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 #if CLITK_USE_PACS_CONNECTION
  52 #include "vvQPacsConnection.h"
  53 #endif
  54 #include "clitkConfiguration.h"
  55 #include "clitkMatrix.h"
  56 #ifdef Q_OS_OSX
  57 # include "vvOSXHelper.h"
  58 #endif
  59
  60 // ITK include
  61 #include <itkImage.h>
  62 #include <itkImageFileReader.h>
  63 #include <itkByteSwapper.h>
  64 #include <itkCommand.h>
  65 #include <itkNumericSeriesFileNames.h>
  66
  67 // VTK include
  68 #include <vtkImageMapper3D.h>
  69 #include <vtkInformation.h>
  70 #include <vtkVersion.h>
  71 #include <vtkImageData.h>
  72 #include <vtkImageActor.h>
  73 #include <vtkCornerAnnotation.h>
  74 #include <vtkRenderWindow.h>
  75 #include <vtkRenderWindowInteractor.h>
  76 #include <vtkRenderer.h>
  77 #include <vtkRendererCollection.h>
  78 #include <vtkWindowToImageFilter.h>
  79 #include <vtkBMPWriter.h>
  80 #include <vtkTIFFWriter.h>
  81 #include <vtkPNMWriter.h>
  82 #include <vtkPNGWriter.h>
  83 #include <vtkJPEGWriter.h>
  84 #include <vtkGenericMovieWriter.h>
  85 #include <vvAnimatedGIFWriter.h>
  86 #ifdef VTK_USE_VIDEO_FOR_WINDOWS
  87 #  include <vtkAVIWriter.h>
  88 #endif
  89 #ifdef VTK_USE_FFMPEG_ENCODER
  90 #  include <vtkFFMPEGWriter.h>
  91 #endif
  92 #ifdef VTK_USE_MPEG2_ENCODER
  93 #  include <vtkMPEG2Writer.h>
  94 #endif
  95 #include <vtkMatrix4x4.h>
  96 #include <vtkTransform.h>
  97
  98 // Standard includes
  99 #include <iostream>
 100 #include <fstream>
 101 #include <sstream>
 102 #include <iomanip>
 103
 104 #define COLUMN_TREE 0
 105 #define COLUMN_UL_VIEW 1
 106 #define COLUMN_UR_VIEW 2
 107 #define COLUMN_DL_VIEW 3
 108 #define COLUMN_DR_VIEW 4
 109 #define COLUMN_CLOSE_IMAGE 5
 110 #define COLUMN_RELOAD_IMAGE 6
 111 #define COLUMN_IMAGE_NAME 7
 112
 113 #ifdef CLITK_PRIVATE_FEATURES
 114 #define EXTENSIONS "Images ( *.bmp *.dcm *.png *.jpeg *.jpg *.tif *.mhd *.mha *.hdr *.vox *.his *.xdr *.SCAN *.nii *.nrrd *.nhdr *.refscan *.nii.gz *.usf *.svl)"
 115 #else
 116 #define EXTENSIONS "Images ( *.bmp *.dcm *.png *.jpeg *.jpg *.tif *.mhd *.mha *.hdr *.vox *.his *.xdr *.SCAN *.nii *.nrrd *.nhdr *.refscan *.nii.gz)"
 117 #endif
 118
 119
 120 /*Data Tree values
 121 0,Qt::UserRole full filename
 122 1,Qt::CheckStateRole checkbutton UL View
 123 1,Qt::UserRole overlay, fusion or vector
 124 2,Qt::CheckStateRole checkbutton UR View
 125 3,Qt::CheckStateRole checkbutton DL View
 126 4,Qt::CheckStateRole checkbutton DR View
 127 5,0  short filename
 128 5,Qt::UserRole mSlicerManager id*/
 129
 130 //------------------------------------------------------------------------------
 131 vvMainWindow::vvMainWindow():vvMainWindowBase()
 132 {
 133   setupUi(this); // this sets up the GUI
 134
 135   setDicomClient();
 136
 137   //Qt::WindowFlags flags = windowFlags();
 138   //setWindowFlags(flags | Qt::WindowStaysOnTopHint);
 139
 140   mInputPathName = "";
 141   mMenuTools = menuTools;
 142   //  mMenuSegmentation = menuSegmentation;
 143   mContextMenu = &contextMenu;
 144   mMenuExperimentalTools = menuExperimental;
 145   mMainWidget = this;
 146   mCurrentTime = -1;
 147   mCurrentSelectedImageId = "";
 148   mCurrentPickedImageId = "";
 149   mCurrentPickedImageIndex = 0;
 150
 151   //Init the contextMenu
 152   this->setContextMenuPolicy(Qt::CustomContextMenu);
 153   contextActions.resize(0);
 154   QAction* actionOpen_new_image = contextMenu.addAction(QIcon(QString::fromUtf8(":/common/icons/fileopen.png")),
 155     tr("O&pen new Image"));
 156   connect(actionOpen_new_image,SIGNAL(triggered()),this,SLOT(OpenImages()));
 157   contextActions.push_back(actionOpen_new_image);
 158   contextMenu.addSeparator();
 159
 160   QAction* actionClose_Image = contextMenu.addAction(QIcon(QString::fromUtf8(":/common/icons/exit.png")),
 161     tr("Close Current Image"));
 162   connect(actionClose_Image,SIGNAL(triggered()),this,SLOT(CloseImage()));
 163   contextActions.push_back(actionClose_Image);
 164
 165   QAction* actionReload_image = contextMenu.addAction(QIcon(QString::fromUtf8(":/common/icons/rotateright.png")),
 166     tr("Reload Current Image"));
 167   connect(actionReload_image,SIGNAL(triggered()),this,SLOT(ReloadImage()));
 168   contextActions.push_back(actionReload_image);
 169
 170   QAction* actionSave_image = contextMenu.addAction(QIcon(QString::fromUtf8(":/common/icons/filesave.png")),
 171     tr("Save Current Image"));
 172   connect(actionSave_image,SIGNAL(triggered()),this,SLOT(SaveAs()));
 173   contextActions.push_back(actionSave_image);
 174
 175   QAction* actionSave_state = contextMenu.addAction(QIcon(QString::fromUtf8(":/common/icons/filesave.png")),
 176     tr("Save Current State"));
 177   connect(actionSave_state,SIGNAL(triggered()),this,SLOT(SaveCurrentState()));
 178   contextActions.push_back(actionSave_state);
 179
 180   QAction* actionRead_state = contextMenu.addAction(QIcon(QString::fromUtf8(":/common/icons/filesave.png")),
 181     tr("Read Saved State"));
 182   connect(actionRead_state,SIGNAL(triggered()),this,SLOT(ReadSavedState()));
 183   contextActions.push_back(actionRead_state);
 184
 185   contextMenu.addSeparator();
 186
 187   contextMenu.addAction(actionAdd_VF_to_current_Image);
 188   contextActions.push_back(actionAdd_VF_to_current_Image);
 189
 190   //QAction* actionAdd_Overlay_to_current_Image = menuOverlay->addAction(QIcon(QString::fromUtf8(":/common/icons/GPSup.png")),
 191   //    tr("Add overlay image to current image"));
 192   contextMenu.addAction(actionAdd_overlay_image_to_current_image);
 193   contextActions.push_back(actionAdd_overlay_image_to_current_image);
 194
 195   contextMenu.addAction(actionAdd_fusion_image);
 196   contextActions.push_back(actionAdd_fusion_image);
 197
 198 #ifdef CLITK_EXPERIMENTAL
 199   contextMenu.addAction(actionAdd_USSequence_toCT);
 200   contextActions.push_back(actionAdd_USSequence_toCT);
 201 #endif
 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 #if CLITK_USE_PACS_CONNECTION
 237      PacsConnection = new vvQPacsConnection();
 238 #endif
 239
 240   inverseButton->setEnabled(0);
 241   actionAdd_overlay_image_to_current_image->setEnabled(0);
 242   actionSave_As->setEnabled(0);
 243   actionAdd_VF_to_current_Image->setEnabled(0);
 244   actionAdd_fusion_image->setEnabled(0);
 245   actionAdd_USSequence_toCT->setEnabled(0);
 246
 247   //init the sliders
 248   verticalSliders.push_back(NOVerticalSlider);
 249   verticalSliders.push_back(NEVerticalSlider);
 250   verticalSliders.push_back(SOVerticalSlider);
 251   verticalSliders.push_back(SEVerticalSlider);
 252
 253   for (int i =0; i < 4; i++)
 254     verticalSliders[i]->hide();
 255
 256   horizontalSliders.push_back(NOHorizontalSlider);
 257   horizontalSliders.push_back(NEHorizontalSlider);
 258   horizontalSliders.push_back(SOHorizontalSlider);
 259   horizontalSliders.push_back(SEHorizontalSlider);
 260
 261   for (int i =0; i < 4; i++)
 262     horizontalSliders[i]->hide();
 263
 264
 265   connect(NOVerticalSlider,SIGNAL(valueChanged(int)),this,SLOT(NOVerticalSliderChanged()));
 266   connect(NEVerticalSlider,SIGNAL(valueChanged(int)),this,SLOT(NEVerticalSliderChanged()));
 267   connect(SOVerticalSlider,SIGNAL(valueChanged(int)),this,SLOT(SOVerticalSliderChanged()));
 268   connect(SEVerticalSlider,SIGNAL(valueChanged(int)),this,SLOT(SEVerticalSliderChanged()));
 269
 270   connect(NOHorizontalSlider,SIGNAL(valueChanged(int)),this,SLOT(NOHorizontalSliderMoved()));
 271   connect(NEHorizontalSlider,SIGNAL(valueChanged(int)),this,SLOT(NEHorizontalSliderMoved()));
 272   connect(SOHorizontalSlider,SIGNAL(valueChanged(int)),this,SLOT(SOHorizontalSliderMoved()));
 273   connect(SEHorizontalSlider,SIGNAL(valueChanged(int)),this,SLOT(SEHorizontalSliderMoved()));
 274
 275   //connect everything
 276   connect(actionCompute_mid_position_image,SIGNAL(triggered()),this,SLOT(ComputeMidPosition()));
 277   connect(actionDeformable_Registration,SIGNAL(triggered()),this,SLOT(ComputeDeformableRegistration()));
 278   connect(actionWarp_image_with_vector_field,SIGNAL(triggered()),this,SLOT(WarpImage()));
 279   connect(actionLoad_images,SIGNAL(triggered()),this,SLOT(OpenImages()));
 280   connect(actionOpen_Dicom,SIGNAL(triggered()),this,SLOT(OpenDicom()));
 281 #if CLITK_USE_PACS_CONNECTION
 282   connect(actionConnect_Pacs,SIGNAL(triggered()),this,SLOT(ConnectPacs()));
 283 #endif
 284   //  connect(actionOpen_Dicom_Struct,SIGNAL(triggered()),this,SLOT(OpenDCStructContour()));
 285   connect(actionOpen_VTK_contour,SIGNAL(triggered()),this,SLOT(OpenVTKContour()));
 286   connect(actionOpen_Multiple_Images_As_One,SIGNAL(triggered()),this,SLOT(MergeImages()));
 287   connect(actionSlice_Image_As_Multiple_Images,SIGNAL(triggered()),this,SLOT(SliceImages()));
 288   connect(actionOpen_Image_With_Time,SIGNAL(triggered()),this,SLOT(OpenImageWithTime()));
 289   connect(actionMerge_images_as_n_dim_t, SIGNAL(triggered()), this, SLOT(MergeImagesWithTime()));
 290   connect(actionSave_As,SIGNAL(triggered()),this,SLOT(SaveAs()));
 291   connect(actionSave_current_state,SIGNAL(triggered()),this,SLOT(SaveCurrentState()));
 292   connect(actionRead_saved_state,SIGNAL(triggered()),this,SLOT(ReadSavedState()));
 293   connect(actionExit,SIGNAL(triggered()),this,SLOT(close()));
 294   connect(actionAdd_VF_to_current_Image,SIGNAL(triggered()),this,SLOT(OpenField()));
 295   connect(actionAdd_fusion_image,SIGNAL(triggered()),this,SLOT(SelectFusionImage()));
 296   connect(actionAdd_overlay_image_to_current_image,SIGNAL(triggered()), this,SLOT(SelectOverlayImage()));
 297   connect(actionAdd_USSequence_toCT,SIGNAL(triggered()), this,SLOT(SelectFusionSequence()));
 298   connect(actionNavigation_Help,SIGNAL(triggered()),this,SLOT(ShowHelpDialog()));
 299
 300   QShortcut *shortcutHelp = new QShortcut(QKeySequence(QKeySequence::HelpContents),this);
 301   shortcutHelp->setContext(Qt::ApplicationShortcut);
 302   QObject::connect(shortcutHelp, SIGNAL(activated()), this, SLOT(ShowHelpDialog()));
 303
 304   connect(actionDocumentation,SIGNAL(triggered()),this,SLOT(ShowDocumentation()));
 305   connect(actionRegister_vv,SIGNAL(triggered()),this,SLOT(PopupRegisterForm()));
 306
 307   connect(overlayPanel, SIGNAL(FusionSequenceCorrespondancesButtonPressed()), this, SLOT(SelectFusionSequenceCorrespondances()));
 308
 309
 310   ///////////////////////////////////////////////
 311   connect(actionSegmentation,SIGNAL(triggered()),this,SLOT(SegmentationOnCurrentImage()));
 312   connect(actionSurface_Viewer,SIGNAL(triggered()),this,SLOT(SurfaceViewerLaunch()));
 313   ///////////////////////////////////////////////
 314
 315   actionNorth_East_Window->setEnabled(0);
 316   actionNorth_West_Window->setEnabled(0);
 317   actionSouth_East_Window->setEnabled(0);
 318   actionSouth_West_Window->setEnabled(0);
 319
 320   connect(actionNorth_East_Window,SIGNAL(triggered()),this,SLOT(SaveNEScreenshot()));
 321   connect(actionNorth_West_Window,SIGNAL(triggered()),this,SLOT(SaveNOScreenshot()));
 322   connect(actionSouth_East_Window,SIGNAL(triggered()),this,SLOT(SaveSEScreenshot()));
 323   connect(actionSouth_West_Window,SIGNAL(triggered()),this,SLOT(SaveSOScreenshot()));
 324   connect(actionSave_all_slices,SIGNAL(triggered()),this,SLOT(SaveScreenshotAllSlices()));
 325
 326   connect(DataTree,SIGNAL(itemSelectionChanged()),this,SLOT(ImageInfoChanged()));
 327   connect(DataTree,SIGNAL(itemClicked(QTreeWidgetItem*, int)),this,
 328     SLOT(DisplayChanged(QTreeWidgetItem*, int)));
 329
 330   connect(viewButton,SIGNAL(clicked()),this, SLOT(ChangeViewMode()) );
 331   connect(windowSpinBox,SIGNAL(editingFinished()),this,SLOT(WindowLevelEdited()));
 332   connect(levelSpinBox,SIGNAL(editingFinished()),this,SLOT(WindowLevelEdited()));
 333   connect(colorMapComboBox,SIGNAL(currentIndexChanged(int)),this,SLOT(UpdateColorMap()));
 334   connect(presetComboBox,SIGNAL(currentIndexChanged(int)),this,SLOT(UpdateWindowLevel()));
 335   connect(slicingPresetComboBox, SIGNAL(currentIndexChanged(int)),this,SLOT(UpdateSlicingPreset()));
 336   connect(inverseButton,SIGNAL(clicked()),this,SLOT(SwitchWindowLevel()));
 337   connect(applyWindowLevelToAllButton,SIGNAL(clicked()),this,SLOT(ApplyWindowLevelToAllImages()));
 338
 339   connect(this,SIGNAL(customContextMenuRequested(QPoint)),this,SLOT(ShowContextMenu(QPoint)));
 340
 341   connect(linkPanel,SIGNAL(addLink(QString,QString,bool)),this,SLOT(AddLink(QString,QString,bool)));
 342   connect(linkPanel,SIGNAL(removeLink(QString,QString)),this,SLOT(RemoveLink(QString,QString)));
 343   connect(overlayPanel,SIGNAL(VFPropertyUpdated(int,int,int,int,double,double,double)),this,SLOT(SetVFProperty(int,int,int,int,double,double,double)));
 344   connect(overlayPanel,SIGNAL(OverlayPropertyUpdated(int,int,double,double)),
 345     this,SLOT(SetOverlayProperty(int,int,double,double)));
 346   connect(overlayPanel,SIGNAL(FusionPropertyUpdated(int,int,int,double,double, bool)),
 347     this,SLOT(SetFusionProperty(int,int,int,double,double, bool)));
 348   connect(landmarksPanel,SIGNAL(UpdateRenderWindows()),this,SLOT(UpdateRenderWindows()));
 349   connect(landmarksPanel,SIGNAL(SelectedPointChanged()),this,SLOT(GoToLandmark()));
 350
 351   connect(overlayPanel,SIGNAL(FusionSequencePropertyUpdated(int, bool, unsigned int, bool)),
 352     this,SLOT(SetFusionSequenceProperty(int, bool,unsigned int, bool)));
 353
 354
 355   playMode = 0;//pause
 356   mFrameRate = 10;
 357   playButton->setEnabled(0);
 358   frameRateLabel->setEnabled(0);
 359   frameRateSpinBox->setEnabled(0);
 360   connect(playButton, SIGNAL(clicked()),this,SLOT(PlayPause()));
 361   connect(frameRateSpinBox, SIGNAL(valueChanged(int)),this,SLOT(ChangeFrameRate(int)));
 362
 363   goToCursorPushButton->setEnabled(0);
 364   connect(goToCursorPushButton, SIGNAL(clicked()),this,SLOT(GoToCursor()));
 365
 366   NOViewWidget->hide();
 367   NEViewWidget->hide();
 368   SOViewWidget->hide();
 369   SEViewWidget->hide();
 370
 371 #ifdef Q_OS_OSX
 372   disableGLHiDPI(NOViewWidget->winId());
 373   disableGLHiDPI(NEViewWidget->winId());
 374   disableGLHiDPI(SOViewWidget->winId());
 375   disableGLHiDPI(SEViewWidget->winId());
 376 #endif
 377
 378   //Recently opened files
 379   std::list<std::string> recent_files = GetRecentlyOpenedImages();
 380   recentlyOpenedFilesMenu=NULL;
 381   if ( !recent_files.empty() ) {
 382     createRecentlyOpenedFilesMenu();
 383     updateRecentlyOpenedFilesMenu(recent_files);
 384   }
 385
 386   // Adding all new tools (insertion in the menu)
 387   vvToolManager::GetInstance()->InsertToolsInMenu(this);
 388   vvToolManager::GetInstance()->EnableToolsInMenu(this, false);
 389
 390 //#ifndef CLITK_EXPERIMENTAL
 391 //#define CLITK_EXPERIMENTAL 0
 392 //#endif
 393 #ifdef CLITK_EXPERIMENTAL
 394   if (!CLITK_EXPERIMENTAL)
 395     menuExperimental->menuAction()->setVisible(false);
 396 #endif
 397
 398 #if !CLITK_USE_PACS_CONNECTION
 399     actionConnect_Pacs->setVisible(false);
 400 #endif
 401
 402   QTimer * timerMemory = new QTimer(this);
 403   //timerMemory->setInterval(5);
 404   connect(timerMemory, SIGNAL(timeout()), this, SLOT(UpdateMemoryUsage()));
 405   timerMemory->start(2000);
 406 }
 407
 408 //------------------------------------------------------------------------------
 409 void vvMainWindow::show()
 410 {
 411   vvMainWindowBase::show();
 412   PopupRegisterForm(true);
 413 }
 414 //------------------------------------------------------------------------------
 415 void vvMainWindow::UpdateMemoryUsage()
 416 {
 417   //  clitk::PrintMemory(true);
 418   if (clitk::GetMemoryUsageInMb() == 0) infoPanel->setMemoryInMb("NA");
 419   else infoPanel->setMemoryInMb(QString::number(clitk::GetMemoryUsageInMb())+" MB");
 420 }
 421 //------------------------------------------------------------------------------
 422
 423
 424 //------------------------------------------------------------------------------
 425 void vvMainWindow::createRecentlyOpenedFilesMenu()
 426 {
 427   recentlyOpenedFilesMenu = new QMenu("Recently opened files...");
 428   recentlyOpenedFilesMenu->setIcon(QIcon(QString::fromUtf8(":/common/icons/open.png")));
 429   menuFile->insertMenu(actionOpen_Image_With_Time,recentlyOpenedFilesMenu);
 430   menuFile->insertSeparator(actionOpen_Image_With_Time);
 431 }
 432 //------------------------------------------------------------------------------
 433
 434
 435 //------------------------------------------------------------------------------
 436
 437 void vvMainWindow::updateRecentlyOpenedFilesMenu(const std::list<std::string> &recent_files)
 438 {
 439   if(recentlyOpenedFilesMenu==NULL) {
 440     createRecentlyOpenedFilesMenu();
 441   } else {
 442     recentlyOpenedFilesMenu->clear();
 443   }
 444   for (std::list<std::string>::const_iterator i = recent_files.begin(); i!=recent_files.end(); i++) {
 445     QAction* current=new QAction(QIcon(QString::fromUtf8(":/common/icons/open.png")), i->c_str(),this);
 446     recentlyOpenedFilesMenu->addAction(current);
 447     connect(current,SIGNAL(triggered()),this,SLOT(OpenRecentImage()));
 448   }
 449 }
 450 //------------------------------------------------------------------------------
 451
 452
 453 //------------------------------------------------------------------------------
 454 void vvMainWindow::ComputeMidPosition()
 455 {
 456   bool ok;
 457   int index=GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
 458   int ref = QInputDialog::getInt(this,"Chose reference phase","Reference phase",0,0,\
 459 mSlicerManagers[index]->GetImage()->GetVTKImages().size()-1,1,&ok);
 460   if (ok) {
 461     vvMidPosition midp;
 462     midp.slicer_manager = mSlicerManagers[index];
 463     midp.reference_image_index = ref;
 464     QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
 465     midp.Update();
 466     if (midp.error)
 467       QMessageBox::warning(this, "Error computing midposition image",midp.error_message.c_str());
 468     else {
 469       QFileInfo info(midp.slicer_manager->GetFileName().c_str());
 470       AddImage(midp.output,info.path().toStdString()+"/"+info.completeBaseName().toStdString()+"_midposition.mhd");
 471     }
 472     QApplication::restoreOverrideCursor();
 473   }
 474 }
 475 //------------------------------------------------------------------------------
 476
 477
 478 //------------------------------------------------------------------------------
 479 void vvMainWindow::AddContour(int image_index, vvMesh::Pointer contour, bool propagation)
 480 {
 481   QTreeWidgetItem *item = new QTreeWidgetItem();
 482   item->setData(0,Qt::UserRole,"filename.vtk");
 483   item->setData(1,Qt::UserRole,tr("contour"));
 484   QBrush brush;
 485   brush.setColor(QColor(contour->r*255,contour->g*255,contour->b*255));
 486   brush.setStyle(Qt::SolidPattern);
 487   item->setData(COLUMN_IMAGE_NAME,Qt::BackgroundRole,brush);
 488   item->setData(COLUMN_IMAGE_NAME,Qt::DisplayRole,contour->structure_name.c_str());
 489
 490   for (int j = 1; j <= 4; j++)
 491     item->setData(j,Qt::CheckStateRole,DataTree->topLevelItem(image_index)->data(j,Qt::CheckStateRole));
 492
 493   QTreePushButton* cButton = new QTreePushButton;
 494   cButton->setItem(item);
 495   cButton->setColumn(COLUMN_CLOSE_IMAGE);
 496   cButton->setToolTip(tr("close image"));
 497   cButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/exit.png")));
 498   connect(cButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
 499     this,SLOT(CloseImage(QTreeWidgetItem*, int)));
 500
 501   QTreePushButton* rButton = new QTreePushButton;
 502   rButton->setItem(item);
 503   rButton->setColumn(COLUMN_RELOAD_IMAGE);
 504   rButton->setToolTip(tr("reload image"));
 505   rButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/rotateright.png")));
 506   rButton->setEnabled(false);
 507   //Not implemented
 508   //connect(rButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
 509   //this,SLOT(ReloadImage(QTreeWidgetItem*, int)));
 510
 511   DataTree->topLevelItem(image_index)->setExpanded(1);
 512   DataTree->topLevelItem(image_index)->addChild(item);
 513   DataTree->setItemWidget(item, COLUMN_CLOSE_IMAGE, cButton);
 514   DataTree->setItemWidget(item, COLUMN_RELOAD_IMAGE, rButton);
 515   QString id = DataTree->topLevelItem(image_index)->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString();
 516   item->setData(COLUMN_IMAGE_NAME,Qt::UserRole,id.toStdString().c_str());
 517
 518   UpdateTree();
 519   mSlicerManagers[image_index]->AddContour(contour,propagation);
