vv/vvMainWindow.cxx

   1 /*=========================================================================
   2 Program:   vv                     http://www.creatis.insa-lyon.fr/rio/vv
   3
   4 Authors belong to:
   5 - University of LYON              http://www.universite-lyon.fr/
   6 - Léon Bérard cancer center       http://www.centreleonberard.fr
   7 - CREATIS CNRS laboratory         http://www.creatis.insa-lyon.fr
   8
   9 This software is distributed WITHOUT ANY WARRANTY; without even
  10 the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
  11 PURPOSE.  See the copyright notices for more information.
  12
  13 It is distributed under dual licence
  14
  15 - BSD        See included LICENSE.txt file
  16 - CeCILL-B   http://www.cecill.info/licences/Licence_CeCILL-B_V1-en.html
  17 ===========================================================================**/
  18
  19 #include <algorithm>
  20 #include <QMessageBox>
  21 #include <QInputDialog>
  22 #include <QTimer>
  23 #include "QTreePushButton.h"
  24 #include <QUrl>
  25 #include <QSettings>
  26 #include <QShortcut>
  27
  28 // VV include
  29 #include "vvMainWindow.h"
  30 #include "vvHelpDialog.h"
  31 #include "vvRegisterForm.h"
  32 #include "vvDocumentation.h"
  33 #include "vvProgressDialog.h"
  34 #include "vvQDicomSeriesSelector.h"
  35 #include "vvSlicerManager.h"
  36 #include "clitkImageCommon.h"
  37 #include "vvSlicer.h"
  38 #include "vvInteractorStyleNavigator.h"
  39 #include "vvImageWriter.h"
  40 #include "vvSegmentationDialog.h"
  41 #include "vvSurfaceViewerDialog.h"
  42 #include "vvDeformationDialog.h"
  43 #include "vvImageWarp.h"
  44 #include "vvUtils.h"
  45 #include "vvMidPosition.h"
  46 #include "vvMesh.h"
  47 #include "vvStructSelector.h"
  48 #include "vvMeshReader.h"
  49 #include "vvSaveState.h"
  50 #include "vvReadState.h"
  51 #include "clitkConfiguration.h"
  52 #include "clitkMatrix.h"
  53 #ifdef Q_OS_OSX
  54 # include "vvOSXHelper.h"
  55 #endif
  56
  57 // ITK include
  58 #include <itkImage.h>
  59 #include <itkImageFileReader.h>
  60 #include <itkByteSwapper.h>
  61 #include <itkCommand.h>
  62 #include <itkNumericSeriesFileNames.h>
  63
  64 // VTK include
  65 #include <vtkImageMapper3D.h>
  66 #include <vtkInformation.h>
  67 #include <vtkVersion.h>
  68 #include <vtkImageData.h>
  69 #include <vtkImageActor.h>
  70 #include <vtkCornerAnnotation.h>
  71 #include <vtkRenderWindow.h>
  72 #include <vtkRenderWindowInteractor.h>
  73 #include <vtkRenderer.h>
  74 #include <vtkRendererCollection.h>
  75 #include <vtkWindowToImageFilter.h>
  76 #include <vtkBMPWriter.h>
  77 #include <vtkTIFFWriter.h>
  78 #include <vtkPNMWriter.h>
  79 #include <vtkPNGWriter.h>
  80 #include <vtkJPEGWriter.h>
  81 #include <vtkGenericMovieWriter.h>
  82 #ifdef CLITK_EXPERIMENTAL
  83 #  include <vvAnimatedGIFWriter.h>
  84 #endif
  85 #ifdef VTK_USE_VIDEO_FOR_WINDOWS
  86 #  include <vtkAVIWriter.h>
  87 #endif
  88 #ifdef VTK_USE_FFMPEG_ENCODER
  89 #  include <vtkFFMPEGWriter.h>
  90 #endif
  91 #ifdef VTK_USE_MPEG2_ENCODER
  92 #  include <vtkMPEG2Writer.h>
  93 #endif
  94 #include <vtkMatrix4x4.h>
  95 #include <vtkTransform.h>
  96
  97 // Standard includes
  98 #include <iostream>
  99 #include <fstream>
 100 #include <sstream>
 101 #include <iomanip>
 102
 103 #define COLUMN_TREE 0
 104 #define COLUMN_UL_VIEW 1
 105 #define COLUMN_UR_VIEW 2
 106 #define COLUMN_DL_VIEW 3
 107 #define COLUMN_DR_VIEW 4
 108 #define COLUMN_CLOSE_IMAGE 5
 109 #define COLUMN_RELOAD_IMAGE 6
 110 #define COLUMN_IMAGE_NAME 7
 111
 112 #ifdef CLITK_PRIVATE_FEATURES
 113 #define EXTENSIONS "Images ( *.bmp *.dcm *.png *.jpeg *.jpg *.tif *.mhd *.mha *.hdr *.vox *.his *.xdr *.SCAN *.nii *.nrrd *.nhdr *.refscan *.nii.gz *.usf *.svl)"
 114 #else
 115 #define EXTENSIONS "Images ( *.bmp *.dcm *.png *.jpeg *.jpg *.tif *.mhd *.mha *.hdr *.vox *.his *.xdr *.SCAN *.nii *.nrrd *.nhdr *.refscan *.nii.gz)"
 116 #endif
 117
 118
 119 /*Data Tree values
 120 0,Qt::UserRole full filename
 121 1,Qt::CheckStateRole checkbutton UL View
 122 1,Qt::UserRole overlay, fusion or vector
 123 2,Qt::CheckStateRole checkbutton UR View
 124 3,Qt::CheckStateRole checkbutton DL View
 125 4,Qt::CheckStateRole checkbutton DR View
 126 5,0  short filename
 127 5,Qt::UserRole mSlicerManager id*/
 128
 129 //------------------------------------------------------------------------------
 130 vvMainWindow::vvMainWindow():vvMainWindowBase()
 131 {
 132   setupUi(this); // this sets up the GUI
 133
 134   //Qt::WindowFlags flags = windowFlags();
 135   //setWindowFlags(flags | Qt::WindowStaysOnTopHint);
 136
 137   mInputPathName = "";
 138   mMenuTools = menuTools;
 139   //  mMenuSegmentation = menuSegmentation;
 140   mContextMenu = &contextMenu;
 141   mMenuExperimentalTools = menuExperimental;
 142   mMainWidget = this;
 143   mCurrentTime = -1;
 144   mCurrentSelectedImageId = "";
 145   mCurrentPickedImageId = "";
 146   mCurrentPickedImageIndex = 0;
 147
 148   //Init the contextMenu
 149   this->setContextMenuPolicy(Qt::CustomContextMenu);
 150   contextActions.resize(0);
 151   QAction* actionOpen_new_image = contextMenu.addAction(QIcon(QString::fromUtf8(":/common/icons/fileopen.png")),
 152     tr("O&pen new Image"));
 153   connect(actionOpen_new_image,SIGNAL(triggered()),this,SLOT(OpenImages()));
 154   contextActions.push_back(actionOpen_new_image);
 155   contextMenu.addSeparator();
 156
 157   QAction* actionClose_Image = contextMenu.addAction(QIcon(QString::fromUtf8(":/common/icons/exit.png")),
 158     tr("Close Current Image"));
 159   connect(actionClose_Image,SIGNAL(triggered()),this,SLOT(CloseImage()));
 160   contextActions.push_back(actionClose_Image);
 161
 162   QAction* actionReload_image = contextMenu.addAction(QIcon(QString::fromUtf8(":/common/icons/rotateright.png")),
 163     tr("Reload Current Image"));
 164   connect(actionReload_image,SIGNAL(triggered()),this,SLOT(ReloadImage()));
 165   contextActions.push_back(actionReload_image);
 166
 167   QAction* actionSave_image = contextMenu.addAction(QIcon(QString::fromUtf8(":/common/icons/filesave.png")),
 168     tr("Save Current Image"));
 169   connect(actionSave_image,SIGNAL(triggered()),this,SLOT(SaveAs()));
 170   contextActions.push_back(actionSave_image);
 171
 172   QAction* actionSave_state = contextMenu.addAction(QIcon(QString::fromUtf8(":/common/icons/filesave.png")),
 173     tr("Save Current State"));
 174   connect(actionSave_state,SIGNAL(triggered()),this,SLOT(SaveCurrentState()));
 175   contextActions.push_back(actionSave_state);
 176
 177   QAction* actionRead_state = contextMenu.addAction(QIcon(QString::fromUtf8(":/common/icons/filesave.png")),
 178     tr("Read Saved State"));
 179   connect(actionRead_state,SIGNAL(triggered()),this,SLOT(ReadSavedState()));
 180   contextActions.push_back(actionRead_state);
 181
 182   contextMenu.addSeparator();
 183
 184   contextMenu.addAction(actionAdd_VF_to_current_Image);
 185   contextActions.push_back(actionAdd_VF_to_current_Image);
 186
 187   //QAction* actionAdd_Overlay_to_current_Image = menuOverlay->addAction(QIcon(QString::fromUtf8(":/common/icons/GPSup.png")),
 188   //    tr("Add overlay image to current image"));
 189   contextMenu.addAction(actionAdd_overlay_image_to_current_image);
 190   contextActions.push_back(actionAdd_overlay_image_to_current_image);
 191
 192   contextMenu.addAction(actionAdd_fusion_image);
 193   contextActions.push_back(actionAdd_fusion_image);
 194
 195 #ifdef CLITK_EXPERIMENTAL
 196   contextMenu.addAction(actionAdd_USSequence_toCT);
 197   contextActions.push_back(actionAdd_USSequence_toCT);
 198 #endif
 199
 200
 201   contextMenu.addSeparator();
 202   QAction* actionResetMatrix = contextMenu.addAction(QIcon(QString::fromUtf8(":/common/icons/identity.png")),
 203     tr("Reset transformation to identity"));
 204   connect(actionResetMatrix, SIGNAL(triggered()), this,SLOT(ResetTransformationToIdentity()));
 205
 206   //init the DataTree
 207   mSlicerManagers.resize(0);
 208
 209   QStringList header;
 210   header.append("");
 211   header.append("TL");
 212   header.append("TR");
 213   header.append("BL");
 214   header.append("BR");
 215   header.append("");
 216   header.append("");
 217   header.append("Name");
 218
 219   DataTree->setHeaderLabels(header);
 220   DataTree->resizeColumnToContents(COLUMN_TREE);
 221   DataTree->resizeColumnToContents(COLUMN_UL_VIEW);
 222   DataTree->resizeColumnToContents(COLUMN_UR_VIEW);
 223   DataTree->resizeColumnToContents(COLUMN_DL_VIEW);
 224   DataTree->resizeColumnToContents(COLUMN_DR_VIEW);
 225   DataTree->resizeColumnToContents(COLUMN_CLOSE_IMAGE);
 226   DataTree->resizeColumnToContents(COLUMN_RELOAD_IMAGE);
 227   DataTree->resizeColumnToContents(COLUMN_IMAGE_NAME);
 228
 229   viewMode = 1;
 230   documentation = new vvDocumentation();
 231   help_dialog = new vvHelpDialog();
 232   dicomSeriesSelector = new vvDicomSeriesSelector();
 233
 234   inverseButton->setEnabled(0);
 235   actionAdd_overlay_image_to_current_image->setEnabled(0);
 236   actionSave_As->setEnabled(0);
 237   actionAdd_VF_to_current_Image->setEnabled(0);
 238   actionAdd_fusion_image->setEnabled(0);
 239   actionAdd_USSequence_toCT->setEnabled(0);
 240
 241   //init the sliders
 242   verticalSliders.push_back(NOVerticalSlider);
 243   verticalSliders.push_back(NEVerticalSlider);
 244   verticalSliders.push_back(SOVerticalSlider);
 245   verticalSliders.push_back(SEVerticalSlider);
 246
 247   for (int i =0; i < 4; i++)
 248     verticalSliders[i]->hide();
 249
 250   horizontalSliders.push_back(NOHorizontalSlider);
 251   horizontalSliders.push_back(NEHorizontalSlider);
 252   horizontalSliders.push_back(SOHorizontalSlider);
 253   horizontalSliders.push_back(SEHorizontalSlider);
 254
 255   for (int i =0; i < 4; i++)
 256     horizontalSliders[i]->hide();
 257
 258
 259   connect(NOVerticalSlider,SIGNAL(valueChanged(int)),this,SLOT(NOVerticalSliderChanged()));
 260   connect(NEVerticalSlider,SIGNAL(valueChanged(int)),this,SLOT(NEVerticalSliderChanged()));
 261   connect(SOVerticalSlider,SIGNAL(valueChanged(int)),this,SLOT(SOVerticalSliderChanged()));
 262   connect(SEVerticalSlider,SIGNAL(valueChanged(int)),this,SLOT(SEVerticalSliderChanged()));
 263
 264   connect(NOHorizontalSlider,SIGNAL(valueChanged(int)),this,SLOT(NOHorizontalSliderMoved()));
 265   connect(NEHorizontalSlider,SIGNAL(valueChanged(int)),this,SLOT(NEHorizontalSliderMoved()));
 266   connect(SOHorizontalSlider,SIGNAL(valueChanged(int)),this,SLOT(SOHorizontalSliderMoved()));
 267   connect(SEHorizontalSlider,SIGNAL(valueChanged(int)),this,SLOT(SEHorizontalSliderMoved()));
 268
 269   //connect everything
 270   connect(actionCompute_mid_position_image,SIGNAL(triggered()),this,SLOT(ComputeMidPosition()));
 271   connect(actionDeformable_Registration,SIGNAL(triggered()),this,SLOT(ComputeDeformableRegistration()));
 272   connect(actionWarp_image_with_vector_field,SIGNAL(triggered()),this,SLOT(WarpImage()));
 273   connect(actionLoad_images,SIGNAL(triggered()),this,SLOT(OpenImages()));
 274   connect(actionOpen_Dicom,SIGNAL(triggered()),this,SLOT(OpenDicom()));
 275   //  connect(actionOpen_Dicom_Struct,SIGNAL(triggered()),this,SLOT(OpenDCStructContour()));
 276   connect(actionOpen_VTK_contour,SIGNAL(triggered()),this,SLOT(OpenVTKContour()));
 277   connect(actionOpen_Multiple_Images_As_One,SIGNAL(triggered()),this,SLOT(MergeImages()));
 278   connect(actionSlice_Image_As_Multiple_Images,SIGNAL(triggered()),this,SLOT(SliceImages()));
 279   connect(actionOpen_Image_With_Time,SIGNAL(triggered()),this,SLOT(OpenImageWithTime()));
 280   connect(actionMerge_images_as_n_dim_t, SIGNAL(triggered()), this, SLOT(MergeImagesWithTime()));
 281   connect(actionSave_As,SIGNAL(triggered()),this,SLOT(SaveAs()));
 282   connect(actionSave_current_state,SIGNAL(triggered()),this,SLOT(SaveCurrentState()));
 283   connect(actionRead_saved_state,SIGNAL(triggered()),this,SLOT(ReadSavedState()));
 284   connect(actionExit,SIGNAL(triggered()),this,SLOT(close()));
 285   connect(actionAdd_VF_to_current_Image,SIGNAL(triggered()),this,SLOT(OpenField()));
 286   connect(actionAdd_fusion_image,SIGNAL(triggered()),this,SLOT(SelectFusionImage()));
 287   connect(actionAdd_overlay_image_to_current_image,SIGNAL(triggered()), this,SLOT(SelectOverlayImage()));
 288   connect(actionAdd_USSequence_toCT,SIGNAL(triggered()), this,SLOT(SelectFusionSequence()));
 289   connect(actionNavigation_Help,SIGNAL(triggered()),this,SLOT(ShowHelpDialog()));
 290
 291   QShortcut *shortcutHelp = new QShortcut(QKeySequence(QKeySequence::HelpContents),this);
 292   shortcutHelp->setContext(Qt::ApplicationShortcut);
 293   QObject::connect(shortcutHelp, SIGNAL(activated()), this, SLOT(ShowHelpDialog()));
 294
 295   connect(actionDocumentation,SIGNAL(triggered()),this,SLOT(ShowDocumentation()));
 296   connect(actionRegister_vv,SIGNAL(triggered()),this,SLOT(PopupRegisterForm()));
 297
 298   connect(overlayPanel, SIGNAL(FusionSequenceCorrespondancesButtonPressed()), this, SLOT(SelectFusionSequenceCorrespondances()));
 299
 300
 301   ///////////////////////////////////////////////
 302   connect(actionSegmentation,SIGNAL(triggered()),this,SLOT(SegmentationOnCurrentImage()));
 303   connect(actionSurface_Viewer,SIGNAL(triggered()),this,SLOT(SurfaceViewerLaunch()));
 304   ///////////////////////////////////////////////
 305
 306   actionNorth_East_Window->setEnabled(0);
 307   actionNorth_West_Window->setEnabled(0);
 308   actionSouth_East_Window->setEnabled(0);
 309   actionSouth_West_Window->setEnabled(0);
 310
 311   connect(actionNorth_East_Window,SIGNAL(triggered()),this,SLOT(SaveNEScreenshot()));
 312   connect(actionNorth_West_Window,SIGNAL(triggered()),this,SLOT(SaveNOScreenshot()));
 313   connect(actionSouth_East_Window,SIGNAL(triggered()),this,SLOT(SaveSEScreenshot()));
 314   connect(actionSouth_West_Window,SIGNAL(triggered()),this,SLOT(SaveSOScreenshot()));
 315   connect(actionSave_all_slices,SIGNAL(triggered()),this,SLOT(SaveScreenshotAllSlices()));
 316
 317   connect(DataTree,SIGNAL(itemSelectionChanged()),this,SLOT(ImageInfoChanged()));
 318   connect(DataTree,SIGNAL(itemClicked(QTreeWidgetItem*, int)),this,
 319     SLOT(DisplayChanged(QTreeWidgetItem*, int)));
 320
 321   connect(viewButton,SIGNAL(clicked()),this, SLOT(ChangeViewMode()) );
 322   connect(windowSpinBox,SIGNAL(editingFinished()),this,SLOT(WindowLevelEdited()));
 323   connect(levelSpinBox,SIGNAL(editingFinished()),this,SLOT(WindowLevelEdited()));
 324   connect(colorMapComboBox,SIGNAL(currentIndexChanged(int)),this,SLOT(UpdateColorMap()));
 325   connect(presetComboBox,SIGNAL(currentIndexChanged(int)),this,SLOT(UpdateWindowLevel()));
 326   connect(slicingPresetComboBox, SIGNAL(currentIndexChanged(int)),this,SLOT(UpdateSlicingPreset()));
 327   connect(inverseButton,SIGNAL(clicked()),this,SLOT(SwitchWindowLevel()));
 328   connect(applyWindowLevelToAllButton,SIGNAL(clicked()),this,SLOT(ApplyWindowLevelToAllImages()));
 329
 330   connect(this,SIGNAL(customContextMenuRequested(QPoint)),this,SLOT(ShowContextMenu(QPoint)));
 331
 332   connect(linkPanel,SIGNAL(addLink(QString,QString,bool)),this,SLOT(AddLink(QString,QString,bool)));
