButton = new QTreePushButton;
2210       cButton->setItem(item);
2211       cButton->setColumn(COLUMN_CLOSE_IMAGE);
2212       cButton->setToolTip(tr("close image"));
2213       cButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/exit.png")));
2214       connect(cButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
2215         this,SLOT(CloseImage(QTreeWidgetItem*, int)));
2216
2217       QTreePushButton* rButton = new QTreePushButton;
2218       rButton->setItem(item);
2219       rButton->setColumn(COLUMN_RELOAD_IMAGE);
2220       rButton->setToolTip(tr("reload image"));
2221       rButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/rotateright.png")));
2222       connect(rButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
2223         this,SLOT(ReloadImage(QTreeWidgetItem*, int)));
2224
2225       DataTree->topLevelItem(index)->setExpanded(1);
2226       DataTree->topLevelItem(index)->addChild(item);
2227       DataTree->setItemWidget(item, COLUMN_CLOSE_IMAGE, cButton);
2228       DataTree->setItemWidget(item, COLUMN_RELOAD_IMAGE, rButton);
2229
2230       //set the id of the image
2231       QString id = DataTree->topLevelItem(index)->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString();
2232       item->setData(COLUMN_IMAGE_NAME,Qt::UserRole,id.toStdString().c_str());
2233       UpdateTree();
2234       qApp->processEvents();
2235       ImageInfoChanged();
2236       QApplication::restoreOverrideCursor();
2237
2238       // Update the display to update, e.g., the sliders
2239       for(int i=0; i<4; i++)
2240         DisplaySliders(index, i);
2241     } else {
2242       QApplication::restoreOverrideCursor();
2243       QString error = "Cannot import the new image.\n";
2244       error += mSlicerManagers[index]->GetLastError().c_str();
2245       QMessageBox::information(this,tr("Problem reading image !"),error);
2246     }
2247     WindowLevelChanged();
2248   }
2249   else
2250     QMessageBox::information(this,tr("Problem reading Fusion !"),"File doesn't exist!");
2251 }
2252 //------------------------------------------------------------------------------
2253 //------------------------------------------------------------------------------
2254 void vvMainWindow::AddLandmarks(int index, std::vector<std::string> files)
2255 {
2256     if (!landmarksPanel->LoadFromFile(files))
2257       QMessageBox::information(this,tr("Problem reading Landmarks !"),"File doesn't exist!");
2258
2259     landmarksPanel->SetCurrentPath(mInputPathName.toStdString());
2260     landmarksPanel->SetCurrentImage(mSlicerManagers[index]->GetFileName().c_str());
2261 }
2262
2263 //------------------------------------------------------------------------------
2264 void vvMainWindow::OpenField()
2265 {
2266   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2267
2268   if (!(CheckAddedImage(index, "vector")))
2269     return;
2270
2271   QString Extensions = "Images ( *.mhd *.mha *.vf *.nii *.nrrd *.nhdr)";
2272   // Extensions += ";;Images ( *.mha)";
2273   // Extensions += ";;VF Images ( *.vf)";
2274   // Extensions += ";;nii Images ( *.nii)";
2275   // Extensions += ";;nrrd Images ( *.nrrd)";
2276   // Extensions += ";;nhdr Images ( *.nhdr)";
2277   Extensions += ";;All Files (*)";
2278   QString file = QFileDialog::getOpenFileName(this,tr("Load deformation field"),mInputPathName,Extensions);
2279   if (!file.isEmpty())
2280     AddField(file,index);
2281 }
2282 //------------------------------------------------------------------------------
2283
2284
2285 //------------------------------------------------------------------------------
2286 void vvMainWindow::AddFieldEntry(QString filename,int index,bool from_disk)
2287 {
2288   //create an item in the tree with good settings
2289   QTreeWidgetItem *item = new QTreeWidgetItem();
2290   item->setData(0,Qt::UserRole,filename.toStdString().c_str());
2291   item->setData(1,Qt::UserRole,tr("vector"));
2292   QFileInfo fileinfo(filename); //Do not show the path
2293   item->setData(COLUMN_IMAGE_NAME,Qt::DisplayRole,fileinfo.fileName());
2294   item->setToolTip(COLUMN_IMAGE_NAME, mSlicerManagers[index]->GetListOfAbsoluteFilePathInOneString("vector").c_str());
2295   qApp->processEvents();
2296
2297   for (int j = 1; j <= 4; j++) {
2298     item->setData(j,Qt::CheckStateRole,DataTree->topLevelItem(index)->data(j,Qt::CheckStateRole));
2299   }
2300
2301   //Create the buttons for reload and close
2302   qApp->processEvents();
2303   QTreePushButton* cButton = new QTreePushButton;
2304   cButton->setItem(item);
2305   cButton->setColumn(COLUMN_CLOSE_IMAGE);
2306   cButton->setToolTip(tr("close vector field"));
2307   cButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/exit.png")));
2308   connect(cButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
2309     this,SLOT(CloseImage(QTreeWidgetItem*, int)));
2310
2311   QTreePushButton* rButton = new QTreePushButton;
2312   rButton->setItem(item);
2313   rButton->setColumn(COLUMN_RELOAD_IMAGE);
2314   rButton->setToolTip(tr("reload vector field"));
2315   rButton->setEnabled(from_disk);
2316   rButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/rotateright.png")));
2317   connect(rButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
2318     this,SLOT(ReloadImage(QTreeWidgetItem*, int)));
2319
2320   DataTree->topLevelItem(index)->setExpanded(1);
2321   DataTree->topLevelItem(index)->addChild(item);
2322   DataTree->setItemWidget(item, COLUMN_RELOAD_IMAGE, rButton);
2323   DataTree->setItemWidget(item, COLUMN_CLOSE_IMAGE, cButton);
2324
2325   //set the id of the image
2326   QString id = DataTree->topLevelItem(index)->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString();
2327   item->setData(COLUMN_IMAGE_NAME,Qt::UserRole,id.toStdString().c_str());
2328   UpdateTree();
2329   qApp->processEvents();
2330   ImageInfoChanged();
2331   QApplication::restoreOverrideCursor();
2332 }
2333 //------------------------------------------------------------------------------
2334
2335
2336 //------------------------------------------------------------------------------
2337 void vvMainWindow::AddField(vvImage::Pointer vf,QString file,int index)
2338 {
2339   QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
2340   vvSlicerManager* imageManager = mSlicerManagers[index];
2341   if (imageManager->SetVF(vf,file.toStdString())) {
2342     AddFieldEntry(file,index,false);
2343 #if VTK_MAJOR_VERSION > 5
2344       for ( unsigned int i = 0; i < mSlicerManagers[index]->GetNumberOfSlicers(); i++)
2345         mSlicerManagers[index]->GetSlicer(i)->ForceUpdateDisplayExtent();
2346 #endif
2347   } else {
2348     QString error = "Cannot import the vector field for this image.\n";
2349     error += imageManager->GetLastError().c_str();
2350     QMessageBox::information(this,tr("Problem reading VF !"),error);
2351   }
2352   QApplication::restoreOverrideCursor();
2353 }
2354 //------------------------------------------------------------------------------
2355
2356
2357 //------------------------------------------------------------------------------
2358 void vvMainWindow::AddField(QString file,int index)
2359 {
2360   if (QFile::exists(file)) {
2361     mInputPathName = itksys::SystemTools::GetFilenamePath(file.toStdString()).c_str();
2362
2363     //init the progress events
2364     QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
2365     vvProgressDialog progress("Opening " + file.toStdString());
2366     qApp->processEvents();
2367
2368     //read the vector and put it in the current mSlicerManager
2369     vvSlicerManager* imageManager = mSlicerManagers[index];
2370     qApp->processEvents();
2371
2372     std::string filename = itksys::SystemTools::GetFilenameWithoutExtension(file.toStdString()).c_str();
2373     if (imageManager->SetVF(file.toStdString())) {
2374       imageManager->Render();
2375       AddFieldEntry(file,index,true);
2376     } else {
2377       QApplication::restoreOverrideCursor();
2378       QString error = "Cannot import the vector field for this image.\n";
2379       error += imageManager->GetLastError().c_str();