 520   mSlicerManagers[image_index]->Render();
 521 }
 522 //------------------------------------------------------------------------------
 523
 524
 525 //------------------------------------------------------------------------------
 526 void vvMainWindow::OpenVTKContour()
 527 {
 528   if (mSlicerManagers.size() > 0) {
 529     QString Extensions = "Images ( *.vtk *.obj)";
 530     Extensions += ";;All Files (*)";
 531     QString file = QFileDialog::getOpenFileName(this,tr("Open vtkPolyData"),mInputPathName,Extensions);
 532     if (file.isNull())
 533       return;
 534     QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
 535     int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
 536     vvMeshReader reader;
 537     reader.SetImage(mSlicerManagers[index]->GetImage());
 538     reader.SetModeToVTK();
 539     reader.SetFilename(file.toStdString());
 540     reader.Update();
 541     AddContour(index,reader.GetOutput()[0],false);
 542     QApplication::restoreOverrideCursor();
 543   }
 544 }
 545 //------------------------------------------------------------------------------
 546
 547
 548 //------------------------------------------------------------------------------
 549 void vvMainWindow::AddDCStructContour(int index, QString file)
 550 {
 551   vvMeshReader reader;
 552   reader.SetFilename(file.toStdString());
 553   vvStructSelector selector;
 554   selector.SetStructures(reader.GetROINames());
 555   if (!mSlicerManagers[index]->GetVF().IsNull())
 556     selector.EnablePropagationCheckBox();
 557   if (selector.exec()) {
 558     QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
 559     reader.SetSelectedItems(selector.getSelectedItems());
 560     reader.SetImage(mSlicerManagers[index]->GetImage());
 561     if (selector.PropagationEnabled())
 562       reader.SetPropagationVF(mSlicerManagers[index]->GetVF());
 563     reader.Update();
 564     std::vector<vvMesh::Pointer> contours=reader.GetOutput();
 565     for (std::vector<vvMesh::Pointer>::iterator i=contours.begin();
 566       i!=contours.end(); i++)
 567       AddContour(index,*i,selector.PropagationEnabled());
 568     QApplication::restoreOverrideCursor();
 569   }
 570 }
 571
 572 //------------------------------------------------------------------------------
 573 void vvMainWindow::OpenDCStructContour()
 574 {
 575   if (mSlicerManagers.size() > 0) {
 576     QString Extensions = "Dicom Files ( *.dcm RS*)";
 577     Extensions += ";;All Files (*)";
 578     QString file = QFileDialog::getOpenFileName(this,tr("Merge Images"),mInputPathName,Extensions);
 579     if (file.isNull())
 580       return;
 581     int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
 582     AddDCStructContour(index, file);
 583   }
 584 }
 585 //------------------------------------------------------------------------------
 586
 587
 588 //------------------------------------------------------------------------------
 589 void vvMainWindow::ComputeDeformableRegistration()
 590 {
 591   if (mSlicerManagers.size() > 0) {
 592     int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
 593     vvDeformationDialog dialog(index,mSlicerManagers);
 594     if (dialog.exec()) {
 595       std::string base_name=itksys::SystemTools::GetFilenameWithoutExtension(mSlicerManagers[dialog.GetInputFileIndex()]->GetFileName());
 596       AddField(dialog.GetOutput(),dialog.getFieldFile(),dialog.GetInputFileIndex());
 597       WarpImage(dialog.GetSelectedSlicer(),dialog.GetReferenceFrameIndex());
 598     } else
 599       std::cout << "Error or user cancellation while computing deformation field..." << std::endl;
 600   } else QMessageBox::information(this, "Need to open image","You must open an image first.");
 601 }
 602 //------------------------------------------------------------------------------
 603
 604
 605 //------------------------------------------------------------------------------
 606 void vvMainWindow::WarpImage()
 607 {
 608   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
 609   if (!mSlicerManagers[index]->GetVF().IsNull()) {
 610     bool ok;
 611     int ref = QInputDialog::getInt(this,"Chose reference phase","Reference phase",0,0,\
 612       mSlicerManagers[index]->GetImage()->GetVTKImages().size()-1,1,&ok);
 613     if (ok) {
 614       WarpImage(mSlicerManagers[index],ref);
 615     }
 616   } else
 617     QMessageBox::warning(this,tr("No vector field"),tr("Sorry, can't warp without a vector field"));
 618 }
 619 //------------------------------------------------------------------------------
 620
 621
 622 //------------------------------------------------------------------------------
 623 void vvMainWindow::WarpImage(vvSlicerManager* selected_slicer,int reference_phase)
 624 {
 625   if (!selected_slicer->GetVF().IsNull()) {
 626     QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
 627     QFileInfo info(selected_slicer->GetFileName().c_str());
 628     vvImageWarp warp(selected_slicer->GetImage(),selected_slicer->GetVF(),
 629       reference_phase,this);
 630     if (warp.ComputeWarpedImage()) {
 631       AddImage(warp.GetWarpedImage(),info.path().toStdString()+"/"+info.completeBaseName().toStdString()+"_warped.mhd");
 632       AddImage(warp.GetDiffImage()  ,info.path().toStdString()+"/"+info.completeBaseName().toStdString()+"_diff.mhd");
 633       AddImage(warp.GetJacobianImage()  ,info.path().toStdString()+"/"+info.completeBaseName().toStdString()+"_jacobian.mhd");
 634       QApplication::restoreOverrideCursor();
 635     } else {
 636       QApplication::restoreOverrideCursor();
 637       QMessageBox::warning(this,tr("Different spacings"),tr("The vector field and image spacings must be the same in order to warp."));
 638     }
 639   } else
 640     QMessageBox::warning(this,tr("No vector field"),tr("Sorry, can't warp without a vector field."));
 641 }
 642 //------------------------------------------------------------------------------
 643
 644
 645 //------------------------------------------------------------------------------
 646 vvMainWindow::~vvMainWindow()
 647 {
 648   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
 649     if (mSlicerManagers[i] != NULL)
 650       delete mSlicerManagers[i];
 651   }
 652   delete documentation;
 653   delete help_dialog;
 654   delete dicomSeriesSelector;
 655 }
 656 //------------------------------------------------------------------------------
 657
 658 //------------------------------------------------------------------------------
 659 QTabWidget * vvMainWindow::GetTab()
 660 {
 661   return tabWidget;
 662 }
 663 //------------------------------------------------------------------------------
 664
 665
 666 //------------------------------------------------------------------------------
 667 void vvMainWindow::MergeImages()
 668 {
 669   QString Extensions = EXTENSIONS;
 670   Extensions += ";;All Files (*)";
 671   QStringList files = QFileDialog::getOpenFileNames(this,tr("Merge Images"),mInputPathName,Extensions);
 672   if (files.isEmpty())
 673     return;
 674   mInputPathName = itksys::SystemTools::GetFilenamePath(files[0].toStdString()).c_str();
 675   std::vector<std::string> vector;
 676
 677   unsigned int currentDim = 0;
 678   std::vector<double> currentSpacing;
 679   std::vector<int> currentSize;
 680   std::vector<double> currentOrigin;
 681
 682   for (int i = 0; i < files.size(); i++) {
 683     itk::ImageIOBase::Pointer reader = itk::ImageIOFactory::CreateImageIO(
 684       files[i].toStdString().c_str(), itk::ImageIOFactory::ReadMode);
 685     reader->SetFileName(files[i].toStdString().c_str());
 686     reader->ReadImageInformation();
 687     if (reader)        {
 688       //NOViewWidget->hide();
 689       //NEViewWidget->hide();
 690       //SOViewWidget->hide();
 691       //SEViewWidget->hide();
 692       if (i == 0)
 693         currentDim = reader->GetNumberOfDimensions();
 694       bool IsOk = true;
 695       for (unsigned int j = 0; j < currentDim; j++) {
 696         if (i == 0) {
 697           if (j == 0) {
 698             currentSpacing.resize(currentDim);
 699             currentSize.resize(currentDim);
 700             currentOrigin.resize(currentDim);
 701           }
 702           currentOrigin[j] = reader->GetOrigin(j);
 703           currentSpacing[j] = reader->GetSpacing(j);
 704           currentSize[j] = reader->GetDimensions(j);
 705         } else if (currentDim != reader->GetNumberOfDimensions()
 706           || currentSpacing[j] != reader->GetSpacing(j)
 707           || currentSize[j] != (int)reader->GetDimensions(j)
 708           || currentOrigin[j] != reader->GetOrigin(j)) {
 709             QString error = "Cannot read file (too different from others ";
 710             error += files[i].toStdString().c_str();
 711             QMessageBox::information(this,tr("Reading problem"),error);
 712             IsOk = false;
 713             break;
 714         }
 715       }
 716       if (IsOk)
 717         vector.push_back(files[i].toStdString());
 718     }
 719   }
 720   if (vector.size() > 0)
 721     LoadImages(vector, vvImageReader::MERGED);
 722 }
 723 //------------------------------------------------------------------------------
 724
 725 //------------------------------------------------------------------------------
 726 void vvMainWindow::SliceImages()
 727 {
 728   QString Extensions = EXTENSIONS;
 729   Extensions += ";;All Files (*)";
 730
 731   QStringList files = QFileDialog::getOpenFileNames(this,tr("Slice Images"),mInputPathName,Extensions);
 732   if (files.isEmpty())
 733     return;
 734   mInputPathName = itksys::SystemTools::GetFilenamePath(files[0].toStdString()).c_str();
 735   std::vector<std::string> vector;
 736   for (int i = 0; i < files.size(); i++)
 737     vector.push_back(files[i].toStdString());
 738   LoadImages(vector, vvImageReader::SLICED);
 739 }
 740 //------------------------------------------------------------------------------
 741
 742 //------------------------------------------------------------------------------
 743 void vvMainWindow::MergeImagesWithTime()
 744 {
 745   QString Extensions = EXTENSIONS;
 746   Extensions += ";;All Files (*)";
 747   QStringList files = QFileDialog::getOpenFileNames(this,tr("Merge Images With Time"),mInputPathName,Extensions);
 748   if (files.isEmpty())
 749     return;
 750   mInputPathName = itksys::SystemTools::GetFilenamePath(files[0].toStdString()).c_str();
 751   std::vector<std::string> vector;
 752
 753   for (int i = 0; i < files.size(); i++)
 754     vector.push_back(files[i].toStdString());
 755   sort(vector.begin(),vector.end());
 756   if (vector.size() > 1)
 757     LoadImages(vector, vvImageReader::MERGEDWITHTIME);
 758   else
 759     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.");
 760 }
 761 //------------------------------------------------------------------------------
 762
 763
 764 //------------------------------------------------------------------------------
 765 void vvMainWindow::OpenDicom()
 766 {
 767   std::vector<std::string> files;
 768
 769   //std::cout << "dicomSeriesSelector " << std::endl;
 770   if (dicomSeriesSelector->exec() == QDialog::Accepted) {
 771     files = *(dicomSeriesSelector->GetFilenames());
 772     LoadImages(files, vvImageReader::DICOM);
 773   }
 774 }
 775 #if CLITK_USE_PACS_CONNECTION
 776 void vvMainWindow::ConnectPacs()
 777 {
 778   std::vector<std::string> files;
 779
 780   //std::cout << "dicomSeriesSelector " << std::endl;
 781 if (PacsConnection->exec() == QDialog::Accepted) {
 782         for (int i = 0; i < PacsConnection->getSeriesCount(); i++)
 783         {
 784                 files = PacsConnection->getFileNames(i);
 785                 LoadImages(files, vvImageReader::DICOM);
 786         }
 787         PacsConnection->clearMove();
 788   }
 789   }
 790
 791 #endif
 792 //------------------------------------------------------------------------------
 793
 794 //------------------------------------------------------------------------------
 795 void vvMainWindow::OpenImages()
 796 {
 797   QString Extensions = EXTENSIONS;
 798   Extensions += ";;All Files (*)";
 799
 800   QStringList files = QFileDialog::getOpenFileNames(this,tr("Load Images"),mInputPathName,Extensions);
 801   if (files.isEmpty())
 802     return;
 803   mInputPathName = itksys::SystemTools::GetFilenamePath(files[0].toStdString()).c_str();
 804   std::vector<std::string> vector;
 805   for (int i = 0; i < files.size(); i++)
 806     vector.push_back(files[i].toStdString());
 807   LoadImages(vector, vvImageReader::IMAGE);
 808 }
 809 //------------------------------------------------------------------------------
 810 void vvMainWindow::OpenRecentImage()
 811 {
 812   QAction * caller = qobject_cast<QAction*>(sender());
 813   std::vector<std::string> images;
 814   images.push_back(caller->text().toStdString());
 815   mInputPathName = itksys::SystemTools::GetFilenamePath(images[0]).c_str();
 816   LoadImages(images, vvImageReader::IMAGE);
 817 }
 818 //------------------------------------------------------------------------------
 819
 820
 821 //------------------------------------------------------------------------------
 822 void vvMainWindow::OpenImageWithTime()
 823 {
 824   QString Extensions = EXTENSIONS;
 825   Extensions += ";;All Files (*)";
 826
 827   QStringList files = QFileDialog::getOpenFileNames(this,tr("Load Images With Time"),mInputPathName,Extensions);
 828   if (files.isEmpty())
 829     return;
 830   mInputPathName = itksys::SystemTools::GetFilenamePath(files[0].toStdString()).c_str();
 831   std::vector<std::string> vector;
 832   for (int i = 0; i < files.size(); i++) {
 833     vector.push_back(files[i].toStdString());
 834   }
 835   LoadImages(vector, vvImageReader::IMAGEWITHTIME);
 836 }
 837 //------------------------------------------------------------------------------
 838
 839
 840 //------------------------------------------------------------------------------
 841 void vvMainWindow::LoadImages(std::vector<std::string> files, vvImageReader::LoadedImageType filetype)
 842 {
 843   //Separate the way to open images and dicoms
 844   int fileSize;
 845   if (filetype == vvImageReader::IMAGE || filetype == vvImageReader::IMAGEWITHTIME)
 846     fileSize = files.size();
 847   else
 848     fileSize = 1;
 849
 850   // For SLICED, we need the number of slices (ndim and #slices)
 851   std::vector<unsigned int> nSlices;
 852   nSlices.resize(files.size());
 853   std::fill(nSlices.begin(), nSlices.end(), 1);
 854   if (filetype == vvImageReader::SLICED) {
 855     for (int i = 0; i < fileSize; i++) {
 856       itk::ImageIOBase::Pointer header = clitk::readImageHeader(files[i]);
 857       QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
 858       if (!header) {
 859         nSlices[i] = 0;
 860         QString error = "Cannot open file \n";
 861         error += files[i].c_str();
 862         QMessageBox::information(this,tr("Reading problem"),error);
 863         return;
 864       }
 865       if (header->GetNumberOfDimensions() < 3) {
 866         nSlices[i] = 0;
 867         QString error = "Dimension problem. Cannot slice \n";
 868         error += files[i].c_str();
 869         QMessageBox::information(this,tr("Reading problem"),error);
 870         return;
 871       }
 872       nSlices[i] = header->GetDimensions( header->GetNumberOfDimensions()-1 );
 873     }
 874   }
 875
 876   //Only add to the list of recently opened files when a single file is opened,
 877   //to avoid polluting the list of recently opened files
 878   if (files.size() == 1) {
 879     QFileInfo finfo=tr(files[0].c_str());
 880     AddToRecentlyOpenedImages(finfo.absoluteFilePath().toStdString());
 881     updateRecentlyOpenedFilesMenu(GetRecentlyOpenedImages());
 882   }
 883   //init the progress events
 884   QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
 885   vvProgressDialog progress("Opening " + files[0],fileSize>1);
 886   qApp->processEvents();
 887
 888   int numberofsuccesulreads=0;
 889   //open images as 1 or multiples
 890   for (int i = 0; i < fileSize; i++) {
 891     progress.SetText("Opening " + files[i]);
 892     progress.SetProgress(i,fileSize);
 893     qApp->processEvents();
 894
 895     for (unsigned int j = 0; j < nSlices[i]; j++) {
 896       //read the image and put it in mSlicerManagers
 897       vvSlicerManager* imageManager = new vvSlicerManager(4);
 898       qApp->processEvents();
 899
 900       bool SetImageSucceed=false;
 901
 902       // Change filename if an image with the same already exist
 903       int number = GetImageDuplicateFilenameNumber(files[i] + std::string("_slice"));
 904
 905       if (filetype == vvImageReader::IMAGE || filetype == vvImageReader::IMAGEWITHTIME || filetype == vvImageReader::SLICED)
 906         SetImageSucceed = imageManager->SetImage(files[i],filetype, number, j);
 907       else if (filetype == vvImageReader::DICOM)
 908         SetImageSucceed = imageManager->SetImages(files,filetype, number, dicomSeriesSelector->IsPatientCoordianteSystemChecked());
 909       else
 910         SetImageSucceed = imageManager->SetImages(files,filetype, number);
 911
 912       if (!SetImageSucceed) {
 913         QApplication::restoreOverrideCursor();
 914         QString error = "Cannot open file \n";
 915         error += imageManager->GetLastError().c_str();
 916         QMessageBox::information(this,tr("Reading problem"),error);
 917         delete imageManager;
 918       } else {
 919
 920         mSlicerManagers.push_back(imageManager);
 921
 922         //create an item in the tree with good settings
 923         QTreeWidgetItem *item = new QTreeWidgetItem();
 924         item->setData(0,Qt::UserRole,files[i].c_str());
 925         QFileInfo fileinfo(imageManager->GetFileName().c_str()); //Do not show the path
 926         item->setData(COLUMN_IMAGE_NAME,Qt::DisplayRole,fileinfo.fileName());
 927         item->setData(1,Qt::UserRole,tr("image"));
 928         item->setToolTip(COLUMN_IMAGE_NAME, imageManager->GetListOfAbsoluteFilePathInOneString("image").c_str());
 929         qApp->processEvents();
 930
 931         //Create the buttons for reload and close
 932         qApp->processEvents();
 933         QTreePushButton* cButton = new QTreePushButton;
 934         cButton->setItem(item);
 935         cButton->setColumn(COLUMN_CLOSE_IMAGE);
 936         cButton->setToolTip(tr("close image"));
 937         cButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/exit.png")));
 938         connect(cButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
 939           this,SLOT(CloseImage(QTreeWidgetItem*, int)));
 940
 941         QTreePushButton* rButton = new QTreePushButton;
 942         rButton->setItem(item);
 943         rButton->setColumn(COLUMN_RELOAD_IMAGE);
 944         rButton->setToolTip(tr("reload image"));
 945         rButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/rotateright.png")));
 946         connect(rButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
 947           this,SLOT(ReloadImage(QTreeWidgetItem*, int)));
 948
 949         DataTree->addTopLevelItem(item);
 950         DataTree->setItemWidget(item, COLUMN_CLOSE_IMAGE, cButton);
 951         DataTree->setItemWidget(item, COLUMN_RELOAD_IMAGE, rButton);
 952
 953         //set the id of the image
 954         QString id = QDir::current().absoluteFilePath(files[i].c_str()) + QString::number(mSlicerManagers.size()-1);
 955         item->setData(COLUMN_IMAGE_NAME,Qt::UserRole,id.toStdString().c_str());
 956         mSlicerManagers.back()->SetId(id.toStdString());
 957
 958         linkPanel->addImage(imageManager->GetFileName(), id.toStdString());
 959
 960         connect(mSlicerManagers.back(), SIGNAL(currentImageChanged(std::string)),
 961           this,SLOT(CurrentImageChanged(std::string)));
 962         connect(mSlicerManagers.back(), SIGNAL(currentPickedImageChanged(std::string)),
 963           this, SLOT(CurrentPickedImageChanged(std::string)));
 964         connect(mSlicerManagers.back(), SIGNAL(UpdatePosition(int, double, double, double, double, double, double, double)),
 965           this,SLOT(MousePositionChanged(int,double, double, double, double, double, double, double)));
 966         connect(mSlicerManagers.back(), SIGNAL(UpdateVector(int, double, double, double, double)),
 967           this, SLOT(VectorChanged(int,double,double,double, double)));
 968         connect(mSlicerManagers.back(), SIGNAL(UpdateOverlay(int, double, double)),