 333   connect(linkPanel,SIGNAL(removeLink(QString,QString)),this,SLOT(RemoveLink(QString,QString)));
 334   connect(overlayPanel,SIGNAL(VFPropertyUpdated(int,int,int,int,double,double,double)),this,SLOT(SetVFProperty(int,int,int,int,double,double,double)));
 335   connect(overlayPanel,SIGNAL(OverlayPropertyUpdated(int,int,double,double)),
 336     this,SLOT(SetOverlayProperty(int,int,double,double)));
 337   connect(overlayPanel,SIGNAL(FusionPropertyUpdated(int,int,int,double,double, bool)),
 338     this,SLOT(SetFusionProperty(int,int,int,double,double, bool)));
 339   connect(landmarksPanel,SIGNAL(UpdateRenderWindows()),this,SLOT(UpdateRenderWindows()));
 340   connect(landmarksPanel,SIGNAL(SelectedPointChanged()),this,SLOT(GoToLandmark()));
 341
 342   connect(overlayPanel,SIGNAL(FusionSequencePropertyUpdated(int, bool, unsigned int, bool)),
 343     this,SLOT(SetFusionSequenceProperty(int, bool,unsigned int, bool)));
 344
 345
 346   playMode = 0;//pause
 347   mFrameRate = 10;
 348   playButton->setEnabled(0);
 349   frameRateLabel->setEnabled(0);
 350   frameRateSpinBox->setEnabled(0);
 351   connect(playButton, SIGNAL(clicked()),this,SLOT(PlayPause()));
 352   connect(frameRateSpinBox, SIGNAL(valueChanged(int)),this,SLOT(ChangeFrameRate(int)));
 353
 354   goToCursorPushButton->setEnabled(0);
 355   connect(goToCursorPushButton, SIGNAL(clicked()),this,SLOT(GoToCursor()));
 356
 357   NOViewWidget->hide();
 358   NEViewWidget->hide();
 359   SOViewWidget->hide();
 360   SEViewWidget->hide();
 361
 362 #ifdef Q_OS_OSX
 363   disableGLHiDPI(NOViewWidget->winId());
 364   disableGLHiDPI(NEViewWidget->winId());
 365   disableGLHiDPI(SOViewWidget->winId());
 366   disableGLHiDPI(SEViewWidget->winId());
 367 #endif
 368
 369   //Recently opened files
 370   std::list<std::string> recent_files = GetRecentlyOpenedImages();
 371   recentlyOpenedFilesMenu=NULL;
 372   if ( !recent_files.empty() ) {
 373     createRecentlyOpenedFilesMenu();
 374     updateRecentlyOpenedFilesMenu(recent_files);
 375   }
 376
 377   // Adding all new tools (insertion in the menu)
 378   vvToolManager::GetInstance()->InsertToolsInMenu(this);
 379   vvToolManager::GetInstance()->EnableToolsInMenu(this, false);
 380
 381 //#ifndef CLITK_EXPERIMENTAL
 382 //#define CLITK_EXPERIMENTAL 0
 383 //#endif
 384 #ifdef CLITK_EXPERIMENTAL
 385   if (!CLITK_EXPERIMENTAL)
 386     menuExperimental->menuAction()->setVisible(false);
 387 #endif
 388
 389   QTimer * timerMemory = new QTimer(this);
 390   //timerMemory->setInterval(5);
 391   connect(timerMemory, SIGNAL(timeout()), this, SLOT(UpdateMemoryUsage()));
 392   timerMemory->start(2000);
 393 }
 394
 395 //------------------------------------------------------------------------------
 396 void vvMainWindow::show()
 397 {
 398   vvMainWindowBase::show();
 399   PopupRegisterForm(true);
 400 }
 401 //------------------------------------------------------------------------------
 402 void vvMainWindow::UpdateMemoryUsage()
 403 {
 404   //  clitk::PrintMemory(true);
 405   if (clitk::GetMemoryUsageInMb() == 0) infoPanel->setMemoryInMb("NA");
 406   else infoPanel->setMemoryInMb(QString::number(clitk::GetMemoryUsageInMb())+" MiB");
 407 }
 408 //------------------------------------------------------------------------------
 409
 410
 411 //------------------------------------------------------------------------------
 412 void vvMainWindow::createRecentlyOpenedFilesMenu()
 413 {
 414   recentlyOpenedFilesMenu = new QMenu("Recently opened files...");
 415   recentlyOpenedFilesMenu->setIcon(QIcon(QString::fromUtf8(":/common/icons/open.png")));
 416   menuFile->insertMenu(actionOpen_Image_With_Time,recentlyOpenedFilesMenu);
 417   menuFile->insertSeparator(actionOpen_Image_With_Time);
 418 }
 419 //------------------------------------------------------------------------------
 420
 421
 422 //------------------------------------------------------------------------------
 423
 424 void vvMainWindow::updateRecentlyOpenedFilesMenu(const std::list<std::string> &recent_files)
 425 {
 426   if(recentlyOpenedFilesMenu==NULL) {
 427     createRecentlyOpenedFilesMenu();
 428   } else {
 429     recentlyOpenedFilesMenu->clear();
 430   }
 431   for (std::list<std::string>::const_iterator i = recent_files.begin(); i!=recent_files.end(); i++) {
 432     QAction* current=new QAction(QIcon(QString::fromUtf8(":/common/icons/open.png")), i->c_str(),this);
 433     recentlyOpenedFilesMenu->addAction(current);
 434     connect(current,SIGNAL(triggered()),this,SLOT(OpenRecentImage()));
 435   }
 436 }
 437 //------------------------------------------------------------------------------
 438
 439
 440 //------------------------------------------------------------------------------
 441 void vvMainWindow::ComputeMidPosition()
 442 {
 443   bool ok;
 444   int index=GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
 445   int ref = QInputDialog::getInt(this,"Chose reference phase","Reference phase",0,0,\
 446 mSlicerManagers[index]->GetImage()->GetVTKImages().size()-1,1,&ok);
 447   if (ok) {
 448     vvMidPosition midp;
 449     midp.slicer_manager = mSlicerManagers[index];
 450     midp.reference_image_index = ref;
 451     QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
 452     midp.Update();
 453     if (midp.error)
 454       QMessageBox::warning(this, "Error computing midposition image",midp.error_message.c_str());
 455     else {
 456       QFileInfo info(midp.slicer_manager->GetFileName().c_str());
 457       AddImage(midp.output,info.path().toStdString()+"/"+info.completeBaseName().toStdString()+"_midposition.mhd");
 458     }
 459     QApplication::restoreOverrideCursor();
 460   }
 461 }
 462 //------------------------------------------------------------------------------
 463
 464
 465 //------------------------------------------------------------------------------
 466 void vvMainWindow::AddContour(int image_index, vvMesh::Pointer contour, bool propagation)
 467 {
 468   QTreeWidgetItem *item = new QTreeWidgetItem();
 469   item->setData(0,Qt::UserRole,"filename.vtk");
 470   item->setData(1,Qt::UserRole,tr("contour"));
 471   QBrush brush;
 472   brush.setColor(QColor(contour->r*255,contour->g*255,contour->b*255));
 473   brush.setStyle(Qt::SolidPattern);
 474   item->setData(COLUMN_IMAGE_NAME,Qt::BackgroundRole,brush);
 475   item->setData(COLUMN_IMAGE_NAME,Qt::DisplayRole,contour->structure_name.c_str());
 476
 477   for (int j = 1; j <= 4; j++)
 478     item->setData(j,Qt::CheckStateRole,DataTree->topLevelItem(image_index)->data(j,Qt::CheckStateRole));
 479
 480   QTreePushButton* cButton = new QTreePushButton;
 481   cButton->setItem(item);
 482   cButton->setColumn(COLUMN_CLOSE_IMAGE);
 483   cButton->setToolTip(tr("close image"));
 484   cButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/exit.png")));
 485   connect(cButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
 486     this,SLOT(CloseImage(QTreeWidgetItem*, int)));
 487
 488   QTreePushButton* rButton = new QTreePushButton;
 489   rButton->setItem(item);
 490   rButton->setColumn(COLUMN_RELOAD_IMAGE);
 491   rButton->setToolTip(tr("reload image"));
 492   rButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/rotateright.png")));
 493   rButton->setEnabled(false);
 494   //Not implemented
 495   //connect(rButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
 496   //this,SLOT(ReloadImage(QTreeWidgetItem*, int)));
 497
 498   DataTree->topLevelItem(image_index)->setExpanded(1);
 499   DataTree->topLevelItem(image_index)->addChild(item);
 500   DataTree->setItemWidget(item, COLUMN_CLOSE_IMAGE, cButton);
 501   DataTree->setItemWidget(item, COLUMN_RELOAD_IMAGE, rButton);
 502   QString id = DataTree->topLevelItem(image_index)->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString();
 503   item->setData(COLUMN_IMAGE_NAME,Qt::UserRole,id.toStdString().c_str());
 504
 505   UpdateTree();
 506   mSlicerManagers[image_index]->AddContour(contour,propagation);
 507   mSlicerManagers[image_index]->Render();
 508 }
 509 //------------------------------------------------------------------------------
 510
 511
 512 //------------------------------------------------------------------------------
 513 void vvMainWindow::OpenVTKContour()
 514 {
 515   if (mSlicerManagers.size() > 0) {
 516     QString Extensions = "Images ( *.vtk *.obj)";
 517     Extensions += ";;All Files (*)";
 518     QString file = QFileDialog::getOpenFileName(this,tr("Open vtkPolyData"),mInputPathName,Extensions);
 519     if (file.isNull())
 520       return;
 521     QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
 522     int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
 523     vvMeshReader reader;
 524     reader.SetImage(mSlicerManagers[index]->GetImage());
 525     reader.SetModeToVTK();
 526     reader.SetFilename(file.toStdString());
 527     reader.Update();
 528     AddContour(index,reader.GetOutput()[0],false);
 529     QApplication::restoreOverrideCursor();
 530   }
 531 }
 532 //------------------------------------------------------------------------------
 533
 534
 535 //------------------------------------------------------------------------------
 536 void vvMainWindow::AddDCStructContour(int index, QString file)
 537 {
 538   vvMeshReader reader;
 539   reader.SetFilename(file.toStdString());
 540   vvStructSelector selector;
 541   selector.SetStructures(reader.GetROINames());
 542   if (!mSlicerManagers[index]->GetVF().IsNull())
 543     selector.EnablePropagationCheckBox();
 544   if (selector.exec()) {
 545     QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
 546     reader.SetSelectedItems(selector.getSelectedItems());
 547     reader.SetImage(mSlicerManagers[index]->GetImage());
 548     if (selector.PropagationEnabled())
 549       reader.SetPropagationVF(mSlicerManagers[index]->GetVF());
 550     reader.Update();
 551     std::vector<vvMesh::Pointer> contours=reader.GetOutput();
 552     for (std::vector<vvMesh::Pointer>::iterator i=contours.begin();
 553       i!=contours.end(); i++)
 554       AddContour(index,*i,selector.PropagationEnabled());
 555     QApplication::restoreOverrideCursor();
 556   }
 557 }
 558
 559 //------------------------------------------------------------------------------
 560 void vvMainWindow::OpenDCStructContour()
 561 {
 562   if (mSlicerManagers.size() > 0) {
 563     QString Extensions = "Dicom Files ( *.dcm RS*)";
 564     Extensions += ";;All Files (*)";
 565     QString file = QFileDialog::getOpenFileName(this,tr("Merge Images"),mInputPathName,Extensions);
 566     if (file.isNull())
 567       return;
 568     int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
 569     AddDCStructContour(index, file);
 570   }
 571 }
 572 //------------------------------------------------------------------------------
 573
 574
 575 //------------------------------------------------------------------------------
 576 void vvMainWindow::ComputeDeformableRegistration()
 577 {
 578   if (mSlicerManagers.size() > 0) {
 579     int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
 580     vvDeformationDialog dialog(index,mSlicerManagers);
 581     if (dialog.exec()) {
 582       std::string base_name=itksys::SystemTools::GetFilenameWithoutExtension(mSlicerManagers[dialog.GetInputFileIndex()]->GetFileName());
 583       AddField(dialog.GetOutput(),dialog.getFieldFile(),dialog.GetInputFileIndex());
 584       WarpImage(dialog.GetSelectedSlicer(),dialog.GetReferenceFrameIndex());
 585     } else
 586       std::cout << "Error or user cancellation while computing deformation field..." << std::endl;
 587   } else QMessageBox::information(this, "Need to open image","You must open an image first.");
 588 }
 589 //------------------------------------------------------------------------------
 590
 591
 592 //------------------------------------------------------------------------------
 593 void vvMainWindow::WarpImage()
 594 {
 595   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
 596   if (!mSlicerManagers[index]->GetVF().IsNull()) {
 597     bool ok;
 598     int ref = QInputDialog::getInt(this,"Chose reference phase","Reference phase",0,0,\
 599       mSlicerManagers[index]->GetImage()->GetVTKImages().size()-1,1,&ok);
 600     if (ok) {
 601       WarpImage(mSlicerManagers[index],ref);
 602     }
 603   } else
 604     QMessageBox::warning(this,tr("No vector field"),tr("Sorry, can't warp without a vector field"));
 605 }
 606 //------------------------------------------------------------------------------
 607
 608
 609 //------------------------------------------------------------------------------
 610 void vvMainWindow::WarpImage(vvSlicerManager* selected_slicer,int reference_phase)
 611 {
 612   if (!selected_slicer->GetVF().IsNull()) {
 613     QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
 614     QFileInfo info(selected_slicer->GetFileName().c_str());
 615     vvImageWarp warp(selected_slicer->GetImage(),selected_slicer->GetVF(),
 616       reference_phase,this);
 617     if (warp.ComputeWarpedImage()) {
 618       AddImage(warp.GetWarpedImage(),info.path().toStdString()+"/"+info.completeBaseName().toStdString()+"_warped.mhd");
 619       AddImage(warp.GetDiffImage()  ,info.path().toStdString()+"/"+info.completeBaseName().toStdString()+"_diff.mhd");
 620       AddImage(warp.GetJacobianImage()  ,info.path().toStdString()+"/"+info.completeBaseName().toStdString()+"_jacobian.mhd");
 621       QApplication::restoreOverrideCursor();
 622     } else {
 623       QApplication::restoreOverrideCursor();
 624       QMessageBox::warning(this,tr("Different spacings"),tr("The vector field and image spacings must be the same in order to warp."));
 625     }
 626   } else
 627     QMessageBox::warning(this,tr("No vector field"),tr("Sorry, can't warp without a vector field."));
 628 }
 629 //------------------------------------------------------------------------------
 630
 631
 632 //------------------------------------------------------------------------------
 633 vvMainWindow::~vvMainWindow()
 634 {
 635   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
 636     if (mSlicerManagers[i] != NULL)
 637       delete mSlicerManagers[i];
 638   }
 639   delete documentation;
 640   delete help_dialog;
 641   delete dicomSeriesSelector;
 642 }
 643 //------------------------------------------------------------------------------
 644
 645 //------------------------------------------------------------------------------
 646 QTabWidget * vvMainWindow::GetTab()
 647 {
 648   return tabWidget;
 649 }
 650 //------------------------------------------------------------------------------
 651
 652
 653 //------------------------------------------------------------------------------
 654 void vvMainWindow::MergeImages()
 655 {
 656   QString Extensions = EXTENSIONS;
 657   Extensions += ";;All Files (*)";
 658   QStringList files = QFileDialog::getOpenFileNames(this,tr("Merge Images"),mInputPathName,Extensions);
 659   if (files.isEmpty())
 660     return;
 661   mInputPathName = itksys::SystemTools::GetFilenamePath(files[0].toStdString()).c_str();
 662   std::vector<std::string> vector;
 663
 664   unsigned int currentDim = 0;
 665   std::vector<double> currentSpacing;
 666   std::vector<int> currentSize;