2380       QMessageBox::information(this,tr("Problem reading VF !"),error);
2381     }
2382   } else
2383     QMessageBox::information(this,tr("Problem reading VF !"),"File doesn't exist!");
2384
2385 }
2386 //------------------------------------------------------------------------------
2387
2388
2389 //------------------------------------------------------------------------------
2390 void vvMainWindow::SetVFProperty(int subsampling, int scale, int log, int width, double r, double g, double b)
2391 {
2392   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2393   if (mSlicerManagers[index]->GetSlicer(0)->GetVF()) {
2394     for (int i = 0; i < 4; i++) {
2395       mSlicerManagers[index]->GetSlicer(i)->SetVFSubSampling(subsampling);
2396       mSlicerManagers[index]->GetSlicer(i)->SetVFScale(scale);
2397       mSlicerManagers[index]->GetSlicer(i)->SetVFWidth(width);
2398       mSlicerManagers[index]->GetSlicer(i)->SetVFColor(r,g,b);
2399       if (log > 0)
2400         mSlicerManagers[index]->GetSlicer(i)->SetVFLog(1);
2401       else
2402         mSlicerManagers[index]->GetSlicer(i)->SetVFLog(0);
2403     }
2404   }
2405 }
2406 //------------------------------------------------------------------------------
2407
2408
2409 //------------------------------------------------------------------------------
2410 void vvMainWindow::SetOverlayProperty(int color, int linked, double window, double level)
2411 {
2412   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2413   if (mSlicerManagers[index]->GetSlicer(0)->GetOverlay()) {
2414     mSlicerManagers[index]->SetOverlayColor(color);
2415     mSlicerManagers[index]->SetColorMap(0);
2416     mSlicerManagers[index]->SetLinkOverlayWindowLevel(linked);
2417     mSlicerManagers[index]->SetOverlayColorWindow(window);
2418     mSlicerManagers[index]->SetOverlayColorLevel(level);
2419     mSlicerManagers[index]->Render();
2420   }
2421 }
2422 //------------------------------------------------------------------------------
2423
2424 //------------------------------------------------------------------------------
2425 void vvMainWindow::SetFusionProperty(int opacity, int thresOpacity, int colormap,double window, double level, bool showLegend)
2426 {
2427   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2428   if (mSlicerManagers[index]->GetSlicer(0)->GetFusion()) {
2429     mSlicerManagers[index]->SetFusionColorMap(colormap);
2430     mSlicerManagers[index]->SetFusionOpacity(opacity);
2431     mSlicerManagers[index]->SetFusionThresholdOpacity(thresOpacity);
2432     mSlicerManagers[index]->SetFusionWindow(window);
2433     mSlicerManagers[index]->SetFusionLevel(level);
2434     mSlicerManagers[index]->SetFusionShowLegend(showLegend);
2435     mSlicerManagers[index]->SetColorMap(0);
2436     mSlicerManagers[index]->Render();
2437   }
2438 }
2439 //------------------------------------------------------------------------------
2440
2441
2442 //------------------------------------------------------------------------------
2443 void vvMainWindow::SelectFusionSequence()
2444 {
2445   //get the index of the slicer manager of the main sequence (CT)
2446   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2447
2448   if (!(CheckAddedImage(index, "fusion")) || !(CheckAddedImage(index, "fusionSequence")))
2449     return;
2450
2451   QString Extensions = EXTENSIONS;
2452   Extensions += ";;All Files (*)";
2453   QStringList files = QFileDialog::getOpenFileNames(this,tr("Load Overlay image sequence"),mInputPathName,Extensions);
2454   if (files.isEmpty())
2455     return;
2456
2457   std::vector<std::string> vecFileNames;
2458   for (int i = 0; i < files.size(); i++) {
2459     vecFileNames.push_back(files[i].toStdString());
2460   }
2461
2462   //associate the secondary sequence (US) to the main one
2463   AddFusionSequence(index,vecFileNames,vvImageReader::MERGEDWITHTIME);
2464 }
2465 //------------------------------------------------------------------------------
2466
2467
2468 //------------------------------------------------------------------------------
2469 void vvMainWindow::SelectFusionSequenceCorrespondances()
2470 {
2471   //make sure the index is right?
2472   //in the end, I should attach the temporal data to the right sequence!
2473   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2474   //in case the other sequence got selected, make sure we select the primary sequence
2475   if ( (!mSlicerManagers[index]->GetSlicer(0)->GetFusion()) && mSlicerManagers[index]->GetFusionSequenceIndexOfLinkedManager()>=0 ) {
2476     index = mSlicerManagers[index]->GetFusionSequenceIndexOfLinkedManager();
2477   }
2478
2479   //open a dialog box to find a file
2480   //QString Extensions = EXTENSIONS;
2481   QString Extensions = ";;All Files (*)";
2482   QString fileName = QFileDialog::getOpenFileName(this,tr("Load respiratory signal for fused sequence"),mInputPathName,Extensions);
2483   if (fileName.isNull())
2484     return;
2485
2486   //read it as a vector of values
2487   vnl_vector<double> tmpVect;
2488
2489   std::ifstream file;
2490   file.open(fileName.toStdString().c_str());
2491   tmpVect.read_ascii(file);
2492   file.close();
2493
2494   //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
2495   bool signalOK = true;
2496   unsigned nbFrameMain = mSlicerManagers[index]->GetImage()->GetTransform().size();
2497   unsigned nbFrameSecondary = mSlicerManagers[index]->GetFusionSequenceNbFrames();
2498   std::cout<<"nbFrameMain = "<<nbFrameMain<<", nbFrameSecondary= "<<nbFrameSecondary<<", signal size: "<<tmpVect.size()<<std::endl;
2499   std::vector<unsigned> temporalCorrespondances;
2500   if ( tmpVect.size() == nbFrameMain + nbFrameSecondary ) {
2501     for (unsigned i=0 ; i<tmpVect.size() ; i++) {
2502       if (i<nbFrameMain) { //first part of the file: i -> index in secondary seq.
2503         if ( tmpVect(i)<nbFrameSecondary ) temporalCorrespondances.push_back(tmpVect(i));
2504         else { signalOK=false; break; } //pointing outside the secondary sequence...
2505       }
2506       else { //first part of the file -> index in secondary seq.
2507         if ( tmpVect(i)<nbFrameMain ) temporalCorrespondances.push_back(tmpVect(i));
2508         else { signalOK=false; break; } //pointing outside the secondary sequence...
2509       }
2510     }
2511   }
2512   else {signalOK=false;}
2513   if (!signalOK) {//else, send a message to signal the failure...
2514     QString error = "The provided temporal correspondances is invalid - check tooltip.\n";
2515     error += "Ignoring file: " + fileName;
2516     QMessageBox::information(this,tr("Problem adding temporal correspondances!"),error);
2517     return;
2518   }
2519   else {
2520     //for convenience, associate this sequence to both the current slicer manager, and to the linked one
2521     mSlicerManagers[index]->SetFusionSequenceCorrespondances(temporalCorrespondances);
2522     mSlicerManagers[ mSlicerManagers[index]->GetFusionSequenceIndexOfLinkedManager() ]->SetFusionSequenceCorrespondances(temporalCorrespondances);
2523     overlayPanel->enableFusionSequenceTemporalSync();
2524   }
2525
2526 }
2527 //------------------------------------------------------------------------------
2528
2529
2530 //------------------------------------------------------------------------------
2531 //when this function is called index is the slicer manager index corresponding to the main sequence (CT)
2532 //the files behind fileNames points to the data for the secondary sequence
2533 void vvMainWindow::AddFusionSequence(int index, std::vector<std::string> fileNames, vvImageReader::LoadedImageType type)
2534 {
2535   QString file(fileNames[0].c_str());
2536   if (QFile::exists(file))
2537   {
2538     mInputPathName = itksys::SystemTools::GetFilenamePath(file.toStdString()).c_str();
2539     itk::ImageIOBase::Pointer reader = itk::ImageIOFactory::CreateImageIO(
2540       file.toStdString().c_str(), itk::ImageIOFactory::ReadMode);
2541     std::sort (fileNames.begin(), fileNames.end());//make sure the files are sorted.