 969           this, SLOT(OverlayChanged(int,double,double)));
 970         connect(mSlicerManagers.back(), SIGNAL(UpdateFusion(int, double)),
 971           this, SLOT(FusionChanged(int,double)));
 972         connect(mSlicerManagers.back(), SIGNAL(WindowLevelChanged()),
 973           this,SLOT(WindowLevelChanged()));
 974         connect(mSlicerManagers.back(), SIGNAL(UpdateSlice(int,int)),
 975           this,SLOT(UpdateSlice(int,int)));
 976         connect(mSlicerManagers.back(), SIGNAL(UpdateTSlice(int, int, int)),
 977           this,SLOT(UpdateTSlice(int, int, int)));
 978         connect(mSlicerManagers.back(), SIGNAL(UpdateTSlice(int, int, int)),
 979           this,SLOT(ImageInfoChanged()));
 980         connect(mSlicerManagers.back(), SIGNAL(UpdateSliceRange(int,int,int,int,int)),
 981           this,SLOT(UpdateSliceRange(int,int,int,int,int)));
 982         connect(mSlicerManagers.back(), SIGNAL(UpdateLinkManager(std::string,int,double,double,double,int)),
 983           this,SLOT(UpdateLinkManager(std::string,int,double,double,double,int)));
 984         connect(mSlicerManagers.back(), SIGNAL(UpdateLinkedNavigation(std::string,vvSlicerManager*,vvSlicer*)),
 985           this,SLOT(UpdateLinkedNavigation(std::string,vvSlicerManager*,vvSlicer*)));
 986         connect(mSlicerManagers.back(), SIGNAL(ChangeImageWithIndexOffset(vvSlicerManager*,int,int)),
 987           this,SLOT(ChangeImageWithIndexOffset(vvSlicerManager*,int,int)));
 988         connect(mSlicerManagers.back(),SIGNAL(LandmarkAdded()),landmarksPanel,SLOT(AddPoint()));
 989         connect(landmarksPanel,SIGNAL(UpdateLandmarkTransform()), mSlicerManagers.back(), SLOT(UpdateLandmark()));
 990         InitSlicers();
 991         numberofsuccesulreads++;
 992       }
 993     }
 994   }
 995
 996   if (numberofsuccesulreads) {
 997     NOViewWidget->show();
 998     NEViewWidget->show();
 999     SOViewWidget->show();
1000     SEViewWidget->show();
1001     UpdateTree();
1002     InitDisplay();
1003     ShowLastImage();
1004
1005     // Try to guess default WindowLevel
1006     double range[2];
1007     mSlicerManagers.back()->GetImage()->GetFirstVTKImageData()->GetScalarRange(range);
1008     if ((range[0] == 0) && (range[1] == 1)) {
1009       presetComboBox->setCurrentIndex(WL_BINARY);// binary
1010     } else {
1011       // TODO
1012     }
1013   }
1014   QApplication::restoreOverrideCursor();
1015 }
1016 //------------------------------------------------------------------------------
1017
1018 //------------------------------------------------------------------------------
1019 void vvMainWindow::UpdateTree()
1020 {
1021   DataTree->resizeColumnToContents(COLUMN_TREE);
1022   DataTree->resizeColumnToContents(COLUMN_UL_VIEW);
1023   DataTree->resizeColumnToContents(COLUMN_UR_VIEW);
1024   DataTree->resizeColumnToContents(COLUMN_DL_VIEW);
1025   DataTree->resizeColumnToContents(COLUMN_DR_VIEW);
1026   DataTree->resizeColumnToContents(COLUMN_IMAGE_NAME);
1027   DataTree->resizeColumnToContents(COLUMN_CLOSE_IMAGE);
1028   DataTree->resizeColumnToContents(COLUMN_RELOAD_IMAGE);
1029 }
1030 //------------------------------------------------------------------------------
1031
1032 //------------------------------------------------------------------------------
1033 void vvMainWindow::CurrentImageChanged(std::string id)
1034 {
1035   if (id == mCurrentSelectedImageId) return; // Do nothing
1036   int selected = 0;
1037   for (int i = 0; i < DataTree->topLevelItemCount(); i++) {
1038     if (DataTree->topLevelItem(i)->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString().toStdString() == id) {
1039       selected = i;
1040     } else {
1041       DataTree->topLevelItem(i)->setSelected(0);
1042     }
1043     for (int child = 0; child < DataTree->topLevelItem(i)->childCount(); child++)
1044       DataTree->topLevelItem(i)->child(child)->setSelected(0);
1045
1046   }
1047   DataTree->topLevelItem(selected)->setSelected(1);
1048   mCurrentSelectedImageId = id;
1049
1050   landmarksPanel->SetCurrentLandmarks(mSlicerManagers[selected]->GetLandmarks(),
1051                                       mSlicerManagers[selected]->GetTSlice());
1052   landmarksPanel->SetCurrentPath(mInputPathName.toStdString());
1053   landmarksPanel->SetCurrentImage(mSlicerManagers[selected]->GetFileName().c_str());
1054
1055   emit SelectedImageHasChanged(mSlicerManagers[selected]);
1056 }
1057 //------------------------------------------------------------------------------
1058
1059 //------------------------------------------------------------------------------
1060 void vvMainWindow::CurrentPickedImageChanged(std::string id)
1061 {
1062   if (id == mCurrentPickedImageId) return; // Do nothing
1063   int selected = 0;
1064   for (int i = 0; i < DataTree->topLevelItemCount(); i++) {
1065     if (DataTree->topLevelItem(i)->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString().toStdString() == id) {
1066       selected = i;
1067     } else {
1068       DataTree->topLevelItem(i)->setSelected(0);
1069     }
1070     for (int child = 0; child < DataTree->topLevelItem(i)->childCount(); child++)
1071       DataTree->topLevelItem(i)->child(child)->setSelected(0);
1072
1073   }
1074   DataTree->topLevelItem(selected)->setSelected(1);
1075   mCurrentPickedImageId = id;
1076   mCurrentPickedImageIndex = selected;
1077 }
1078 //------------------------------------------------------------------------------
1079
1080 //------------------------------------------------------------------------------
1081 void vvMainWindow::ImageInfoChanged()
1082 {
1083   contextActions[6]->setEnabled(1);
1084   contextActions[5]->setEnabled(1);
1085   actionSave_As->setEnabled(1);
1086   actionAdd_VF_to_current_Image->setEnabled(1);
1087   actionAdd_fusion_image->setEnabled(1);
1088   actionAdd_overlay_image_to_current_image->setEnabled(1);
1089   actionAdd_USSequence_toCT->setEnabled(1);
1090   actionNorth_East_Window->setEnabled(1);
1091   actionNorth_West_Window->setEnabled(1);
1092   actionSouth_East_Window->setEnabled(1);
1093   actionSouth_West_Window->setEnabled(1);
1094   vvToolManager::GetInstance()->EnableToolsInMenu(this, true);
1095   inverseButton->setEnabled(1);
1096
1097   goToCursorPushButton->setEnabled(1);
1098
1099   if (DataTree->selectedItems().size()) {
1100     int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1101
1102     colorMapComboBox->setEnabled(1);
1103     for (int i = 0; i < DataTree->topLevelItem(index)->childCount(); i++) {
1104       if (DataTree->topLevelItem(index)->child(i)->data(1,Qt::UserRole).toString() == "overlay" ||
1105         DataTree->topLevelItem(index)->child(i)->data(1,Qt::UserRole).toString() == "fusion" ||
1106         DataTree->topLevelItem(index)->child(i)->data(1,Qt::UserRole).toString() == "fusionSequence") {
1107           colorMapComboBox->setEnabled(0);
1108           break;
1109       }
1110     }
1111
1112     std::vector<double> origin;
1113     std::vector<double> inputSpacing;
1114     std::vector<int> inputSize;
1115     std::vector<double> sizeMM;
1116     vtkSmartPointer<vtkMatrix4x4> transformation;
1117     int dimension=0;
1118     QString pixelType;
1119     QString inputSizeInBytes;
1120     QString image = DataTree->selectedItems()[0]->data(COLUMN_IMAGE_NAME,Qt::DisplayRole).toString();
1121
1122     int nframes = mSlicerManagers[index]->GetSlicer(0)->GetTMax();
1123
1124     if (nframes > 1 || playMode == 1) {
1125       playButton->setEnabled(1);
1126       frameRateLabel->setEnabled(1);
1127       frameRateSpinBox->setEnabled(1);
1128     } else {
1129       playButton->setEnabled(0);
1130       frameRateLabel->setEnabled(0);
1131       frameRateSpinBox->setEnabled(0);
1132     }
1133
1134     //read image header
1135     int NPixel = 1;
1136
1137     int tSlice = 0;
1138     vvImage::Pointer imageSelected;
1139     if (DataTree->topLevelItem(index) == DataTree->selectedItems()[0]) {
1140       imageSelected = mSlicerManagers[index]->GetSlicer(0)->GetImage();
1141       tSlice = mSlicerManagers[index]->GetSlicer(0)->GetTSlice();
1142     } else if (DataTree->selectedItems()[0]->data(1,Qt::UserRole).toString() == "vector") {
1143       imageSelected = mSlicerManagers[index]->GetSlicer(0)->GetVF();
1144       tSlice = mSlicerManagers[index]->GetSlicer(0)->GetOverlayTSlice();
1145     } else if (DataTree->selectedItems()[0]->data(1,Qt::UserRole).toString() == "overlay") {
1146       imageSelected = mSlicerManagers[index]->GetSlicer(0)->GetOverlay();
1147       tSlice = mSlicerManagers[index]->GetSlicer(0)->GetOverlayTSlice();
1148     } else if (DataTree->selectedItems()[0]->data(1,Qt::UserRole).toString() == "fusion") {
1149       imageSelected = mSlicerManagers[index]->GetSlicer(0)->GetFusion();
1150       tSlice = mSlicerManagers[index]->GetSlicer(0)->GetFusionTSlice();
1151     }
1152     else if (DataTree->selectedItems()[0]->data(1,Qt::UserRole).toString() == "fusionSequence") {
1153       imageSelected = mSlicerManagers[index]->GetSlicer(0)->GetFusion();
1154       tSlice = mSlicerManagers[index]->GetSlicer(0)->GetFusionTSlice();
1155     }
1156     else if (DataTree->selectedItems()[0]->data(1,Qt::UserRole).toString() == "contour") {
1157       imageSelected = mSlicerManagers[index]->GetSlicer(0)->GetImage();
1158       tSlice = mSlicerManagers[index]->GetSlicer(0)->GetTSlice();
1159     }
1160     else {
1161       imageSelected = mSlicerManagers[index]->GetSlicer(0)->GetImage();
1162       tSlice = mSlicerManagers[index]->GetSlicer(0)->GetTSlice();
1163     }
1164
1165     dimension = imageSelected->GetNumberOfDimensions();
1166     origin.resize(dimension);
1167     inputSpacing.resize(dimension);
1168     inputSize.resize(dimension);
1169     sizeMM.resize(dimension);
1170     pixelType = mSlicerManagers[index]->GetImage()->GetScalarTypeAsITKString().c_str();
1171     for (int i = 0; i < dimension; i++) {
1172       origin[i] = imageSelected->GetOrigin()[i];
1173       inputSpacing[i] = imageSelected->GetSpacing()[i];
1174       inputSize[i] = imageSelected->GetSize()[i];
1175       sizeMM[i] = inputSize[i]*inputSpacing[i];
1176       NPixel *= inputSize[i];
1177     }
1178     inputSizeInBytes = GetSizeInBytes(imageSelected->GetActualMemorySize());
1179
1180     QString dim = QString::number(dimension) + " (";
1181     dim += pixelType + ")";
1182
1183     infoPanel->setFileName(image);
1184     std::string creationImageTimeValue("No creation time");
1185     itk::ExposeMetaData< std::string > (*imageSelected->GetFirstMetaDataDictionary(), "creationImageTime", creationImageTimeValue);
1186     infoPanel->setImageCreationTime(QString(creationImageTimeValue.c_str()));
1187     infoPanel->setDimension(dim);
1188     infoPanel->setSizePixel(GetVectorIntAsString(inputSize));
1189     infoPanel->setSizeMM(GetVectorDoubleAsString(sizeMM));
1190     infoPanel->setOrigin(GetVectorDoubleAsString(origin));
1191     infoPanel->setSpacing(GetVectorDoubleAsString(inputSpacing));
1192     infoPanel->setNPixel(QString::number(NPixel)+" ("+inputSizeInBytes+")");
1193
1194     transformation = imageSelected->GetTransform()[tSlice]->GetMatrix();
1195     infoPanel->setTransformation(clitk::Get4x4MatrixDoubleAsString(transformation).c_str());
1196
1197     landmarksPanel->SetCurrentLandmarks(mSlicerManagers[index]->GetLandmarks(),
1198                                         mSlicerManagers[index]->GetTSlice());
1199     landmarksPanel->SetCurrentPath(mInputPathName.toStdString());
1200     landmarksPanel->SetCurrentImage(mSlicerManagers[index]->GetFileName().c_str());
1201
1202     overlayPanel->getCurrentImageName(mSlicerManagers[index]->GetFileName().c_str());
1203     for (int i = 0; i < 4; i++) {
1204       if (DataTree->selectedItems()[0]->data(i+1,Qt::CheckStateRole).toInt() > 0 || i == 3) {
1205         mSlicerManagers[index]->UpdateInfoOnCursorPosition(i);
1206         break;
1207       }
1208     }
1209
1210 //     infoPanel->setFileName(image);
1211 //     infoPanel->setDimension(dim);
1212 //     infoPanel->setSizePixel(GetVectorIntAsString(inputSize));
1213 //     infoPanel->setSizeMM(GetVectorDoubleAsString(sizeMM));
1214 //     infoPanel->setOrigin(GetVectorDoubleAsString(origin));
1215 //     infoPanel->setSpacing(GetVectorDoubleAsString(inputSpacing));
1216 //     infoPanel->setNPixel(QString::number(NPixel)+" ("+inputSizeInBytes+")");
1217 //
1218 //     landmarksPanel->SetCurrentLandmarks(mSlicerManagers[index]->GetLandmarks(),
1219 //                                         mSlicerManagers[index]->GetTSlice());
1220 //     landmarksPanel->SetCurrentPath(mInputPathName.toStdString());
1221 //     landmarksPanel->SetCurrentImage(mSlicerManagers[index]->GetFileName().c_str());
1222 //
1223 //     overlayPanel->getCurrentImageName(mSlicerManagers[index]->GetFileName().c_str());
1224 //     for (int i = 0; i < 4; i++) {
1225 //       if (DataTree->selectedItems()[0]->data(i+1,Qt::CheckStateRole).toInt() > 0 || i == 3) {
1226 //         mSlicerManagers[index]->UpdateInfoOnCursorPosition(i);
1227 //         break;
1228 //       }
1229 //     }
1230     WindowLevelChanged();
1231
1232     slicingPresetComboBox->setCurrentIndex(mSlicerManagers[index]->GetSlicingPreset());
1233
1234     if (mSlicerManagers[index]->GetSlicer(0)->GetVF()) {
1235       overlayPanel->getVFName(mSlicerManagers[index]->GetVFName().c_str());
1236       overlayPanel->getVFProperty(mSlicerManagers[index]->GetSlicer(0)->GetVFSubSampling(),
1237         mSlicerManagers[index]->GetSlicer(0)->GetVFScale(),
1238         mSlicerManagers[index]->GetSlicer(0)->GetVFLog());
1239     } else {
1240       overlayPanel->getVFName(mSlicerManagers[index]->GetVFName().c_str());
1241       overlayPanel->getVFProperty(-1,-1,-1);
1242     }
1243     if (mSlicerManagers[index]->GetSlicer(0)->GetOverlay()) {
1244       overlayPanel->getOverlayName(mSlicerManagers[index]->GetOverlayName().c_str());
1245     } else {
1246       overlayPanel->getOverlayName(mSlicerManagers[index]->GetOverlayName().c_str());
1247     }
1248
1249     if (mSlicerManagers[index]->GetSlicer(0)->GetFusion()) {
1250       overlayPanel->getFusionName(mSlicerManagers[index]->GetFusionName().c_str());
1251     } else {
1252       overlayPanel->getFusionName(mSlicerManagers[index]->GetFusionName().c_str());
1253     }
1254   }
1255 }
1256 //------------------------------------------------------------------------------
1257
1258 //------------------------------------------------------------------------------
1259 void vvMainWindow::ShowDocumentation()
1260 {
1261   documentation->show();
1262 }
1263 //------------------------------------------------------------------------------
1264
1265 //------------------------------------------------------------------------------
1266 void vvMainWindow::PopupRegisterForm(bool checkCanPush)
1267 {
1268   vvRegisterForm* registerForm = new vvRegisterForm(QUrl("http://www.creatis.insa-lyon.fr/~dsarrut/vvregister/write.php"), getVVSettingsPath(), getSettingsOptionFormat());
1269   if(!checkCanPush) {
1270     registerForm->show();
1271   } else {
1272     if(registerForm->canPush()) {
1273       registerForm->show();
1274       registerForm->acquitPushed();//too bad if there is not internet connection anymore.
1275     }
1276   }
1277 }
1278 //------------------------------------------------------------------------------
1279
1280 //------------------------------------------------------------------------------
1281 void vvMainWindow::ShowHelpDialog()
1282 {
1283   help_dialog->show();
1284 }
1285 //------------------------------------------------------------------------------
1286
1287 //------------------------------------------------------------------------------
1288 void vvMainWindow::ChangeViewMode()
1289 {
1290   typedef struct _SIZE{
1291     QSplitter* splitter;
1292     QList<int> size1, size2;
1293     int cols[3];
1294   }SplitterSize;
1295   SplitterSize sizes[4];
1296   sizes[0].splitter = OSplitter;
1297   sizes[0].size1.push_back(1);
1298   sizes[0].size1.push_back(0);
1299   sizes[0].size2.push_back(1);
1300   sizes[0].size2.push_back(0);
1301   sizes[0].cols[0] = 2;
1302   sizes[0].cols[1] = 3;
1303   sizes[0].cols[2] = 4;
1304
1305   sizes[1].splitter = ESplitter;
1306   sizes[1].size1.push_back(0);
1307   sizes[1].size1.push_back(1);
1308   sizes[1].size2.push_back(1);
1309   sizes[1].size2.push_back(0);
1310   sizes[1].cols[0] = 1;
1311   sizes[1].cols[1] = 3;
1312   sizes[1].cols[2] = 4;
1313
1314   sizes[2].splitter = OSplitter;
1315   sizes[2].size1.push_back(1);
1316   sizes[2].size1.push_back(0);
1317   sizes[2].size2.push_back(0);
1318   sizes[2].size2.push_back(1);
1319   sizes[2].cols[0] = 1;
1320   sizes[2].cols[1] = 2;
1321   sizes[2].cols[2] = 4;
1322
1323   sizes[3].splitter = ESplitter;
1324   sizes[3].size1.push_back(0);
1325   sizes[3].size1.push_back(1);
1326   sizes[3].size2.push_back(0);
1327   sizes[3].size2.push_back(1);
1328   sizes[3].cols[0] = 1;
1329   sizes[3].cols[1] = 2;
1330   sizes[3].cols[2] = 3;
1331
1332   int slicer = mSlicerManagers[mCurrentPickedImageIndex]->GetSelectedSlicer();
1333   if (viewMode == 1) {
1334     if (slicer >= 0) {
1335       viewMode = 0;
1336       splitter_3->setSizes(sizes[slicer].size1);
1337       sizes[slicer].splitter->setSizes(sizes[slicer].size2);
1338       DataTree->setColumnHidden(sizes[slicer].cols[0],1);
1339       DataTree->setColumnHidden(sizes[slicer].cols[1],1);
1340       DataTree->setColumnHidden(sizes[slicer].cols[2],1);
1341     }
1342   } else {
1343     QList<int> size;
1344     if (slicer >= 0) {
1345       viewMode = 1;
1346       size.push_back(1);
1347       size.push_back(1);
1348       splitter_3->setSizes(size);
1349       sizes[slicer].splitter->setSizes(size);
1350       DataTree->setColumnHidden(sizes[slicer].cols[0],0);
1351       DataTree->setColumnHidden(sizes[slicer].cols[1],0);
1352       DataTree->setColumnHidden(sizes[slicer].cols[2],0);
1353     }
1354   }
1355   UpdateRenderWindows();
1356   /*
1357   ** I don't know why but for both resized QVTKWidget we also need to render
1358   ** the associated Slicer to redraw crosses.
1359   */
1360   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
1361     //     if (DataTree->topLevelItem(i)->data(COLUMN_UL_VIEW,Qt::CheckStateRole).toInt() > 1)
1362     mSlicerManagers[i]->GetSlicer(0)->Render();
1363     mSlicerManagers[i]->GetSlicer(1)->Render();
1364     //     if (DataTree->topLevelItem(i)->data(COLUMN_DL_VIEW,Qt::CheckStateRole).toInt() > 1)
1365     mSlicerManagers[i]->GetSlicer(2)->Render();
1366     mSlicerManagers[i]->GetSlicer(3)->Render();
1367   }
1368 }
1369 //------------------------------------------------------------------------------
1370
1371 //------------------------------------------------------------------------------
1372 QString vvMainWindow::GetSizeInBytes(unsigned long size)
1373 {
1374   QString result = "";// QString::number(size);
1375   //result += " bytes (";
1376   if (size > 1000000000) {
1377     size /= 1000000000;
1378     result += QString::number(size);
1379     result += "GB";//)";
1380   } else if (size > 1000000) {
1381     size /= 1000000;
1382     result += QString::number(size);
1383     result += "MB";//)";
1384   } else if (size > 1000) {
1385     size /= 1000;
1386     result += QString::number(size);
1387     result += "kB";//)";
1388   }
1389   return result;
1390 }
1391 //------------------------------------------------------------------------------
1392
1393 //------------------------------------------------------------------------------
1394 QString vvMainWindow::GetVectorDoubleAsString(std::vector<double> vectorDouble)
1395 {
1396   QString result;
1397   for (unsigned int i= 0; i < vectorDouble.size(); i++) {
1398     if (i != 0)
1399       result += " ";
1400     result += QString::number(vectorDouble[i]);
1401   }
1402   return result;
1403 }
1404 //------------------------------------------------------------------------------
1405
1406 //------------------------------------------------------------------------------
1407 QString vvMainWindow::GetVectorIntAsString(std::vector<int> vectorInt)
1408 {
1409   QString result;
1410   for (unsigned int i= 0; i < vectorInt.size(); i++) {
1411     if (i != 0)
1412       result += " ";
1413     result += QString::number(vectorInt[i]);
1414   }
1415   return result;
1416 }
1417 //------------------------------------------------------------------------------
1418
1419 //------------------------------------------------------------------------------
1420 //this actually returns the SlicerManager index!
