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