2542     reader->SetFileName(fileNames[0].c_str());
2543     reader->ReadImageInformation();
2544     std::string component = reader->GetComponentTypeAsString(reader->GetComponentType());
2545     int dimension = reader->GetNumberOfDimensions();
2546     QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
2547     vvProgressDialog progress("Opening " + file.toStdString());
2548     qApp->processEvents();
2549
2550     std::string filename = itksys::SystemTools::GetFilenameWithoutExtension(file.toStdString()).c_str();
2551
2552     if (mSlicerManagers[index]->SetFusionSequence(fileNames,dimension, component,type)) {
2553       //create an item in the tree with good settings
2554       QTreeWidgetItem *item = new QTreeWidgetItem();
2555       item->setData(0,Qt::UserRole,file.toStdString().c_str());
2556       item->setData(1,Qt::UserRole,tr("fusionSequence"));
2557
2558       QFileInfo fileinfo(file); //Do not show the path
2559       item->setData(COLUMN_IMAGE_NAME,Qt::DisplayRole,fileinfo.fileName());
2560       item->setToolTip(COLUMN_IMAGE_NAME, mSlicerManagers[index]->GetListOfAbsoluteFilePathInOneString("fusionSequence").c_str());
2561       qApp->processEvents();
2562 #if VTK_MAJOR_VERSION > 5
2563       for ( unsigned int i = 0; i < mSlicerManagers[index]->GetNumberOfSlicers(); i++)
2564         mSlicerManagers[index]->GetSlicer(i)->ForceUpdateDisplayExtent();
2565 #endif
2566       for (int j = 1; j <= 4; j++) {
2567         item->setData(j,Qt::CheckStateRole,DataTree->topLevelItem(index)->data(j,Qt::CheckStateRole));
2568       }
2569
2570       //Create the buttons for reload and close
2571       qApp->processEvents();
2572       QTreePushButton* cButton = new QTreePushButton;
2573       cButton->setItem(item);
2574       cButton->setColumn(COLUMN_CLOSE_IMAGE);
2575       cButton->setToolTip(tr("close image"));
2576       cButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/exit.png")));
2577       connect(cButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
2578         this,SLOT(CloseImage(QTreeWidgetItem*, int)));
2579
2580       QTreePushButton* rButton = new QTreePushButton;
2581       rButton->setItem(item);
2582       rButton->setColumn(COLUMN_RELOAD_IMAGE);
2583       rButton->setToolTip(tr("reload image"));
2584       rButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/rotateright.png")));
2585       connect(rButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
2586         this,SLOT(ReloadImage(QTreeWidgetItem*, int)));
2587
2588       DataTree->topLevelItem(index)->setExpanded(1);
2589       DataTree->topLevelItem(index)->addChild(item);
2590       DataTree->setItemWidget(item, COLUMN_CLOSE_IMAGE, cButton);
2591       DataTree->setItemWidget(item, COLUMN_RELOAD_IMAGE, rButton);
2592
2593       //store the original transform matrix
2594       int indexParent = GetSlicerIndexFromItem( DataTree->topLevelItem(index) );
2595       mSlicerManagers[indexParent]->SetFusionSequenceMainTransformMatrix( mSlicerManagers[indexParent]->GetSlicer(0)->GetImage()->GetTransform()[0]->GetMatrix() );
2596
2597       //set the id of the image
2598       QString id = DataTree->topLevelItem(index)->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString();
2599       item->setData(COLUMN_IMAGE_NAME,Qt::UserRole,id.toStdString().c_str());
2600       UpdateTree();
2601       qApp->processEvents();
2602
2603       //ImageInfoChanged();
2604
2605       QApplication::restoreOverrideCursor();
2606       // Update the display to update, e.g., the sliders
2607       for(int i=0; i<4; i++)
2608         DisplaySliders(index, i);
2609
2610
2611       //This loads the secondary sequence (US) as an independent sequence
2612       LoadImages(fileNames, type);
2613       //reset the transforms to identity
2614       //FIX -- and set the thickness of the US slices to a large value (necessary for visualization purposes...)
2615       double sp_x, sp_y, sp_z;
2616       mSlicerManagers[indexParent]->GetImage()->GetVTKImages()[0]->GetSpacing(sp_x, sp_y, sp_z);
2617       sp_z = std::max(sp_x, std::max(sp_y, sp_z)) + 0.5; //
2618       for (unsigned i=0 ; i<mSlicerManagers.back()->GetImage()->GetTransform().size() ; i++) {
2619         sp_x = mSlicerManagers.back()->GetImage()->GetVTKImages()[i]->GetSpacing()[0];
2620         sp_y = mSlicerManagers.back()->GetImage()->GetVTKImages()[i]->GetSpacing()[1];
2621         mSlicerManagers.back()->GetImage()->GetVTKImages()[i]->SetSpacing( sp_x, sp_y, sp_z);
2622         mSlicerManagers.back()->GetImage()->GetTransform()[i]->Identity();
2623         mSlicerManagers.back()->GetImage()->GetTransform()[i]->Update();
2624       }
2625
2626       //automatically link both images...
2627       AddLink(mSlicerManagers[indexParent]->GetId().c_str(), mSlicerManagers.back()->GetId().c_str(), false);
2628
2629       //tie the main and secondary sequences by raising flags and informing each another of their respective SlicerManager indices
2630       mSlicerManagers[indexParent]->SetFusionSequenceIndexOfLinkedManager(mSlicerManagers.size()-1);
2631       mSlicerManagers[indexParent]->SetFusionSequenceInvolvmentCode(0); //main sequence
2632       mSlicerManagers.back()->SetFusionSequenceIndexOfLinkedManager(indexParent);
2633       mSlicerManagers.back()->SetFusionSequenceInvolvmentCode(1); //secondary sequence
2634       for (unsigned i=0 ; i<4 ; i++) {
2635         mSlicerManagers.back()->GetSlicer(i)->SetFusionSequenceCode(1); //flag the slicers of the secondary sequence
2636       }
2637
2638     } else {
2639       QApplication::restoreOverrideCursor();
2640       QString error = "Cannot import the new image.\n";
2641       error += mSlicerManagers[index]->GetLastError().c_str();
2642       QMessageBox::information(this,tr("Problem reading image !"),error);
2643     }
2644     WindowLevelChanged();
2645     ImageInfoChanged(); //this internally calls WindowLevelChanged...
2646   }
2647   else {
2648     QMessageBox::information(this,tr("Problem reading fusion sequence !"),"File doesn't exist!");
2649     return;
2650   }
2651
2652 }
2653 //------------------------------------------------------------------------------
2654
2655
2656 //------------------------------------------------------------------------------
2657 //fusionSequenceFrameIndex and fusionSequenceNbFrames are relative to the secondary sequence (US)
2658 void vvMainWindow::SetFusionSequenceProperty(int fusionSequenceFrameIndex, bool spatialSyncFlag, unsigned int fusionSequenceNbFrames, bool temporalSyncFlag)
2659 {
2660   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2661
2662   if (!mSlicerManagers[index]->IsInvolvedInFusionSequence()) return;
2663
2664   //check if the focus moved to the linked sequence, and in this case, select the master sequence instead
2665   if (!mSlicerManagers[index]->IsMainSequenceOfFusionSequence()) {
2666     index = mSlicerManagers[index]->GetFusionSequenceIndexOfLinkedManager();
2667   }
2668   int secondaryIndex = mSlicerManagers[index]->GetFusionSequenceIndexOfLinkedManager();
2669   if (secondaryIndex==-1) return; //this should never happen
2670   if ( (!mSlicerManagers[index]->IsMainSequenceOfFusionSequence()) ||
2671     (!mSlicerManagers[secondaryIndex]->IsSecondarySequenceOfFusionSequence()) )
2672   {return;} //this should never happen, raise an exception?
2673
2674   if (mSlicerManagers[index]->GetSlicer(0)->GetFusion()) {
2675
2676     //First, if the spatialSync button is unchecked, then reposition the parent sequence (CT) in its original coordinate frame
2677     if ( (!spatialSyncFlag) && (mSlicerManagers[index]->GetFusionSequenceSpatialSyncFlag()) ) {
2678       for ( unsigned i=0 ; i<mSlicerManagers[index]->GetSlicer(0)->GetImage()->GetTransform().size() ; i++ ) {
2679         mSlicerManagers[index]->GetSlicer(0)->GetImage()->GetTransform()[i]->SetMatrix( mSlicerManagers[index]->GetFusionSequenceMainTransformMatrix() );
2680         mSlicerManagers[index]->GetSlicer(0)->GetImage()->GetTransform()[i]->Update();
2681       }
2682
2683       for (int i=0; i<mSlicerManagers[index]->GetNumberOfSlicers(); i++) {
2684         mSlicerManagers[index]->GetSlicer(i)->ForceUpdateDisplayExtent();
2685         mSlicerManagers[index]->GetSlicer(i)->Render();
2686       }
2687     }
2688
2689     //then, update the property values in the slicer manager
2690     mSlicerManagers[index]->SetFusionSequenceLength(fusionSequenceNbFrames);
2691     mSlicerManagers[index]->SetFusionSequenceSpatialSyncFlag(spatialSyncFlag);
2692     mSlicerManagers[index]->SetFusionSequenceTemporalSyncFlag(temporalSyncFlag);
2693     mSlicerManagers[index]->SetFusionSequenceFrameIndex(fusionSequenceFrameIndex);
2694
2695     //select the right frame of the US sequence
2696     mSlicerManagers[index]->SetFusionSequenceTSlice(fusionSequenceFrameIndex); //here, I should only update the overlayed sequence
2697     mSlicerManagers[secondaryIndex]->SetTSlice(fusionSequenceFrameIndex, false); //this should update the secondary sequence (individual version)
2698
2699     //update the horizontal sliders of the main window
2700     overlayPanel->updateFusionSequenceSliderValueFromWindow(fusionSequenceFrameIndex, false);
2701
2702     if (spatialSyncFlag) { //reslice the CT
2703
2704       if (temporalSyncFlag) { //do the temporal synchronisation
2705         int mainSequenceFrameIndex=0;
2706         //estimate the TSlice to set to the CT
2707         unsigned nbFramesMain = mSlicerManagers[index]->GetImage()->GetTransform().size();
2708         mainSequenceFrameIndex = mSlicerManagers[index]->GetFusionSequenceCorrespondances()[ nbFramesMain + fusionSequenceFrameIndex];
2709         //and set it!
2710         mSlicerManagers[index]->SetTSlice(mainSequenceFrameIndex, false);
2711         //warning, there is a loopback, and modification of the TSlice in main sequence forces an update of the TSlice in secondary, etc...