1421 int vvMainWindow::GetSlicerIndexFromItem(QTreeWidgetItem* item)
1422 {
1423   QString id = item->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString();
1424   for (int i = 0; i < DataTree->topLevelItemCount(); i++) {
1425     if (DataTree->topLevelItem(i)->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString() == id)
1426       return i;
1427   }
1428   return -1;
1429 }
1430 //------------------------------------------------------------------------------
1431
1432 //------------------------------------------------------------------------------
1433 QTreeWidgetItem* vvMainWindow::GetItemFromSlicerManager(vvSlicerManager* sm)
1434 {
1435   QString id = sm->GetId().c_str();
1436   for (int i = 0; i < DataTree->topLevelItemCount(); i++) {
1437     if (DataTree->topLevelItem(i)->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString() == id)
1438       return DataTree->topLevelItem(i);
1439   }
1440   return NULL;
1441 }
1442 //------------------------------------------------------------------------------
1443
1444 //------------------------------------------------------------------------------
1445 void vvMainWindow::DisplayChanged(QTreeWidgetItem *clickedItem, int column)
1446 {
1447   if ( column >= COLUMN_CLOSE_IMAGE || column <= 0)
1448     return;
1449
1450   // Get parent information (might be the same item)
1451   int slicerManagerIndex = GetSlicerIndexFromItem(clickedItem);
1452   QTreeWidgetItem* clickedParentItem = DataTree->topLevelItem(slicerManagerIndex);
1453   vvSlicer* clickedSlicer = mSlicerManagers[slicerManagerIndex]->GetSlicer(column-1);
1454
1455   // Go over the complete item tree (only 2 levels, parents and children)
1456   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
1457     // Trick to avoid redoing twice the job for a key (sr)
1458     mSlicerManagers[i]->GetSlicer(column-1)->GetRenderWindow()->GetInteractor()->SetKeySym("Crap");
1459
1460     QTreeWidgetItem* currentParentItem = DataTree->topLevelItem(i);
1461     if(currentParentItem != clickedParentItem) {
1462       // Not the branch of the clicked item, uncheck all
1463
1464       // Parent
1465       currentParentItem->setData(column,Qt::CheckStateRole, 0);
1466       mSlicerManagers[i]->UpdateSlicer(column-1, false);
1467
1468       // Children
1469       for (int iChild = 0; iChild < currentParentItem->childCount(); iChild++) {
1470         currentParentItem->child(iChild)->setData(column,Qt::CheckStateRole, 0);
1471       }
1472     }
1473     else {
1474       // Branch of the clicked one: get check status from actor visibility in slicer
1475       // and toggle the clicked one
1476
1477       // Parent
1478       bool vis = clickedSlicer->GetActorVisibility("image", 0);
1479       bool draw = clickedSlicer->GetRenderer()->GetDraw();
1480
1481       // Update slicer (after getting visibility)
1482       mSlicerManagers[slicerManagerIndex]->UpdateSlicer(column-1, true);
1483       mSlicerManagers[slicerManagerIndex]->UpdateInfoOnCursorPosition(column-1);
1484       DisplaySliders(slicerManagerIndex, column-1);
1485       if(clickedParentItem == clickedItem) {
1486         // Toggle
1487         vis = !draw || !vis;
1488       }
1489       clickedSlicer->SetActorVisibility("image", 0, vis);
1490       clickedParentItem->setData(column, Qt::CheckStateRole, vis?2:0);
1491
1492       // Children
1493       std::map<std::string, int> actorTypeCounts;
1494       for (int iChild = 0; iChild < clickedParentItem->childCount(); iChild++) {
1495         QTreeWidgetItem* currentChildItem = clickedParentItem->child(iChild);
1496         std::string actorType = currentChildItem->data(1,Qt::UserRole).toString().toStdString();
1497         vis = clickedSlicer->GetActorVisibility(actorType, actorTypeCounts[actorType]);
1498         if(currentChildItem == clickedItem) {
1499           // Toggle or force visibility if it was not on this branch so far
1500           vis = !draw || !vis;
1501           clickedSlicer->SetActorVisibility(actorType, actorTypeCounts[actorType], vis);
1502         }
1503         currentChildItem->setData(column, Qt::CheckStateRole, vis?2:0);
1504         actorTypeCounts[actorType]++;
1505       }
1506     }
1507   }
1508
1509   clickedSlicer->Render();
1510 }
1511 //------------------------------------------------------------------------------
1512
1513 void vvMainWindow::InitSlicers()
1514 {
1515   if (mSlicerManagers.size()) {
1516     mSlicerManagers.back()->GenerateDefaultLookupTable();
1517     mSlicerManagers.back()->SetSlicerWindow(0,NOViewWidget->GetRenderWindow());
1518     mSlicerManagers.back()->SetSlicerWindow(1,NEViewWidget->GetRenderWindow());
1519     mSlicerManagers.back()->SetSlicerWindow(2,SOViewWidget->GetRenderWindow());
1520     mSlicerManagers.back()->SetSlicerWindow(3,SEViewWidget->GetRenderWindow());
1521 #if VTK_MAJOR_VERSION <= 5
1522     mSlicerManagers.back()->Render(); // SR: displayed #slice is wrong without this / TB: With VTK6 and multiple images, all slicers are updated, not only the first
1523 #endif
1524   }
1525 }
1526
1527 //------------------------------------------------------------------------------
1528 void vvMainWindow::InitDisplay()
1529 {
1530   if (mSlicerManagers.size()) {
1531     //BE CAREFUL : this is absolutely necessary to set the interactor style
1532     //in order to have the same style instanciation for all SlicerManagers in
1533     // a same window
1534     for (int j = 0; j < 4; j++) {
1535       vvInteractorStyleNavigator* style = vvInteractorStyleNavigator::New();
1536       style->SetAutoAdjustCameraClippingRange(1);
1537       bool AlreadySelected = false;
1538       for (int i = 0; i < DataTree->topLevelItemCount(); i++) {
1539         mSlicerManagers[i]->SetInteractorStyleNavigator(j,style);
1540         //select the image only if previous are not selected
1541         if (DataTree->topLevelItem(i)->data(j+1,Qt::CheckStateRole).toInt() > 1) {
1542           mSlicerManagers[i]->UpdateSlicer(j,1);
1543           AlreadySelected = true;
1544         } else if (i == DataTree->topLevelItemCount()-1 && !AlreadySelected) {
1545           if (DataTree->selectedItems().size() == 0) {
1546             DataTree->topLevelItem(i)->setSelected(1);
1547           }
1548           DataTree->topLevelItem(i)->setData(j+1,Qt::CheckStateRole,2);
1549           mSlicerManagers[i]->UpdateSlicer(j,1);
1550           DisplaySliders(i,j);
1551         } else {
1552           DataTree->topLevelItem(i)->setData(j+1,Qt::CheckStateRole,0);
1553           mSlicerManagers[i]->UpdateSlicer(j,0);
1554         }
1555       }
1556       style->Delete();
1557     }
1558   }
1559 }
1560 //------------------------------------------------------------------------------
1561
1562 //------------------------------------------------------------------------------
1563 void vvMainWindow::DisplaySliders(int slicer, int window)
1564 {
1565   if(!mSlicerManagers[slicer]->GetSlicer(window)->GetRenderer()->GetDraw())
1566     return;
1567
1568   int range[2];
1569   mSlicerManagers[slicer]->GetSlicer(window)->GetSliceRange(range);
1570   int position = mSlicerManagers[slicer]->GetSlicer(window)->GetSlice();
1571   if (range[1]>0)
1572     verticalSliders[window]->show();
1573   else
1574     verticalSliders[window]->hide();
1575   verticalSliders[window]->setRange(range[0],range[1]);
1576   verticalSliders[window]->setValue(position);
1577
1578   int tRange[2];
1579   tRange[0] = 0;
1580   tRange[1] = mSlicerManagers[slicer]->GetSlicer(window)->GetTMax();
1581   if (tRange[1]>0)
1582     horizontalSliders[window]->show();
1583   else
1584     horizontalSliders[window]->hide();
1585   horizontalSliders[window]->setRange(tRange[0],tRange[1]);
1586   int tPosition = mSlicerManagers[slicer]->GetSlicer(window)->GetMaxCurrentTSlice();
1587   horizontalSliders[window]->setValue(tPosition);
1588 }
1589 //------------------------------------------------------------------------------
1590
1591 //------------------------------------------------------------------------------
1592 void vvMainWindow::CloseImage(QTreeWidgetItem* item, int column)
1593 {
1594   int index = GetSlicerIndexFromItem(item);
1595
1596   if (DataTree->topLevelItem(index) != item) {
1597     QString warning = "Do you really want to close the overlay : ";
1598     warning += item->data(COLUMN_IMAGE_NAME,Qt::DisplayRole).toString();
1599     QMessageBox msgBox(QMessageBox::Warning, tr("Close Overlay"),
1600       warning, 0, this);
1601     msgBox.addButton(tr("Close"), QMessageBox::AcceptRole);
1602     msgBox.addButton(tr("Cancel"), QMessageBox::RejectRole);
1603     if (msgBox.exec() == QMessageBox::AcceptRole) {
1604       std::string overlay_type=item->data(1,Qt::UserRole).toString().toStdString();
1605       int overlay_index=0;
1606       for (int child = 0; child < DataTree->topLevelItem(index)->childCount(); child++) {
1607         if (DataTree->topLevelItem(index)->\
1608           child(child)->data(1,Qt::UserRole).toString().toStdString() == overlay_type)
1609           overlay_index++;
1610         if (DataTree->topLevelItem(index)->child(child) == item) break;
1611       }
1612       if (overlay_type=="fusionSequence") {
1613         //removing the overlay sequence in a fusion sequence visualization mode
1614         //reset the transforms
1615         overlayPanel->getFusionSequenceProperty(-1, false, 0, false);
1616
1617         //unlink and untie the slicer managers
1618         RemoveLink(mSlicerManagers[index]->GetId().c_str(), mSlicerManagers[mSlicerManagers[index]->GetFusionSequenceIndexOfLinkedManager()]->GetId().c_str());
1619         mSlicerManagers[index]->SetFusionSequenceInvolvmentCode(-1);
1620         mSlicerManagers[mSlicerManagers[index]->GetFusionSequenceIndexOfLinkedManager()]->SetFusionSequenceInvolvmentCode(-1);
1621         for (unsigned i=0 ; i<4 ; i++) {
1622             mSlicerManagers[index]->GetSlicer(i)->SetFusionSequenceCode(-1);
1623             mSlicerManagers[mSlicerManagers[index]->GetFusionSequenceIndexOfLinkedManager()]->GetSlicer(i)->SetFusionSequenceCode(-1);
1624         }
1625
1626       }
1627       mSlicerManagers[index]->RemoveActor(overlay_type, overlay_index-1);
1628       mSlicerManagers[index]->SetColorMap(0);
1629       DataTree->topLevelItem(index)->takeChild(DataTree->topLevelItem(index)->indexOfChild(item));
1630       mSlicerManagers[index]->Render();
1631     }
1632   } else if (DataTree->topLevelItemCount() <= 1) {
1633     QString warning = "Do you really want to close the image : ";
1634     warning += item->data(COLUMN_IMAGE_NAME,Qt::DisplayRole).toString();
1635     warning += "\nThis is the last image, you're about to close vv !!!";
1636     QMessageBox msgBox(QMessageBox::Warning, tr("Close Image"),
1637       warning, 0, this);
1638     msgBox.addButton(tr("Close vv"), QMessageBox::AcceptRole);
1639     msgBox.addButton(tr("Cancel"), QMessageBox::RejectRole);
1640     if (msgBox.exec() == QMessageBox::AcceptRole) {
1641       this->close();
1642     }
1643   } else {
1644     QString warning = "Do you really want to close the image : ";
1645     warning += item->data(COLUMN_IMAGE_NAME,Qt::DisplayRole).toString();
1646     QMessageBox msgBox(QMessageBox::Warning, tr("Close Image"),
1647       warning, 0, this);
1648     msgBox.addButton(tr("Close"), QMessageBox::AcceptRole);
1649     msgBox.addButton(tr("Cancel"), QMessageBox::RejectRole);
1650     if (msgBox.exec() == QMessageBox::AcceptRole) {
1651
1652       // Tell tools that we close an image
1653       emit AnImageIsBeingClosed(mSlicerManagers[index]);
1654
1655       std::vector<vvSlicerManager*>::iterator Manageriter = mSlicerManagers.begin();
1656       DataTree->takeTopLevelItem(index);
1657       for (int i = 0; i < index; i++) {
1658         Manageriter++;
1659       }
1660       //if the slicer manager was involved in a fusion sequence visualization...
1661       if ( mSlicerManagers[index]->IsInvolvedInFusionSequence() ) {
1662         //in both cases, close the overlay: find it... and close it
1663         //ideally, I should duplicate the code, and avoid calling CloseImage, since this pops up another interactive box
1664         QTreeWidgetItem* overlayItem;
1665         if (mSlicerManagers[index]->IsMainSequenceOfFusionSequence()) {
1666           for (unsigned i=0 ; i<item->childCount() ; i++) {
1667             overlayItem = item->child(i);
1668             this->CloseImage( overlayItem, 0 );
1669           }
1670         }
1671         else {
1672           QTreeWidgetItem* linkedItem = this->GetItemFromSlicerManager( mSlicerManagers[mSlicerManagers[index]->GetFusionSequenceIndexOfLinkedManager()] );
1673           for (unsigned i=0 ; i<linkedItem->childCount() ; i++) {
1674             overlayItem = linkedItem->child(i);
1675             this->CloseImage( overlayItem, 0 );
1676           }
1677         }
1678
1679         /* -- this is normally already done when closing the overlay.
1680         //reset the transforms
1681         overlayPanel->getFusionSequenceProperty(-1, false, 0, false);
1682
1683         //unlink and untie the slicer managers
1684         RemoveLink(mSlicerManagers[index]->GetId().c_str(), mSlicerManagers[mSlicerManagers[index]->GetFusionSequenceIndexOfLinkedManager()]->GetId().c_str());
1685         mSlicerManagers[index]->SetFusionSequenceInvolvmentCode(-1);
1686         mSlicerManagers[mSlicerManagers[index]->GetFusionSequenceIndexOfLinkedManager()]->SetFusionSequenceInvolvmentCode(-1);
1687         for (unsigned i=0 ; i<4 ; i++) {
1688             mSlicerManagers[index]->GetSlicer(i)->SetFusionSequenceCode(-1);
1689             mSlicerManagers[mSlicerManagers[index]->GetFusionSequenceIndexOfLinkedManager()]->GetSlicer(i)->SetFusionSequenceCode(-1);
1690         }
1691         */
1692       }
1693
1694       linkPanel->removeImage(index);
1695       mSlicerManagers[index]->RemoveActors();
1696
1697       //remove the slicer manager
1698       delete mSlicerManagers[index];
1699       mSlicerManagers.erase(Manageriter);
1700
1701       //
1702       InitDisplay();
1703     }
1704   }
1705   ImageInfoChanged();
1706 }
1707 //------------------------------------------------------------------------------
1708
1709 //------------------------------------------------------------------------------
1710 void vvMainWindow::ReloadImage(QTreeWidgetItem* item, int column)
1711 {
1712   // int index = GetSlicerIndexFromItem(item);
1713   //   QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
1714   //   if (item->data(1,Qt::UserRole).toString() == "vector")
1715   //     mSlicerManagers[index]->ReloadVF();
1716   //   else
1717   //     mSlicerManagers[index]->Reload();
1718
1719   //   QApplication::restoreOverrideCursor();
1720   int index = GetSlicerIndexFromItem(item);
1721   QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
1722   QString role=item->data(1,Qt::UserRole).toString();
1723   if ( role == "vector") {
1724     mSlicerManagers[index]->ReloadVF();
1725   }
1726   else if (role == "overlay") {
1727     mSlicerManagers[index]->ReloadOverlay();
1728   }
1729   else if (role == "fusion") {
1730     mSlicerManagers[index]->ReloadFusion();
1731   }
1732   else if (role == "fusionSequence") {
1733     //both versions of the secondary sequence must be updated.
1734     mSlicerManagers[index]->ReloadFusionSequence();
1735     mSlicerManagers[mSlicerManagers[index]->GetFusionSequenceIndexOfLinkedManager()]->Reload();
1736   }
1737   else {
1738     mSlicerManagers[index]->Reload();
1739     //if we update the secondary sequence, then the overlay of the main sequence should also be updated
1740     if (mSlicerManagers[index]->IsSecondarySequenceOfFusionSequence()) mSlicerManagers[mSlicerManagers[index]->GetFusionSequenceIndexOfLinkedManager()]->ReloadFusionSequence();
1741   }
1742   // Update view and info
1743   ImageInfoChanged();
1744   mSlicerManagers[index]->Render();
1745   QApplication::restoreOverrideCursor();
1746 }
1747 //------------------------------------------------------------------------------
1748
1749 //------------------------------------------------------------------------------
1750 void vvMainWindow::MousePositionChanged(int visibility,double x, double y, double z, double X, double Y, double Z , double value)
1751 {
1752   infoPanel->setCurrentInfo(visibility,x,y,z,X,Y,Z,value);
1753 }
1754 //------------------------------------------------------------------------------
1755
1756 //------------------------------------------------------------------------------
1757 void vvMainWindow::VectorChanged(int visibility,double x, double y, double z, double value)
1758 {
1759   overlayPanel->getCurrentVectorInfo(visibility,x,y,z,value);
1760 }
1761 //------------------------------------------------------------------------------
1762
1763 //------------------------------------------------------------------------------
1764 void vvMainWindow::OverlayChanged(int visibility, double valueOver, double valueRef)
1765 {
1766   overlayPanel->getCurrentOverlayInfo(visibility,valueOver, valueRef);
1767 }
1768 //------------------------------------------------------------------------------
1769
1770 //------------------------------------------------------------------------------
1771 void vvMainWindow::FusionChanged(int visibility, double value)
1772 {
1773   overlayPanel->getCurrentFusionInfo(visibility,value);
1774 }
1775 //------------------------------------------------------------------------------
1776
1777 //------------------------------------------------------------------------------
1778 //called when AddOverlayImage, AddFusionSequence
1779 //or when UpdateWindowLevel() is called ; when slicerManager emits WindowLevelChanged
1780 //when ImageInfoChanged() is called
1781 void vvMainWindow::WindowLevelChanged()
1782 {
1783   // Base image
1784   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1785   if(index==-1) return;
1786   windowSpinBox->setValue(mSlicerManagers[index]->GetColorWindow());
1787   levelSpinBox->setValue(mSlicerManagers[index]->GetColorLevel());
1788   colorMapComboBox->setCurrentIndex(mSlicerManagers[index]->GetColorMap());
1789   presetComboBox->setCurrentIndex(mSlicerManagers[index]->GetPreset());
1790
1791   // Overlay image
1792   if (mSlicerManagers[index]->GetSlicer(0)->GetOverlay())
1793     overlayPanel->getOverlayProperty(mSlicerManagers[index]->GetOverlayColor(),
1794     mSlicerManagers[index]->GetLinkOverlayWindowLevel(),
1795     mSlicerManagers[index]->GetOverlayColorWindow(),
1796     mSlicerManagers[index]->GetOverlayColorLevel());
1797   else
1798     overlayPanel->getOverlayProperty(-1,0,0.,0.);
1799
1800   // Fusion & SequenceFusion image
1801   if (mSlicerManagers[index]->GetSlicer(0)->GetFusion()) {
1802     overlayPanel->getFusionProperty(mSlicerManagers[index]->GetFusionOpacity(),
1803       mSlicerManagers[index]->GetFusionThresholdOpacity(),
1804       mSlicerManagers[index]->GetFusionColorMap(),
1805       mSlicerManagers[index]->GetFusionWindow(),
1806       mSlicerManagers[index]->GetFusionLevel());
1807     if (mSlicerManagers[index]->IsMainSequenceOfFusionSequence()) {
1808       overlayPanel->getFusionSequenceProperty(mSlicerManagers[index]->GetFusionSequenceFrameIndex(),
1809         mSlicerManagers[index]->GetFusionSequenceSpatialSyncFlag(),
1810         mSlicerManagers[index]->GetFusionSequenceNbFrames(),
1811         mSlicerManagers[index]->GetFusionSequenceTemporalSyncFlag());
1812     }
1813   }
1814   else if ( mSlicerManagers[index]->IsSecondarySequenceOfFusionSequence() ) {
1815     //if the image is involved in a fusion sequence, preserve the overlay panel!