 667   std::vector<double> currentOrigin;
 668
 669   for (int i = 0; i < files.size(); i++) {
 670     itk::ImageIOBase::Pointer reader = itk::ImageIOFactory::CreateImageIO(
 671       files[i].toStdString().c_str(), itk::ImageIOFactory::ReadMode);
 672     reader->SetFileName(files[i].toStdString().c_str());
 673     reader->ReadImageInformation();
 674     if (reader)        {
 675       //NOViewWidget->hide();
 676       //NEViewWidget->hide();
 677       //SOViewWidget->hide();
 678       //SEViewWidget->hide();
 679       if (i == 0)
 680         currentDim = reader->GetNumberOfDimensions();
 681       bool IsOk = true;
 682       for (unsigned int j = 0; j < currentDim; j++) {
 683         if (i == 0) {
 684           if (j == 0) {
 685             currentSpacing.resize(currentDim);
 686             currentSize.resize(currentDim);
 687             currentOrigin.resize(currentDim);
 688           }
 689           currentOrigin[j] = reader->GetOrigin(j);
 690           currentSpacing[j] = reader->GetSpacing(j);
 691           currentSize[j] = reader->GetDimensions(j);
 692         } else if (currentDim != reader->GetNumberOfDimensions()
 693           || currentSpacing[j] != reader->GetSpacing(j)
 694           || currentSize[j] != (int)reader->GetDimensions(j)
 695           || currentOrigin[j] != reader->GetOrigin(j)) {
 696             QString error = "Cannot read file (too different from others ";
 697             error += files[i].toStdString().c_str();
 698             QMessageBox::information(this,tr("Reading problem"),error);
 699             IsOk = false;
 700             break;
 701         }
 702       }
 703       if (IsOk)
 704         vector.push_back(files[i].toStdString());
 705     }
 706   }
 707   if (vector.size() > 0)
 708     LoadImages(vector, vvImageReader::MERGED);
 709 }
 710 //------------------------------------------------------------------------------
 711
 712 //------------------------------------------------------------------------------
 713 void vvMainWindow::SliceImages()
 714 {
 715   QString Extensions = EXTENSIONS;
 716   Extensions += ";;All Files (*)";
 717
 718   QStringList files = QFileDialog::getOpenFileNames(this,tr("Slice Images"),mInputPathName,Extensions);
 719   if (files.isEmpty())
 720     return;
 721   mInputPathName = itksys::SystemTools::GetFilenamePath(files[0].toStdString()).c_str();
 722   std::vector<std::string> vector;
 723   for (int i = 0; i < files.size(); i++)
 724     vector.push_back(files[i].toStdString());
 725   LoadImages(vector, vvImageReader::SLICED);
 726 }
 727 //------------------------------------------------------------------------------
 728
 729 //------------------------------------------------------------------------------
 730 void vvMainWindow::MergeImagesWithTime()
 731 {
 732   QString Extensions = EXTENSIONS;
 733   Extensions += ";;All Files (*)";
 734   QStringList files = QFileDialog::getOpenFileNames(this,tr("Merge Images With Time"),mInputPathName,Extensions);
 735   if (files.isEmpty())
 736     return;
 737   mInputPathName = itksys::SystemTools::GetFilenamePath(files[0].toStdString()).c_str();
 738   std::vector<std::string> vector;
 739
 740   for (int i = 0; i < files.size(); i++)
 741     vector.push_back(files[i].toStdString());
 742   sort(vector.begin(),vector.end());
 743   if (vector.size() > 1)
 744     LoadImages(vector, vvImageReader::MERGEDWITHTIME);
 745   else
 746     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.");
 747 }
 748 //------------------------------------------------------------------------------
 749
 750
 751 //------------------------------------------------------------------------------
 752 void vvMainWindow::OpenDicom()
 753 {
 754   std::vector<std::string> files;
 755
 756   //std::cout << "dicomSeriesSelector " << std::endl;
 757   if (dicomSeriesSelector->exec() == QDialog::Accepted) {
 758     files = *(dicomSeriesSelector->GetFilenames());
 759     LoadImages(files, vvImageReader::DICOM);
 760   }
 761 }
 762 //------------------------------------------------------------------------------
 763
 764 //------------------------------------------------------------------------------
 765 void vvMainWindow::OpenImages()
 766 {
 767   QString Extensions = EXTENSIONS;
 768   Extensions += ";;All Files (*)";
 769
 770   QStringList files = QFileDialog::getOpenFileNames(this,tr("Load Images"),mInputPathName,Extensions);
 771   if (files.isEmpty())
 772     return;
 773   mInputPathName = itksys::SystemTools::GetFilenamePath(files[0].toStdString()).c_str();
 774   std::vector<std::string> vector;
 775   for (int i = 0; i < files.size(); i++)
 776     vector.push_back(files[i].toStdString());
 777   LoadImages(vector, vvImageReader::IMAGE);
 778 }
 779 //------------------------------------------------------------------------------
 780 void vvMainWindow::OpenRecentImage()
 781 {
 782   QAction * caller = qobject_cast<QAction*>(sender());
 783   std::vector<std::string> images;
 784   images.push_back(caller->text().toStdString());
 785   mInputPathName = itksys::SystemTools::GetFilenamePath(images[0]).c_str();
 786   LoadImages(images, vvImageReader::IMAGE);
 787 }
 788 //------------------------------------------------------------------------------
 789
 790
 791 //------------------------------------------------------------------------------
 792 void vvMainWindow::OpenImageWithTime()
 793 {
 794   QString Extensions = EXTENSIONS;
 795   Extensions += ";;All Files (*)";
 796
 797   QStringList files = QFileDialog::getOpenFileNames(this,tr("Load Images With Time"),mInputPathName,Extensions);
 798   if (files.isEmpty())
 799     return;
 800   mInputPathName = itksys::SystemTools::GetFilenamePath(files[0].toStdString()).c_str();
 801   std::vector<std::string> vector;
 802   for (int i = 0; i < files.size(); i++) {
 803     vector.push_back(files[i].toStdString());
 804   }
 805   LoadImages(vector, vvImageReader::IMAGEWITHTIME);
 806 }
 807 //------------------------------------------------------------------------------
 808
 809
 810 //------------------------------------------------------------------------------
 811 void vvMainWindow::LoadImages(std::vector<std::string> files, vvImageReader::LoadedImageType filetype)
 812 {
 813   //Separate the way to open images and dicoms
 814   int fileSize;
 815   if (filetype == vvImageReader::IMAGE || filetype == vvImageReader::IMAGEWITHTIME)
 816     fileSize = files.size();
 817   else
 818     fileSize = 1;
 819
 820   // For SLICED, we need the number of slices (ndim and #slices)
 821   std::vector<unsigned int> nSlices;
 822   nSlices.resize(files.size());
 823   std::fill(nSlices.begin(), nSlices.end(), 1);
 824   if (filetype == vvImageReader::SLICED) {
 825     for (int i = 0; i < fileSize; i++) {
 826       itk::ImageIOBase::Pointer header = clitk::readImageHeader(files[i]);
 827       QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
 828       if (!header) {
 829         nSlices[i] = 0;
 830         QString error = "Cannot open file \n";
 831         error += files[i].c_str();
 832         QMessageBox::information(this,tr("Reading problem"),error);
 833         return;
 834       }
 835       if (header->GetNumberOfDimensions() < 3) {
 836         nSlices[i] = 0;
 837         QString error = "Dimension problem. Cannot slice \n";
 838         error += files[i].c_str();
 839         QMessageBox::information(this,tr("Reading problem"),error);
 840         return;
 841       }
 842       nSlices[i] = header->GetDimensions( header->GetNumberOfDimensions()-1 );
 843     }
 844   }
 845
 846   //Only add to the list of recently opened files when a single file is opened,
 847   //to avoid polluting the list of recently opened files
 848   if (files.size() == 1) {
 849     QFileInfo finfo=tr(files[0].c_str());
 850     AddToRecentlyOpenedImages(finfo.absoluteFilePath().toStdString());
 851     updateRecentlyOpenedFilesMenu(GetRecentlyOpenedImages());
 852   }
 853   //init the progress events
 854   QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
 855   vvProgressDialog progress("Opening " + files[0],fileSize>1);
 856   qApp->processEvents();
 857
 858   int numberofsuccesulreads=0;
 859   //open images as 1 or multiples
 860   for (int i = 0; i < fileSize; i++) {
 861     progress.SetText("Opening " + files[i]);
 862     progress.SetProgress(i,fileSize);
 863     qApp->processEvents();
 864
 865     for (unsigned int j = 0; j < nSlices[i]; j++) {
 866       //read the image and put it in mSlicerManagers
 867       vvSlicerManager* imageManager = new vvSlicerManager(4);
 868       qApp->processEvents();
 869
 870       bool SetImageSucceed=false;
 871
 872       // Change filename if an image with the same already exist
 873       int number = GetImageDuplicateFilenameNumber(files[i] + std::string("_slice"));
 874
 875       if (filetype == vvImageReader::IMAGE || filetype == vvImageReader::IMAGEWITHTIME || filetype == vvImageReader::SLICED) {
 876         SetImageSucceed = imageManager->SetImage(files[i],filetype, number, j);
 877       } else {
 878         SetImageSucceed = imageManager->SetImages(files,filetype, number);
 879       }
 880       if (!SetImageSucceed) {
 881         QApplication::restoreOverrideCursor();
 882         QString error = "Cannot open file \n";
 883         error += imageManager->GetLastError().c_str();
 884         QMessageBox::information(this,tr("Reading problem"),error);
 885         delete imageManager;
 886       } else {
 887
 888         mSlicerManagers.push_back(imageManager);
 889
 890         //create an item in the tree with good settings
 891         QTreeWidgetItem *item = new QTreeWidgetItem();
 892         item->setData(0,Qt::UserRole,files[i].c_str());
 893         QFileInfo fileinfo(imageManager->GetFileName().c_str()); //Do not show the path
 894         item->setData(COLUMN_IMAGE_NAME,Qt::DisplayRole,fileinfo.fileName());
 895         item->setData(1,Qt::UserRole,tr("image"));
 896         item->setToolTip(COLUMN_IMAGE_NAME, imageManager->GetListOfAbsoluteFilePathInOneString("image").c_str());
 897         qApp->processEvents();
 898
 899         //Create the buttons for reload and close
 900         qApp->processEvents();
 901         QTreePushButton* cButton = new QTreePushButton;
 902         cButton->setItem(item);
 903         cButton->setColumn(COLUMN_CLOSE_IMAGE);
 904         cButton->setToolTip(tr("close image"));
 905         cButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/exit.png")));
 906         connect(cButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
 907           this,SLOT(CloseImage(QTreeWidgetItem*, int)));
 908
 909         QTreePushButton* rButton = new QTreePushButton;
 910         rButton->setItem(item);
 911         rButton->setColumn(COLUMN_RELOAD_IMAGE);
 912         rButton->setToolTip(tr("reload image"));
 913         rButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/rotateright.png")));
 914         connect(rButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
 915           this,SLOT(ReloadImage(QTreeWidgetItem*, int)));
 916
 917         DataTree->addTopLevelItem(item);
 918         DataTree->setItemWidget(item, COLUMN_CLOSE_IMAGE, cButton);
 919         DataTree->setItemWidget(item, COLUMN_RELOAD_IMAGE, rButton);
 920
 921         //set the id of the image
 922         QString id = QDir::current().absoluteFilePath(files[i].c_str()) + QString::number(mSlicerManagers.size()-1);
 923         item->setData(COLUMN_IMAGE_NAME,Qt::UserRole,id.toStdString().c_str());
 924         mSlicerManagers.back()->SetId(id.toStdString());
 925
 926         linkPanel->addImage(imageManager->GetFileName(), id.toStdString());
 927
 928         connect(mSlicerManagers.back(), SIGNAL(currentImageChanged(std::string)),
 929           this,SLOT(CurrentImageChanged(std::string)));
 930         connect(mSlicerManagers.back(), SIGNAL(currentPickedImageChanged(std::string)),
 931           this, SLOT(CurrentPickedImageChanged(std::string)));
 932         connect(mSlicerManagers.back(), SIGNAL(UpdatePosition(int, double, double, double, double, double, double, double)),
 933           this,SLOT(MousePositionChanged(int,double, double, double, double, double, double, double)));
 934         connect(mSlicerManagers.back(), SIGNAL(UpdateVector(int, double, double, double, double)),
 935           this, SLOT(VectorChanged(int,double,double,double, double)));
 936         connect(mSlicerManagers.back(), SIGNAL(UpdateOverlay(int, double, double)),
 937           this, SLOT(OverlayChanged(int,double,double)));
 938         connect(mSlicerManagers.back(), SIGNAL(UpdateFusion(int, double)),
 939           this, SLOT(FusionChanged(int,double)));
 940         connect(mSlicerManagers.back(), SIGNAL(WindowLevelChanged()),
 941           this,SLOT(WindowLevelChanged()));
 942         connect(mSlicerManagers.back(), SIGNAL(UpdateSlice(int,int)),
 943           this,SLOT(UpdateSlice(int,int)));
 944         connect(mSlicerManagers.back(), SIGNAL(UpdateTSlice(int, int, int)),
 945           this,SLOT(UpdateTSlice(int, int, int)));
 946         connect(mSlicerManagers.back(), SIGNAL(UpdateTSlice(int, int, int)),
 947           this,SLOT(ImageInfoChanged()));
 948         connect(mSlicerManagers.back(), SIGNAL(UpdateSliceRange(int,int,int,int,int)),
 949           this,SLOT(UpdateSliceRange(int,int,int,int,int)));
 950         connect(mSlicerManagers.back(), SIGNAL(UpdateLinkManager(std::string,int,double,double,double,int)),
 951           this,SLOT(UpdateLinkManager(std::string,int,double,double,double,int)));
 952         connect(mSlicerManagers.back(), SIGNAL(UpdateLinkedNavigation(std::string,vvSlicerManager*,vvSlicer*)),
 953           this,SLOT(UpdateLinkedNavigation(std::string,vvSlicerManager*,vvSlicer*)));
 954         connect(mSlicerManagers.back(), SIGNAL(ChangeImageWithIndexOffset(vvSlicerManager*,int,int)),
 955           this,SLOT(ChangeImageWithIndexOffset(vvSlicerManager*,int,int)));
 956         connect(mSlicerManagers.back(),SIGNAL(LandmarkAdded()),landmarksPanel,SLOT(AddPoint()));
 957         InitSlicers();
 958         numberofsuccesulreads++;
 959       }
 960     }
 961   }
 962
 963   if (numberofsuccesulreads) {
 964     NOViewWidget->show();
 965     NEViewWidget->show();
 966     SOViewWidget->show();
 967     SEViewWidget->show();
 968     UpdateTree();
 969     InitDisplay();
 970     ShowLastImage();
 971
 972     // Try to guess default WindowLevel
 973     double range[2];
 974     mSlicerManagers.back()->GetImage()->GetFirstVTKImageData()->GetScalarRange(range);
 975     if ((range[0] == 0) && (range[1] == 1)) {
 976       presetComboBox->setCurrentIndex(WL_BINARY);// binary
 977     } else {
 978       // TODO
 979     }
 980   }
 981   QApplication::restoreOverrideCursor();
 982 }
 983 //------------------------------------------------------------------------------
 984
 985 //------------------------------------------------------------------------------
 986 void vvMainWindow::UpdateTree()
 987 {
 988   DataTree->resizeColumnToContents(COLUMN_TREE);
 989   DataTree->resizeColumnToContents(COLUMN_UL_VIEW);
 990   DataTree->resizeColumnToContents(COLUMN_UR_VIEW);
 991   DataTree->resizeColumnToContents(COLUMN_DL_VIEW);