2712       }
2713
2714
2715       //Set the transform matrix of the parent sequence (typically CT / 4DCT)
2716       vtkSmartPointer<vtkMatrix4x4> tmpMat = vtkSmartPointer<vtkMatrix4x4>::New();
2717       vtkMatrix4x4::Invert( mSlicerManagers[index]->GetFusionSequenceInitialTransformMatrixAtFrame(fusionSequenceFrameIndex), tmpMat );
2718       for ( unsigned i=0 ; i<mSlicerManagers[index]->GetSlicer(0)->GetImage()->GetTransform().size() ; i++ ) {
2719         mSlicerManagers[index]->GetSlicer(0)->GetImage()->GetTransform()[i]->SetMatrix( mSlicerManagers[index]->GetFusionSequenceMainTransformMatrix() );
2720         mSlicerManagers[index]->GetSlicer(0)->GetImage()->GetTransform()[i]->PreMultiply();
2721         mSlicerManagers[index]->GetSlicer(0)->GetImage()->GetTransform()[i]->Concatenate( tmpMat );
2722         mSlicerManagers[index]->GetSlicer(0)->GetImage()->GetTransform()[i]->Update();
2723       }
2724
2725       for (int i=0; i<mSlicerManagers[index]->GetNumberOfSlicers(); i++) {
2726         mSlicerManagers[index]->GetSlicer(i)->ForceUpdateDisplayExtent();
2727         mSlicerManagers[index]->GetSlicer(i)->Render();
2728       }
2729
2730     }
2731
2732   }
2733 }
2734 //------------------------------------------------------------------------------
2735
2736
2737 //------------------------------------------------------------------------------
2738 void vvMainWindow::SaveAs()
2739 {
2740   if (DataTree->selectedItems()[0]->data(1,Qt::UserRole).toString() == "vector") {
2741     QMessageBox::warning(this,tr("Unsupported type"),tr("Sorry, saving a vector field is unsupported for the moment"));
2742     return;
2743   }
2744
2745   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2746   int dimension = mSlicerManagers[index]->GetDimension();
2747   QStringList OutputListeFormat;
2748   OutputListeFormat.clear();
2749   if (dimension == 1) {
2750     OutputListeFormat.push_back(".mhd");
2751     OutputListeFormat.push_back(".mha");
2752   }
2753   if (dimension == 2) {
2754     OutputListeFormat.push_back(".bmp");
2755     OutputListeFormat.push_back(".png");
2756     OutputListeFormat.push_back(".jpeg");
2757     OutputListeFormat.push_back(".tif");
2758     OutputListeFormat.push_back(".mhd");
2759     OutputListeFormat.push_back(".mha");
2760     OutputListeFormat.push_back(".hdr");
2761     OutputListeFormat.push_back(".vox");
2762   } else if (dimension == 3) {
2763     OutputListeFormat.push_back(".mhd");
2764     OutputListeFormat.push_back(".mha");
2765     OutputListeFormat.push_back(".nii");
2766     OutputListeFormat.push_back(".nrrd");
2767     OutputListeFormat.push_back(".nhdr");
2768     OutputListeFormat.push_back(".hdr");
2769     OutputListeFormat.push_back(".vox");
2770   } else if (dimension == 4) {
2771     OutputListeFormat.push_back(".mhd");
2772     OutputListeFormat.push_back(".mha");
2773     OutputListeFormat.push_back(".nii");
2774     OutputListeFormat.push_back(".nrrd");
2775     OutputListeFormat.push_back(".nhdr");
2776   }
2777   QString Extensions = "AllFiles(*.*)";
2778   for (int i = 0; i < OutputListeFormat.count(); i++) {
2779     Extensions += ";;Images ( *";
2780     Extensions += OutputListeFormat[i];
2781     Extensions += ")";
2782   }
2783   QString fileName = QFileDialog::getSaveFileName(this,
2784     tr("Save As"),
2785     mSlicerManagers[index]->GetFileName().c_str(),
2786     Extensions);
2787   if (!fileName.isEmpty()) {
2788     std::string fileformat = itksys::SystemTools::GetFilenameLastExtension(fileName.toStdString());
2789     if (OutputListeFormat.contains(
2790       fileformat.c_str())) {
2791         QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
2792         std::string action = "Saving";
2793         vvProgressDialog progress("Saving "+fileName.toStdString());
2794         qApp->processEvents();
2795         vvImageWriter::Pointer writer = vvImageWriter::New();
2796         writer->SetOutputFileName(fileName.toStdString());
2797         writer->SetInput(mSlicerManagers[index]->GetImage());
2798
2799         // Check on transform and prompt user
2800         writer->SetSaveTransform(false);
2801         bool bId = true;
2802         for(int i=0; i<4; i++)
2803           for(int j=0; j<4; j++) {
2804             // TODO SR and BP: check on the list of transforms and not the first only
2805             double elt = mSlicerManagers[index]->GetImage()->GetTransform()[0]->GetMatrix()->GetElement(i,j);
2806             if(i==j && elt!=1.)
2807               bId = false;
2808             if(i!=j && elt!=0.)
2809               bId = false;
2810           }
2811           if( !bId ) {
2812             QString warning = "The image has an associated linear transform. Do you want to save it along?";
2813             QMessageBox msgBox(QMessageBox::Warning, tr("Save transform"), warning, 0, this);
2814             msgBox.addButton(tr("Yes"), QMessageBox::AcceptRole);
2815             msgBox.addButton(tr("No"), QMessageBox::RejectRole);
2816             if (msgBox.exec() == QMessageBox::AcceptRole)
2817               writer->SetSaveTransform(true);
2818           }
2819
2820           writer->Update();
2821           QApplication::restoreOverrideCursor();
2822           if (writer->GetLastError().size()) {
2823             QString error = "Saving did not succeed\n";
2824             error += writer->GetLastError().c_str();
2825             QMessageBox::information(this,tr("Saving Problem"),error);
2826             SaveAs();
2827           }
2828     } else {
2829       QString error = fileformat.c_str();
2830       if (error.isEmpty())
2831         error += "no file format specified !";
2832       else
2833         error += " format unknown !!!\n";
2834       QMessageBox::information(this,tr("Saving Problem"),error);
2835       SaveAs();
2836     }
2837   }
2838 }
2839 //------------------------------------------------------------------------------
2840
2841 //------------------------------------------------------------------------------
2842 void vvMainWindow::SaveCurrentState()
2843 {
2844   QString Extensions = "XML Files(*.xml)";
2845   QString fileName = QFileDialog::getSaveFileName(this,
2846     tr("Save Current Window State"),
2847     "",
2848     Extensions);
2849
2850   SaveCurrentStateAs(fileName.toStdString());
2851 }
2852 //------------------------------------------------------------------------------
2853
2854 //------------------------------------------------------------------------------
2855 void vvMainWindow::SaveCurrentStateAs(const std::string& stateFile)
2856 {
2857   vvSaveState save_state;
2858   save_state.Run(this, stateFile);
2859 }
2860
2861 //------------------------------------------------------------------------------
2862 void vvMainWindow::ReadSavedState()
2863 {
2864   QString Extensions = "XML Files(*.xml)";
2865   QString fileName = QFileDialog::getOpenFileName(this,
2866     tr("Load Window State"),
2867     "",
2868     Extensions);
2869
2870   ReadSavedStateFile(fileName.toStdString());
2871 }
2872 //------------------------------------------------------------------------------
2873
2874 //------------------------------------------------------------------------------
2875 void vvMainWindow::ReadSavedStateFile(const std::string& stateFile)
2876 {
2877   vvReadState read_state;
2878   read_state.Run(this, stateFile);
2879 }
2880 //------------------------------------------------------------------------------
2881
2882 //------------------------------------------------------------------------------
2883 void vvMainWindow::LinkAllImages()
2884 {
2885   linkPanel->linkAll();
2886 }
2887
2888 //------------------------------------------------------------------------------
2889 void vvMainWindow::AddLink(QString image1,QString image2,bool fromPanel)
2890 {
2891   if (!fromPanel) {
2892     // delegate to linkPanel if call came from elsewhere...