1816     int ind = mSlicerManagers[index]->GetFusionSequenceIndexOfLinkedManager();
1817     overlayPanel->getFusionProperty(mSlicerManagers[ind]->GetFusionOpacity(),
1818       mSlicerManagers[ind]->GetFusionThresholdOpacity(),
1819       mSlicerManagers[ind]->GetFusionColorMap(),
1820       mSlicerManagers[ind]->GetFusionWindow(),
1821       mSlicerManagers[ind]->GetFusionLevel());
1822     overlayPanel->getFusionSequenceProperty(mSlicerManagers[ind]->GetFusionSequenceFrameIndex(),
1823       mSlicerManagers[ind]->GetFusionSequenceSpatialSyncFlag(),
1824       mSlicerManagers[ind]->GetFusionSequenceNbFrames(),
1825       mSlicerManagers[ind]->GetFusionSequenceTemporalSyncFlag());
1826   }
1827   else
1828   {
1829     overlayPanel->getFusionProperty(-1, -1, -1, -1, -1);
1830     overlayPanel->getFusionSequenceProperty(-1, false, 0, false);
1831   }
1832 }
1833 //------------------------------------------------------------------------------
1834
1835 //------------------------------------------------------------------------------
1836 void vvMainWindow::WindowLevelEdited()
1837 {
1838   presetComboBox->setCurrentIndex(WL_USER);
1839   UpdateWindowLevel();
1840 }
1841 //------------------------------------------------------------------------------
1842
1843 //------------------------------------------------------------------------------
1844 void vvMainWindow::SetWindowLevel(double w, double l)
1845 {
1846   windowSpinBox->setValue(w);
1847   levelSpinBox->setValue(l);
1848   presetComboBox->setCurrentIndex(WL_USER);
1849   colorMapComboBox->setCurrentIndex(0);
1850   UpdateWindowLevel();
1851 }
1852 //------------------------------------------------------------------------------
1853
1854 //------------------------------------------------------------------------------
1855 void vvMainWindow::UpdateWindowLevel()
1856 {
1857   if (DataTree->selectedItems().size()) {
1858     if (presetComboBox->currentIndex() == WL_VENTILATION) //For ventilation
1859       colorMapComboBox->setCurrentIndex(5);
1860     int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1861     mSlicerManagers[index]->SetColorWindow(windowSpinBox->value());
1862     mSlicerManagers[index]->SetColorLevel(levelSpinBox->value());
1863     mSlicerManagers[index]->SetPreset(presetComboBox->currentIndex());
1864     mSlicerManagers[index]->Render();
1865     WindowLevelChanged();
1866   }
1867 }
1868 //------------------------------------------------------------------------------
1869
1870 //------------------------------------------------------------------------------
1871 void vvMainWindow::UpdateSlicingPreset()
1872 {
1873   if (DataTree->selectedItems().size()) {
1874     int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1875     mSlicerManagers[index]->SetSlicingPreset(vvSlicerManager::SlicingPresetType(slicingPresetComboBox->currentIndex()));
1876   }
1877 }
1878 //------------------------------------------------------------------------------
1879
1880 //------------------------------------------------------------------------------
1881 void vvMainWindow::UpdateColorMap()
1882 {
1883   if (DataTree->selectedItems().size()) {
1884     int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1885     mSlicerManagers[index]->SetColorMap(colorMapComboBox->currentIndex());
1886     mSlicerManagers[index]->Render();
1887   }
1888 }
1889 //------------------------------------------------------------------------------
1890 void vvMainWindow::SwitchWindowLevel()
1891 {
1892   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1893   int window = mSlicerManagers[index]->GetColorWindow();
1894   presetComboBox->setCurrentIndex(WL_USER);
1895   windowSpinBox->setValue(-window);
1896   UpdateWindowLevel();
1897 }
1898 //------------------------------------------------------------------------------
1899
1900 //------------------------------------------------------------------------------
1901 void vvMainWindow::ApplyWindowLevelToAllImages()
1902 {
1903   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1904   if(index==-1) return;
1905   double window = mSlicerManagers[index]->GetColorWindow();
1906   double level = mSlicerManagers[index]->GetColorLevel();
1907
1908   double fusWindow = mSlicerManagers[index]->GetFusionWindow();
1909   double fusLevel = mSlicerManagers[index]->GetFusionLevel();
1910
1911   double overWindow = mSlicerManagers[index]->GetOverlayColorWindow();
1912   double overLevel = mSlicerManagers[index]->GetOverlayColorLevel();
1913
1914   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
1915     if (mSlicerManagers[i] == NULL)
1916       continue;
1917     mSlicerManagers[i]->SetColorWindow(window);
1918     mSlicerManagers[i]->SetColorLevel(level);
1919     mSlicerManagers[i]->SetPreset(WL_USER);
1920     mSlicerManagers[i]->SetFusionWindow(fusWindow);
1921     mSlicerManagers[i]->SetFusionLevel(fusLevel);
1922     mSlicerManagers[i]->SetOverlayColorWindow(overWindow);
1923     mSlicerManagers[i]->SetOverlayColorLevel(overLevel);
1924     mSlicerManagers[i]->Render();
1925   }
1926 }
1927 //------------------------------------------------------------------------------
1928
1929 //------------------------------------------------------------------------------
1930 void vvMainWindow::ApplyWindowToSetOfImages(double window, unsigned int indexMin, unsigned int indexMax)
1931 {
1932   for (unsigned int i = indexMin; i <= indexMax && i < mSlicerManagers.size(); i++) {
1933     if (mSlicerManagers[i] == NULL)
1934       continue;
1935     SetWindowLevel(window, mSlicerManagers[i]->GetColorLevel());
1936     mSlicerManagers[i]->SetColorWindow(window);
1937     mSlicerManagers[i]->SetPreset(WL_USER);
1938     mSlicerManagers[i]->Render();
1939   }
1940 }
1941 //------------------------------------------------------------------------------
1942
1943 //------------------------------------------------------------------------------
1944 void vvMainWindow::ApplyLevelToSetOfImages(double level, unsigned int indexMin, unsigned int indexMax)
1945 {
1946   for (unsigned int i = indexMin; i <= indexMax && i < mSlicerManagers.size(); i++) {
1947     if (mSlicerManagers[i] == NULL)
1948       continue;
1949     SetWindowLevel(mSlicerManagers[i]->GetColorWindow(), level);
1950     mSlicerManagers[i]->SetColorLevel(level);
1951     mSlicerManagers[i]->SetPreset(WL_USER);
1952     mSlicerManagers[i]->Render();
1953   }
1954 }
1955 //------------------------------------------------------------------------------
1956
1957 //------------------------------------------------------------------------------
1958 void vvMainWindow::UpdateLinkManager(std::string id, int slicer, double x, double y, double z, int temps)
1959 {
1960   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
1961     if (mSlicerManagers[i]->GetId() == id) {
1962       mSlicerManagers[i]->GetSlicer(slicer)->SetCurrentPosition(x,y,z,temps);
1963       mSlicerManagers[i]->UpdateViews(0,slicer);
1964       break;
1965     }
1966   }
1967 }
1968 //------------------------------------------------------------------------------
1969
1970 //------------------------------------------------------------------------------
1971 void vvMainWindow::UpdateLinkedNavigation(std::string id, vvSlicerManager * sm, vvSlicer* refSlicer)
1972 {
1973   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
1974     if (id == mSlicerManagers[i]->GetId()) {
1975       mSlicerManagers[i]->UpdateLinkedNavigation(refSlicer);
1976     }
1977   }
1978 }
1979 //------------------------------------------------------------------------------
1980
1981 //------------------------------------------------------------------------------
1982 void vvMainWindow::ShowContextMenu(QPoint point)
1983 {
1984   if (!DataTree->selectedItems().size()) {
1985     contextActions[1]->setEnabled(0);
1986     contextActions[2]->setEnabled(0);
1987     contextActions[3]->setEnabled(0);
1988     contextActions[4]->setEnabled(0);
1989     contextActions[5]->setEnabled(0);
1990     contextActions[6]->setEnabled(0);
1991   } else {
1992     int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1993     contextActions[1]->setEnabled(1);
1994     contextActions[2]->setEnabled(
1995       DataTree->itemWidget(DataTree->selectedItems()[0],
1996       COLUMN_RELOAD_IMAGE)->isEnabled());
1997     contextActions[3]->setEnabled(1);
1998     contextActions[5]->setEnabled(1);
1999     contextActions[6]->setEnabled(1);
2000
2001     if (mSlicerManagers[index]->GetDimension() < 3)
2002       contextActions[4]->setEnabled(0);
2003     else
2004       contextActions[4]->setEnabled(1);
2005   }
2006   contextMenu.exec(QCursor::pos());
2007 }
2008 //------------------------------------------------------------------------------
2009
2010 //------------------------------------------------------------------------------
2011 void vvMainWindow::CloseImage()
2012 {
2013   CloseImage(DataTree->selectedItems()[0],0);
2014 }
2015 //------------------------------------------------------------------------------
2016
2017 //------------------------------------------------------------------------------
2018 void vvMainWindow::ReloadImage()
2019 {
2020   ReloadImage(DataTree->selectedItems()[0],0);
2021 }
2022 //------------------------------------------------------------------------------
2023
2024 //------------------------------------------------------------------------------
2025 void vvMainWindow::SelectOverlayImage()
2026 {
2027   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2028
2029   if (!(CheckAddedImage(index, "overlay")))
2030     return;
2031
2032   QString Extensions = EXTENSIONS;
2033   Extensions += ";;All Files (*)";
2034   QStringList files = QFileDialog::getOpenFileNames(this,tr("Load Overlay image"),mInputPathName,Extensions);
2035   if (files.isEmpty())
2036     return;
2037
2038   std::vector<std::string> vecFileNames;
2039   for (int i = 0; i < files.size(); i++) {
2040     vecFileNames.push_back(files[i].toStdString());
2041   }
2042
2043   AddOverlayImage(index,vecFileNames,vvImageReader::IMAGE);
2044 }
2045 //------------------------------------------------------------------------------
2046
2047 //------------------------------------------------------------------------------
2048 bool vvMainWindow::CheckAddedImage(int index, QString imageType)
2049 {
2050   //check if one overlay image is added
2051   for (int child = 0; child < DataTree->topLevelItem(index)->childCount(); child++)
2052     if (DataTree->topLevelItem(index)->child(child)->data(1,Qt::UserRole).toString().compare(imageType) == 0) {
2053       QString error = "Cannot add more than one compared image\n";
2054       error += "Please remove first ";
2055       error += DataTree->topLevelItem(index)->child(child)->data(COLUMN_IMAGE_NAME,Qt::DisplayRole).toString();
2056       QMessageBox::information(this,tr("Problem adding compared image !"),error);
2057       return false;
2058     }
2059     return true;
2060 }
2061 //------------------------------------------------------------------------------
2062
2063 //------------------------------------------------------------------------------
2064 void vvMainWindow::AddOverlayImage(int index, std::vector<std::string> fileNames, vvImageReader::LoadedImageType type)
2065 {
2066   QString file(fileNames[0].c_str());
2067   if (QFile::exists(file))
2068   {
2069     mInputPathName = itksys::SystemTools::GetFilenamePath(file.toStdString()).c_str();
2070     itk::ImageIOBase::Pointer reader = itk::ImageIOFactory::CreateImageIO(
2071       file.toStdString().c_str(), itk::ImageIOFactory::ReadMode);
2072     reader->SetFileName(fileNames[0].c_str());
2073     reader->ReadImageInformation();
2074     std::string component = reader->GetComponentTypeAsString(reader->GetComponentType());
2075     int dimension = reader->GetNumberOfDimensions();
2076     QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
2077     vvProgressDialog progress("Opening " + file.toStdString());
2078     qApp->processEvents();
2079
2080     std::string filename = itksys::SystemTools::GetFilenameWithoutExtension(file.toStdString()).c_str();
2081     if (mSlicerManagers[index]->SetOverlay(fileNames,dimension, component,type)) {
2082       //create an item in the tree with good settings
2083       QTreeWidgetItem *item = new QTreeWidgetItem();
2084       item->setData(0,Qt::UserRole,file.toStdString().c_str());
2085       item->setData(1,Qt::UserRole,tr("overlay"));
2086       QFileInfo fileinfo(file); //Do not show the path
2087       item->setData(COLUMN_IMAGE_NAME,Qt::DisplayRole,fileinfo.fileName());
2088       item->setToolTip(COLUMN_IMAGE_NAME, mSlicerManagers[index]->GetListOfAbsoluteFilePathInOneString("overlay").c_str());
2089       qApp->processEvents();
2090 #if VTK_MAJOR_VERSION > 5
2091       for ( unsigned int i = 0; i < mSlicerManagers[index]->GetNumberOfSlicers(); i++)
2092         mSlicerManagers[index]->GetSlicer(i)->ForceUpdateDisplayExtent();
2093 #endif
2094
2095       for (int j = 1; j <= 4; j++) {
2096         item->setData(j,Qt::CheckStateRole,DataTree->topLevelItem(index)->data(j,Qt::CheckStateRole));
2097       }
2098
2099       //Create the buttons for reload and close
2100       qApp->processEvents();
2101       QTreePushButton* cButton = new QTreePushButton;
2102       cButton->setItem(item);
2103       cButton->setColumn(COLUMN_CLOSE_IMAGE);
2104       cButton->setToolTip(tr("close image"));
2105       cButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/exit.png")));
2106       connect(cButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
2107         this,SLOT(CloseImage(QTreeWidgetItem*, int)));
2108
2109       QTreePushButton* rButton = new QTreePushButton;
2110       rButton->setItem(item);
2111       rButton->setColumn(COLUMN_RELOAD_IMAGE);
2112       rButton->setToolTip(tr("reload image"));
2113       rButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/rotateright.png")));
2114       connect(rButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
2115         this,SLOT(ReloadImage(QTreeWidgetItem*, int)));
2116
2117       DataTree->topLevelItem(index)->setExpanded(1);
2118       DataTree->topLevelItem(index)->addChild(item);
2119       DataTree->setItemWidget(item, COLUMN_CLOSE_IMAGE, cButton);
2120       DataTree->setItemWidget(item, COLUMN_RELOAD_IMAGE, rButton);
2121
2122       //set the id of the image
2123       QString id = DataTree->topLevelItem(index)->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString();
2124       item->setData(COLUMN_IMAGE_NAME,Qt::UserRole,id.toStdString().c_str());
2125       UpdateTree();
2126       qApp->processEvents();
2127       ImageInfoChanged();
2128       QApplication::restoreOverrideCursor();
2129
2130       // Update the display to update, e.g., the sliders
2131       for(int i=0; i<4; i++)
2132         DisplaySliders(index, i);
2133     } else {
2134       QApplication::restoreOverrideCursor();
2135       QString error = "Cannot import the new image.\n";
2136       error += mSlicerManagers[index]->GetLastError().c_str();
2137       QMessageBox::information(this,tr("Problem reading image !"),error);
2138     }
2139     WindowLevelChanged();
2140   }
2141   else
2142     QMessageBox::information(this,tr("Problem reading Overlay !"),"File doesn't exist!");
2143 }
2144 //------------------------------------------------------------------------------
2145
2146
2147 //------------------------------------------------------------------------------
2148 void vvMainWindow::AddROI(int index, QString file)
2149 {
2150   /*
2151   // Get slice manager
2152
2153   // Load image
2154
2155   vvImageReader * mReader = new vvImageReader;
2156   mReader->SetInputFilename(filename.toStdString());
2157   mReader->Update(IMAGE);
2158   if (mReader->GetLastError().size() != 0) {
2159   std::cerr << "Error while reading " << filename.toStdString() << std::endl;
2160   QString error = "Cannot open file \n";
2161   error += mReader->GetLastError().c_str();
2162   QMessageBox::information(this,tr("Reading problem"),error);
2163   delete mReader;
2164   return;
2165   }
2166   vvImage::Pointer roi = mReader->GetOutput();
2167
2168   // Create roi in new tool
2169   vvToolStructureSetManager::AddImage(mCurrentSlicerManager, roi);
2170   */
2171 }
2172 //------------------------------------------------------------------------------
2173
2174 //------------------------------------------------------------------------------
2175 void vvMainWindow::SelectFusionImage()
2176 {
2177   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2178
2179   if (!(CheckAddedImage(index, "fusion")) || !(CheckAddedImage(index, "fusionSequence")))
2180     return;
2181
2182   QString Extensions = EXTENSIONS;
2183   Extensions += ";;All Files (*)";
2184   QStringList files = QFileDialog::getOpenFileNames(this,tr("Load Fusion image"),mInputPathName,Extensions);
2185   if (files.isEmpty())
2186     return;
2187
2188   std::vector<std::string> vecFileNames;
2189   for (int i = 0; i < files.size(); i++) {
2190     vecFileNames.push_back(files[i].toStdString());
2191   }
2192   AddFusionImage(index,vecFileNames,vvImageReader::IMAGE);
2193 }
2194 //------------------------------------------------------------------------------
2195
2196 //------------------------------------------------------------------------------
2197 void vvMainWindow::ResetTransformationToIdentity()
2198 {
2199   std::string actorType = DataTree->selectedItems()[0]->data(1,Qt::UserRole).toString().toStdString();
2200   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2201   mSlicerManagers[index]->ResetTransformationToIdentity(actorType);
2202   ImageInfoChanged();
2203 }
2204 //------------------------------------------------------------------------------
2205
2206 //------------------------------------------------------------------------------
2207 void vvMainWindow::AddFusionImage(int index, std::vector<std::string> fileNames, vvImageReader::LoadedImageType type)
2208 {
2209   QString file(fileNames[0].c_str());
2210   if (QFile::exists(file))
2211   {
2212     mInputPathName = itksys::SystemTools::GetFilenamePath(file.toStdString()).c_str();
2213     itk::ImageIOBase::Pointer reader = itk::ImageIOFactory::CreateImageIO(
2214       file.toStdString().c_str(), itk::ImageIOFactory::ReadMode);
2215     reader->SetFileName(fileNames[0].c_str());
2216     reader->ReadImageInformation();
2217     std::string component = reader->GetComponentTypeAsString(reader->GetComponentType());
2218     int dimension = reader->GetNumberOfDimensions();
2219     QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
2220     vvProgressDialog progress("Opening fusion");
2221     qApp->processEvents();
2222
2223     std::string filename = itksys::SystemTools::GetFilenameWithoutExtension(file.toStdString()).c_str();
2224     if (mSlicerManagers[index]->SetFusion(fileNames,dimension, component,type)) {
2225       //create an item in the tree with good settings
2226       QTreeWidgetItem *item = new QTreeWidgetItem();
2227       item->setData(0,Qt::UserRole,file.toStdString().c_str());
2228       item->setData(1,Qt::UserRole,tr("fusion"));
2229       QFileInfo fileinfo(file); //Do not show the path
2230           item->setData(COLUMN_IMAGE_NAME,Qt::DisplayRole,fileinfo.fileName());
2231           item->setToolTip(COLUMN_IMAGE_NAME, mSlicerManagers[index]->GetListOfAbsoluteFilePathInOneString("fusion").c_str());
2232           qApp->processEvents();
2233 #if VTK_MAJOR_VERSION > 5
2234       for ( unsigned int i = 0; i < mSlicerManagers[index]->GetNumberOfSlicers(); i++)
2235         mSlicerManagers[index]->GetSlicer(i)->ForceUpdateDisplayExtent();
2236 #endif
2237       for (int j = 1; j <= 4; j++) {
2238         item->setData(j,Qt::CheckStateRole,DataTree->topLevelItem(index)->data(j,Qt::CheckStateRole));
2239       }
2240
2241       //Create the buttons for reload and close
2242       qApp->processEvents();
2243       QTreePushButton* cButton = new QTreePushButton;
2244       cButton->setItem(item);
2245       cButton->setColumn(COLUMN_CLOSE_IMAGE);
2246       cButton->setToolTip(tr("close image"));
2247       cButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/exit.png")));
2248       connect(cButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
2249         this,SLOT(CloseImage(QTreeWidgetItem*, int)));
2250
2251       QTreePushButton* rButton = new QTreePushButton;
2252       rButton->setItem(item);
2253       rButton->setColumn(COLUMN_RELOAD_IMAGE);
2254       rButton->setToolTip(tr("reload image"));
2255       rButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/rotateright.png")));
2256       connect(rButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
2257         this,SLOT(ReloadImage(QTreeWidgetItem*, int)));
2258
2259       DataTree->topLevelItem(index)->setExpanded(1);
2260       DataTree->topLevelItem(index)->addChild(item);
2261       DataTree->setItemWidget(item, COLUMN_CLOSE_IMAGE, cButton);
2262       DataTree->setItemWidget(item, COLUMN_RELOAD_IMAGE, rButton);
2263
2264       //set the id of the image
2265       QString id = DataTree->topLevelItem(index)->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString();
2266       item->setData(COLUMN_IMAGE_NAME,Qt::UserRole,id.toStdString().c_str());
2267       UpdateTree();
2268       qApp->processEvents();
2269       ImageInfoChanged();
2270       QApplication::restoreOverrideCursor();
2271
2272       // Update the display to update, e.g., the sliders
2273       for(int i=0; i<4; i++)
2274         DisplaySliders(index, i);
2275     } else {
2276       QApplication::restoreOverrideCursor();
2277       QString error = "Cannot import the new image.\n";
2278       error += mSlicerManagers[index]->GetLastError().c_str();
2279       QMessageBox::information(this,tr("Problem reading image !"),error);
2280     }
2281     WindowLevelChanged();
2282   }
2283   else
2284     QMessageBox::information(this,tr("Problem reading Fusion !"),"File doesn't exist!");
2285 }
2286 //------------------------------------------------------------------------------
2287 //------------------------------------------------------------------------------
2288 void vvMainWindow::AddLandmarks(int index, std::vector<std::string> files)
2289 {
2290     if (!landmarksPanel->LoadFromFile(files))
2291       QMessageBox::information(this,tr("Problem reading Landmarks !"),"File doesn't exist!");
2292
2293     landmarksPanel->SetCurrentPath(mInputPathName.toStdString());
2294     landmarksPanel->SetCurrentImage(mSlicerManagers[index]->GetFileName().c_str());
2295 }
2296
2297 //------------------------------------------------------------------------------
2298 void vvMainWindow::OpenField()
2299 {
2300   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2301
2302   if (!(CheckAddedImage(index, "vector")))
2303     return;
2304
2305   QString Extensions = "Images ( *.mhd *.mha *.vf *.nii *.nrrd *.nhdr)";
2306   // Extensions += ";;Images ( *.mha)";
2307   // Extensions += ";;VF Images ( *.vf)";
