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