2893     linkPanel->addLinkFromIds(image1, image2);
2894     return;
2895   }
2896
2897   unsigned int sm1 = 0;
2898   unsigned int sm2 = 0;
2899
2900   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
2901     if (image1.toStdString() == mSlicerManagers[i]->GetId()) {
2902       mSlicerManagers[i]->AddLink(image2.toStdString());
2903       sm1 = i;
2904     }
2905     if (image2.toStdString() == mSlicerManagers[i]->GetId()) {
2906       mSlicerManagers[i]->AddLink(image1.toStdString());
2907       sm2 = i;
2908     }
2909   }
2910
2911   if (linkPanel->isLinkAll())   {
2912     emit UpdateLinkedNavigation(mSlicerManagers[sm1]->GetId(), mSlicerManagers[mCurrentPickedImageIndex], mSlicerManagers[mCurrentPickedImageIndex]->GetSlicer(0));
2913     emit UpdateLinkedNavigation(mSlicerManagers[sm2]->GetId(), mSlicerManagers[mCurrentPickedImageIndex], mSlicerManagers[mCurrentPickedImageIndex]->GetSlicer(0));
2914   } else {
2915     emit UpdateLinkedNavigation(mSlicerManagers[sm2]->GetId(), mSlicerManagers[sm1], mSlicerManagers[sm1]->GetSlicer(0));
2916   }
2917 }
2918
2919 //------------------------------------------------------------------------------
2920
2921
2922 //------------------------------------------------------------------------------
2923 void vvMainWindow::RemoveLink(QString image1,QString image2)
2924 {
2925   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
2926     if (image1.toStdString() == mSlicerManagers[i]->GetId()) {
2927       mSlicerManagers[i]->RemoveLink(image2.toStdString());
2928     }
2929     if (image2.toStdString() == mSlicerManagers[i]->GetId()) {
2930       mSlicerManagers[i]->RemoveLink(image1.toStdString());
2931     }
2932   }
2933 }
2934 //------------------------------------------------------------------------------
2935
2936 //------------------------------------------------------------------------------
2937 void vvMainWindow::ChangeImageWithIndexOffset(vvSlicerManager *sm, int slicer, int offset)
2938 {
2939   if(mSlicerManagers.size()==1)
2940     return;
2941
2942   int index = 0;
2943   while(sm != mSlicerManagers[index])
2944     index++;
2945   index = (index+offset+mSlicerManagers.size()) % mSlicerManagers.size();
2946
2947   QTreeWidgetItem* item = GetItemFromSlicerManager(mSlicerManagers[index]);
2948   item->setData(slicer+1,Qt::CheckStateRole,2);         //change checkbox
2949   CurrentImageChanged(mSlicerManagers[index]->GetId()); //select new image
2950   DisplayChanged(item,slicer+1);
2951 }
2952 //------------------------------------------------------------------------------
2953 void vvMainWindow::HorizontalSliderMoved(int value,int column, int slicer_index)
2954 {
2955   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
2956     if (DataTree->topLevelItem(i)->data(column,Qt::CheckStateRole).toInt() > 1) {
2957       //i is the SlicerManager that is in charge of this slicer.
2958       if (mSlicerManagers[i]->IsInvolvedInFusionSequence()) {
2959         //if the slicerManager is involved in a fusionSequence as the secondary sequence, then update the slider position in the overlay panel and everything accordingly
2960         if (mSlicerManagers[i]->IsSecondarySequenceOfFusionSequence()) {
2961           overlayPanel->updateFusionSequenceSliderValueFromWindow(value, true);
2962         }
2963         else { //if this is the primary sequence that has been modified
2964           if (mSlicerManagers[i]->GetFusionSequenceTemporalSyncFlag()) {
2965             //WARNING: for some obscure reason, there are problems when accessing mSlicerManagers[mSlicerManagers[i]->GetFusionSequenceIndexOfLinkedManager()]->GetFusionSequenceFrameIndex();
2966
2967             int estimatedValue=0;
2968             //estimate a corresponding time index for the secondary (US) sequence, and update it accordingly.
2969             estimatedValue = mSlicerManagers[i]->GetFusionSequenceCorrespondances()[ value ];
2970             //TODO: at the moment, there is a loop in TSlice modifications
2971             //modifying sequence 1 causes seq 2 to update, which in turns update seq1...
2972             //I disable control on seq1 at the moment.
2973             //overlayPanel->updateFusionSequenceSliderValueFromWindow(estimatedValue, true);
2974           }
2975         }
2976       }
2977
2978       for (int j = 0; j < 4; j++) {
2979         mSlicerManagers[i]->SetTSliceInSlicer(value,j);
2980       }
2981       mSlicerManagers[i]->GetSlicer(slicer_index)->Render();
2982       break;
2983     }
2984   }
2985 }
2986 //------------------------------------------------------------------------------
2987
2988
2989 //------------------------------------------------------------------------------
2990 void vvMainWindow::NOHorizontalSliderMoved()
2991 {
2992   // if (mCurrentTime == NOHorizontalSlider->value()) return;
2993   HorizontalSliderMoved(NOHorizontalSlider->value(),COLUMN_UL_VIEW,0);
2994   //  mCurrentTime = NOHorizontalSlider->value();
2995 }
2996 //------------------------------------------------------------------------------
2997
2998
2999 //------------------------------------------------------------------------------
3000 void vvMainWindow::NEHorizontalSliderMoved()
3001 {
3002   // if (mCurrentTime == NEHorizontalSlider->value()) return;
3003   HorizontalSliderMoved(NEHorizontalSlider->value(),COLUMN_UR_VIEW,1);
3004   //  mCurrentTime = NEHorizontalSlider->value();
3005 }
3006 //------------------------------------------------------------------------------
3007
3008
3009 //------------------------------------------------------------------------------
3010 void vvMainWindow::SOHorizontalSliderMoved()
3011 {
3012   // if (mCurrentTime == SOHorizontalSlider->value()) return;
3013   HorizontalSliderMoved(SOHorizontalSlider->value(),COLUMN_DL_VIEW,2);
3014   // mCurrentTime = SOHorizontalSlider->value();
3015 }
3016 //------------------------------------------------------------------------------
3017
3018
3019 //------------------------------------------------------------------------------
3020 void vvMainWindow::SEHorizontalSliderMoved()
3021 {
3022   // if (mCurrentTime == SEHorizontalSlider->value()) return;
3023   HorizontalSliderMoved(SEHorizontalSlider->value(),COLUMN_DR_VIEW,3);
3024   // mCurrentTime = SEHorizontalSlider->value();
3025 }
3026 //------------------------------------------------------------------------------
3027
3028 //------------------------------------------------------------------------------
3029 void vvMainWindow::NOVerticalSliderChanged()
3030 {
3031   static int value=-1;
3032   if (value == NOVerticalSlider->value()) return;
3033   else value = NOVerticalSlider->value();
3034   //  int value = NOVerticalSlider->value();
3035   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
3036     if (DataTree->topLevelItem(i)->data(COLUMN_UL_VIEW,Qt::CheckStateRole).toInt() > 1) {
3037       if (mSlicerManagers[i]->GetSlicer(0)->GetSlice() != value) {
3038         mSlicerManagers[i]->GetSlicer(0)->SetSlice(value);
3039         mSlicerManagers[i]->VerticalSliderHasChanged(0, value);
3040
3041         // If nor Update/Render -> slider not work
3042         // only render = ok navigation, but for contour Update needed but slower ?
3043
3044         mSlicerManagers[i]->UpdateSlice(0);  // <-- DS add this. Not too much update ? YES. but needed for ImageContour ...
3045         //mSlicerManagers[i]->GetSlicer(0)->Render(); // <-- DS add this, needed for contour, seems ok ? not too slow ?
3046       }
3047       break;
3048     }
3049   }
3050 }
3051 //------------------------------------------------------------------------------
3052
3053
3054 //------------------------------------------------------------------------------
3055 void vvMainWindow::NEVerticalSliderChanged()
3056 {
3057   static int value=-1;
3058   if (value == NEVerticalSlider->value()) return;
3059   else value = NEVerticalSlider->value();
3060   //  int value = NEVerticalSlider->value();
3061   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
3062     if (DataTree->topLevelItem(i)->data(COLUMN_UR_VIEW,Qt::CheckStateRole).toInt() > 1) {
3063       if (mSlicerManagers[i]->GetSlicer(1)->GetSlice() != value) {
3064         mSlicerManagers[i]->GetSlicer(1)->SetSlice(value);
3065         mSlicerManagers[i]->VerticalSliderHasChanged(1, value);
3066         mSlicerManagers[i]->UpdateSlice(1);
3067         //mSlicerManagers[i]->GetSlicer(1)->Render(); // <-- DS add this, needed for contour, seems ok ? not too slow ?
3068       }
3069       break;
3070     }
3071   }
3072 }
3073 //------------------------------------------------------------------------------
3074
3075
3076 //------------------------------------------------------------------------------
3077 void vvMainWindow::SOVerticalSliderChanged()
3078 {
3079   static int value=-1;
3080   if (value == SOVerticalSlider->value()) return;
3081   else value = SOVerticalSlider->value();
3082   //int value = SOVerticalSlider->value();
3083   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
3084     if (DataTree->topLevelItem(i)->data(COLUMN_DL_VIEW,Qt::CheckStateRole).toInt() > 1) {
3085       if (mSlicerManagers[i]->GetSlicer(2)->GetSlice() != value) {
3086         mSlicerManagers[i]->GetSlicer(2)->SetSlice(value);
3087         mSlicerManagers[i]->VerticalSliderHasChanged(2, value);
3088         mSlicerManagers[i]->UpdateSlice(2);
3089         //mSlicerManagers[i]->GetSlicer(2)->Render(); // <-- DS add this, needed for contour, seems ok ? not too slow ?
3090       }
3091       // else { DD("avoid SOVerticalSlider slicer update"); }
3092       break;
3093     }
3094   }
3095 }
3096 //------------------------------------------------------------------------------
3097
3098
3099 //------------------------------------------------------------------------------
3100 void vvMainWindow::SEVerticalSliderChanged()
3101 {
3102   static int value=-1;
3103   if (value == SEVerticalSlider->value()) return;
3104   else value = SEVerticalSlider->value();
3105   // int value = SEVerticalSlider->value();
3106   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
3107     if (DataTree->topLevelItem(i)->data(COLUMN_DR_VIEW,Qt::CheckStateRole).toInt() > 1) {
3108       if (mSlicerManagers[i]->GetSlicer(3)->GetSlice() != value) {
3109         mSlicerManagers[i]->GetSlicer(3)->SetSlice(value);
3110         mSlicerManagers[i]->VerticalSliderHasChanged(3, value);
3111         mSlicerManagers[i]->UpdateSlice(3);
3112         //mSlicerManagers[i]->GetSlicer(3)->Render(); // <-- DS add this, needed for contour, seems ok ? not too slow ?