2308   // Extensions += ";;nii Images ( *.nii)";
2309   // Extensions += ";;nrrd Images ( *.nrrd)";
2310   // Extensions += ";;nhdr Images ( *.nhdr)";
2311   Extensions += ";;All Files (*)";
2312   QString file = QFileDialog::getOpenFileName(this,tr("Load deformation field"),mInputPathName,Extensions);
2313   if (!file.isEmpty())
2314     AddField(file,index);
2315 }
2316 //------------------------------------------------------------------------------
2317
2318
2319 //------------------------------------------------------------------------------
2320 void vvMainWindow::AddFieldEntry(QString filename,int index,bool from_disk)
2321 {
2322   //create an item in the tree with good settings
2323   QTreeWidgetItem *item = new QTreeWidgetItem();
2324   item->setData(0,Qt::UserRole,filename.toStdString().c_str());
2325   item->setData(1,Qt::UserRole,tr("vector"));
2326   QFileInfo fileinfo(filename); //Do not show the path
2327   item->setData(COLUMN_IMAGE_NAME,Qt::DisplayRole,fileinfo.fileName());
2328   item->setToolTip(COLUMN_IMAGE_NAME, mSlicerManagers[index]->GetListOfAbsoluteFilePathInOneString("vector").c_str());
2329   qApp->processEvents();
2330
2331   for (int j = 1; j <= 4; j++) {
2332     item->setData(j,Qt::CheckStateRole,DataTree->topLevelItem(index)->data(j,Qt::CheckStateRole));
2333   }
2334
2335   //Create the buttons for reload and close
2336   qApp->processEvents();
2337   QTreePushButton* cButton = new QTreePushButton;
2338   cButton->setItem(item);
2339   cButton->setColumn(COLUMN_CLOSE_IMAGE);
2340   cButton->setToolTip(tr("close vector field"));
2341   cButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/exit.png")));
2342   connect(cButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
2343     this,SLOT(CloseImage(QTreeWidgetItem*, int)));
2344
2345   QTreePushButton* rButton = new QTreePushButton;
2346   rButton->setItem(item);
2347   rButton->setColumn(COLUMN_RELOAD_IMAGE);
2348   rButton->setToolTip(tr("reload vector field"));
2349   rButton->setEnabled(from_disk);
2350   rButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/rotateright.png")));
2351   connect(rButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
2352     this,SLOT(ReloadImage(QTreeWidgetItem*, int)));
2353
2354   DataTree->topLevelItem(index)->setExpanded(1);
2355   DataTree->topLevelItem(index)->addChild(item);
2356   DataTree->setItemWidget(item, COLUMN_RELOAD_IMAGE, rButton);
2357   DataTree->setItemWidget(item, COLUMN_CLOSE_IMAGE, cButton);
2358
2359   //set the id of the image
2360   QString id = DataTree->topLevelItem(index)->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString();
2361   item->setData(COLUMN_IMAGE_NAME,Qt::UserRole,id.toStdString().c_str());
2362   UpdateTree();
2363   qApp->processEvents();
2364   ImageInfoChanged();
2365   QApplication::restoreOverrideCursor();
2366 }
2367 //------------------------------------------------------------------------------
2368
2369
2370 //------------------------------------------------------------------------------
2371 void vvMainWindow::AddField(vvImage::Pointer vf,QString file,int index)
2372 {
2373   QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
2374   vvSlicerManager* imageManager = mSlicerManagers[index];
2375   if (imageManager->SetVF(vf,file.toStdString())) {
2376     AddFieldEntry(file,index,false);
2377 #if VTK_MAJOR_VERSION > 5
2378       for ( unsigned int i = 0; i < mSlicerManagers[index]->GetNumberOfSlicers(); i++)
2379         mSlicerManagers[index]->GetSlicer(i)->ForceUpdateDisplayExtent();
2380 #endif
2381   } else {
2382     QString error = "Cannot import the vector field for this image.\n";
2383     error += imageManager->GetLastError().c_str();
2384     QMessageBox::information(this,tr("Problem reading VF !"),error);
2385   }
2386   QApplication::restoreOverrideCursor();
2387 }
2388 //------------------------------------------------------------------------------
2389
2390
2391 //------------------------------------------------------------------------------
2392 void vvMainWindow::AddField(QString file,int index)
2393 {
2394   if (QFile::exists(file)) {
2395     mInputPathName = itksys::SystemTools::GetFilenamePath(file.toStdString()).c_str();
2396
2397     //init the progress events
2398     QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
2399     vvProgressDialog progress("Opening " + file.toStdString());
2400     qApp->processEvents();
2401
2402     //read the vector and put it in the current mSlicerManager
2403     vvSlicerManager* imageManager = mSlicerManagers[index];
2404     qApp->processEvents();
2405
2406     std::string filename = itksys::SystemTools::GetFilenameWithoutExtension(file.toStdString()).c_str();
2407     if (imageManager->SetVF(file.toStdString())) {
2408       imageManager->Render();
2409       AddFieldEntry(file,index,true);
2410     } else {
2411       QApplication::restoreOverrideCursor();
2412       QString error = "Cannot import the vector field for this image.\n";
2413       error += imageManager->GetLastError().c_str();
2414       QMessageBox::information(this,tr("Problem reading VF !"),error);
2415     }
2416   } else
2417     QMessageBox::information(this,tr("Problem reading VF !"),"File doesn't exist!");
2418
2419 }
2420 //------------------------------------------------------------------------------
2421
2422
2423 //------------------------------------------------------------------------------
2424 void vvMainWindow::SetVFProperty(int subsampling, int scale, int log, int width, double r, double g, double b)
2425 {
2426   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2427   if (mSlicerManagers[index]->GetSlicer(0)->GetVF()) {
2428     for (int i = 0; i < 4; i++) {
2429       mSlicerManagers[index]->GetSlicer(i)->SetVFSubSampling(subsampling);
2430       mSlicerManagers[index]->GetSlicer(i)->SetVFScale(scale);
2431       mSlicerManagers[index]->GetSlicer(i)->SetVFWidth(width);
2432       mSlicerManagers[index]->GetSlicer(i)->SetVFColor(r,g,b);
2433       if (log > 0)
2434         mSlicerManagers[index]->GetSlicer(i)->SetVFLog(1);
2435       else
2436         mSlicerManagers[index]->GetSlicer(i)->SetVFLog(0);
2437     }
2438   }
2439 }
2440 //------------------------------------------------------------------------------
2441
2442
2443 //------------------------------------------------------------------------------
2444 void vvMainWindow::SetOverlayProperty(int color, int linked, double window, double level)
2445 {
2446   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2447   if (mSlicerManagers[index]->GetSlicer(0)->GetOverlay()) {
2448     mSlicerManagers[index]->SetOverlayColor(color);
2449     mSlicerManagers[index]->SetColorMap(0);
2450     mSlicerManagers[index]->SetLinkOverlayWindowLevel(linked);
2451     mSlicerManagers[index]->SetOverlayColorWindow(window);
2452     mSlicerManagers[index]->SetOverlayColorLevel(level);
2453     mSlicerManagers[index]->Render();
2454   }
2455 }
2456 //------------------------------------------------------------------------------
2457
2458 //------------------------------------------------------------------------------
2459 void vvMainWindow::SetFusionProperty(int opacity, int thresOpacity, int colormap,double window, double level, bool showLegend)
2460 {
2461   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2462   if (mSlicerManagers[index]->GetSlicer(0)->GetFusion()) {
2463     mSlicerManagers[index]->SetFusionColorMap(colormap);
2464     mSlicerManagers[index]->SetFusionOpacity(opacity);
2465     mSlicerManagers[index]->SetFusionThresholdOpacity(thresOpacity);
2466     mSlicerManagers[index]->SetFusionWindow(window);
2467     mSlicerManagers[index]->SetFusionLevel(level);
2468     mSlicerManagers[index]->SetFusionShowLegend(showLegend);
2469     mSlicerManagers[index]->SetColorMap(0);
2470     mSlicerManagers[index]->Render();
2471   }
2472 }
2473 //------------------------------------------------------------------------------
2474
2475
2476 //------------------------------------------------------------------------------
2477 void vvMainWindow::SelectFusionSequence()
2478 {
2479   //get the index of the slicer manager of the main sequence (CT)
2480   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2481
2482   if (!(CheckAddedImage(index, "fusion")) || !(CheckAddedImage(index, "fusionSequence")))
2483     return;
2484
2485   QString Extensions = EXTENSIONS;
2486   Extensions += ";;All Files (*)";
2487   QStringList files = QFileDialog::getOpenFileNames(this,tr("Load Overlay image sequence"),mInputPathName,Extensions);
2488   if (files.isEmpty())
2489     return;
2490
2491   std::vector<std::string> vecFileNames;
2492   for (int i = 0; i < files.size(); i++) {
2493     vecFileNames.push_back(files[i].toStdString());
2494   }
2495
2496   //associate the secondary sequence (US) to the main one
2497   AddFusionSequence(index,vecFileNames,vvImageReader::MERGEDWITHTIME);
2498 }
2499 //------------------------------------------------------------------------------
2500
2501
2502 //------------------------------------------------------------------------------
2503 void vvMainWindow::SelectFusionSequenceCorrespondances()
2504 {
2505   //make sure the index is right?
2506   //in the end, I should attach the temporal data to the right sequence!
2507   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2508   //in case the other sequence got selected, make sure we select the primary sequence
2509   if ( (!mSlicerManagers[index]->GetSlicer(0)->GetFusion()) && mSlicerManagers[index]->GetFusionSequenceIndexOfLinkedManager()>=0 ) {
2510     index = mSlicerManagers[index]->GetFusionSequenceIndexOfLinkedManager();
2511   }
2512
2513   //open a dialog box to find a file
2514   //QString Extensions = EXTENSIONS;
2515   QString Extensions = ";;All Files (*)";
2516   QString fileName = QFileDialog::getOpenFileName(this,tr("Load respiratory signal for fused sequence"),mInputPathName,Extensions);
2517   if (fileName.isNull())
2518     return;
2519
2520   //read it as a vector of values
2521   vnl_vector<double> tmpVect;
2522
2523   std::ifstream file;
2524   file.open(fileName.toStdString().c_str());
2525   tmpVect.read_ascii(file);
2526   file.close();
2527
2528   //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
2529   bool signalOK = true;
2530   unsigned nbFrameMain = mSlicerManagers[index]->GetImage()->GetTransform().size();
2531   unsigned nbFrameSecondary = mSlicerManagers[index]->GetFusionSequenceNbFrames();
2532   std::cout<<"nbFrameMain = "<<nbFrameMain<<", nbFrameSecondary= "<<nbFrameSecondary<<", signal size: "<<tmpVect.size()<<std::endl;
2533   std::vector<unsigned> temporalCorrespondances;
2534   if ( tmpVect.size() == nbFrameMain + nbFrameSecondary ) {
2535     for (unsigned i=0 ; i<tmpVect.size() ; i++) {
2536       if (i<nbFrameMain) { //first part of the file: i -> index in secondary seq.
2537         if ( tmpVect(i)<nbFrameSecondary ) temporalCorrespondances.push_back(tmpVect(i));
2538         else { signalOK=false; break; } //pointing outside the secondary sequence...
2539       }
2540       else { //first part of the file -> index in secondary seq.
2541         if ( tmpVect(i)<nbFrameMain ) temporalCorrespondances.push_back(tmpVect(i));
2542         else { signalOK=false; break; } //pointing outside the secondary sequence...
2543       }
2544     }
2545   }
2546   else {signalOK=false;}
2547   if (!signalOK) {//else, send a message to signal the failure...
2548     QString error = "The provided temporal correspondances is invalid - check tooltip.\n";
2549     error += "Ignoring file: " + fileName;
2550     QMessageBox::information(this,tr("Problem adding temporal correspondances!"),error);
2551     return;
2552   }
2553   else {
2554     //for convenience, associate this sequence to both the current slicer manager, and to the linked one
2555     mSlicerManagers[index]->SetFusionSequenceCorrespondances(temporalCorrespondances);
2556     mSlicerManagers[ mSlicerManagers[index]->GetFusionSequenceIndexOfLinkedManager() ]->SetFusionSequenceCorrespondances(temporalCorrespondances);
2557     overlayPanel->enableFusionSequenceTemporalSync();
2558   }
2559
2560 }
2561 //------------------------------------------------------------------------------
2562
2563
2564 //------------------------------------------------------------------------------
2565 //when this function is called index is the slicer manager index corresponding to the main sequence (CT)
2566 //the files behind fileNames points to the data for the secondary sequence
2567 void vvMainWindow::AddFusionSequence(int index, std::vector<std::string> fileNames, vvImageReader::LoadedImageType type)
2568 {
2569   QString file(fileNames[0].c_str());
2570   if (QFile::exists(file))
2571   {
2572     mInputPathName = itksys::SystemTools::GetFilenamePath(file.toStdString()).c_str();
2573     itk::ImageIOBase::Pointer reader = itk::ImageIOFactory::CreateImageIO(
2574       file.toStdString().c_str(), itk::ImageIOFactory::ReadMode);
2575     std::sort (fileNames.begin(), fileNames.end());//make sure the files are sorted.
2576     reader->SetFileName(fileNames[0].c_str());
2577     reader->ReadImageInformation();
2578     std::string component = reader->GetComponentTypeAsString(reader->GetComponentType());
2579     int dimension = reader->GetNumberOfDimensions();
2580     QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
2581     vvProgressDialog progress("Opening " + file.toStdString());
2582     qApp->processEvents();
2583
2584     std::string filename = itksys::SystemTools::GetFilenameWithoutExtension(file.toStdString()).c_str();
2585
2586     if (mSlicerManagers[index]->SetFusionSequence(fileNames,dimension, component,type)) {
2587       //create an item in the tree with good settings
2588       QTreeWidgetItem *item = new QTreeWidgetItem();
2589       item->setData(0,Qt::UserRole,file.toStdString().c_str());
2590       item->setData(1,Qt::UserRole,tr("fusionSequence"));
2591
2592       QFileInfo fileinfo(file); //Do not show the path
2593       item->setData(COLUMN_IMAGE_NAME,Qt::DisplayRole,fileinfo.fileName());
2594       item->setToolTip(COLUMN_IMAGE_NAME, mSlicerManagers[index]->GetListOfAbsoluteFilePathInOneString("fusionSequence").c_str());
2595       qApp->processEvents();
2596 #if VTK_MAJOR_VERSION > 5
2597       for ( unsigned int i = 0; i < mSlicerManagers[index]->GetNumberOfSlicers(); i++)
2598         mSlicerManagers[index]->GetSlicer(i)->ForceUpdateDisplayExtent();
2599 #endif
2600       for (int j = 1; j <= 4; j++) {
2601         item->setData(j,Qt::CheckStateRole,DataTree->topLevelItem(index)->data(j,Qt::CheckStateRole));
2602       }
2603
2604       //Create the buttons for reload and close
2605       qApp->processEvents();
2606       QTreePushButton* cButton = new QTreePushButton;
2607       cButton->setItem(item);
2608       cButton->setColumn(COLUMN_CLOSE_IMAGE);
2609       cButton->setToolTip(tr("close image"));
2610       cButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/exit.png")));
2611       connect(cButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
2612         this,SLOT(CloseImage(QTreeWidgetItem*, int)));
2613
2614       QTreePushButton* rButton = new QTreePushButton;
2615       rButton->setItem(item);
2616       rButton->setColumn(COLUMN_RELOAD_IMAGE);
2617       rButton->setToolTip(tr("reload image"));
2618       rButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/rotateright.png")));
2619       connect(rButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
2620         this,SLOT(ReloadImage(QTreeWidgetItem*, int)));
2621
2622       DataTree->topLevelItem(index)->setExpanded(1);
2623       DataTree->topLevelItem(index)->addChild(item);
2624       DataTree->setItemWidget(item, COLUMN_CLOSE_IMAGE, cButton);
2625       DataTree->setItemWidget(item, COLUMN_RELOAD_IMAGE, rButton);
2626
2627       //store the original transform matrix
2628       int indexParent = GetSlicerIndexFromItem( DataTree->topLevelItem(index) );
2629       mSlicerManagers[indexParent]->SetFusionSequenceMainTransformMatrix( mSlicerManagers[indexParent]->GetSlicer(0)->GetImage()->GetTransform()[0]->GetMatrix() );
2630
2631       //set the id of the image
2632       QString id = DataTree->topLevelItem(index)->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString();
2633       item->setData(COLUMN_IMAGE_NAME,Qt::UserRole,id.toStdString().c_str());
2634       UpdateTree();
2635       qApp->processEvents();
2636
2637       //ImageInfoChanged();
2638
2639       QApplication::restoreOverrideCursor();
2640       // Update the display to update, e.g., the sliders
2641       for(int i=0; i<4; i++)
2642         DisplaySliders(index, i);
2643
2644
2645       //This loads the secondary sequence (US) as an independent sequence
2646       LoadImages(fileNames, type);
2647       //reset the transforms to identity
2648       //FIX -- and set the thickness of the US slices to a large value (necessary for visualization purposes...)
2649       double sp_x, sp_y, sp_z;
2650       mSlicerManagers[indexParent]->GetImage()->GetVTKImages()[0]->GetSpacing(sp_x, sp_y, sp_z);
2651       sp_z = std::max(sp_x, std::max(sp_y, sp_z)) + 0.5; //
2652       for (unsigned i=0 ; i<mSlicerManagers.back()->GetImage()->GetTransform().size() ; i++) {
2653         sp_x = mSlicerManagers.back()->GetImage()->GetVTKImages()[i]->GetSpacing()[0];
2654         sp_y = mSlicerManagers.back()->GetImage()->GetVTKImages()[i]->GetSpacing()[1];
2655         mSlicerManagers.back()->GetImage()->GetVTKImages()[i]->SetSpacing( sp_x, sp_y, sp_z);
2656         mSlicerManagers.back()->GetImage()->GetTransform()[i]->Identity();
2657         mSlicerManagers.back()->GetImage()->GetTransform()[i]->Update();
2658       }
2659
2660       //automatically link both images...
2661       AddLink(mSlicerManagers[indexParent]->GetId().c_str(), mSlicerManagers.back()->GetId().c_str(), false);
2662
2663       //tie the main and secondary sequences by raising flags and informing each another of their respective SlicerManager indices
2664       mSlicerManagers[indexParent]->SetFusionSequenceIndexOfLinkedManager(mSlicerManagers.size()-1);
2665       mSlicerManagers[indexParent]->SetFusionSequenceInvolvmentCode(0); //main sequence
2666       mSlicerManagers.back()->SetFusionSequenceIndexOfLinkedManager(indexParent);
2667       mSlicerManagers.back()->SetFusionSequenceInvolvmentCode(1); //secondary sequence
2668       for (unsigned i=0 ; i<4 ; i++) {
2669         mSlicerManagers.back()->GetSlicer(i)->SetFusionSequenceCode(1); //flag the slicers of the secondary sequence
2670       }
2671
2672     } else {
2673       QApplication::restoreOverrideCursor();
2674       QString error = "Cannot import the new image.\n";
2675       error += mSlicerManagers[index]->GetLastError().c_str();
2676       QMessageBox::information(this,tr("Problem reading image !"),error);
2677     }
2678     WindowLevelChanged();
2679     ImageInfoChanged(); //this internally calls WindowLevelChanged...
2680   }
2681   else {
2682     QMessageBox::information(this,tr("Problem reading fusion sequence !"),"File doesn't exist!");
2683     return;
2684   }
2685
2686 }
2687 //------------------------------------------------------------------------------
2688
2689
2690 //------------------------------------------------------------------------------
2691 //fusionSequenceFrameIndex and fusionSequenceNbFrames are relative to the secondary sequence (US)
2692 void vvMainWindow::SetFusionSequenceProperty(int fusionSequenceFrameIndex, bool spatialSyncFlag, unsigned int fusionSequenceNbFrames, bool temporalSyncFlag)
2693 {
2694   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2695
2696   if (!mSlicerManagers[index]->IsInvolvedInFusionSequence()) return;
2697
2698   //check if the focus moved to the linked sequence, and in this case, select the master sequence instead
2699   if (!mSlicerManagers[index]->IsMainSequenceOfFusionSequence()) {
2700     index = mSlicerManagers[index]->GetFusionSequenceIndexOfLinkedManager();
2701   }
2702   int secondaryIndex = mSlicerManagers[index]->GetFusionSequenceIndexOfLinkedManager();
2703   if (secondaryIndex==-1) return; //this should never happen
2704   if ( (!mSlicerManagers[index]->IsMainSequenceOfFusionSequence()) ||
2705     (!mSlicerManagers[secondaryIndex]->IsSecondarySequenceOfFusionSequence()) )
2706   {return;} //this should never happen, raise an exception?
2707
2708   if (mSlicerManagers[index]->GetSlicer(0)->GetFusion()) {
2709
2710     //First, if the spatialSync button is unchecked, then reposition the parent sequence (CT) in its original coordinate frame
2711     if ( (!spatialSyncFlag) && (mSlicerManagers[index]->GetFusionSequenceSpatialSyncFlag()) ) {
2712       for ( unsigned i=0 ; i<mSlicerManagers[index]->GetSlicer(0)->GetImage()->GetTransform().size() ; i++ ) {
2713         mSlicerManagers[index]->GetSlicer(0)->GetImage()->GetTransform()[i]->SetMatrix( mSlicerManagers[index]->GetFusionSequenceMainTransformMatrix() );
2714         mSlicerManagers[index]->GetSlicer(0)->GetImage()->GetTransform()[i]->Update();
2715       }
2716
2717       for (int i=0; i<mSlicerManagers[index]->GetNumberOfSlicers(); i++) {
2718         mSlicerManagers[index]->GetSlicer(i)->ForceUpdateDisplayExtent();
2719         mSlicerManagers[index]->GetSlicer(i)->Render();
2720       }
2721     }
2722
2723     //then, update the property values in the slicer manager
2724     mSlicerManagers[index]->SetFusionSequenceLength(fusionSequenceNbFrames);
2725     mSlicerManagers[index]->SetFusionSequenceSpatialSyncFlag(spatialSyncFlag);
2726     mSlicerManagers[index]->SetFusionSequenceTemporalSyncFlag(temporalSyncFlag);
2727     mSlicerManagers[index]->SetFusionSequenceFrameIndex(fusionSequenceFrameIndex);
2728
2729     //select the right frame of the US sequence
2730     mSlicerManagers[index]->SetFusionSequenceTSlice(fusionSequenceFrameIndex); //here, I should only update the overlayed sequence
2731     mSlicerManagers[secondaryIndex]->SetTSlice(fusionSequenceFrameIndex, false); //this should update the secondary sequence (individual version)
2732
2733     //update the horizontal sliders of the main window
2734     overlayPanel->updateFusionSequenceSliderValueFromWindow(fusionSequenceFrameIndex, false);
2735
2736     if (spatialSyncFlag) { //reslice the CT
2737
2738       if (temporalSyncFlag) { //do the temporal synchronisation
2739         int mainSequenceFrameIndex=0;
2740         //estimate the TSlice to set to the CT
2741         unsigned nbFramesMain = mSlicerManagers[index]->GetImage()->GetTransform().size();
2742         mainSequenceFrameIndex = mSlicerManagers[index]->GetFusionSequenceCorrespondances()[ nbFramesMain + fusionSequenceFrameIndex];
2743         //and set it!
2744         mSlicerManagers[index]->SetTSlice(mainSequenceFrameIndex, false);
2745         //warning, there is a loopback, and modification of the TSlice in main sequence forces an update of the TSlice in secondary, etc...