 992   DataTree->resizeColumnToContents(COLUMN_DR_VIEW);
 993   DataTree->resizeColumnToContents(COLUMN_IMAGE_NAME);
 994   DataTree->resizeColumnToContents(COLUMN_CLOSE_IMAGE);
 995   DataTree->resizeColumnToContents(COLUMN_RELOAD_IMAGE);
 996 }
 997 //------------------------------------------------------------------------------
 998
 999 //------------------------------------------------------------------------------
1000 void vvMainWindow::CurrentImageChanged(std::string id)
1001 {
1002   if (id == mCurrentSelectedImageId) return; // Do nothing
1003   int selected = 0;
1004   for (int i = 0; i < DataTree->topLevelItemCount(); i++) {
1005     if (DataTree->topLevelItem(i)->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString().toStdString() == id) {
1006       selected = i;
1007     } else {
1008       DataTree->topLevelItem(i)->setSelected(0);
1009     }
1010     for (int child = 0; child < DataTree->topLevelItem(i)->childCount(); child++)
1011       DataTree->topLevelItem(i)->child(child)->setSelected(0);
1012
1013   }
1014   DataTree->topLevelItem(selected)->setSelected(1);
1015   mCurrentSelectedImageId = id;
1016
1017   landmarksPanel->SetCurrentLandmarks(mSlicerManagers[selected]->GetLandmarks(),
1018                                       mSlicerManagers[selected]->GetTSlice());
1019   landmarksPanel->SetCurrentPath(mInputPathName.toStdString());
1020   landmarksPanel->SetCurrentImage(mSlicerManagers[selected]->GetFileName().c_str());
1021
1022   emit SelectedImageHasChanged(mSlicerManagers[selected]);
1023 }
1024 //------------------------------------------------------------------------------
1025
1026 //------------------------------------------------------------------------------
1027 void vvMainWindow::CurrentPickedImageChanged(std::string id)
1028 {
1029   if (id == mCurrentPickedImageId) return; // Do nothing
1030   int selected = 0;
1031   for (int i = 0; i < DataTree->topLevelItemCount(); i++) {
1032     if (DataTree->topLevelItem(i)->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString().toStdString() == id) {
1033       selected = i;
1034     } else {
1035       DataTree->topLevelItem(i)->setSelected(0);
1036     }
1037     for (int child = 0; child < DataTree->topLevelItem(i)->childCount(); child++)
1038       DataTree->topLevelItem(i)->child(child)->setSelected(0);
1039
1040   }
1041   DataTree->topLevelItem(selected)->setSelected(1);
1042   mCurrentPickedImageId = id;
1043   mCurrentPickedImageIndex = selected;
1044 }
1045 //------------------------------------------------------------------------------
1046
1047 //------------------------------------------------------------------------------
1048 void vvMainWindow::ImageInfoChanged()
1049 {
1050   contextActions[6]->setEnabled(1);
1051   contextActions[5]->setEnabled(1);
1052   actionSave_As->setEnabled(1);
1053   actionAdd_VF_to_current_Image->setEnabled(1);
1054   actionAdd_fusion_image->setEnabled(1);
1055   actionAdd_overlay_image_to_current_image->setEnabled(1);
1056   actionAdd_USSequence_toCT->setEnabled(1);
1057   actionNorth_East_Window->setEnabled(1);
1058   actionNorth_West_Window->setEnabled(1);
1059   actionSouth_East_Window->setEnabled(1);
1060   actionSouth_West_Window->setEnabled(1);
1061   vvToolManager::GetInstance()->EnableToolsInMenu(this, true);
1062   inverseButton->setEnabled(1);
1063
1064   goToCursorPushButton->setEnabled(1);
1065
1066   if (DataTree->selectedItems().size()) {
1067     int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1068
1069     colorMapComboBox->setEnabled(1);
1070     for (int i = 0; i < DataTree->topLevelItem(index)->childCount(); i++) {
1071       if (DataTree->topLevelItem(index)->child(i)->data(1,Qt::UserRole).toString() == "overlay" ||
1072         DataTree->topLevelItem(index)->child(i)->data(1,Qt::UserRole).toString() == "fusion" ||
1073         DataTree->topLevelItem(index)->child(i)->data(1,Qt::UserRole).toString() == "fusionSequence") {
1074           colorMapComboBox->setEnabled(0);
1075           break;
1076       }
1077     }
1078
1079     std::vector<double> origin;
1080     std::vector<double> inputSpacing;
1081     std::vector<int> inputSize;
1082     std::vector<double> sizeMM;
1083     vtkSmartPointer<vtkMatrix4x4> transformation;
1084     int dimension=0;
1085     QString pixelType;
1086     QString inputSizeInBytes;
1087     QString image = DataTree->selectedItems()[0]->data(COLUMN_IMAGE_NAME,Qt::DisplayRole).toString();
1088
1089     int nframes = mSlicerManagers[index]->GetSlicer(0)->GetTMax();
1090
1091     if (nframes > 1 || playMode == 1) {
1092       playButton->setEnabled(1);
1093       frameRateLabel->setEnabled(1);
1094       frameRateSpinBox->setEnabled(1);
1095     } else {
1096       playButton->setEnabled(0);
1097       frameRateLabel->setEnabled(0);
1098       frameRateSpinBox->setEnabled(0);
1099     }
1100
1101     //read image header
1102     int NPixel = 1;
1103
1104     int tSlice = 0;
1105     vvImage::Pointer imageSelected;
1106     if (DataTree->topLevelItem(index) == DataTree->selectedItems()[0]) {
1107       imageSelected = mSlicerManagers[index]->GetSlicer(0)->GetImage();
1108       tSlice = mSlicerManagers[index]->GetSlicer(0)->GetTSlice();
1109     } else if (DataTree->selectedItems()[0]->data(1,Qt::UserRole).toString() == "vector") {
1110       imageSelected = mSlicerManagers[index]->GetSlicer(0)->GetVF();
1111       tSlice = mSlicerManagers[index]->GetSlicer(0)->GetOverlayTSlice();
1112     } else if (DataTree->selectedItems()[0]->data(1,Qt::UserRole).toString() == "overlay") {
1113       imageSelected = mSlicerManagers[index]->GetSlicer(0)->GetOverlay();
1114       tSlice = mSlicerManagers[index]->GetSlicer(0)->GetOverlayTSlice();
1115     } else if (DataTree->selectedItems()[0]->data(1,Qt::UserRole).toString() == "fusion") {
1116       imageSelected = mSlicerManagers[index]->GetSlicer(0)->GetFusion();
1117       tSlice = mSlicerManagers[index]->GetSlicer(0)->GetFusionTSlice();
1118     }
1119     else if (DataTree->selectedItems()[0]->data(1,Qt::UserRole).toString() == "fusionSequence") {
1120       imageSelected = mSlicerManagers[index]->GetSlicer(0)->GetFusion();
1121       tSlice = mSlicerManagers[index]->GetSlicer(0)->GetFusionTSlice();
1122     }
1123     else if (DataTree->selectedItems()[0]->data(1,Qt::UserRole).toString() == "contour") {
1124       imageSelected = mSlicerManagers[index]->GetSlicer(0)->GetImage();
1125       tSlice = mSlicerManagers[index]->GetSlicer(0)->GetTSlice();
1126     }
1127     else {
1128       imageSelected = mSlicerManagers[index]->GetSlicer(0)->GetImage();
1129       tSlice = mSlicerManagers[index]->GetSlicer(0)->GetTSlice();
1130     }
1131
1132     dimension = imageSelected->GetNumberOfDimensions();
1133     origin.resize(dimension);
1134     inputSpacing.resize(dimension);
1135     inputSize.resize(dimension);
1136     sizeMM.resize(dimension);
1137     pixelType = mSlicerManagers[index]->GetImage()->GetScalarTypeAsITKString().c_str();
1138     for (int i = 0; i < dimension; i++) {
1139       origin[i] = imageSelected->GetOrigin()[i];
1140       inputSpacing[i] = imageSelected->GetSpacing()[i];
1141       inputSize[i] = imageSelected->GetSize()[i];
1142       sizeMM[i] = inputSize[i]*inputSpacing[i];
1143       NPixel *= inputSize[i];
1144     }
1145     inputSizeInBytes = GetSizeInBytes(imageSelected->GetActualMemorySize()*1000);
1146
1147     QString dim = QString::number(dimension) + " (";
1148     dim += pixelType + ")";
1149
1150     infoPanel->setFileName(image);
1151     std::string creationImageTimeValue("No creation time");
1152     itk::ExposeMetaData< std::string > (*imageSelected->GetFirstMetaDataDictionary(), "creationImageTime", creationImageTimeValue);
1153     infoPanel->setImageCreationTime(QString(creationImageTimeValue.c_str()));
1154     infoPanel->setDimension(dim);
1155     infoPanel->setSizePixel(GetVectorIntAsString(inputSize));
1156     infoPanel->setSizeMM(GetVectorDoubleAsString(sizeMM));
1157     infoPanel->setOrigin(GetVectorDoubleAsString(origin));
1158     infoPanel->setSpacing(GetVectorDoubleAsString(inputSpacing));
1159     infoPanel->setNPixel(QString::number(NPixel)+" ("+inputSizeInBytes+")");
1160
1161     transformation = imageSelected->GetTransform()[tSlice]->GetMatrix();
1162     infoPanel->setTransformation(clitk::Get4x4MatrixDoubleAsString(transformation).c_str());
1163
1164     landmarksPanel->SetCurrentLandmarks(mSlicerManagers[index]->GetLandmarks(),
1165                                         mSlicerManagers[index]->GetTSlice());
1166     landmarksPanel->SetCurrentPath(mInputPathName.toStdString());
1167     landmarksPanel->SetCurrentImage(mSlicerManagers[index]->GetFileName().c_str());
1168
1169     overlayPanel->getCurrentImageName(mSlicerManagers[index]->GetFileName().c_str());
1170     for (int i = 0; i < 4; i++) {
1171       if (DataTree->selectedItems()[0]->data(i+1,Qt::CheckStateRole).toInt() > 0 || i == 3) {
1172         mSlicerManagers[index]->UpdateInfoOnCursorPosition(i);
1173         break;
1174       }
1175     }
1176
1177 //     infoPanel->setFileName(image);
1178 //     infoPanel->setDimension(dim);
1179 //     infoPanel->setSizePixel(GetVectorIntAsString(inputSize));
1180 //     infoPanel->setSizeMM(GetVectorDoubleAsString(sizeMM));
1181 //     infoPanel->setOrigin(GetVectorDoubleAsString(origin));
1182 //     infoPanel->setSpacing(GetVectorDoubleAsString(inputSpacing));
1183 //     infoPanel->setNPixel(QString::number(NPixel)+" ("+inputSizeInBytes+")");
1184 //
1185 //     landmarksPanel->SetCurrentLandmarks(mSlicerManagers[index]->GetLandmarks(),
1186 //                                         mSlicerManagers[index]->GetTSlice());
1187 //     landmarksPanel->SetCurrentPath(mInputPathName.toStdString());
1188 //     landmarksPanel->SetCurrentImage(mSlicerManagers[index]->GetFileName().c_str());
1189 //
1190 //     overlayPanel->getCurrentImageName(mSlicerManagers[index]->GetFileName().c_str());
1191 //     for (int i = 0; i < 4; i++) {
1192 //       if (DataTree->selectedItems()[0]->data(i+1,Qt::CheckStateRole).toInt() > 0 || i == 3) {
1193 //         mSlicerManagers[index]->UpdateInfoOnCursorPosition(i);
1194 //         break;
1195 //       }
1196 //     }
1197     WindowLevelChanged();
1198
1199     slicingPresetComboBox->setCurrentIndex(mSlicerManagers[index]->GetSlicingPreset());
1200
1201     if (mSlicerManagers[index]->GetSlicer(0)->GetVF()) {
1202       overlayPanel->getVFName(mSlicerManagers[index]->GetVFName().c_str());
1203       overlayPanel->getVFProperty(mSlicerManagers[index]->GetSlicer(0)->GetVFSubSampling(),
1204         mSlicerManagers[index]->GetSlicer(0)->GetVFScale(),
1205         mSlicerManagers[index]->GetSlicer(0)->GetVFLog());
1206     } else {
1207       overlayPanel->getVFName(mSlicerManagers[index]->GetVFName().c_str());
1208       overlayPanel->getVFProperty(-1,-1,-1);
1209     }
1210     if (mSlicerManagers[index]->GetSlicer(0)->GetOverlay()) {
1211       overlayPanel->getOverlayName(mSlicerManagers[index]->GetOverlayName().c_str());
1212     } else {
1213       overlayPanel->getOverlayName(mSlicerManagers[index]->GetOverlayName().c_str());
1214     }
1215
1216     if (mSlicerManagers[index]->GetSlicer(0)->GetFusion()) {
1217       overlayPanel->getFusionName(mSlicerManagers[index]->GetFusionName().c_str());
1218     } else {
1219       overlayPanel->getFusionName(mSlicerManagers[index]->GetFusionName().c_str());
1220     }
1221   }
1222 }
1223 //------------------------------------------------------------------------------
1224
1225 //------------------------------------------------------------------------------
1226 void vvMainWindow::ShowDocumentation()
1227 {
1228   documentation->show();
1229 }
1230 //------------------------------------------------------------------------------
1231
1232 //------------------------------------------------------------------------------
1233 void vvMainWindow::PopupRegisterForm(bool checkCanPush)
1234 {
1235   vvRegisterForm* registerForm = new vvRegisterForm(QUrl("http://www.creatis.insa-lyon.fr/~dsarrut/vvregister/write.php"), getVVSettingsPath(), getSettingsOptionFormat());
1236   if(!checkCanPush) {
1237     registerForm->show();
1238   } else {
1239     if(registerForm->canPush()) {
1240       registerForm->show();
1241       registerForm->acquitPushed();//too bad if there is not internet connection anymore.
1242     }
1243   }
1244 }
1245 //------------------------------------------------------------------------------
1246
1247 //------------------------------------------------------------------------------
1248 void vvMainWindow::ShowHelpDialog()
1249 {
1250   help_dialog->show();
1251 }
1252 //------------------------------------------------------------------------------
1253
1254 //------------------------------------------------------------------------------
1255 void vvMainWindow::ChangeViewMode()
1256 {
1257   typedef struct _SIZE{
1258     QSplitter* splitter;
1259     QList<int> size1, size2;
1260     int cols[3];
1261   }SplitterSize;
1262   SplitterSize sizes[4];
1263   sizes[0].splitter = OSplitter;
1264   sizes[0].size1.push_back(1);
1265   sizes[0].size1.push_back(0);
1266   sizes[0].size2.push_back(1);
1267   sizes[0].size2.push_back(0);
1268   sizes[0].cols[0] = 2;
1269   sizes[0].cols[1] = 3;
1270   sizes[0].cols[2] = 4;
1271
1272   sizes[1].splitter = ESplitter;
1273   sizes[1].size1.push_back(0);
1274   sizes[1].size1.push_back(1);
1275   sizes[1].size2.push_back(1);
1276   sizes[1].size2.push_back(0);
1277   sizes[1].cols[0] = 1;
1278   sizes[1].cols[1] = 3;
1279   sizes[1].cols[2] = 4;
1280
1281   sizes[2].splitter = OSplitter;
1282   sizes[2].size1.push_back(1);
1283   sizes[2].size1.push_back(0);
1284   sizes[2].size2.push_back(0);
1285   sizes[2].size2.push_back(1);
1286   sizes[2].cols[0] = 1;
1287   sizes[2].cols[1] = 2;
1288   sizes[2].cols[2] = 4;
1289
1290   sizes[3].splitter = ESplitter;
1291   sizes[3].size1.push_back(0);
1292   sizes[3].size1.push_back(1);
1293   sizes[3].size2.push_back(0);
1294   sizes[3].size2.push_back(1);
1295   sizes[3].cols[0] = 1;
1296   sizes[3].cols[1] = 2;
1297   sizes[3].cols[2] = 3;
1298
1299   int slicer = mSlicerManagers[mCurrentPickedImageIndex]->GetSelectedSlicer();
1300   if (viewMode == 1) {
1301     if (slicer >= 0) {
1302       viewMode = 0;
1303       splitter_3->setSizes(sizes[slicer].size1);
1304       sizes[slicer].splitter->setSizes(sizes[slicer].size2);
1305       DataTree->setColumnHidden(sizes[slicer].cols[0],1);
1306       DataTree->setColumnHidden(sizes[slicer].cols[1],1);
1307       DataTree->setColumnHidden(sizes[slicer].cols[2],1);
1308     }
1309   } else {
1310     QList<int> size;
1311     if (slicer >= 0) {
1312       viewMode = 1;
1313       size.push_back(1);
1314       size.push_back(1);
1315       splitter_3->setSizes(size);
1316       sizes[slicer].splitter->setSizes(size);
1317       DataTree->setColumnHidden(sizes[slicer].cols[0],0);
1318       DataTree->setColumnHidden(sizes[slicer].cols[1],0);
1319       DataTree->setColumnHidden(sizes[slicer].cols[2],0);
1320     }
1321   }
1322   UpdateRenderWindows();
1323   /*
1324   ** I don't know why but for both resized QVTKWidget we also need to render
1325   ** the associated Slicer to redraw crosses.