3113       }
3114       break;
3115     }
3116   }
3117 }
3118 //------------------------------------------------------------------------------
3119
3120
3121 //------------------------------------------------------------------------------
3122 void vvMainWindow::UpdateSlice(int slicer, int slice)
3123 {
3124   // DD("vvMainWindow::UpdateSlice");
3125   //   DD(slicer);
3126   //   DD(slice);
3127   if (slicer == 0) {
3128     //    if (slice != NOVerticalSlider->value())
3129     NOVerticalSlider->setValue(slice);
3130   } else {
3131     if (slicer == 1)
3132       NEVerticalSlider->setValue(slice);
3133     else {
3134       if (slicer == 2)
3135         SOVerticalSlider->setValue(slice);
3136       else {
3137         if (slicer == 3)
3138           SEVerticalSlider->setValue(slice);
3139       }
3140     }
3141   }
3142   // DD("vvMainWindow:UpdateSlice END");
3143 }
3144 //------------------------------------------------------------------------------
3145
3146
3147 //------------------------------------------------------------------------------
3148 void vvMainWindow::UpdateTSlice(int slicer, int slice, int code)
3149 {
3150   //FusionSequence: the slider value should be updated for slicers which show the same sequence as requested
3151   bool doUpdate=false;
3152   if (code==-1) doUpdate=true;
3153   else {
3154     for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
3155       if (DataTree->topLevelItem(i)->data(slicer+1,Qt::CheckStateRole).toInt() > 1) {
3156         //i is the active SlicerManager
3157         if (mSlicerManagers[i]->GetFusionSequenceInvolvmentCode()==code) doUpdate=true;
3158         break;
3159       }
3160     }
3161   }
3162   if (!doUpdate) return;
3163
3164   switch (slicer) {
3165   case 0:
3166     if (NOHorizontalSlider->value()==slice) return;
3167     NOHorizontalSlider->setValue(slice);
3168     break;
3169   case 1:
3170     if (NEHorizontalSlider->value()==slice) return;
3171     NEHorizontalSlider->setValue(slice);
3172     break;
3173   case 2:
3174     if (SOHorizontalSlider->value()==slice) return;
3175     SOHorizontalSlider->setValue(slice);
3176     break;
3177   case 3:
3178     if (SEHorizontalSlider->value()==slice) return;
3179     SEHorizontalSlider->setValue(slice);
3180     break;
3181   }
3182 }
3183 //------------------------------------------------------------------------------
3184
3185
3186 //------------------------------------------------------------------------------
3187 void vvMainWindow::UpdateSliceRange(int slicer, int min, int max, int tmin, int tmax)
3188 {
3189   //int position = int((min+max)/2);
3190   int position = mSlicerManagers[mCurrentPickedImageIndex]->GetSlicer(slicer)->GetSlice();
3191   if (slicer == 0) {
3192     NOVerticalSlider->setRange(min,max);
3193     NOHorizontalSlider->setRange(tmin,tmax);
3194     NOVerticalSlider->setValue(position);
3195   } else if (slicer == 1) {
3196     NEVerticalSlider->setRange(min,max);
3197     NEHorizontalSlider->setRange(tmin,tmax);
3198     NEVerticalSlider->setValue(position);
3199   } else if (slicer == 2) {
3200     SOVerticalSlider->setRange(min,max);
3201     SOHorizontalSlider->setRange(tmin,tmax);
3202     SOVerticalSlider->setValue(position);
3203   } else if (slicer == 3) {
3204     SEVerticalSlider->setRange(min,max);
3205     SEHorizontalSlider->setRange(tmin,tmax);
3206     SEVerticalSlider->setValue(position);
3207   }
3208 }
3209 //------------------------------------------------------------------------------
3210
3211
3212 //------------------------------------------------------------------------------
3213 void vvMainWindow::SaveNOScreenshot()
3214 {
3215   SaveScreenshot(NOViewWidget);
3216 }
3217 //------------------------------------------------------------------------------
3218
3219
3220 //------------------------------------------------------------------------------
3221 void vvMainWindow::SaveNEScreenshot()
3222 {
3223   SaveScreenshot(NEViewWidget);
3224 }
3225 //------------------------------------------------------------------------------
3226
3227
3228 //------------------------------------------------------------------------------
3229 void vvMainWindow::SaveSOScreenshot()
3230 {
3231   SaveScreenshot(SOViewWidget);
3232 }
3233 //------------------------------------------------------------------------------
3234
3235
3236 //------------------------------------------------------------------------------
3237 void vvMainWindow::SaveSEScreenshot()
3238 {
3239   SaveScreenshot(SEViewWidget);
3240 }
3241 //------------------------------------------------------------------------------
3242
3243
3244 //------------------------------------------------------------------------------
3245 void vvMainWindow::SaveScreenshotAllSlices()
3246 {
3247   QVTKWidget *widget = NOViewWidget;
3248
3249   int index = 0;// GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
3250   vvSlicerManager * SM = mSlicerManagers[index];
3251   vvImage * image = SM->GetImage();
3252   vvSlicer * slicer = SM->GetSlicer(0);
3253   int orientation = slicer->GetOrientation();
3254   int nbSlices = image->GetSize()[orientation];
3255   vtkSmartPointer<vtkRenderWindow>  renderWindow = widget->GetRenderWindow();
3256
3257   // Select filename base
3258   QString filename = QFileDialog::getSaveFileName(this,
3259     tr("Save As (filename will be completed by slice number)"),
3260     itksys::SystemTools::GetFilenamePath(mSlicerManagers[index]->GetFileName()).c_str(),
3261     "Images( *.png);;Images( *.jpg)");
3262
3263   // Loop on slices
3264   for(int i=0; i<nbSlices; i++) {
3265     // Change the slice
3266     slicer->SetSlice(i); // -> change the slice of the current slicer
3267     SM->UpdateSlice(0); // --> this one emit UpdateSlice
3268     QCoreApplication::flush(); // -> needed to force display of contours
3269
3270     // Screenshot
3271     vtkSmartPointer<vtkWindowToImageFilter> windowToImageFilter = vtkSmartPointer<vtkWindowToImageFilter>::New();
3272     windowToImageFilter->SetInput(renderWindow);
3273     windowToImageFilter->SetMagnification(1);
3274     windowToImageFilter->SetInputBufferTypeToRGBA(); //also record the alpha (transparency) channel
3275     windowToImageFilter->Update();
3276
3277     vtkSmartPointer<vtkPNGWriter> writer = vtkSmartPointer<vtkPNGWriter>::New();
3278     std::string fn = itksys::SystemTools::GetFilenameWithoutLastExtension(filename.toStdString());
3279     std::string num = clitk::toString(i);
3280     if (i<10) num = "0"+num;
3281     if (i<100) num = "0"+num;
3282     if (i<1000) num = "0"+num;
3283
3284     fn = itksys::SystemTools::GetFilenamePath(filename.toStdString()) + "/"+ fn
3285       + "_" + num + itksys::SystemTools::GetFilenameLastExtension(filename.toStdString());
3286     writer->SetFileName(fn.c_str());
3287 #if VTK_MAJOR_VERSION <= 5
3288     writer->SetInput(windowToImageFilter->GetOutput());
3289 #else
3290     writer->SetInputConnection(windowToImageFilter->GetOutputPort());
3291 #endif
3292     writer->Write();
3293   }
3294 }
3295 //------------------------------------------------------------------------------
3296
3297
3298 //------------------------------------------------------------------------------
3299 void vvMainWindow::SaveScreenshot(QVTKWidget *widget)
3300 {
3301   QString Extensions = "Images( *.png);;";
3302   Extensions += "Images( *.jpg);;";
3303   Extensions += "Images( *.bmp);;";
3304   Extensions += "Images( *.tif);;";
3305   Extensions += "Images( *.ppm)";
3306 #if defined(VTK_USE_FFMPEG_ENCODER) || defined(VTK_USE_VIDEO_FOR_WINDOWS)
3307   Extensions += ";;Video( *.avi)";
3308 #endif
3309 #ifdef VTK_USE_MPEG2_ENCODER
3310   Extensions += ";;Video( *.mpg)";
3311 #endif
3312 #ifdef CLITK_EXPERIMENTAL
3313   Extensions += ";;Video( *.gif)";
3314 #endif
3315
3316   int smIndex=GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
3317   QString fileName = QFileDialog::getSaveFileName(this,
3318     tr("Save As"),
3319     itksys::SystemTools::GetFilenamePath(mSlicerManagers[smIndex]->GetFileName()).c_str(),
3320     Extensions);
3321
3322   if (!fileName.isEmpty()) {