2746       }
2747
2748
2749       //Set the transform matrix of the parent sequence (typically CT / 4DCT)
2750       vtkSmartPointer<vtkMatrix4x4> tmpMat = vtkSmartPointer<vtkMatrix4x4>::New();
2751       vtkMatrix4x4::Invert( mSlicerManagers[index]->GetFusionSequenceInitialTransformMatrixAtFrame(fusionSequenceFrameIndex), tmpMat );
2752       for ( unsigned i=0 ; i<mSlicerManagers[index]->GetSlicer(0)->GetImage()->GetTransform().size() ; i++ ) {
2753         mSlicerManagers[index]->GetSlicer(0)->GetImage()->GetTransform()[i]->SetMatrix( mSlicerManagers[index]->GetFusionSequenceMainTransformMatrix() );
2754         mSlicerManagers[index]->GetSlicer(0)->GetImage()->GetTransform()[i]->PreMultiply();
2755         mSlicerManagers[index]->GetSlicer(0)->GetImage()->GetTransform()[i]->Concatenate( tmpMat );
2756         mSlicerManagers[index]->GetSlicer(0)->GetImage()->GetTransform()[i]->Update();
2757       }
2758
2759       for (int i=0; i<mSlicerManagers[index]->GetNumberOfSlicers(); i++) {
2760         mSlicerManagers[index]->GetSlicer(i)->ForceUpdateDisplayExtent();
2761         mSlicerManagers[index]->GetSlicer(i)->Render();
2762       }
2763
2764     }
2765
2766   }
2767 }
2768 //------------------------------------------------------------------------------
2769
2770
2771 //------------------------------------------------------------------------------
2772 void vvMainWindow::SaveAs()
2773 {
2774   if (DataTree->selectedItems()[0]->data(1,Qt::UserRole).toString() == "vector") {
2775     QMessageBox::warning(this,tr("Unsupported type"),tr("Sorry, saving a vector field is unsupported for the moment"));
2776     return;
2777   }
2778
2779   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2780   int dimension = mSlicerManagers[index]->GetDimension();
2781   QStringList OutputListeFormat;
2782   OutputListeFormat.clear();
2783   if (dimension == 1) {
2784     OutputListeFormat.push_back(".mhd");
2785     OutputListeFormat.push_back(".mha");
2786   }
2787   if (dimension == 2) {
2788     OutputListeFormat.push_back(".bmp");
2789     OutputListeFormat.push_back(".png");
2790     OutputListeFormat.push_back(".jpeg");
2791     OutputListeFormat.push_back(".tif");
2792     OutputListeFormat.push_back(".mhd");
2793     OutputListeFormat.push_back(".mha");
2794     OutputListeFormat.push_back(".hdr");
2795     OutputListeFormat.push_back(".vox");
2796   } else if (dimension == 3) {
2797     OutputListeFormat.push_back(".mhd");
2798     OutputListeFormat.push_back(".mha");
2799     OutputListeFormat.push_back(".nii");
2800     OutputListeFormat.push_back(".nrrd");
2801     OutputListeFormat.push_back(".nhdr");
2802     OutputListeFormat.push_back(".hdr");
2803     OutputListeFormat.push_back(".vox");
2804   } else if (dimension == 4) {
2805     OutputListeFormat.push_back(".mhd");
2806     OutputListeFormat.push_back(".mha");
2807     OutputListeFormat.push_back(".nii");
2808     OutputListeFormat.push_back(".nrrd");
2809     OutputListeFormat.push_back(".nhdr");
2810   }
2811   QString Extensions = "AllFiles(*.*)";
2812   for (int i = 0; i < OutputListeFormat.count(); i++) {
2813     Extensions += ";;Images ( *";
2814     Extensions += OutputListeFormat[i];
2815     Extensions += ")";
2816   }
2817   QString fileName = QFileDialog::getSaveFileName(this,
2818     tr("Save As"),
2819     mSlicerManagers[index]->GetFileName().c_str(),
2820     Extensions);
2821   if (!fileName.isEmpty()) {
2822     std::string fileformat = itksys::SystemTools::GetFilenameLastExtension(fileName.toStdString());
2823     if (OutputListeFormat.contains(
2824       fileformat.c_str())) {
2825         QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
2826         std::string action = "Saving";
2827         vvProgressDialog progress("Saving "+fileName.toStdString());
2828         qApp->processEvents();
2829         vvImageWriter::Pointer writer = vvImageWriter::New();
2830         writer->SetOutputFileName(fileName.toStdString());
2831         writer->SetInput(mSlicerManagers[index]->GetImage());
2832
2833         // Check on transform and prompt user
2834         writer->SetSaveTransform(false);
2835         bool bId = true;
2836         for(int i=0; i<4; i++)
2837           for(int j=0; j<4; j++) {
2838             // TODO SR and BP: check on the list of transforms and not the first only
2839             double elt = mSlicerManagers[index]->GetImage()->GetTransform()[0]->GetMatrix()->GetElement(i,j);
2840             if(i==j && elt!=1.)
2841               bId = false;
2842             if(i!=j && elt!=0.)
2843               bId = false;
2844           }
2845           if( !bId ) {
2846             QString warning = "The image has an associated linear transform. Do you want to save it along?";
2847             QMessageBox msgBox(QMessageBox::Warning, tr("Save transform"), warning, 0, this);
2848             msgBox.addButton(tr("Yes"), QMessageBox::AcceptRole);
2849             msgBox.addButton(tr("No"), QMessageBox::RejectRole);
2850             if (msgBox.exec() == QMessageBox::AcceptRole)
2851               writer->SetSaveTransform(true);
2852           }
2853
2854           writer->Update();
2855           QApplication::restoreOverrideCursor();
2856           if (writer->GetLastError().size()) {
2857             QString error = "Saving did not succeed\n";
2858             error += writer->GetLastError().c_str();
2859             QMessageBox::information(this,tr("Saving Problem"),error);
2860             SaveAs();
2861           }
2862     } else {
2863       QString error = fileformat.c_str();
2864       if (error.isEmpty())
2865         error += "no file format specified !";
2866       else
2867         error += " format unknown !!!\n";
2868       QMessageBox::information(this,tr("Saving Problem"),error);
2869       SaveAs();
2870     }
2871   }
2872 }
2873 //------------------------------------------------------------------------------
2874
2875 //------------------------------------------------------------------------------
2876 void vvMainWindow::SaveCurrentState()
2877 {
2878   QString Extensions = "XML Files(*.xml)";
2879   QString fileName = QFileDialog::getSaveFileName(this,
2880     tr("Save Current Window State"),
2881     "",
2882     Extensions);
2883
2884   SaveCurrentStateAs(fileName.toStdString());
2885 }
2886 //------------------------------------------------------------------------------
2887
2888 //------------------------------------------------------------------------------
2889 void vvMainWindow::SaveCurrentStateAs(const std::string& stateFile)
2890 {
2891   vvSaveState save_state;
2892   save_state.Run(this, stateFile);
2893 }
2894
2895 //------------------------------------------------------------------------------
2896 void vvMainWindow::ReadSavedState()
2897 {
2898   QString Extensions = "XML Files(*.xml)";
2899   QString fileName = QFileDialog::getOpenFileName(this,
2900     tr("Load Window State"),
2901     "",
2902     Extensions);
2903
2904   ReadSavedStateFile(fileName.toStdString());
2905 }
2906 //------------------------------------------------------------------------------
2907
2908 //------------------------------------------------------------------------------
2909 void vvMainWindow::ReadSavedStateFile(const std::string& stateFile)
2910 {
2911   vvReadState read_state;
2912   read_state.Run(this, stateFile);
2913 }
2914 //------------------------------------------------------------------------------
2915
2916 //------------------------------------------------------------------------------
2917 void vvMainWindow::LinkAllImages()
2918 {
2919   linkPanel->linkAll();
2920 }
2921
2922 //------------------------------------------------------------------------------
2923 void vvMainWindow::AddLink(QString image1,QString image2,bool fromPanel)
2924 {
2925   if (!fromPanel) {
2926     // delegate to linkPanel if call came from elsewhere...
2927     linkPanel->addLinkFromIds(image1, image2);
2928     return;
2929   }
2930
2931   unsigned int sm1 = 0;
2932   unsigned int sm2 = 0;
2933
2934   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
2935     if (image1.toStdString() == mSlicerManagers[i]->GetId()) {
2936       mSlicerManagers[i]->AddLink(image2.toStdString());
2937       sm1 = i;
2938     }
2939     if (image2.toStdString() == mSlicerManagers[i]->GetId()) {
2940       mSlicerManagers[i]->AddLink(image1.toStdString());
2941       sm2 = i;
2942     }
2943   }
2944
2945   if (linkPanel->isLinkAll())   {
2946     emit UpdateLinkedNavigation(mSlicerManagers[sm1]->GetId(), mSlicerManagers[mCurrentPickedImageIndex], mSlicerManagers[mCurrentPickedImageIndex]->GetSlicer(0));
2947     emit UpdateLinkedNavigation(mSlicerManagers[sm2]->GetId(), mSlicerManagers[mCurrentPickedImageIndex], mSlicerManagers[mCurrentPickedImageIndex]->GetSlicer(0));
2948   } else {
2949     emit UpdateLinkedNavigation(mSlicerManagers[sm2]->GetId(), mSlicerManagers[sm1], mSlicerManagers[sm1]->GetSlicer(0));
2950   }
2951 }
2952
2953 //------------------------------------------------------------------------------
2954
2955
2956 //------------------------------------------------------------------------------
2957 void vvMainWindow::RemoveLink(QString image1,QString image2)
2958 {
2959   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
2960     if (image1.toStdString() == mSlicerManagers[i]->GetId()) {
2961       mSlicerManagers[i]->RemoveLink(image2.toStdString());
2962     }
2963     if (image2.toStdString() == mSlicerManagers[i]->GetId()) {
2964       mSlicerManagers[i]->RemoveLink(image1.toStdString());
2965     }
2966   }
2967 }
2968 //------------------------------------------------------------------------------
2969
2970 //------------------------------------------------------------------------------
2971 void vvMainWindow::ChangeImageWithIndexOffset(vvSlicerManager *sm, int slicer, int offset)
2972 {
2973   if(mSlicerManagers.size()==1)
2974     return;
2975
2976   int index = 0;
2977   while(sm != mSlicerManagers[index])
2978     index++;
2979   index = (index+offset+mSlicerManagers.size()) % mSlicerManagers.size();
2980
2981   QTreeWidgetItem* item = GetItemFromSlicerManager(mSlicerManagers[index]);
2982   item->setData(slicer+1,Qt::CheckStateRole,2);         //change checkbox
2983   CurrentImageChanged(mSlicerManagers[index]->GetId()); //select new image
2984   DisplayChanged(item,slicer+1);
2985 }
2986 //------------------------------------------------------------------------------
2987 void vvMainWindow::HorizontalSliderMoved(int value,int column, int slicer_index)
2988 {
2989   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
2990     if (DataTree->topLevelItem(i)->data(column,Qt::CheckStateRole).toInt() > 1) {
2991       //i is the SlicerManager that is in charge of this slicer.
2992       if (mSlicerManagers[i]->IsInvolvedInFusionSequence()) {
2993         //if the slicerManager is involved in a fusionSequence as the secondary sequence, then update the slider position in the overlay panel and everything accordingly
2994         if (mSlicerManagers[i]->IsSecondarySequenceOfFusionSequence()) {
2995           overlayPanel->updateFusionSequenceSliderValueFromWindow(value, true);
2996         }
2997         else { //if this is the primary sequence that has been modified
2998           if (mSlicerManagers[i]->GetFusionSequenceTemporalSyncFlag()) {
2999             //WARNING: for some obscure reason, there are problems when accessing mSlicerManagers[mSlicerManagers[i]->GetFusionSequenceIndexOfLinkedManager()]->GetFusionSequenceFrameIndex();
3000
3001             int estimatedValue=0;
3002             //estimate a corresponding time index for the secondary (US) sequence, and update it accordingly.
3003             estimatedValue = mSlicerManagers[i]->GetFusionSequenceCorrespondances()[ value ];
3004             //TODO: at the moment, there is a loop in TSlice modifications
3005             //modifying sequence 1 causes seq 2 to update, which in turns update seq1...
3006             //I disable control on seq1 at the moment.
3007             //overlayPanel->updateFusionSequenceSliderValueFromWindow(estimatedValue, true);
3008           }
3009         }
3010       }
3011
3012       for (int j = 0; j < 4; j++) {
3013         mSlicerManagers[i]->SetTSliceInSlicer(value,j);
3014       }
3015       mSlicerManagers[i]->GetSlicer(slicer_index)->Render();
3016       break;
3017     }
3018   }
3019 }
3020 //------------------------------------------------------------------------------
3021
3022
3023 //------------------------------------------------------------------------------
3024 void vvMainWindow::NOHorizontalSliderMoved()
3025 {
3026   // if (mCurrentTime == NOHorizontalSlider->value()) return;
3027   HorizontalSliderMoved(NOHorizontalSlider->value(),COLUMN_UL_VIEW,0);
3028   //  mCurrentTime = NOHorizontalSlider->value();
3029 }
3030 //------------------------------------------------------------------------------
3031
3032
3033 //------------------------------------------------------------------------------
3034 void vvMainWindow::NEHorizontalSliderMoved()
3035 {
3036   // if (mCurrentTime == NEHorizontalSlider->value()) return;
3037   HorizontalSliderMoved(NEHorizontalSlider->value(),COLUMN_UR_VIEW,1);
3038   //  mCurrentTime = NEHorizontalSlider->value();
3039 }
3040 //------------------------------------------------------------------------------
3041
3042
3043 //------------------------------------------------------------------------------
3044 void vvMainWindow::SOHorizontalSliderMoved()
3045 {
3046   // if (mCurrentTime == SOHorizontalSlider->value()) return;
3047   HorizontalSliderMoved(SOHorizontalSlider->value(),COLUMN_DL_VIEW,2);
3048   // mCurrentTime = SOHorizontalSlider->value();
3049 }
3050 //------------------------------------------------------------------------------
3051
3052
3053 //------------------------------------------------------------------------------
3054 void vvMainWindow::SEHorizontalSliderMoved()
3055 {
3056   // if (mCurrentTime == SEHorizontalSlider->value()) return;
3057   HorizontalSliderMoved(SEHorizontalSlider->value(),COLUMN_DR_VIEW,3);
3058   // mCurrentTime = SEHorizontalSlider->value();
3059 }
3060 //------------------------------------------------------------------------------
3061
3062 //------------------------------------------------------------------------------
3063 void vvMainWindow::NOVerticalSliderChanged()
3064 {
3065   static int value=-1;
3066   if (value == NOVerticalSlider->value()) return;
3067   else value = NOVerticalSlider->value();
3068   //  int value = NOVerticalSlider->value();
3069   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
3070     if (DataTree->topLevelItem(i)->data(COLUMN_UL_VIEW,Qt::CheckStateRole).toInt() > 1) {
3071       if (mSlicerManagers[i]->GetSlicer(0)->GetSlice() != value) {
3072         mSlicerManagers[i]->GetSlicer(0)->SetSlice(value);
3073         mSlicerManagers[i]->VerticalSliderHasChanged(0, value);
3074
3075         // If nor Update/Render -> slider not work
3076         // only render = ok navigation, but for contour Update needed but slower ?
3077
3078         mSlicerManagers[i]->UpdateSlice(0);  // <-- DS add this. Not too much update ? YES. but needed for ImageContour ...
3079         //mSlicerManagers[i]->GetSlicer(0)->Render(); // <-- DS add this, needed for contour, seems ok ? not too slow ?
3080       }
3081       break;
3082     }
3083   }
3084 }
3085 //------------------------------------------------------------------------------
3086
3087
3088 //------------------------------------------------------------------------------
3089 void vvMainWindow::NEVerticalSliderChanged()
3090 {
3091   static int value=-1;
3092   if (value == NEVerticalSlider->value()) return;
3093   else value = NEVerticalSlider->value();
3094   //  int value = NEVerticalSlider->value();
3095   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
3096     if (DataTree->topLevelItem(i)->data(COLUMN_UR_VIEW,Qt::CheckStateRole).toInt() > 1) {
3097       if (mSlicerManagers[i]->GetSlicer(1)->GetSlice() != value) {
3098         mSlicerManagers[i]->GetSlicer(1)->SetSlice(value);
3099         mSlicerManagers[i]->VerticalSliderHasChanged(1, value);
3100         mSlicerManagers[i]->UpdateSlice(1);
3101         //mSlicerManagers[i]->GetSlicer(1)->Render(); // <-- DS add this, needed for contour, seems ok ? not too slow ?
3102       }
3103       break;
3104     }
3105   }
3106 }
3107 //------------------------------------------------------------------------------
3108
3109
3110 //------------------------------------------------------------------------------
3111 void vvMainWindow::SOVerticalSliderChanged()
3112 {
3113   static int value=-1;
3114   if (value == SOVerticalSlider->value()) return;
3115   else value = SOVerticalSlider->value();
3116   //int value = SOVerticalSlider->value();
3117   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
3118     if (DataTree->topLevelItem(i)->data(COLUMN_DL_VIEW,Qt::CheckStateRole).toInt() > 1) {
3119       if (mSlicerManagers[i]->GetSlicer(2)->GetSlice() != value) {
3120         mSlicerManagers[i]->GetSlicer(2)->SetSlice(value);
3121         mSlicerManagers[i]->VerticalSliderHasChanged(2, value);
3122         mSlicerManagers[i]->UpdateSlice(2);
3123         //mSlicerManagers[i]->GetSlicer(2)->Render(); // <-- DS add this, needed for contour, seems ok ? not too slow ?
3124       }
3125       // else { DD("avoid SOVerticalSlider slicer update"); }
3126       break;
3127     }
3128   }
3129 }
3130 //------------------------------------------------------------------------------
3131
3132
3133 //------------------------------------------------------------------------------
3134 void vvMainWindow::SEVerticalSliderChanged()
3135 {
3136   static int value=-1;
3137   if (value == SEVerticalSlider->value()) return;
3138   else value = SEVerticalSlider->value();
3139   // int value = SEVerticalSlider->value();
3140   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
3141     if (DataTree->topLevelItem(i)->data(COLUMN_DR_VIEW,Qt::CheckStateRole).toInt() > 1) {
3142       if (mSlicerManagers[i]->GetSlicer(3)->GetSlice() != value) {
3143         mSlicerManagers[i]->GetSlicer(3)->SetSlice(value);
3144         mSlicerManagers[i]->VerticalSliderHasChanged(3, value);
3145         mSlicerManagers[i]->UpdateSlice(3);
3146         //mSlicerManagers[i]->GetSlicer(3)->Render(); // <-- DS add this, needed for contour, seems ok ? not too slow ?