1326   */
1327   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
1328     //     if (DataTree->topLevelItem(i)->data(COLUMN_UL_VIEW,Qt::CheckStateRole).toInt() > 1)
1329     mSlicerManagers[i]->GetSlicer(0)->Render();
1330     mSlicerManagers[i]->GetSlicer(1)->Render();
1331     //     if (DataTree->topLevelItem(i)->data(COLUMN_DL_VIEW,Qt::CheckStateRole).toInt() > 1)
1332     mSlicerManagers[i]->GetSlicer(2)->Render();
1333     mSlicerManagers[i]->GetSlicer(3)->Render();
1334   }
1335 }
1336 //------------------------------------------------------------------------------
1337
1338 //------------------------------------------------------------------------------
1339 QString vvMainWindow::GetSizeInBytes(unsigned long size)
1340 {
1341   QString result = "";// QString::number(size);
1342   //result += " bytes (";
1343   if (size > 1000000000) {
1344     size /= 1000000000;
1345     result += QString::number(size);
1346     result += "Gb";//)";
1347   } else if (size > 1000000) {
1348     size /= 1000000;
1349     result += QString::number(size);
1350     result += "Mb";//)";
1351   } else if (size > 1000) {
1352     size /= 1000;
1353     result += QString::number(size);
1354     result += "kb";//)";
1355   }
1356   return result;
1357 }
1358 //------------------------------------------------------------------------------
1359
1360 //------------------------------------------------------------------------------
1361 QString vvMainWindow::GetVectorDoubleAsString(std::vector<double> vectorDouble)
1362 {
1363   QString result;
1364   for (unsigned int i= 0; i < vectorDouble.size(); i++) {
1365     if (i != 0)
1366       result += " ";
1367     result += QString::number(vectorDouble[i]);
1368   }
1369   return result;
1370 }
1371 //------------------------------------------------------------------------------
1372
1373 //------------------------------------------------------------------------------
1374 QString vvMainWindow::GetVectorIntAsString(std::vector<int> vectorInt)
1375 {
1376   QString result;
1377   for (unsigned int i= 0; i < vectorInt.size(); i++) {
1378     if (i != 0)
1379       result += " ";
1380     result += QString::number(vectorInt[i]);
1381   }
1382   return result;
1383 }
1384 //------------------------------------------------------------------------------
1385
1386 //------------------------------------------------------------------------------
1387 //this actually returns the SlicerManager index!
1388 int vvMainWindow::GetSlicerIndexFromItem(QTreeWidgetItem* item)
1389 {
1390   QString id = item->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString();
1391   for (int i = 0; i < DataTree->topLevelItemCount(); i++) {
1392     if (DataTree->topLevelItem(i)->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString() == id)
1393       return i;
1394   }
1395   return -1;
1396 }
1397 //------------------------------------------------------------------------------
1398
1399 //------------------------------------------------------------------------------
1400 QTreeWidgetItem* vvMainWindow::GetItemFromSlicerManager(vvSlicerManager* sm)
1401 {
1402   QString id = sm->GetId().c_str();
1403   for (int i = 0; i < DataTree->topLevelItemCount(); i++) {
1404     if (DataTree->topLevelItem(i)->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString() == id)
1405       return DataTree->topLevelItem(i);
1406   }
1407   return NULL;
1408 }
1409 //------------------------------------------------------------------------------
1410
1411 //------------------------------------------------------------------------------
1412 void vvMainWindow::DisplayChanged(QTreeWidgetItem *clickedItem, int column)
1413 {
1414   if ( column >= COLUMN_CLOSE_IMAGE || column <= 0)
1415     return;
1416
1417   // Get parent information (might be the same item)
1418   int slicerManagerIndex = GetSlicerIndexFromItem(clickedItem);
1419   QTreeWidgetItem* clickedParentItem = DataTree->topLevelItem(slicerManagerIndex);
1420   vvSlicer* clickedSlicer = mSlicerManagers[slicerManagerIndex]->GetSlicer(column-1);
1421
1422   // Go over the complete item tree (only 2 levels, parents and children)
1423   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
1424     // Trick to avoid redoing twice the job for a key (sr)
1425     mSlicerManagers[i]->GetSlicer(column-1)->GetRenderWindow()->GetInteractor()->SetKeySym("Crap");
1426
1427     QTreeWidgetItem* currentParentItem = DataTree->topLevelItem(i);
1428     if(currentParentItem != clickedParentItem) {
1429       // Not the branch of the clicked item, uncheck all
1430
1431       // Parent
1432       currentParentItem->setData(column,Qt::CheckStateRole, 0);
1433       mSlicerManagers[i]->UpdateSlicer(column-1, false);
1434
1435       // Children
1436       for (int iChild = 0; iChild < currentParentItem->childCount(); iChild++) {
1437         currentParentItem->child(iChild)->setData(column,Qt::CheckStateRole, 0);
1438       }
1439     }
1440     else {
1441       // Branch of the clicked one: get check status from actor visibility in slicer
1442       // and toggle the clicked one
1443
1444       // Parent
1445       bool vis = clickedSlicer->GetActorVisibility("image", 0);
1446       bool draw = clickedSlicer->GetRenderer()->GetDraw();
1447
1448       // Update slicer (after getting visibility)
1449       mSlicerManagers[slicerManagerIndex]->UpdateSlicer(column-1, true);
1450       mSlicerManagers[slicerManagerIndex]->UpdateInfoOnCursorPosition(column-1);
1451       DisplaySliders(slicerManagerIndex, column-1);
1452       if(clickedParentItem == clickedItem) {
1453         // Toggle
1454         vis = !draw || !vis;
1455       }
1456       clickedSlicer->SetActorVisibility("image", 0, vis);
1457       clickedParentItem->setData(column, Qt::CheckStateRole, vis?2:0);
1458
1459       // Children
1460       std::map<std::string, int> actorTypeCounts;
1461       for (int iChild = 0; iChild < clickedParentItem->childCount(); iChild++) {
1462         QTreeWidgetItem* currentChildItem = clickedParentItem->child(iChild);
1463         std::string actorType = currentChildItem->data(1,Qt::UserRole).toString().toStdString();
1464         vis = clickedSlicer->GetActorVisibility(actorType, actorTypeCounts[actorType]);
1465         if(currentChildItem == clickedItem) {
1466           // Toggle or force visibility if it was not on this branch so far
1467           vis = !draw || !vis;
1468           clickedSlicer->SetActorVisibility(actorType, actorTypeCounts[actorType], vis);
1469         }
1470         currentChildItem->setData(column, Qt::CheckStateRole, vis?2:0);
1471         actorTypeCounts[actorType]++;
1472       }
1473     }
1474   }
1475
1476   clickedSlicer->Render();
1477 }
1478 //------------------------------------------------------------------------------
1479
1480 void vvMainWindow::InitSlicers()
1481 {
1482   if (mSlicerManagers.size()) {
1483     mSlicerManagers.back()->GenerateDefaultLookupTable();
1484     mSlicerManagers.back()->SetSlicerWindow(0,NOViewWidget->GetRenderWindow());
1485     mSlicerManagers.back()->SetSlicerWindow(1,NEViewWidget->GetRenderWindow());
1486     mSlicerManagers.back()->SetSlicerWindow(2,SOViewWidget->GetRenderWindow());
1487     mSlicerManagers.back()->SetSlicerWindow(3,SEViewWidget->GetRenderWindow());
1488 #if VTK_MAJOR_VERSION <= 5
1489     mSlicerManagers.back()->Render(); // SR: displayed #slice is wrong without this / TB: With VTK6 and multiple images, all slicers are updated, not only the first
1490 #endif
1491   }
1492 }
1493
1494 //------------------------------------------------------------------------------
1495 void vvMainWindow::InitDisplay()
1496 {
1497   if (mSlicerManagers.size()) {
1498     //BE CAREFUL : this is absolutely necessary to set the interactor style
1499     //in order to have the same style instanciation for all SlicerManagers in
1500     // a same window
1501     for (int j = 0; j < 4; j++) {
1502       vvInteractorStyleNavigator* style = vvInteractorStyleNavigator::New();
1503       style->SetAutoAdjustCameraClippingRange(1);
1504       bool AlreadySelected = false;
1505       for (int i = 0; i < DataTree->topLevelItemCount(); i++) {
1506         mSlicerManagers[i]->SetInteractorStyleNavigator(j,style);
1507         //select the image only if previous are not selected
1508         if (DataTree->topLevelItem(i)->data(j+1,Qt::CheckStateRole).toInt() > 1) {
1509           mSlicerManagers[i]->UpdateSlicer(j,1);
1510           AlreadySelected = true;
1511         } else if (i == DataTree->topLevelItemCount()-1 && !AlreadySelected) {
1512           if (DataTree->selectedItems().size() == 0) {
1513             DataTree->topLevelItem(i)->setSelected(1);
1514           }
1515           DataTree->topLevelItem(i)->setData(j+1,Qt::CheckStateRole,2);
1516           mSlicerManagers[i]->UpdateSlicer(j,1);
1517           DisplaySliders(i,j);
1518         } else {
1519           DataTree->topLevelItem(i)->setData(j+1,Qt::CheckStateRole,0);
1520           mSlicerManagers[i]->UpdateSlicer(j,0);
1521         }
1522       }
1523       style->Delete();
1524     }
1525   }
1526 }
1527 //------------------------------------------------------------------------------
1528
1529 //------------------------------------------------------------------------------
1530 void vvMainWindow::DisplaySliders(int slicer, int window)
1531 {
1532   if(!mSlicerManagers[slicer]->GetSlicer(window)->GetRenderer()->GetDraw())
1533     return;
1534
1535   int range[2];
1536   mSlicerManagers[slicer]->GetSlicer(window)->GetSliceRange(range);
1537   int position = mSlicerManagers[slicer]->GetSlicer(window)->GetSlice();
1538   if (range[1]>0)
1539     verticalSliders[window]->show();
1540   else
1541     verticalSliders[window]->hide();
1542   verticalSliders[window]->setRange(range[0],range[1]);
1543   verticalSliders[window]->setValue(position);
1544
1545   int tRange[2];
1546   tRange[0] = 0;
1547   tRange[1] = mSlicerManagers[slicer]->GetSlicer(window)->GetTMax();
1548   if (tRange[1]>0)
1549     horizontalSliders[window]->show();
1550   else
1551     horizontalSliders[window]->hide();
1552   horizontalSliders[window]->setRange(tRange[0],tRange[1]);
1553   int tPosition = mSlicerManagers[slicer]->GetSlicer(window)->GetMaxCurrentTSlice();
1554   horizontalSliders[window]->setValue(tPosition);
1555 }
1556 //------------------------------------------------------------------------------
1557
1558 //------------------------------------------------------------------------------
1559 void vvMainWindow::CloseImage(QTreeWidgetItem* item, int column)
1560 {
1561   int index = GetSlicerIndexFromItem(item);
1562
1563   if (DataTree->topLevelItem(index) != item) {
1564     QString warning = "Do you really want to close the overlay : ";
1565     warning += item->data(COLUMN_IMAGE_NAME,Qt::DisplayRole).toString();
1566     QMessageBox msgBox(QMessageBox::Warning, tr("Close Overlay"),
1567       warning, 0, this);
1568     msgBox.addButton(tr("Close"), QMessageBox::AcceptRole);
1569     msgBox.addButton(tr("Cancel"), QMessageBox::RejectRole);
1570     if (msgBox.exec() == QMessageBox::AcceptRole) {
1571       std::string overlay_type=item->data(1,Qt::UserRole).toString().toStdString();
1572       int overlay_index=0;
1573       for (int child = 0; child < DataTree->topLevelItem(index)->childCount(); child++) {
1574         if (DataTree->topLevelItem(index)->\
1575           child(child)->data(1,Qt::UserRole).toString().toStdString() == overlay_type)
1576           overlay_index++;
1577         if (DataTree->topLevelItem(index)->child(child) == item) break;
1578       }
1579       if (overlay_type=="fusionSequence") {
1580         //removing the overlay sequence in a fusion sequence visualization mode
1581         //reset the transforms
1582         overlayPanel->getFusionSequenceProperty(-1, false, 0, false);
1583
1584         //unlink and untie the slicer managers
1585         RemoveLink(mSlicerManagers[index]->GetId().c_str(), mSlicerManagers[mSlicerManagers[index]->GetFusionSequenceIndexOfLinkedManager()]->GetId().c_str());
1586         mSlicerManagers[index]->SetFusionSequenceInvolvmentCode(-1);
1587         mSlicerManagers[mSlicerManagers[index]->GetFusionSequenceIndexOfLinkedManager()]->SetFusionSequenceInvolvmentCode(-1);
1588         for (unsigned i=0 ; i<4 ; i++) {
1589             mSlicerManagers[index]->GetSlicer(i)->SetFusionSequenceCode(-1);
1590             mSlicerManagers[mSlicerManagers[index]->GetFusionSequenceIndexOfLinkedManager()]->GetSlicer(i)->SetFusionSequenceCode(-1);
1591         }
1592
1593       }
1594       mSlicerManagers[index]->RemoveActor(overlay_type, overlay_index-1);
1595       mSlicerManagers[index]->SetColorMap(0);
1596       DataTree->topLevelItem(index)->takeChild(DataTree->topLevelItem(index)->indexOfChild(item));
1597       mSlicerManagers[index]->Render();
1598     }
1599   } else if (DataTree->topLevelItemCount() <= 1) {
1600     QString warning = "Do you really want to close the image : ";
1601     warning += item->data(COLUMN_IMAGE_NAME,Qt::DisplayRole).toString();
1602     warning += "\nThis is the last image, you're about to close vv !!!";
1603     QMessageBox msgBox(QMessageBox::Warning, tr("Close Image"),
1604       warning, 0, this);
1605     msgBox.addButton(tr("Close vv"), QMessageBox::AcceptRole);
1606     msgBox.addButton(tr("Cancel"), QMessageBox::RejectRole);
1607     if (msgBox.exec() == QMessageBox::AcceptRole) {
1608       this->close();
1609     }
1610   } else {
1611     QString warning = "Do you really want to close the image : ";
1612     warning += item->data(COLUMN_IMAGE_NAME,Qt::DisplayRole).toString();
1613     QMessageBox msgBox(QMessageBox::Warning, tr("Close Image"),
1614       warning, 0, this);
1615     msgBox.addButton(tr("Close"), QMessageBox::AcceptRole);
1616     msgBox.addButton(tr("Cancel"), QMessageBox::RejectRole);
1617     if (msgBox.exec() == QMessageBox::AcceptRole) {
1618
1619       // Tell tools that we close an image
1620       emit AnImageIsBeingClosed(mSlicerManagers[index]);
1621
1622       std::vector<vvSlicerManager*>::iterator Manageriter = mSlicerManagers.begin();
1623       DataTree->takeTopLevelItem(index);
1624       for (int i = 0; i < index; i++) {
1625         Manageriter++;
1626       }
1627       //if the slicer manager was involved in a fusion sequence visualization...
1628       if ( mSlicerManagers[index]->IsInvolvedInFusionSequence() ) {
1629         //in both cases, close the overlay: find it... and close it
1630         //ideally, I should duplicate the code, and avoid calling CloseImage, since this pops up another interactive box
1631         QTreeWidgetItem* overlayItem;
1632         if (mSlicerManagers[index]->IsMainSequenceOfFusionSequence()) {
1633           for (unsigned i=0 ; i<item->childCount() ; i++) {
1634             overlayItem = item->child(i);
1635             this->CloseImage( overlayItem, 0 );
1636           }
1637         }
1638         else {
1639           QTreeWidgetItem* linkedItem = this->GetItemFromSlicerManager( mSlicerManagers[mSlicerManagers[index]->GetFusionSequenceIndexOfLinkedManager()] );
1640           for (unsigned i=0 ; i<linkedItem->childCount() ; i++) {
1641             overlayItem = linkedItem->child(i);
1642             this->CloseImage( overlayItem, 0 );
1643           }
1644         }
1645
1646         /* -- this is normally already done when closing the overlay.