3323     vtkSmartPointer<vtkWindowToImageFilter> w2i = vtkSmartPointer<vtkWindowToImageFilter>::New();
3324     w2i->SetInput(widget->GetRenderWindow());
3325     w2i->Update();
3326     vtkImageData *image = w2i->GetOutput();
3327
3328     std::string ext(itksys::SystemTools::GetFilenameLastExtension(fileName.toStdString()));
3329
3330     // Image
3331     vtkImageWriter *imgwriter = NULL;
3332     if (ext==".bmp")
3333       imgwriter = vtkBMPWriter::New();
3334     else if (ext==".tif")
3335       imgwriter = vtkTIFFWriter::New();
3336     else if (ext==".ppm")
3337       imgwriter = vtkPNMWriter::New();
3338     else if (ext==".png")
3339       imgwriter = vtkPNGWriter::New();
3340     else if (ext==".jpg")
3341       imgwriter = vtkJPEGWriter::New();
3342
3343     // Snapshot image if not null
3344     if(imgwriter!=NULL) {
3345 #if VTK_MAJOR_VERSION <= 5
3346       imgwriter->SetInput(image);
3347 #else
3348       imgwriter->SetInputConnection(w2i->GetOutputPort());
3349 #endif
3350       imgwriter->SetFileName(fileName.toStdString().c_str());
3351       imgwriter->Write();
3352       return;
3353     }
3354
3355     // Video
3356     vtkGenericMovieWriter *vidwriter = NULL;
3357 #if CLITK_EXPERIMENTAL == 1
3358     if (ext==".gif") {
3359       vvAnimatedGIFWriter *gif = vvAnimatedGIFWriter::New();
3360       vidwriter = gif;
3361
3362       // FPS
3363       bool ok;
3364       int fps = QInputDialog::getInt(this, tr("Number of frames per second"),
3365         tr("FPS:"), 5, 0, 1000, 1, &ok);
3366       if(ok)
3367         gif->SetRate(fps);
3368
3369       // Loops
3370       int loops = QInputDialog::getInt(this, tr("Loops"),
3371         tr("Number of loops (0 means infinite):"), 0, 0, 1000000000, 1, &ok);
3372       if(ok)
3373         gif->SetLoops(loops);
3374
3375       // Dithering
3376       QString msg = "Would you like to activate dithering?";
3377       QMessageBox msgBox(QMessageBox::Question, tr("Dithering"),msg, 0, this);
3378       msgBox.addButton(tr("Yes"), QMessageBox::AcceptRole);
3379       msgBox.addButton(tr("No"), QMessageBox::RejectRole);
3380       gif->SetDither(msgBox.exec() == QMessageBox::AcceptRole);
3381     }
3382 #endif
3383 #ifdef VTK_USE_VIDEO_FOR_WINDOWS
3384     if (ext==".avi") {
3385       vtkAVIWriter *mpg = vtkAVIWriter::New();
3386       vidwriter = mpg;
3387       mpg->SetQuality(2);
3388       bool ok;
3389       int fps = QInputDialog::getInteger(this, tr("Number of frames per second"),
3390         tr("FPS:"), 5, 0, 1024, 1, &ok);
3391       if(!ok)
3392         fps = 5;
3393       mpg->SetRate(fps);
3394     }
3395 #endif
3396 #ifdef VTK_USE_FFMPEG_ENCODER
3397     if (ext==".avi") {
3398       vtkFFMPEGWriter *mpg = vtkFFMPEGWriter::New();
3399       vidwriter = mpg;
3400       mpg->SetQuality(2);
3401       bool ok;
3402       int fps = QInputDialog::getInteger(this, tr("Number of frames per second"),
3403         tr("FPS:"), 5, 0, 1024, 1, &ok);
3404       if(!ok)
3405         fps = 5;
3406       mpg->SetRate(fps);
3407       mpg->SetBitRateTolerance(int(ceil(12.0*1024*1024/fps)));
3408     }
3409 #endif
3410 #ifdef VTK_USE_MPEG2_ENCODER
3411     if (ext==".mpg") {
3412       vtkMPEG2Writer *mpg = vtkMPEG2Writer::New();
3413       vidwriter = mpg;
3414     }
3415 #endif
3416
3417     // Take video if not null
3418     if(vidwriter!=NULL){
3419 #if VTK_MAJOR_VERSION <= 5
3420       vidwriter->SetInput(image);
3421 #else
3422       vidwriter->SetInputConnection(w2i->GetOutputPort());
3423 #endif
3424       vidwriter->SetFileName(fileName.toStdString().c_str());
3425       vidwriter->Start();
3426       int nSlice = mSlicerManagers[smIndex]->GetSlicer(0)->GetTMax();
3427       for(int i=0; i<=nSlice; i++) {
3428         mSlicerManagers[smIndex]->SetNextTSlice(0);
3429         vtkSmartPointer<vtkWindowToImageFilter> w2i = vtkSmartPointer<vtkWindowToImageFilter>::New();
3430         w2i->SetInput(widget->GetRenderWindow());
3431         w2i->Update();
3432 #if VTK_MAJOR_VERSION <= 5
3433         vidwriter->SetInput(w2i->GetOutput());
3434 #else
3435         vidwriter->SetInputConnection(w2i->GetOutputPort());
3436 #endif
3437         vidwriter->Write();
3438       }
3439       vidwriter->End();
3440       vidwriter->Delete();
3441       return;
3442     }
3443
3444     QMessageBox::information(this,tr("Problem saving screenshot !"),tr("Cannot save image.\nPlease set a file extension !!!"));
3445   }
3446 }
3447 //------------------------------------------------------------------------------
3448
3449
3450 //------------------------------------------------------------------------------
3451 void vvMainWindow::GoToCursor()
3452 {
3453   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
3454   for (int column = 1; column < 5; column++) {
3455     if (DataTree->selectedItems()[0]->data(column,Qt::CheckStateRole).toInt() > 1) {
3456       double* cursorPos = mSlicerManagers[index]->GetSlicer(column-1)->GetCursorPosition();
3457       mSlicerManagers[index]->GetSlicer(column-1)->SetCurrentPosition(
3458         cursorPos[0],cursorPos[1],cursorPos[2],cursorPos[3]);
3459       mSlicerManagers[index]->UpdateViews(1,column-1);
3460       mSlicerManagers[index]->UpdateLinked(column-1);
3461       break;
3462     }
3463   }
3464 }
3465 //------------------------------------------------------------------------------
3466
3467 //------------------------------------------------------------------------------
3468 void vvMainWindow::GoToLandmark()
3469 {
3470   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
3471   for (int column = 1; column < 5; column++) {
3472     if (DataTree->selectedItems()[0]->data(column,Qt::CheckStateRole).toInt() > 1) {
3473       double* cursorPos = landmarksPanel->GetSelectedPoint();
3474       mSlicerManagers[index]->GetSlicer(column-1)->SetCurrentPosition(
3475         cursorPos[0],cursorPos[1],cursorPos[2],cursorPos[3]);
3476       mSlicerManagers[index]->UpdateViews(1,column-1);
3477       mSlicerManagers[index]->UpdateLinked(column-1);
3478       break;
3479     }
3480   }
3481 }
3482 //------------------------------------------------------------------------------
3483
3484 //------------------------------------------------------------------------------
3485 void vvMainWindow::PlayPause()
3486 {
3487   if (playMode) {
3488     playMode = 0;
3489     playButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/player_play.png")));
3490     ImageInfoChanged();
3491     return;
3492   } else {
3493     int image_number=DataTree->topLevelItemCount();
3494     bool has_temporal;
3495     for (int i=0; i<image_number; i++)
3496       if (mSlicerManagers[i]->GetSlicer(0)->GetTMax() > 0) {
3497         has_temporal=true;
3498         break;
3499       }
3500       if (has_temporal) {
3501         playMode = 1;
3502         playButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/player_pause.png")));
3503         QTimer::singleShot(1000/mFrameRate, this, SLOT(PlayNext()));
3504       }
3505   }
3506 }
3507 //------------------------------------------------------------------------------
3508
3509 //------------------------------------------------------------------------------
3510 void vvMainWindow::PlayNext()
3511 {
3512   if (playMode && !this->isHidden()) {
3513     int image_number=DataTree->topLevelItemCount();
3514     ///Only play one slicer per SM, and only if the SM is being displayed
3515     for (int i=0; i<image_number; i++)
3516       for (int j=0; j<4; j++)
3517         if (mSlicerManagers[i]->GetSlicer(0)->GetTMax() > 0 &&
3518           DataTree->topLevelItem(i)->data(j+1,Qt::CheckStateRole).toInt() > 0) {
3519             mSlicerManagers[i]->SetNextTSlice(j);
3520             break;
3521         }
3522         QTimer::singleShot(1000/mFrameRate, this, SLOT(PlayNext()));
3523   }
3524 }
3525 //------------------------------------------------------------------------------
3526
3527 void vvMainWindow::ShowLastImage()
3528 {
3529   if (mSlicerManagers.size() > 1) {
3530     QTreeWidgetItem * item=DataTree->topLevelItem(DataTree->topLevelItemCount()-1);
3531     CurrentImageChanged(mSlicerManagers.back()->GetId()); //select new image