3147       }
3148       break;
3149     }
3150   }
3151 }
3152 //------------------------------------------------------------------------------
3153
3154
3155 //------------------------------------------------------------------------------
3156 void vvMainWindow::UpdateSlice(int slicer, int slice)
3157 {
3158   // DD("vvMainWindow::UpdateSlice");
3159   //   DD(slicer);
3160   //   DD(slice);
3161   if (slicer == 0) {
3162     //    if (slice != NOVerticalSlider->value())
3163     NOVerticalSlider->setValue(slice);
3164   } else {
3165     if (slicer == 1)
3166       NEVerticalSlider->setValue(slice);
3167     else {
3168       if (slicer == 2)
3169         SOVerticalSlider->setValue(slice);
3170       else {
3171         if (slicer == 3)
3172           SEVerticalSlider->setValue(slice);
3173       }
3174     }
3175   }
3176   // DD("vvMainWindow:UpdateSlice END");
3177 }
3178 //------------------------------------------------------------------------------
3179
3180
3181 //------------------------------------------------------------------------------
3182 void vvMainWindow::UpdateTSlice(int slicer, int slice, int code)
3183 {
3184   //FusionSequence: the slider value should be updated for slicers which show the same sequence as requested
3185   bool doUpdate=false;
3186   if (code==-1) doUpdate=true;
3187   else {
3188     for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
3189       if (DataTree->topLevelItem(i)->data(slicer+1,Qt::CheckStateRole).toInt() > 1) {
3190         //i is the active SlicerManager
3191         if (mSlicerManagers[i]->GetFusionSequenceInvolvmentCode()==code) doUpdate=true;
3192         break;
3193       }
3194     }
3195   }
3196   if (!doUpdate) return;
3197
3198   switch (slicer) {
3199   case 0:
3200     if (NOHorizontalSlider->value()==slice) return;
3201     NOHorizontalSlider->setValue(slice);
3202     break;
3203   case 1:
3204     if (NEHorizontalSlider->value()==slice) return;
3205     NEHorizontalSlider->setValue(slice);
3206     break;
3207   case 2:
3208     if (SOHorizontalSlider->value()==slice) return;
3209     SOHorizontalSlider->setValue(slice);
3210     break;
3211   case 3:
3212     if (SEHorizontalSlider->value()==slice) return;
3213     SEHorizontalSlider->setValue(slice);
3214     break;
3215   }
3216 }
3217 //------------------------------------------------------------------------------
3218
3219
3220 //------------------------------------------------------------------------------
3221 void vvMainWindow::UpdateSliceRange(int slicer, int min, int max, int tmin, int tmax)
3222 {
3223   //int position = int((min+max)/2);
3224   int position = mSlicerManagers[mCurrentPickedImageIndex]->GetSlicer(slicer)->GetSlice();
3225   if (slicer == 0) {
3226     NOVerticalSlider->setRange(min,max);
3227     NOHorizontalSlider->setRange(tmin,tmax);
3228     NOVerticalSlider->setValue(position);
3229   } else if (slicer == 1) {
3230     NEVerticalSlider->setRange(min,max);
3231     NEHorizontalSlider->setRange(tmin,tmax);
3232     NEVerticalSlider->setValue(position);
3233   } else if (slicer == 2) {
3234     SOVerticalSlider->setRange(min,max);
3235     SOHorizontalSlider->setRange(tmin,tmax);
3236     SOVerticalSlider->setValue(position);
3237   } else if (slicer == 3) {
3238     SEVerticalSlider->setRange(min,max);
3239     SEHorizontalSlider->setRange(tmin,tmax);
3240     SEVerticalSlider->setValue(position);
3241   }
3242 }
3243 //------------------------------------------------------------------------------
3244
3245
3246 //------------------------------------------------------------------------------
3247 void vvMainWindow::SaveNOScreenshot()
3248 {
3249   SaveScreenshot(NOViewWidget);
3250 }
3251 //------------------------------------------------------------------------------
3252
3253
3254 //------------------------------------------------------------------------------
3255 void vvMainWindow::SaveNEScreenshot()
3256 {
3257   SaveScreenshot(NEViewWidget);
3258 }
3259 //------------------------------------------------------------------------------
3260
3261
3262 //------------------------------------------------------------------------------
3263 void vvMainWindow::SaveSOScreenshot()
3264 {
3265   SaveScreenshot(SOViewWidget);
3266 }
3267 //------------------------------------------------------------------------------
3268
3269
3270 //------------------------------------------------------------------------------
3271 void vvMainWindow::SaveSEScreenshot()
3272 {
3273   SaveScreenshot(SEViewWidget);
3274 }
3275 //------------------------------------------------------------------------------
3276
3277
3278 //------------------------------------------------------------------------------
3279 void vvMainWindow::SaveScreenshotAllSlices()
3280 {
3281   QVTKWidget *widget = NOViewWidget;
3282
3283   int index = 0;// GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
3284   vvSlicerManager * SM = mSlicerManagers[index];
3285   vvImage * image = SM->GetImage();
3286   vvSlicer * slicer = SM->GetSlicer(0);
3287   int orientation = slicer->GetOrientation();
3288   int nbSlices = image->GetSize()[orientation];
3289   vtkSmartPointer<vtkRenderWindow>  renderWindow = widget->GetRenderWindow();
3290
3291   // Select filename base
3292   QString filename = QFileDialog::getSaveFileName(this,
3293     tr("Save As (filename will be completed by slice number)"),
3294     itksys::SystemTools::GetFilenamePath(mSlicerManagers[index]->GetFileName()).c_str(),
3295     "Images( *.png);;Images( *.jpg)");
3296
3297   // Loop on slices
3298   for(int i=0; i<nbSlices; i++) {
3299     // Change the slice
3300     slicer->SetSlice(i); // -> change the slice of the current slicer
3301     SM->UpdateSlice(0); // --> this one emit UpdateSlice
3302     QCoreApplication::flush(); // -> needed to force display of contours
3303
3304     // Screenshot
3305     vtkSmartPointer<vtkWindowToImageFilter> windowToImageFilter = vtkSmartPointer<vtkWindowToImageFilter>::New();
3306     windowToImageFilter->SetInput(renderWindow);
3307 #if (VTK_MAJOR_VERSION >= 8 && VTK_MINOR_VERSION >= 1) || VTK_MAJOR_VERSION >= 9
3308     windowToImageFilter->SetScale(1);
3309 #else
3310     windowToImageFilter->SetMagnification(1);
3311 #endif
3312     windowToImageFilter->SetInputBufferTypeToRGBA(); //also record the alpha (transparency) channel
3313     windowToImageFilter->Update();
3314
3315     vtkSmartPointer<vtkPNGWriter> writer = vtkSmartPointer<vtkPNGWriter>::New();
3316     std::string fn = itksys::SystemTools::GetFilenameWithoutLastExtension(filename.toStdString());
3317     std::string num = clitk::toString(i);
3318     if (i<10) num = "0"+num;
3319     if (i<100) num = "0"+num;
3320     if (i<1000) num = "0"+num;
3321
3322     fn = itksys::SystemTools::GetFilenamePath(filename.toStdString()) + "/"+ fn
3323       + "_" + num + itksys::SystemTools::GetFilenameLastExtension(filename.toStdString());
3324     writer->SetFileName(fn.c_str());
3325 #if VTK_MAJOR_VERSION <= 5
3326     writer->SetInput(windowToImageFilter->GetOutput());
3327 #else
3328     writer->SetInputConnection(windowToImageFilter->GetOutputPort());
3329 #endif
3330     writer->Write();
3331   }
3332 }
3333 //------------------------------------------------------------------------------
3334
3335
3336 //------------------------------------------------------------------------------
3337 void vvMainWindow::SaveScreenshot(QVTKWidget *widget)
3338 {
3339   QString Extensions = "Images( *.png);;";
3340   Extensions += "Images( *.jpg);;";
3341   Extensions += "Images( *.bmp);;";
3342   Extensions += "Images( *.tif);;";
3343   Extensions += "Images( *.ppm)";
3344 #if defined(VTK_USE_FFMPEG_ENCODER) || defined(VTK_USE_VIDEO_FOR_WINDOWS)
3345   Extensions += ";;Video( *.avi)";
3346 #endif
3347 #ifdef VTK_USE_MPEG2_ENCODER
3348   Extensions += ";;Video( *.mpg)";
3349 #endif
3350   Extensions += ";;Video( *.gif)";
3351
3352   int smIndex=GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
3353   QString fileName = QFileDialog::getSaveFileName(this,
3354     tr("Save As"),
3355     itksys::SystemTools::GetFilenamePath(mSlicerManagers[smIndex]->GetFileName()).c_str(),
3356     Extensions);
3357
3358   if (!fileName.isEmpty()) {
3359     vtkSmartPointer<vtkWindowToImageFilter> w2i = vtkSmartPointer<vtkWindowToImageFilter>::New();
3360     w2i->SetInput(widget->GetRenderWindow());
3361 #if (VTK_MAJOR_VERSION >= 8 && VTK_MINOR_VERSION >= 1) || VTK_MAJOR_VERSION >= 9
3362     w2i->SetScale(1);
3363 #else
3364     w2i->SetMagnification(1);
3365 #endif
3366     w2i->SetInputBufferTypeToRGBA(); //also record the alpha (transparency) channel
3367     w2i->Update();
3368     vtkImageData *image = w2i->GetOutput();
3369
3370     std::string ext(itksys::SystemTools::GetFilenameLastExtension(fileName.toStdString()));
3371
3372     // Image
3373     vtkImageWriter *imgwriter = NULL;
3374     if (ext==".bmp")
3375       imgwriter = vtkBMPWriter::New();
3376     else if (ext==".tif")
3377       imgwriter = vtkTIFFWriter::New();
3378     else if (ext==".ppm")
3379       imgwriter = vtkPNMWriter::New();
3380     else if (ext==".png")
3381       imgwriter = vtkPNGWriter::New();
3382     else if (ext==".jpg")
3383       imgwriter = vtkJPEGWriter::New();
3384
3385     // Snapshot image if not null
3386     if(imgwriter!=NULL) {
3387 #if VTK_MAJOR_VERSION <= 5
3388       imgwriter->SetInput(image);
3389 #else
3390       imgwriter->SetInputConnection(w2i->GetOutputPort());
3391 #endif
3392       imgwriter->SetFileName(fileName.toStdString().c_str());
3393       imgwriter->Write();
3394       return;
3395     }
3396
3397     // Video
3398     vtkGenericMovieWriter *vidwriter = NULL;
3399     if (ext==".gif") {
3400       vvAnimatedGIFWriter *gif = vvAnimatedGIFWriter::New();
3401       vidwriter = gif;
3402
3403       // FPS
3404       bool ok;
3405       int fps = QInputDialog::getInt(this, tr("Number of frames per second"),
3406         tr("FPS:"), 5, 0, 1000, 1, &ok);
3407       if(ok)
3408         gif->SetRate(fps);
3409
3410       // Loops
3411       int loops = QInputDialog::getInt(this, tr("Loops"),
3412         tr("Number of loops (0 means infinite):"), 0, 0, 1000000000, 1, &ok);
3413       if(ok)
3414         gif->SetLoops(loops);
3415
3416       // Dithering
3417       QString msg = "Would you like to activate dithering?";
3418       QMessageBox msgBox(QMessageBox::Question, tr("Dithering"),msg, 0, this);
3419       msgBox.addButton(tr("Yes"), QMessageBox::AcceptRole);
3420       msgBox.addButton(tr("No"), QMessageBox::RejectRole);
3421       gif->SetDither(msgBox.exec() == QMessageBox::AcceptRole);
3422     }
3423 #ifdef VTK_USE_VIDEO_FOR_WINDOWS
3424     if (ext==".avi") {
3425       vtkAVIWriter *mpg = vtkAVIWriter::New();
3426       vidwriter = mpg;
3427       mpg->SetQuality(2);
3428       bool ok;
3429       int fps = QInputDialog::getInt(this, tr("Number of frames per second"),
3430         tr("FPS:"), 5, 0, 1024, 1, &ok);
3431       if(!ok)
3432         fps = 5;
3433       mpg->SetRate(fps);
3434     }
3435 #endif
3436 #ifdef VTK_USE_FFMPEG_ENCODER
3437     if (ext==".avi") {
3438       vtkFFMPEGWriter *mpg = vtkFFMPEGWriter::New();
3439       vidwriter = mpg;
3440       mpg->SetQuality(2);
3441       bool ok;
3442       int fps = QInputDialog::getInt(this, tr("Number of frames per second"),
3443         tr("FPS:"), 5, 0, 1024, 1, &ok);
3444       if(!ok)
3445         fps = 5;
3446       mpg->SetRate(fps);
3447       mpg->SetBitRateTolerance(int(ceil(12.0*1024*1024/fps)));
3448     }
3449 #endif
3450 #ifdef VTK_USE_MPEG2_ENCODER
3451     if (ext==".mpg") {
3452       vtkMPEG2Writer *mpg = vtkMPEG2Writer::New();
3453       vidwriter = mpg;
3454     }
3455 #endif
3456
3457     // Take video if not null
3458     if(vidwriter!=NULL){
3459 #if VTK_MAJOR_VERSION <= 5
3460       vidwriter->SetInput(image);
3461 #else
3462       vidwriter->SetInputConnection(w2i->GetOutputPort());
3463 #endif
3464       vidwriter->SetFileName(fileName.toStdString().c_str());
3465       vidwriter->Start();
3466       int nSlice = mSlicerManagers[smIndex]->GetSlicer(0)->GetTMax();
3467       for(int i=0; i<=nSlice; i++) {
3468         mSlicerManagers[smIndex]->SetNextTSlice(0);
3469         vtkSmartPointer<vtkWindowToImageFilter> w2i = vtkSmartPointer<vtkWindowToImageFilter>::New();
3470         w2i->SetInput(widget->GetRenderWindow());
3471         w2i->Update();
3472 #if VTK_MAJOR_VERSION <= 5
3473         vidwriter->SetInput(w2i->GetOutput());
3474 #else
3475         vidwriter->SetInputConnection(w2i->GetOutputPort());
3476 #endif
3477         vidwriter->Write();
3478       }
3479       vidwriter->End();
3480       vidwriter->Delete();
3481       return;
3482     }
3483
3484     QMessageBox::information(this,tr("Problem saving screenshot !"),tr("Cannot save image.\nPlease set a file extension !!!"));
3485   }
3486 }
3487 //------------------------------------------------------------------------------
3488
3489
3490 //------------------------------------------------------------------------------
3491 void vvMainWindow::GoToCursor()
3492 {
3493   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
3494   for (int column = 1; column < 5; column++) {
3495     if (DataTree->selectedItems()[0]->data(column,Qt::CheckStateRole).toInt() > 1) {
3496       double* cursorPos = mSlicerManagers[index]->GetSlicer(column-1)->GetCursorPosition();
3497       mSlicerManagers[index]->GetSlicer(column-1)->SetCurrentPosition(
3498         cursorPos[0],cursorPos[1],cursorPos[2],cursorPos[3]);
3499       mSlicerManagers[index]->UpdateViews(1,column-1);
3500       mSlicerManagers[index]->UpdateLinked(column-1);
3501       break;
3502     }
3503   }
3504 }
3505 //------------------------------------------------------------------------------
3506
3507 //------------------------------------------------------------------------------
3508 void vvMainWindow::GoToLandmark()
3509 {
3510   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
3511   for (int column = 1; column < 5; column++) {
3512     if (DataTree->selectedItems()[0]->data(column,Qt::CheckStateRole).toInt() > 1) {
3513       double* cursorPos = landmarksPanel->GetSelectedPoint();
3514       mSlicerManagers[index]->GetSlicer(column-1)->SetCurrentPosition(
3515         cursorPos[0],cursorPos[1],cursorPos[2],cursorPos[3]);
3516       mSlicerManagers[index]->UpdateViews(1,column-1);
3517       mSlicerManagers[index]->UpdateLinked(column-1);
3518       break;
3519     }
3520   }
3521 }
3522 //------------------------------------------------------------------------------
3523
3524 //------------------------------------------------------------------------------
3525 void vvMainWindow::PlayPause()
3526 {
3527   if (playMode) {
3528     playMode = 0;
3529     playButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/player_play.png")));
3530     ImageInfoChanged();
3531     return;
3532   } else {
3533     int image_number=DataTree->topLevelItemCount();
3534     bool has_temporal;
3535     for (int i=0; i<image_number; i++)
3536       if (mSlicerManagers[i]->GetSlicer(0)->GetTMax() > 0) {
3537         has_temporal=true;
3538         break;
3539       }
3540       if (has_temporal) {
3541         playMode = 1;
3542         playButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/player_pause.png")));
3543         QTimer::singleShot(1000/mFrameRate, this, SLOT(PlayNext()));
3544       }
3545   }
3546 }
3547 //------------------------------------------------------------------------------
3548
3549 //------------------------------------------------------------------------------
3550 void vvMainWindow::PlayNext()
3551 {
3552   if (playMode && !this->isHidden()) {
3553     int image_number=DataTree->topLevelItemCount();
3554     ///Only play one slicer per SM, and only if the SM is being displayed
3555     for (int i=0; i<image_number; i++)
3556       for (int j=0; j<4; j++)
3557         if (mSlicerManagers[i]->GetSlicer(0)->GetTMax() > 0 &&
3558           DataTree->topLevelItem(i)->data(j+1,Qt::CheckStateRole).toInt() > 0) {
3559             mSlicerManagers[i]->SetNextTSlice(j);
3560             break;
3561         }
3562         QTimer::singleShot(1000/mFrameRate, this, SLOT(PlayNext()));
3563   }
3564 }
3565 //------------------------------------------------------------------------------
3566
3567 void vvMainWindow::ShowLastImage()
3568 {
3569   if (mSlicerManagers.size() > 1) {
3570     QTreeWidgetItem * item=DataTree->topLevelItem(DataTree->topLevelItemCount()-1);
3571     CurrentImageChanged(mSlicerManagers.back()->GetId()); //select new image
3572     item->setData(1,Qt::CheckStateRole,2); //show the new image in the first panel
3573     //mSlicerManagers[GetSlicerIndexFromItem(item)]->GetSlicer(0)->SetActorVisibility("image", 0, 1); //Set the Last Image visibles
3574     DisplayChanged(item,1);
3575   }
3576 }
3577
3578 //------------------------------------------------------------------------------
3579 void vvMainWindow::UpdateRenderWindows()
3580 {
3581   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
3582       for (unsigned int j = 0; j < 4; ++j) {
3583         mSlicerManagers[i]->GetSlicer(j)->RemoveLandmarks();
3584         mSlicerManagers[i]->GetSlicer(j)->DisplayLandmarks();
3585       }
3586   }
3587   if (NOViewWidget->GetRenderWindow()) NOViewWidget->GetRenderWindow()->Render();
3588   if (NEViewWidget->GetRenderWindow()) NEViewWidget->GetRenderWindow()->Render();
3589   if (SOViewWidget->GetRenderWindow()) SOViewWidget->GetRenderWindow()->Render();
3590   if (SEViewWidget->GetRenderWindow()) SEViewWidget->GetRenderWindow()->Render();
3591 }
3592 //------------------------------------------------------------------------------
3593
3594 //------------------------------------------------------------------------------
3595 void vvMainWindow::SegmentationOnCurrentImage()
3596 {
3597   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
3598
3599   vvSegmentationDialog segmentation;
3600   segmentation.SetImage(mSlicerManagers[index]->GetSlicer(0)->GetImage());
3601   segmentation.exec();
3602 }
3603 //------------------------------------------------------------------------------
3604
3605 void vvMainWindow::SurfaceViewerLaunch()
3606 {
3607   vvSurfaceViewerDialog surfaceViewer;
3608   surfaceViewer.exec();
3609 }
3610 //------------------------------------------------------------------------------
3611
3612
3613 //------------------------------------------------------------------------------
3614 int vvMainWindow::GetImageDuplicateFilenameNumber(std::string filename)
3615 {
3616   int number=0;
3617   for(unsigned int l=0; l<mSlicerManagers.size(); l++) {
3618     vvSlicerManager * v = mSlicerManagers[l];
3619     if (v->GetBaseFileName() ==
3620       vtksys::SystemTools::GetFilenameName(vtksys::SystemTools::GetFilenameWithoutLastExtension(filename))) {
3621         number = std::max(number, v->GetBaseFileNameNumber()+1);
3622     }
3623   }
3624   return number;
3625 }
3626 //------------------------------------------------------------------------------
3627
3628
3629 //------------------------------------------------------------------------------
3630 vvSlicerManager* vvMainWindow::AddImage(vvImage::Pointer image,std::string filename)
3631 {
3632   // Change filename if another image exist with the same name
3633   int number = GetImageDuplicateFilenameNumber(filename);
3634
3635   // Create new SliceManager
3636   vvSlicerManager* slicer_manager = new vvSlicerManager(4);
3637   slicer_manager->SetImage(image);//, IMAGE, number);
3638   //  filename = filename+"_"+clitk::toString(number);
3639   slicer_manager->SetFilename(filename, number);
3640   mSlicerManagers.push_back(slicer_manager);
3641
3642   //create an item in the tree with good settings
3643   QTreeWidgetItem *item = new QTreeWidgetItem();
3644   item->setData(0,Qt::UserRole,slicer_manager->GetFileName().c_str());//files[i].c_str());
3645   item->setData(1,Qt::UserRole,tr("image"));
3646   item->setData(COLUMN_IMAGE_NAME,Qt::DisplayRole,slicer_manager->GetFileName().c_str());//filename.c_str());
3647   qApp->processEvents();
3648
3649   for (int j = 1; j <= 4; j++) item->setData(j,Qt::CheckStateRole,1);
3650
3651   //Create the buttons for reload and close
3652   qApp->processEvents();
3653   QTreePushButton* cButton = new QTreePushButton;
3654   cButton->setItem(item);
3655   cButton->setColumn(COLUMN_CLOSE_IMAGE);
3656   cButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/exit.png")));
3657   connect(cButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
3658     this,SLOT(CloseImage(QTreeWidgetItem*, int)));
3659
3660   QTreePushButton* rButton = new QTreePushButton;
3661   rButton->setItem(item);
3662   rButton->setColumn(COLUMN_RELOAD_IMAGE);
3663   rButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/rotateright.png")));
3664   rButton->setEnabled(0);
3665   connect(rButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
3666     this,SLOT(ReloadImage(QTreeWidgetItem*, int)));
3667
3668   DataTree->addTopLevelItem(item);
3669   DataTree->setItemWidget(item, COLUMN_CLOSE_IMAGE, cButton);
3670   DataTree->setItemWidget(item, COLUMN_RELOAD_IMAGE, rButton);
3671
3672   //set the id of the image
3673   QString id = QDir::current().absoluteFilePath(slicer_manager->GetFileName().c_str()) + QString::number(mSlicerManagers.size()-1);
3674   item->setData(COLUMN_IMAGE_NAME,Qt::UserRole,id.toStdString().c_str());
3675   mSlicerManagers.back()->SetId(id.toStdString());
3676
3677   linkPanel->addImage(slicer_manager->GetFileName().c_str()// filename
3678     , id.toStdString());
3679
3680   connect(mSlicerManagers.back(), SIGNAL(currentImageChanged(std::string)),
3681     this, SLOT(CurrentImageChanged(std::string)));
3682   connect(mSlicerManagers.back(), SIGNAL(currentPickedImageChanged(std::string)),
3683     this, SLOT(CurrentPickedImageChanged(std::string)));
3684   connect(mSlicerManagers.back(), SIGNAL(UpdatePosition(int, double, double, double, double, double, double, double)),
3685     this, SLOT(MousePositionChanged(int,double, double, double, double, double, double, double)));
3686   connect(mSlicerManagers.back(), SIGNAL(UpdateVector(int, double, double, double, double)),
3687     this, SLOT(VectorChanged(int,double,double,double, double)));
3688   connect(mSlicerManagers.back(), SIGNAL(UpdateOverlay(int, double, double)),
3689     this, SLOT(OverlayChanged(int,double,double)));
3690   connect(mSlicerManagers.back(), SIGNAL(UpdateFusion(int, double)),
3691     this, SLOT(FusionChanged(int,double)));
3692   //connect(mSlicerManagers.back(), SIGNAL(UpdateFusionSequence(int, bool, unsigned int)),
3693   //  this, SLOT(FusionSequenceChanged(int, bool, unsigned int)));
3694   connect(mSlicerManagers.back(), SIGNAL(WindowLevelChanged()),
3695     this,SLOT(WindowLevelChanged()));
3696   connect(mSlicerManagers.back(), SIGNAL(UpdateSlice(int,int)),
3697     this,SLOT(UpdateSlice(int,int)));
3698   connect(mSlicerManagers.back(), SIGNAL(UpdateTSlice(int, int, int)),
3699     this,SLOT(UpdateTSlice(int, int, int)));
3700   connect(mSlicerManagers.back(), SIGNAL(UpdateTSlice(int, int, int)),
3701     this,SLOT(ImageInfoChanged()));
3702   connect(mSlicerManagers.back(), SIGNAL(UpdateSliceRange(int,int,int,int,int)),
3703     this,SLOT(UpdateSliceRange(int,int,int,int,int)));
3704   connect(mSlicerManagers.back(), SIGNAL(UpdateLinkManager(std::string,int,double,double,double,int)),
3705     this,SLOT(UpdateLinkManager(std::string,int,double,double,double,int)));
3706   connect(mSlicerManagers.back(), SIGNAL(UpdateLinkedNavigation(std::string,vvSlicerManager*,vvSlicer*)),
3707     this,SLOT(UpdateLinkedNavigation(std::string,vvSlicerManager*,vvSlicer*)));
3708   connect(mSlicerManagers.back(), SIGNAL(ChangeImageWithIndexOffset(vvSlicerManager*,int,int)),
3709     this,SLOT(ChangeImageWithIndexOffset(vvSlicerManager*,int,int)));
3710   connect(mSlicerManagers.back(), SIGNAL(LandmarkAdded()),landmarksPanel,SLOT(AddPoint()));
3711   connect(landmarksPanel,SIGNAL(UpdateLandmarkTransform()), mSlicerManagers.back(), SLOT(UpdateLandmark()));
3712
3713
3714
3715   InitSlicers();
3716   UpdateTree();
3717   qApp->processEvents();
3718   InitDisplay();
3719   ShowLastImage();
3720   qApp->processEvents();
3721   // End
3722   ImageInfoChanged();
3723   return slicer_manager;
3724 }
3725 //------------------------------------------------------------------------------
3726
3727
3728 //------------------------------------------------------------------------------
3729 void vvMainWindow::UpdateCurrentSlicer()
3730 {
3731   int index = -1;
3732   if (DataTree->selectedItems().size() > 0) {
3733     index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
3734   }
3735   mSlicerManagerCurrentIndex = index;
3736 }
3737 //------------------------------------------------------------------------------