1647         //reset the transforms
1648         overlayPanel->getFusionSequenceProperty(-1, false, 0, false);
1649
1650         //unlink and untie the slicer managers
1651         RemoveLink(mSlicerManagers[index]->GetId().c_str(), mSlicerManagers[mSlicerManagers[index]->GetFusionSequenceIndexOfLinkedManager()]->GetId().c_str());
1652         mSlicerManagers[index]->SetFusionSequenceInvolvmentCode(-1);
1653         mSlicerManagers[mSlicerManagers[index]->GetFusionSequenceIndexOfLinkedManager()]->SetFusionSequenceInvolvmentCode(-1);
1654         for (unsigned i=0 ; i<4 ; i++) {
1655             mSlicerManagers[index]->GetSlicer(i)->SetFusionSequenceCode(-1);
1656             mSlicerManagers[mSlicerManagers[index]->GetFusionSequenceIndexOfLinkedManager()]->GetSlicer(i)->SetFusionSequenceCode(-1);
1657         }
1658         */
1659       }
1660
1661       linkPanel->removeImage(index);
1662       mSlicerManagers[index]->RemoveActors();
1663
1664       //remove the slicer manager
1665       delete mSlicerManagers[index];
1666       mSlicerManagers.erase(Manageriter);
1667
1668       //
1669       InitDisplay();
1670     }
1671   }
1672   ImageInfoChanged();
1673 }
1674 //------------------------------------------------------------------------------
1675
1676 //------------------------------------------------------------------------------
1677 void vvMainWindow::ReloadImage(QTreeWidgetItem* item, int column)
1678 {
1679   // int index = GetSlicerIndexFromItem(item);
1680   //   QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
1681   //   if (item->data(1,Qt::UserRole).toString() == "vector")
1682   //     mSlicerManagers[index]->ReloadVF();
1683   //   else
1684   //     mSlicerManagers[index]->Reload();
1685
1686   //   QApplication::restoreOverrideCursor();
1687   int index = GetSlicerIndexFromItem(item);
1688   QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
1689   QString role=item->data(1,Qt::UserRole).toString();
1690   if ( role == "vector") {
1691     mSlicerManagers[index]->ReloadVF();
1692   }
1693   else if (role == "overlay") {
1694     mSlicerManagers[index]->ReloadOverlay();
1695   }
1696   else if (role == "fusion") {
1697     mSlicerManagers[index]->ReloadFusion();
1698   }
1699   else if (role == "fusionSequence") {
1700     //both versions of the secondary sequence must be updated.
1701     mSlicerManagers[index]->ReloadFusionSequence();
1702     mSlicerManagers[mSlicerManagers[index]->GetFusionSequenceIndexOfLinkedManager()]->Reload();
1703   }
1704   else {
1705     mSlicerManagers[index]->Reload();
1706     //if we update the secondary sequence, then the overlay of the main sequence should also be updated
1707     if (mSlicerManagers[index]->IsSecondarySequenceOfFusionSequence()) mSlicerManagers[mSlicerManagers[index]->GetFusionSequenceIndexOfLinkedManager()]->ReloadFusionSequence();
1708   }
1709   // Update view and info
1710   ImageInfoChanged();
1711   mSlicerManagers[index]->Render();
1712   QApplication::restoreOverrideCursor();
1713 }
1714 //------------------------------------------------------------------------------
1715
1716 //------------------------------------------------------------------------------
1717 void vvMainWindow::MousePositionChanged(int visibility,double x, double y, double z, double X, double Y, double Z , double value)
1718 {
1719   infoPanel->setCurrentInfo(visibility,x,y,z,X,Y,Z,value);
1720 }
1721 //------------------------------------------------------------------------------
1722
1723 //------------------------------------------------------------------------------
1724 void vvMainWindow::VectorChanged(int visibility,double x, double y, double z, double value)
1725 {
1726   overlayPanel->getCurrentVectorInfo(visibility,x,y,z,value);
1727 }
1728 //------------------------------------------------------------------------------
1729
1730 //------------------------------------------------------------------------------
1731 void vvMainWindow::OverlayChanged(int visibility, double valueOver, double valueRef)
1732 {
1733   overlayPanel->getCurrentOverlayInfo(visibility,valueOver, valueRef);
1734 }
1735 //------------------------------------------------------------------------------
1736
1737 //------------------------------------------------------------------------------
1738 void vvMainWindow::FusionChanged(int visibility, double value)
1739 {
1740   overlayPanel->getCurrentFusionInfo(visibility,value);
1741 }
1742 //------------------------------------------------------------------------------
1743
1744 //------------------------------------------------------------------------------
1745 //called when AddOverlayImage, AddFusionSequence
1746 //or when UpdateWindowLevel() is called ; when slicerManager emits WindowLevelChanged
1747 //when ImageInfoChanged() is called
1748 void vvMainWindow::WindowLevelChanged()
1749 {
1750   // Base image
1751   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1752   if(index==-1) return;
1753   windowSpinBox->setValue(mSlicerManagers[index]->GetColorWindow());
1754   levelSpinBox->setValue(mSlicerManagers[index]->GetColorLevel());
1755   colorMapComboBox->setCurrentIndex(mSlicerManagers[index]->GetColorMap());
1756   presetComboBox->setCurrentIndex(mSlicerManagers[index]->GetPreset());
1757
1758   // Overlay image
1759   if (mSlicerManagers[index]->GetSlicer(0)->GetOverlay())
1760     overlayPanel->getOverlayProperty(mSlicerManagers[index]->GetOverlayColor(),
1761     mSlicerManagers[index]->GetLinkOverlayWindowLevel(),
1762     mSlicerManagers[index]->GetOverlayColorWindow(),
1763     mSlicerManagers[index]->GetOverlayColorLevel());
1764   else
1765     overlayPanel->getOverlayProperty(-1,0,0.,0.);
1766
1767   // Fusion & SequenceFusion image
1768   if (mSlicerManagers[index]->GetSlicer(0)->GetFusion()) {
1769     overlayPanel->getFusionProperty(mSlicerManagers[index]->GetFusionOpacity(),
1770       mSlicerManagers[index]->GetFusionThresholdOpacity(),
1771       mSlicerManagers[index]->GetFusionColorMap(),
1772       mSlicerManagers[index]->GetFusionWindow(),
1773       mSlicerManagers[index]->GetFusionLevel());
1774     if (mSlicerManagers[index]->IsMainSequenceOfFusionSequence()) {
1775       overlayPanel->getFusionSequenceProperty(mSlicerManagers[index]->GetFusionSequenceFrameIndex(),
1776         mSlicerManagers[index]->GetFusionSequenceSpatialSyncFlag(),
1777         mSlicerManagers[index]->GetFusionSequenceNbFrames(),
1778         mSlicerManagers[index]->GetFusionSequenceTemporalSyncFlag());
1779     }
1780   }
1781   else if ( mSlicerManagers[index]->IsSecondarySequenceOfFusionSequence() ) {
1782     //if the image is involved in a fusion sequence, preserve the overlay panel!
1783     int ind = mSlicerManagers[index]->GetFusionSequenceIndexOfLinkedManager();
1784     overlayPanel->getFusionProperty(mSlicerManagers[ind]->GetFusionOpacity(),
1785       mSlicerManagers[ind]->GetFusionThresholdOpacity(),
1786       mSlicerManagers[ind]->GetFusionColorMap(),
1787       mSlicerManagers[ind]->GetFusionWindow(),
1788       mSlicerManagers[ind]->GetFusionLevel());
1789     overlayPanel->getFusionSequenceProperty(mSlicerManagers[ind]->GetFusionSequenceFrameIndex(),
1790       mSlicerManagers[ind]->GetFusionSequenceSpatialSyncFlag(),
1791       mSlicerManagers[ind]->GetFusionSequenceNbFrames(),
1792       mSlicerManagers[ind]->GetFusionSequenceTemporalSyncFlag());
1793   }
1794   else
1795   {
1796     overlayPanel->getFusionProperty(-1, -1, -1, -1, -1);
1797     overlayPanel->getFusionSequenceProperty(-1, false, 0, false);
1798   }
1799 }
1800 //------------------------------------------------------------------------------
1801
1802 //------------------------------------------------------------------------------
1803 void vvMainWindow::WindowLevelEdited()
1804 {
1805   presetComboBox->setCurrentIndex(WL_USER);
1806   UpdateWindowLevel();
1807 }
1808 //------------------------------------------------------------------------------
1809
1810 //------------------------------------------------------------------------------
1811 void vvMainWindow::SetWindowLevel(double w, double l)
1812 {
1813   windowSpinBox->setValue(w);
1814   levelSpinBox->setValue(l);
1815   presetComboBox->setCurrentIndex(WL_USER);
1816   colorMapComboBox->setCurrentIndex(0);
1817   UpdateWindowLevel();
1818 }
1819 //------------------------------------------------------------------------------
1820
1821 //------------------------------------------------------------------------------
1822 void vvMainWindow::UpdateWindowLevel()
1823 {
1824   if (DataTree->selectedItems().size()) {
1825     if (presetComboBox->currentIndex() == WL_VENTILATION) //For ventilation
1826       colorMapComboBox->setCurrentIndex(5);
1827     int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1828     mSlicerManagers[index]->SetColorWindow(windowSpinBox->value());
1829     mSlicerManagers[index]->SetColorLevel(levelSpinBox->value());
1830     mSlicerManagers[index]->SetPreset(presetComboBox->currentIndex());
1831     mSlicerManagers[index]->Render();
1832     WindowLevelChanged();
1833   }
1834 }
1835 //------------------------------------------------------------------------------
1836
1837 //------------------------------------------------------------------------------
1838 void vvMainWindow::UpdateSlicingPreset()
1839 {
1840   if (DataTree->selectedItems().size()) {
1841     int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1842     mSlicerManagers[index]->SetSlicingPreset(vvSlicerManager::SlicingPresetType(slicingPresetComboBox->currentIndex()));
1843   }
1844 }
1845 //------------------------------------------------------------------------------
1846
1847 //------------------------------------------------------------------------------
1848 void vvMainWindow::UpdateColorMap()
1849 {
1850   if (DataTree->selectedItems().size()) {
1851     int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1852     mSlicerManagers[index]->SetColorMap(colorMapComboBox->currentIndex());
1853     mSlicerManagers[index]->Render();
1854   }
1855 }
1856 //------------------------------------------------------------------------------
1857 void vvMainWindow::SwitchWindowLevel()
1858 {
1859   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1860   int window = mSlicerManagers[index]->GetColorWindow();
1861   presetComboBox->setCurrentIndex(WL_USER);
1862   windowSpinBox->setValue(-window);
1863   UpdateWindowLevel();
1864 }
1865 //------------------------------------------------------------------------------
1866
1867 //------------------------------------------------------------------------------
1868 void vvMainWindow::ApplyWindowLevelToAllImages()
1869 {
1870   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1871   if(index==-1) return;
1872   double window = mSlicerManagers[index]->GetColorWindow();
1873   double level = mSlicerManagers[index]->GetColorLevel();
1874
1875   double fusWindow = mSlicerManagers[index]->GetFusionWindow();
1876   double fusLevel = mSlicerManagers[index]->GetFusionLevel();
1877
1878   double overWindow = mSlicerManagers[index]->GetOverlayColorWindow();
1879   double overLevel = mSlicerManagers[index]->GetOverlayColorLevel();
1880
1881   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
1882     if (mSlicerManagers[i] == NULL)
1883       continue;
1884     mSlicerManagers[i]->SetColorWindow(window);
1885     mSlicerManagers[i]->SetColorLevel(level);
1886     mSlicerManagers[i]->SetPreset(WL_USER);
1887     mSlicerManagers[i]->SetFusionWindow(fusWindow);
1888     mSlicerManagers[i]->SetFusionLevel(fusLevel);
1889     mSlicerManagers[i]->SetOverlayColorWindow(overWindow);
1890     mSlicerManagers[i]->SetOverlayColorLevel(overLevel);
1891     mSlicerManagers[i]->Render();
1892   }
1893 }
1894 //------------------------------------------------------------------------------
1895
1896 //------------------------------------------------------------------------------
1897 void vvMainWindow::ApplyWindowToSetOfImages(double window, unsigned int indexMin, unsigned int indexMax)
1898 {
1899   for (unsigned int i = indexMin; i <= indexMax && i < mSlicerManagers.size(); i++) {
1900     if (mSlicerManagers[i] == NULL)
1901       continue;
1902     SetWindowLevel(window, mSlicerManagers[i]->GetColorLevel());
1903     mSlicerManagers[i]->SetColorWindow(window);
1904     mSlicerManagers[i]->SetPreset(WL_USER);
1905     mSlicerManagers[i]->Render();
1906   }
1907 }
1908 //------------------------------------------------------------------------------
1909
1910 //------------------------------------------------------------------------------
1911 void vvMainWindow::ApplyLevelToSetOfImages(double level, unsigned int indexMin, unsigned int indexMax)
1912 {
1913   for (unsigned int i = indexMin; i <= indexMax && i < mSlicerManagers.size(); i++) {
1914     if (mSlicerManagers[i] == NULL)
1915       continue;
1916     SetWindowLevel(mSlicerManagers[i]->GetColorWindow(), level);
1917     mSlicerManagers[i]->SetColorLevel(level);
1918     mSlicerManagers[i]->SetPreset(WL_USER);
1919     mSlicerManagers[i]->Render();
1920   }
1921 }
1922 //------------------------------------------------------------------------------
1923
1924 //------------------------------------------------------------------------------
1925 void vvMainWindow::UpdateLinkManager(std::string id, int slicer, double x, double y, double z, int temps)
1926 {
1927   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
1928     if (mSlicerManagers[i]->GetId() == id) {
1929       mSlicerManagers[i]->GetSlicer(slicer)->SetCurrentPosition(x,y,z,temps);
1930       mSlicerManagers[i]->UpdateViews(0,slicer);
1931       break;
1932     }
1933   }
1934 }
1935 //------------------------------------------------------------------------------
1936
1937 //------------------------------------------------------------------------------
1938 void vvMainWindow::UpdateLinkedNavigation(std::string id, vvSlicerManager * sm, vvSlicer* refSlicer)
1939 {
1940   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
1941     if (id == mSlicerManagers[i]->GetId()) {
1942       mSlicerManagers[i]->UpdateLinkedNavigation(refSlicer);
1943     }
1944   }
1945 }
1946 //------------------------------------------------------------------------------
1947
1948 //------------------------------------------------------------------------------
1949 void vvMainWindow::ShowContextMenu(QPoint point)
1950 {
1951   if (!DataTree->selectedItems().size()) {
1952     contextActions[1]->setEnabled(0);
1953     contextActions[2]->setEnabled(0);
1954     contextActions[3]->setEnabled(0);
1955     contextActions[4]->setEnabled(0);
1956     contextActions[5]->setEnabled(0);
1957     contextActions[6]->setEnabled(0);
1958   } else {
1959     int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1960     contextActions[1]->setEnabled(1);
1961     contextActions[2]->setEnabled(
1962       DataTree->itemWidget(DataTree->selectedItems()[0],
1963       COLUMN_RELOAD_IMAGE)->isEnabled());
1964     contextActions[3]->setEnabled(1);
1965     contextActions[5]->setEnabled(1);
1966     contextActions[6]->setEnabled(1);
1967
1968     if (mSlicerManagers[index]->GetDimension() < 3)
1969       contextActions[4]->setEnabled(0);
1970     else
1971       contextActions[4]->setEnabled(1);
1972   }
1973   contextMenu.exec(QCursor::pos());
1974 }
1975 //------------------------------------------------------------------------------
1976
1977 //------------------------------------------------------------------------------
1978 void vvMainWindow::CloseImage()
1979 {
1980   CloseImage(DataTree->selectedItems()[0],0);
1981 }
1982 //------------------------------------------------------------------------------
1983
1984 //------------------------------------------------------------------------------
1985 void vvMainWindow::ReloadImage()
1986 {
1987   ReloadImage(DataTree->selectedItems()[0],0);
1988 }
1989 //------------------------------------------------------------------------------
1990
1991 //------------------------------------------------------------------------------
1992 void vvMainWindow::SelectOverlayImage()
1993 {
1994   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1995
1996   if (!(CheckAddedImage(index, "overlay")))
1997     return;
1998
1999   QString Extensions = EXTENSIONS;
2000   Extensions += ";;All Files (*)";
2001   QStringList files = QFileDialog::getOpenFileNames(this,tr("Load Overlay image"),mInputPathName,Extensions);
2002   if (files.isEmpty())
2003     return;
2004
2005   std::vector<std::string> vecFileNames;
2006   for (int i = 0; i < files.size(); i++) {
2007     vecFileNames.push_back(files[i].toStdString());
2008   }
2009
2010   AddOverlayImage(index,vecFileNames,vvImageReader::IMAGE);
2011 }
2012 //------------------------------------------------------------------------------
2013
2014 //------------------------------------------------------------------------------
2015 bool vvMainWindow::CheckAddedImage(int index, QString imageType)
2016 {
2017   //check if one overlay image is added
2018   for (int child = 0; child < DataTree->topLevelItem(index)->childCount(); child++)
2019     if (DataTree->topLevelItem(index)->child(child)->data(1,Qt::UserRole).toString().compare(imageType) == 0) {
2020       QString error = "Cannot add more than one compared image\n";
2021       error += "Please remove first ";
2022       error += DataTree->topLevelItem(index)->child(child)->data(COLUMN_IMAGE_NAME,Qt::DisplayRole).toString();
2023       QMessageBox::information(this,tr("Problem adding compared image !"),error);
2024       return false;
2025     }
2026     return true;
2027 }
2028 //------------------------------------------------------------------------------
2029
2030 //------------------------------------------------------------------------------
2031 void vvMainWindow::AddOverlayImage(int index, std::vector<std::string> fileNames, vvImageReader::LoadedImageType type)
2032 {
2033   QString file(fileNames[0].c_str());
2034   if (QFile::exists(file))
2035   {
2036     mInputPathName = itksys::SystemTools::GetFilenamePath(file.toStdString()).c_str();
2037     itk::ImageIOBase::Pointer reader = itk::ImageIOFactory::CreateImageIO(
2038       file.toStdString().c_str(), itk::ImageIOFactory::ReadMode);
2039     reader->SetFileName(fileNames[0].c_str());
2040     reader->ReadImageInformation();
2041     std::string component = reader->GetComponentTypeAsString(reader->GetComponentType());
2042     int dimension = reader->GetNumberOfDimensions();
2043     QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
2044     vvProgressDialog progress("Opening " + file.toStdString());
2045     qApp->processEvents();
2046
2047     std::string filename = itksys::SystemTools::GetFilenameWithoutExtension(file.toStdString()).c_str();
2048     if (mSlicerManagers[index]->SetOverlay(fileNames,dimension, component,type)) {
2049       //create an item in the tree with good settings
2050       QTreeWidgetItem *item = new QTreeWidgetItem();
2051       item->setData(0,Qt::UserRole,file.toStdString().c_str());
2052       item->setData(1,Qt::UserRole,tr("overlay"));
2053       QFileInfo fileinfo(file); //Do not show the path
2054       item->setData(COLUMN_IMAGE_NAME,Qt::DisplayRole,fileinfo.fileName());
2055       item->setToolTip(COLUMN_IMAGE_NAME, mSlicerManagers[index]->GetListOfAbsoluteFilePathInOneString("overlay").c_str());
2056       qApp->processEvents();
2057 #if VTK_MAJOR_VERSION > 5