3532     item->setData(1,Qt::CheckStateRole,2); //show the new image in the first panel
3533     //mSlicerManagers[GetSlicerIndexFromItem(item)]->GetSlicer(0)->SetActorVisibility("image", 0, 1); //Set the Last Image visibles
3534     DisplayChanged(item,1);
3535   }
3536 }
3537
3538 //------------------------------------------------------------------------------
3539 void vvMainWindow::UpdateRenderWindows()
3540 {
3541   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
3542       for (unsigned int j = 0; j < 4; ++j) {
3543         mSlicerManagers[i]->GetSlicer(j)->RemoveLandmarks();
3544         mSlicerManagers[i]->GetSlicer(j)->DisplayLandmarks();
3545       }
3546   }
3547   if (NOViewWidget->GetRenderWindow()) NOViewWidget->GetRenderWindow()->Render();
3548   if (NEViewWidget->GetRenderWindow()) NEViewWidget->GetRenderWindow()->Render();
3549   if (SOViewWidget->GetRenderWindow()) SOViewWidget->GetRenderWindow()->Render();
3550   if (SEViewWidget->GetRenderWindow()) SEViewWidget->GetRenderWindow()->Render();
3551 }
3552 //------------------------------------------------------------------------------
3553
3554 //------------------------------------------------------------------------------
3555 void vvMainWindow::SegmentationOnCurrentImage()
3556 {
3557   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
3558
3559   vvSegmentationDialog segmentation;
3560   segmentation.SetImage(mSlicerManagers[index]->GetSlicer(0)->GetImage());
3561   segmentation.exec();
3562 }
3563 //------------------------------------------------------------------------------
3564
3565 void vvMainWindow::SurfaceViewerLaunch()
3566 {
3567   vvSurfaceViewerDialog surfaceViewer;
3568   surfaceViewer.exec();
3569 }
3570 //------------------------------------------------------------------------------
3571
3572
3573 //------------------------------------------------------------------------------
3574 int vvMainWindow::GetImageDuplicateFilenameNumber(std::string filename)
3575 {
3576   int number=0;
3577   for(unsigned int l=0; l<mSlicerManagers.size(); l++) {
3578     vvSlicerManager * v = mSlicerManagers[l];
3579     if (v->GetBaseFileName() ==
3580       vtksys::SystemTools::GetFilenameName(vtksys::SystemTools::GetFilenameWithoutLastExtension(filename))) {
3581         number = std::max(number, v->GetBaseFileNameNumber()+1);
3582     }
3583   }
3584   return number;
3585 }
3586 //------------------------------------------------------------------------------
3587
3588
3589 //------------------------------------------------------------------------------
3590 vvSlicerManager* vvMainWindow::AddImage(vvImage::Pointer image,std::string filename)
3591 {
3592   // Change filename if another image exist with the same name
3593   int number = GetImageDuplicateFilenameNumber(filename);
3594
3595   // Create new SliceManager
3596   vvSlicerManager* slicer_manager = new vvSlicerManager(4);
3597   slicer_manager->SetImage(image);//, IMAGE, number);
3598   //  filename = filename+"_"+clitk::toString(number);
3599   slicer_manager->SetFilename(filename, number);
3600   mSlicerManagers.push_back(slicer_manager);
3601
3602   //create an item in the tree with good settings
3603   QTreeWidgetItem *item = new QTreeWidgetItem();
3604   item->setData(0,Qt::UserRole,slicer_manager->GetFileName().c_str());//files[i].c_str());
3605   item->setData(1,Qt::UserRole,tr("image"));
3606   item->setData(COLUMN_IMAGE_NAME,Qt::DisplayRole,slicer_manager->GetFileName().c_str());//filename.c_str());
3607   qApp->processEvents();
3608
3609   for (int j = 1; j <= 4; j++) item->setData(j,Qt::CheckStateRole,1);
3610
3611   //Create the buttons for reload and close
3612   qApp->processEvents();
3613   QTreePushButton* cButton = new QTreePushButton;
3614   cButton->setItem(item);
3615   cButton->setColumn(COLUMN_CLOSE_IMAGE);
3616   cButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/exit.png")));
3617   connect(cButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
3618     this,SLOT(CloseImage(QTreeWidgetItem*, int)));
3619
3620   QTreePushButton* rButton = new QTreePushButton;
3621   rButton->setItem(item);
3622   rButton->setColumn(COLUMN_RELOAD_IMAGE);
3623   rButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/rotateright.png")));
3624   rButton->setEnabled(0);
3625   connect(rButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
3626     this,SLOT(ReloadImage(QTreeWidgetItem*, int)));
3627
3628   DataTree->addTopLevelItem(item);
3629   DataTree->setItemWidget(item, COLUMN_CLOSE_IMAGE, cButton);
3630   DataTree->setItemWidget(item, COLUMN_RELOAD_IMAGE, rButton);
3631
3632   //set the id of the image
3633   QString id = QDir::current().absoluteFilePath(slicer_manager->GetFileName().c_str()) + QString::number(mSlicerManagers.size()-1);
3634   item->setData(COLUMN_IMAGE_NAME,Qt::UserRole,id.toStdString().c_str());
3635   mSlicerManagers.back()->SetId(id.toStdString());
3636
3637   linkPanel->addImage(slicer_manager->GetFileName().c_str()// filename
3638     , id.toStdString());
3639
3640   connect(mSlicerManagers.back(), SIGNAL(currentImageChanged(std::string)),
3641     this, SLOT(CurrentImageChanged(std::string)));
3642   connect(mSlicerManagers.back(), SIGNAL(currentPickedImageChanged(std::string)),
3643     this, SLOT(CurrentPickedImageChanged(std::string)));
3644   connect(mSlicerManagers.back(), SIGNAL(UpdatePosition(int, double, double, double, double, double, double, double)),
3645     this, SLOT(MousePositionChanged(int,double, double, double, double, double, double, double)));
3646   connect(mSlicerManagers.back(), SIGNAL(UpdateVector(int, double, double, double, double)),
3647     this, SLOT(VectorChanged(int,double,double,double, double)));
3648   connect(mSlicerManagers.back(), SIGNAL(UpdateOverlay(int, double, double)),
3649     this, SLOT(OverlayChanged(int,double,double)));
3650   connect(mSlicerManagers.back(), SIGNAL(UpdateFusion(int, double)),
3651     this, SLOT(FusionChanged(int,double)));
3652   //connect(mSlicerManagers.back(), SIGNAL(UpdateFusionSequence(int, bool, unsigned int)),
3653   //  this, SLOT(FusionSequenceChanged(int, bool, unsigned int)));
3654   connect(mSlicerManagers.back(), SIGNAL(WindowLevelChanged()),
3655     this,SLOT(WindowLevelChanged()));
3656   connect(mSlicerManagers.back(), SIGNAL(UpdateSlice(int,int)),
3657     this,SLOT(UpdateSlice(int,int)));
3658   connect(mSlicerManagers.back(), SIGNAL(UpdateTSlice(int, int, int)),
3659     this,SLOT(UpdateTSlice(int, int, int)));
3660   connect(mSlicerManagers.back(), SIGNAL(UpdateTSlice(int, int, int)),
3661     this,SLOT(ImageInfoChanged()));
3662   connect(mSlicerManagers.back(), SIGNAL(UpdateSliceRange(int,int,int,int,int)),
3663     this,SLOT(UpdateSliceRange(int,int,int,int,int)));
3664   connect(mSlicerManagers.back(), SIGNAL(UpdateLinkManager(std::string,int,double,double,double,int)),
3665     this,SLOT(UpdateLinkManager(std::string,int,double,double,double,int)));
3666   connect(mSlicerManagers.back(), SIGNAL(UpdateLinkedNavigation(std::string,vvSlicerManager*,vvSlicer*)),
3667     this,SLOT(UpdateLinkedNavigation(std::string,vvSlicerManager*,vvSlicer*)));
3668   connect(mSlicerManagers.back(), SIGNAL(ChangeImageWithIndexOffset(vvSlicerManager*,int,int)),
3669     this,SLOT(ChangeImageWithIndexOffset(vvSlicerManager*,int,int)));
3670   connect(mSlicerManagers.back(), SIGNAL(LandmarkAdded()),landmarksPanel,SLOT(AddPoint()));
3671
3672
3673
3674   InitSlicers();
3675   UpdateTree();
3676   qApp->processEvents();
3677   InitDisplay();
3678   ShowLastImage();
3679   qApp->processEvents();
3680   // End
3681   ImageInfoChanged();
3682   return slicer_manager;
3683 }
3684 //------------------------------------------------------------------------------
3685
3686
3687 //------------------------------------------------------------------------------
3688 void vvMainWindow::UpdateCurrentSlicer()
3689 {
3690   int index = -1;
3691   if (DataTree->selectedItems().size() > 0) {
3692     index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
3693   }
3694   mSlicerManagerCurrentIndex = index;
3695 }
3696 //------------------------------------------------------------------------------