2058       for ( unsigned int i = 0; i < mSlicerManagers[index]->GetNumberOfSlicers(); i++)
2059         mSlicerManagers[index]->GetSlicer(i)->ForceUpdateDisplayExtent();
2060 #endif
2061
2062       for (int j = 1; j <= 4; j++) {
2063         item->setData(j,Qt::CheckStateRole,DataTree->topLevelItem(index)->data(j,Qt::CheckStateRole));
2064       }
2065
2066       //Create the buttons for reload and close
2067       qApp->processEvents();
2068       QTreePushButton* cButton = new QTreePushButton;
2069       cButton->setItem(item);
2070       cButton->setColumn(COLUMN_CLOSE_IMAGE);
2071       cButton->setToolTip(tr("close image"));
2072       cButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/exit.png")));
2073       connect(cButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
2074         this,SLOT(CloseImage(QTreeWidgetItem*, int)));
2075
2076       QTreePushButton* rButton = new QTreePushButton;
2077       rButton->setItem(item);
2078       rButton->setColumn(COLUMN_RELOAD_IMAGE);
2079       rButton->setToolTip(tr("reload image"));
2080       rButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/rotateright.png")));
2081       connect(rButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
2082         this,SLOT(ReloadImage(QTreeWidgetItem*, int)));
2083
2084       DataTree->topLevelItem(index)->setExpanded(1);
2085       DataTree->topLevelItem(index)->addChild(item);
2086       DataTree->setItemWidget(item, COLUMN_CLOSE_IMAGE, cButton);
2087       DataTree->setItemWidget(item, COLUMN_RELOAD_IMAGE, rButton);
2088
2089       //set the id of the image
2090       QString id = DataTree->topLevelItem(index)->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString();
2091       item->setData(COLUMN_IMAGE_NAME,Qt::UserRole,id.toStdString().c_str());
2092       UpdateTree();
2093       qApp->processEvents();
2094       ImageInfoChanged();
2095       QApplication::restoreOverrideCursor();
2096
2097       // Update the display to update, e.g., the sliders
2098       for(int i=0; i<4; i++)
2099         DisplaySliders(index, i);
2100     } else {
2101       QApplication::restoreOverrideCursor();
2102       QString error = "Cannot import the new image.\n";
2103       error += mSlicerManagers[index]->GetLastError().c_str();
2104       QMessageBox::information(this,tr("Problem reading image !"),error);
2105     }
2106     WindowLevelChanged();
2107   }
2108   else
2109     QMessageBox::information(this,tr("Problem reading Overlay !"),"File doesn't exist!");
2110 }
2111 //------------------------------------------------------------------------------
2112
2113
2114 //------------------------------------------------------------------------------
2115 void vvMainWindow::AddROI(int index, QString file)
2116 {
2117   /*
2118   // Get slice manager
2119
2120   // Load image
2121
2122   vvImageReader * mReader = new vvImageReader;
2123   mReader->SetInputFilename(filename.toStdString());
2124   mReader->Update(IMAGE);
2125   if (mReader->GetLastError().size() != 0) {
2126   std::cerr << "Error while reading " << filename.toStdString() << std::endl;
2127   QString error = "Cannot open file \n";
2128   error += mReader->GetLastError().c_str();
2129   QMessageBox::information(this,tr("Reading problem"),error);
2130   delete mReader;
2131   return;
2132   }
2133   vvImage::Pointer roi = mReader->GetOutput();
2134
2135   // Create roi in new tool
2136   vvToolStructureSetManager::AddImage(mCurrentSlicerManager, roi);
2137   */
2138 }
2139 //------------------------------------------------------------------------------
2140
2141 //------------------------------------------------------------------------------
2142 void vvMainWindow::SelectFusionImage()
2143 {
2144   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2145
2146   if (!(CheckAddedImage(index, "fusion")) || !(CheckAddedImage(index, "fusionSequence")))
2147     return;
2148
2149   QString Extensions = EXTENSIONS;
2150   Extensions += ";;All Files (*)";
2151   QStringList files = QFileDialog::getOpenFileNames(this,tr("Load Fusion image"),mInputPathName,Extensions);
2152   if (files.isEmpty())
2153     return;
2154
2155   std::vector<std::string> vecFileNames;
2156   for (int i = 0; i < files.size(); i++) {
2157     vecFileNames.push_back(files[i].toStdString());
2158   }
2159   AddFusionImage(index,vecFileNames,vvImageReader::IMAGE);
2160 }
2161 //------------------------------------------------------------------------------
2162
2163 //------------------------------------------------------------------------------
2164 void vvMainWindow::ResetTransformationToIdentity()
2165 {
2166   std::string actorType = DataTree->selectedItems()[0]->data(1,Qt::UserRole).toString().toStdString();
2167   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2168   mSlicerManagers[index]->ResetTransformationToIdentity(actorType);
2169   ImageInfoChanged();
2170 }
2171 //------------------------------------------------------------------------------
2172
2173 //------------------------------------------------------------------------------
2174 void vvMainWindow::AddFusionImage(int index, std::vector<std::string> fileNames, vvImageReader::LoadedImageType type)
2175 {
2176   QString file(fileNames[0].c_str());
2177   if (QFile::exists(file))
2178   {
2179     mInputPathName = itksys::SystemTools::GetFilenamePath(file.toStdString()).c_str();
2180     itk::ImageIOBase::Pointer reader = itk::ImageIOFactory::CreateImageIO(
2181       file.toStdString().c_str(), itk::ImageIOFactory::ReadMode);
2182     reader->SetFileName(fileNames[0].c_str());
2183     reader->ReadImageInformation();
2184     std::string component = reader->GetComponentTypeAsString(reader->GetComponentType());
2185     int dimension = reader->GetNumberOfDimensions();
2186     QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
2187     vvProgressDialog progress("Opening fusion");
2188     qApp->processEvents();
2189
2190     std::string filename = itksys::SystemTools::GetFilenameWithoutExtension(file.toStdString()).c_str();
2191     if (mSlicerManagers[index]->SetFusion(fileNames,dimension, component,type)) {
2192       //create an item in the tree with good settings
2193       QTreeWidgetItem *item = new QTreeWidgetItem();
2194       item->setData(0,Qt::UserRole,file.toStdString().c_str());
2195       item->setData(1,Qt::UserRole,tr("fusion"));
2196       QFileInfo fileinfo(file); //Do not show the path
2197           item->setData(COLUMN_IMAGE_NAME,Qt::DisplayRole,fileinfo.fileName());
2198           item->setToolTip(COLUMN_IMAGE_NAME, mSlicerManagers[index]->GetListOfAbsoluteFilePathInOneString("fusion").c_str());
2199           qApp->processEvents();
2200 #if VTK_MAJOR_VERSION > 5
2201       for ( unsigned int i = 0; i < mSlicerManagers[index]->GetNumberOfSlicers(); i++)
2202         mSlicerManagers[index]->GetSlicer(i)->ForceUpdateDisplayExtent();
2203 #endif
2204       for (int j = 1; j <= 4; j++) {
2205         item->setData(j,Qt::CheckStateRole,DataTree->topLevelItem(index)->data(j,Qt::CheckStateRole));
2206       }
2207
2208       //Create the buttons for reload and close
2209       qApp->processEvents();
2210       QTreePushButton* cButton = new QTreePushButton;
2211       cButton->setItem(item);
2212       cButton->setColumn(COLUMN_CLOSE_IMAGE);
2213       cButton->setToolTip(tr("close image"));
2214       cButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/exit.png")));
2215       connect(cButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
2216         this,SLOT(CloseImage(QTreeWidgetItem*, int)));
2217
2218       QTreePushButton* rButton = new QTreePushButton;
2219       rButton->setItem(item);
2220       rButton->setColumn(COLUMN_RELOAD_IMAGE);
2221       rButton->setToolTip(tr("reload image"));
2222       rButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/rotateright.png")));
2223       connect(rButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
2224         this,SLOT(ReloadImage(QTreeWidgetItem*, int)));
2225
2226       DataTree->topLevelItem(index)->setExpanded(1);
2227       DataTree->topLevelItem(index)->addChild(item);
2228       DataTree->setItemWidget(item, COLUMN_CLOSE_IMAGE, cButton);
2229       DataTree->setItemWidget(item, COLUMN_RELOAD_IMAGE, rButton);
2230
2231       //set the id of the image
2232       QString id = DataTree->topLevelItem(index)->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString();
2233       item->setData(COLUMN_IMAGE_NAME,Qt::UserRole,id.toStdString().c_str());
2234       UpdateTree();
2235       qApp->processEvents();
2236       ImageInfoChanged();
2237       QApplication::restoreOverrideCursor();
2238
2239       // Update the display to update, e.g., the sliders
2240       for(int i=0; i<4; i++)
2241         DisplaySliders(index, i);
2242     } else {
2243       QApplication::restoreOverrideCursor();
2244       QString error = "Cannot import the new image.\n";
2245       error += mSlicerManagers[index]->GetLastError().c_str();
2246       QMessageBox::information(this,tr("Problem reading image !"),error);
2247     }
2248     WindowLevelChanged();
2249   }
2250   else
2251     QMessageBox::information(this,tr("Problem reading Fusion !"),"File doesn't exist!");
2252 }
2253 //------------------------------------------------------------------------------
2254 //------------------------------------------------------------------------------
2255 void vvMainWindow::AddLandmarks(int index, std::vector<std::string> files)
2256 {
2257     if (!landmarksPanel->LoadFromFile(files))
2258       QMessageBox::information(this,tr("Problem reading Landmarks !"),"File doesn't exist!");
2259
2260     landmarksPanel->SetCurrentPath(mInputPathName.toStdString());
2261     landmarksPanel->SetCurrentImage(mSlicerManagers[index]->GetFileName().c_str());
2262 }
2263
2264 //------------------------------------------------------------------------------
2265 void vvMainWindow::OpenField()
2266 {
2267   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2268
2269   if (!(CheckAddedImage(index, "vector")))
2270     return;
2271
2272   QString Extensions = "Images ( *.mhd *.mha *.vf *.nii *.nrrd *.nhdr)";
2273   // Extensions += ";;Images ( *.mha)";
2274   // Extensions += ";;VF Images ( *.vf)";
2275   // Extensions += ";;nii Images ( *.nii)";
2276   // Extensions += ";;nrrd Images ( *.nrrd)";
2277   // Extensions += ";;nhdr Images ( *.nhdr)";
2278   Extensions += ";;All Files (*)";
2279   QString file = QFileDialog::getOpenFileName(this,tr("Load deformation field"),mInputPathName,Extensions);
2280   if (!file.isEmpty())
2281     AddField(file,index);
2282 }
2283 //------------------------------------------------------------------------------
2284
2285
2286 //------------------------------------------------------------------------------
2287 void vvMainWindow::AddFieldEntry(QString filename,int index,bool from_disk)
2288 {
2289   //create an item in the tree with good settings
2290   QTreeWidgetItem *item = new QTreeWidgetItem();
2291   item->setData(0,Qt::UserRole,filename.toStdString().c_str());
2292   item->setData(1,Qt::UserRole,tr("vector"));
2293   QFileInfo fileinfo(filename); //Do not show the path
2294   item->setData(COLUMN_IMAGE_NAME,Qt::DisplayRole,fileinfo.fileName());
2295   item->setToolTip(COLUMN_IMAGE_NAME, mSlicerManagers[index]->GetListOfAbsoluteFilePathInOneString("vector").c_str());
2296   qApp->processEvents();
2297
2298   for (int j = 1; j <= 4; j++) {
2299     item->setData(j,Qt::CheckStateRole,DataTree->topLevelItem(index)->data(j,Qt::CheckStateRole));
2300   }
2301
2302   //Create the buttons for reload and close
2303   qApp->processEvents();
2304   QTreePushButton* cButton = new QTreePushButton;
2305   cButton->setItem(item);
2306   cButton->setColumn(COLUMN_CLOSE_IMAGE);
2307   cButton->setToolTip(tr("close vector field"));
2308   cButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/exit.png")));
2309   connect(cButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
2310     this,SLOT(CloseImage(QTreeWidgetItem*, int)));
2311
2312   QTreePushButton* rButton = new QTreePushButton;
2313   rButton->setItem(item);
2314   rButton->setColumn(COLUMN_RELOAD_IMAGE);
2315   rButton->setToolTip(tr("reload vector field"));
2316   rButton->setEnabled(from_disk);
2317   rButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/rotateright.png")));
2318   connect(rButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
2319     this,SLOT(ReloadImage(QTreeWidgetItem*, int)));
2320
2321   DataTree->topLevelItem(index)->setExpanded(1);
2322   DataTree->topLevelItem(index)->addChild(item);
2323   DataTree->setItemWidget(item, COLUMN_RELOAD_IMAGE, rButton);
2324   DataTree->setItemWidget(item, COLUMN_CLOSE_IMAGE, cButton);
2325
2326   //set the id of the image
2327   QString id = DataTree->topLevelItem(index)->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString();
2328   item->setData(COLUMN_IMAGE_NAME,Qt::UserRole,id.toStdString().c_str());
2329   UpdateTree();
2330   qApp->processEvents();
2331   ImageInfoChanged();
2332   QApplication::restoreOverrideCursor();
2333 }
2334 //------------------------------------------------------------------------------
2335
2336
2337 //------------------------------------------------------------------------------
2338 void vvMainWindow::AddField(vvImage::Pointer vf,QString file,int index)
2339 {
2340   QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
2341   vvSlicerManager* imageManager = mSlicerManagers[index];
2342   if (imageManager->SetVF(vf,file.toStdString())) {
2343     AddFieldEntry(file,index,false);
2344 #if VTK_MAJOR_VERSION > 5
2345       for ( unsigned int i = 0; i < mSlicerManagers[index]->GetNumberOfSlicers(); i++)
2346         mSlicerManagers[index]->GetSlicer(i)->ForceUpdateDisplayExtent();
2347 #endif
2348   } else {
2349     QString error = "Cannot import the vector field for this image.\n";
2350     error += imageManager->GetLastError().c_str();
2351     QMessageBox::information(this,tr("Problem reading VF !"),error);
2352   }
2353   QApplication::restoreOverrideCursor();
2354 }
2355 //------------------------------------------------------------------------------
2356
2357
2358 //------------------------------------------------------------------------------
2359 void vvMainWindow::AddField(QString file,int index)
2360 {
2361   if (QFile::exists(file)) {
2362     mInputPathName = itksys::SystemTools::GetFilenamePath(file.toStdString()).c_str();
2363
2364     //init the progress events
2365     QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
2366     vvProgressDialog progress("Opening " + file.toStdString());
2367     qApp->processEvents();
2368
2369     //read the vector and put it in the current mSlicerManager
2370     vvSlicerManager* imageManager = mSlicerManagers[index];
2371     qApp->processEvents();
2372
2373     std::string filename = itksys::SystemTools::GetFilenameWithoutExtension(file.toStdString()).c_str();
2374     if (imageManager->SetVF(file.toStdString())) {
2375       imageManager->Render();
2376       AddFieldEntry(file,index,true);
2377     } else {
2378       QApplication::restoreOverrideCursor();
2379       QString error = "Cannot import the vector field for this image.\n";
2380       error += imageManager->GetLastError().c_str();
2381       QMessageBox::information(this,tr("Problem reading VF !"),error);
2382     }
2383   } else
2384     QMessageBox::information(this,tr("Problem reading VF !"),"File doesn't exist!");
2385
2386 }
2387 //------------------------------------------------------------------------------
2388
2389
2390 //------------------------------------------------------------------------------
2391 void vvMainWindow::SetVFProperty(int subsampling, int scale, int log, int width, double r, double g, double b)
2392 {
2393   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2394   if (mSlicerManagers[index]->GetSlicer(0)->GetVF()) {
2395     for (int i = 0; i < 4; i++) {
2396       mSlicerManagers[index]->GetSlicer(i)->SetVFSubSampling(subsampling);
2397       mSlicerManagers[index]->GetSlicer(i)->SetVFScale(scale);
2398       mSlicerManagers[index]->GetSlicer(i)->SetVFWidth(width);
2399       mSlicerManagers[index]->GetSlicer(i)->SetVFColor(r,g,b);
2400       if (log > 0)
2401         mSlicerManagers[index]->GetSlicer(i)->SetVFLog(1);
2402       else
2403         mSlicerManagers[index]->GetSlicer(i)->SetVFLog(0);
2404     }
2405   }
2406 }
2407 //------------------------------------------------------------------------------
2408
2409
2410 //------------------------------------------------------------------------------
2411 void vvMainWindow::SetOverlayProperty(int color, int linked, double window, double level)
2412 {
2413   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2414   if (mSlicerManagers[index]->GetSlicer(0)->GetOverlay()) {
2415     mSlicerManagers[index]->SetOverlayColor(color);
2416     mSlicerManagers[index]->SetColorMap(0);
2417     mSlicerManagers[index]->SetLinkOverlayWindowLevel(linked);
2418     mSlicerManagers[index]->SetOverlayColorWindow(window);
2419     mSlicerManagers[index]->SetOverlayColorLevel(level);
2420     mSlicerManagers[index]->Render();
2421   }
2422 }
2423 //------------------------------------------------------------------------------
2424
2425 //------------------------------------------------------------------------------
2426 void vvMainWindow::SetFusionProperty(int opacity, int thresOpacity, int colormap,double window, double level, bool showLegend)
2427 {
2428   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2429   if (mSlicerManagers[index]->GetSlicer(0)->GetFusion()) {
2430     mSlicerManagers[index]->SetFusionColorMap(colormap);
2431     mSlicerManagers[index]->SetFusionOpacity(opacity);
2432     mSlicerManagers[index]->SetFusionThresholdOpacity(thresOpacity);
2433     mSlicerManagers[index]->SetFusionWindow(window);
2434     mSlicerManagers[index]->SetFusionLevel(level);
2435     mSlicerManagers[index]->SetFusionShowLegend(showLegend);
2436     mSlicerManagers[index]->SetColorMap(0);
2437     mSlicerManagers[index]->Render();
2438   }
2439 }
2440 //------------------------------------------------------------------------------
2441
2442
2443 //------------------------------------------------------------------------------
2444 void vvMainWindow::SelectFusionSequence()
2445 {
2446   //get the index of the slicer manager of the main sequence (CT)
2447   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2448
2449   if (!(CheckAddedImage(index, "fusion")) || !(CheckAddedImage(index, "fusionSequence")))
2450     return;
2451
2452   QString Extensions = EXTENSIONS;
2453   Extensions += ";;All Files (*)";
2454   QStringList files = QFileDialog::getOpenFileNames(this,tr("Load Overlay image sequence"),mInputPathName,Extensions);
2455   if (files.isEmpty())
2456     return;
2457
2458   std::vector<std::string> vecFileNames;
2459   for (int i = 0; i < files.size(); i++) {
2460     vecFileNames.push_back(files[i].toStdString());
2461   }
2462
2463   //associate the secondary sequence (US) to the main one
2464   AddFusionSequence(index,vecFileNames,vvImageReader::MERGEDWITHTIME);
2465 }
2466 //------------------------------------------------------------------------------
2467
2468
2469 //------------------------------------------------------------------------------
2470 void vvMainWindow::SelectFusionSequenceCorrespondances()
2471 {
2472   //make sure the index is right?
2473   //in the end, I should attach the temporal data to the right sequence!
2474   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2475   //in case the other sequence got selected, make sure we select the primary sequence
2476   if ( (!mSlicerManagers[index]->GetSlicer(0)->GetFusion()) && mSlicerManagers[index]->GetFusionSequenceIndexOfLinkedManager()>=0 ) {
2477     index = mSlicerManagers[index]->GetFusionSequenceIndexOfLinkedManager();
2478   }
2479
2480   //open a dialog box to find a file
2481   //QString Extensions = EXTENSIONS;
2482   QString Extensions = ";;All Files (*)";
2483   QString fileName = QFileDialog::getOpenFileName(this,tr("Load respiratory signal for fused sequence"),mInputPathName,Extensions);
2484   if (fileName.isNull())
2485     return;
2486
2487   //read it as a vector of values
2488   vnl_vector<double> tmpVect;
2489
2490   std::ifstream file;
2491   file.open(fileName.toStdString().c_str());
2492   tmpVect.read_ascii(file);
2493   file.close();
2494
2495   //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
2496   bool signalOK = true;
2497   unsigned nbFrameMain = mSlicerManagers[index]->GetImage()->GetTransform().size();
2498   unsigned nbFrameSecondary = mSlicerManagers[index]->GetFusionSequenceNbFrames();
2499   std::cout<<"nbFrameMain = "<<nbFrameMain<<", nbFrameSecondary= "<<nbFrameSecondary<<", signal size: "<<tmpVect.size()<<std::endl;
2500   std::vector<unsigned> temporalCorrespondances;
2501   if ( tmpVect.size() == nbFrameMain + nbFrameSecondary ) {
2502     for (unsigned i=0 ; i<tmpVect.size() ; i++) {
2503       if (i<nbFrameMain) { //first part of the file: i -> index in secondary seq.
2504         if ( tmpVect(i)<nbFrameSecondary ) temporalCorrespondances.push_back(tmpVect(i));
2505         else { signalOK=false; break; } //pointing outside the secondary sequence...
2506       }
2507       else { //first part of the file -> index in secondary seq.
2508         if ( tmpVect(i)<nbFrameMain ) temporalCorrespondances.push_back(tmpVect(i));
2509         else { signalOK=false; break; } //pointing outside the secondary sequence...
2510       }
2511     }
2512   }
2513   else {signalOK=false;}
2514   if (!signalOK) {//else, send a message to signal the failure...
2515     QString error = "The provided temporal correspondances is invalid - check tooltip.\n";
2516     error += "Ignoring file: " + fileName;
2517     QMessageBox::information(this,tr("Problem adding temporal correspondances!"),error);
2518     return;
2519   }
2520   else {
2521     //for convenience, associate this sequence to both the current slicer manager, and to the linked one
2522     mSlicerManagers[index]->SetFusionSequenceCorrespondances(temporalCorrespondances);
2523     mSlicerManagers[ mSlicerManagers[index]->GetFusionSequenceIndexOfLinkedManager() ]->SetFusionSequenceCorrespondances(temporalCorrespondances);
2524     overlayPanel->enableFusionSequenceTemporalSync();
2525   }
2526
2527 }
2528 //------------------------------------------------------------------------------
2529
2530
2531 //------------------------------------------------------------------------------
2532 //when this function is called index is the slicer manager index corresponding to the main sequence (CT)
2533 //the files behind fileNames points to the data for the secondary sequence
2534 void vvMainWindow::AddFusionSequence(int index, std::vector<std::string> fileNames, vvImageReader::LoadedImageType type)
2535 {
2536   QString file(fileNames[0].c_str());
2537   if (QFile::exists(file))
2538   {
2539     mInputPathName = itksys::SystemTools::GetFilenamePath(file.toStdString()).c_str();
2540     itk::ImageIOBase::Pointer reader = itk::ImageIOFactory::CreateImageIO(
2541       file.toStdString().c_str(), itk::ImageIOFactory::ReadMode);
2542     std::sort (fileNames.begin(), fileNames.end());//make sure the files are sorted.
2543     reader->SetFileName(fileNames[0].c_str());
2544     reader->ReadImageInformation();
2545     std::string component = reader->GetComponentTypeAsString(reader->GetComponentType());
2546     int dimension = reader->GetNumberOfDimensions();
2547     QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
2548     vvProgressDialog progress("Opening " + file.toStdString());
2549     qApp->processEvents();
2550
2551     std::string filename = itksys::SystemTools::GetFilenameWithoutExtension(file.toStdString()).c_str();
2552
2553     if (mSlicerManagers[index]->SetFusionSequence(fileNames,dimension, component,type)) {
2554       //create an item in the tree with good settings
2555       QTreeWidgetItem *item = new QTreeWidgetItem();
2556       item->setData(0,Qt::UserRole,file.toStdString().c_str());
2557       item->setData(1,Qt::UserRole,tr("fusionSequence"));
2558
2559       QFileInfo fileinfo(file); //Do not show the path
2560       item->setData(COLUMN_IMAGE_NAME,Qt::DisplayRole,fileinfo.fileName());
2561       item->setToolTip(COLUMN_IMAGE_NAME, mSlicerManagers[index]->GetListOfAbsoluteFilePathInOneString("fusionSequence").c_str());
2562       qApp->processEvents();
2563 #if VTK_MAJOR_VERSION > 5
2564       for ( unsigned int i = 0; i < mSlicerManagers[index]->GetNumberOfSlicers(); i++)
2565         mSlicerManagers[index]->GetSlicer(i)->ForceUpdateDisplayExtent();
2566 #endif
2567       for (int j = 1; j <= 4; j++) {
2568         item->setData(j,Qt::CheckStateRole,DataTree->topLevelItem(index)->data(j,Qt::CheckStateRole));
2569       }
2570
2571       //Create the buttons for reload and close
2572       qApp->processEvents();
2573       QTreePushButton* cButton = new QTreePushButton;
2574       cButton->setItem(item);
2575       cButton->setColumn(COLUMN_CLOSE_IMAGE);
2576       cButton->setToolTip(tr("close image"));
2577       cButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/exit.png")));
2578       connect(cButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
2579         this,SLOT(CloseImage(QTreeWidgetItem*, int)));
2580
2581       QTreePushButton* rButton = new QTreePushButton;
2582       rButton->setItem(item);
2583       rButton->setColumn(COLUMN_RELOAD_IMAGE);
2584       rButton->setToolTip(tr("reload image"));
2585       rButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/rotateright.png")));
2586       connect(rButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
2587         this,SLOT(ReloadImage(QTreeWidgetItem*, int)));
2588
2589       DataTree->topLevelItem(index)->setExpanded(1);
2590       DataTree->topLevelItem(index)->addChild(item);
2591       DataTree->setItemWidget(item, COLUMN_CLOSE_IMAGE, cButton);
2592       DataTree->setItemWidget(item, COLUMN_RELOAD_IMAGE, rButton);
2593
2594       //store the original transform matrix
2595       int indexParent = GetSlicerIndexFromItem( DataTree->topLevelItem(index) );
2596       mSlicerManagers[indexParent]->SetFusionSequenceMainTransformMatrix( mSlicerManagers[indexParent]->GetSlicer(0)->GetImage()->GetTransform()[0]->GetMatrix() );
2597
2598       //set the id of the image
2599       QString id = DataTree->topLevelItem(index)->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString();
2600       item->setData(COLUMN_IMAGE_NAME,Qt::UserRole,id.toStdString().c_str());
2601       UpdateTree();
2602       qApp->processEvents();
2603
2604       //ImageInfoChanged();
2605
2606       QApplication::restoreOverrideCursor();
2607       // Update the display to update, e.g., the sliders
2608       for(int i=0; i<4; i++)
2609         DisplaySliders(index, i);
2610
2611
2612       //This loads the secondary sequence (US) as an independent sequence
2613       LoadImages(fileNames, type);
2614       //reset the transforms to identity
2615       //FIX -- and set the thickness of the US slices to a large value (necessary for visualization purposes...)
2616       double sp_x, sp_y, sp_z;
2617       mSlicerManagers[indexParent]->GetImage()->GetVTKImages()[0]->GetSpacing(sp_x, sp_y, sp_z);
2618       sp_z = std::max(sp_x, std::max(sp_y, sp_z)) + 0.5; //
2619       for (unsigned i=0 ; i<mSlicerManagers.back()->GetImage()->GetTransform().size() ; i++) {
2620         sp_x = mSlicerManagers.back()->GetImage()->GetVTKImages()[i]->GetSpacing()[0];
2621         sp_y = mSlicerManagers.back()->GetImage()->GetVTKImages()[i]->GetSpacing()[1];
2622         mSlicerManagers.back()->GetImage()->GetVTKImages()[i]->SetSpacing( sp_x, sp_y, sp_z);
2623         mSlicerManagers.back()->GetImage()->GetTransform()[i]->Identity();
2624         mSlicerManagers.back()->GetImage()->GetTransform()[i]->Update();
2625       }
2626
2627       //automatically link both images...
2628       AddLink(mSlicerManagers[indexParent]->GetId().c_str(), mSlicerManagers.back()->GetId().c_str(), false);
2629
2630       //tie the main and secondary sequences by raising flags and informing each another of their respective SlicerManager indices
2631       mSlicerManagers[indexParent]->SetFusionSequenceIndexOfLinkedManager(mSlicerManagers.size()-1);
2632       mSlicerManagers[indexParent]->SetFusionSequenceInvolvmentCode(0); //main sequence
2633       mSlicerManagers.back()->SetFusionSequenceIndexOfLinkedManager(indexParent);
2634       mSlicerManagers.back()->SetFusionSequenceInvolvmentCode(1); //secondary sequence
2635       for (unsigned i=0 ; i<4 ; i++) {
2636         mSlicerManagers.back()->GetSlicer(i)->SetFusionSequenceCode(1); //flag the slicers of the secondary sequence
2637       }
2638
2639     } else {
2640       QApplication::restoreOverrideCursor();
2641       QString error = "Cannot import the new image.\n";
2642       error += mSlicerManagers[index]->GetLastError().c_str();
2643       QMessageBox::information(this,tr("Problem reading image !"),error);
2644     }
2645     WindowLevelChanged();
2646     ImageInfoChanged(); //this internally calls WindowLevelChanged...
2647   }
2648   else {
2649     QMessageBox::information(this,tr("Problem reading fusion sequence !"),"File doesn't exist!");
2650     return;
2651   }
2652
2653 }
2654 //------------------------------------------------------------------------------
2655
2656
2657 //------------------------------------------------------------------------------
2658 //fusionSequenceFrameIndex and fusionSequenceNbFrames are relative to the secondary sequence (US)
2659 void vvMainWindow::SetFusionSequenceProperty(int fusionSequenceFrameIndex, bool spatialSyncFlag, unsigned int fusionSequenceNbFrames, bool temporalSyncFlag)
2660 {
2661   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2662
2663   if (!mSlicerManagers[index]->IsInvolvedInFusionSequence()) return;
2664
2665   //check if the focus moved to the linked sequence, and in this case, select the master sequence instead
2666   if (!mSlicerManagers[index]->IsMainSequenceOfFusionSequence()) {
2667     index = mSlicerManagers[index]->GetFusionSequenceIndexOfLinkedManager();
2668   }
2669   int secondaryIndex = mSlicerManagers[index]->GetFusionSequenceIndexOfLinkedManager();
2670   if (secondaryIndex==-1) return; //this should never happen
2671   if ( (!mSlicerManagers[index]->IsMainSequenceOfFusionSequence()) ||
2672     (!mSlicerManagers[secondaryIndex]->IsSecondarySequenceOfFusionSequence()) )
2673   {return;} //this should never happen, raise an exception?
2674
2675   if (mSlicerManagers[index]->GetSlicer(0)->GetFusion()) {
2676
2677     //First, if the spatialSync button is unchecked, then reposition the parent sequence (CT) in its original coordinate frame
2678     if ( (!spatialSyncFlag) && (mSlicerManagers[index]->GetFusionSequenceSpatialSyncFlag()) ) {
2679       for ( unsigned i=0 ; i<mSlicerManagers[index]->GetSlicer(0)->GetImage()->GetTransform().size() ; i++ ) {
2680         mSlicerManagers[index]->GetSlicer(0)->GetImage()->GetTransform()[i]->SetMatrix( mSlicerManagers[index]->GetFusionSequenceMainTransformMatrix() );
2681         mSlicerManagers[index]->GetSlicer(0)->GetImage()->GetTransform()[i]->Update();
2682       }
2683
2684       for (int i=0; i<mSlicerManagers[index]->GetNumberOfSlicers(); i++) {
2685         mSlicerManagers[index]->GetSlicer(i)->ForceUpdateDisplayExtent();
2686         mSlicerManagers[index]->GetSlicer(i)->Render();
2687       }
2688     }
2689
2690     //then, update the property values in the slicer manager
2691     mSlicerManagers[index]->SetFusionSequenceLength(fusionSequenceNbFrames);
2692     mSlicerManagers[index]->SetFusionSequenceSpatialSyncFlag(spatialSyncFlag);
2693     mSlicerManagers[index]->SetFusionSequenceTemporalSyncFlag(temporalSyncFlag);
2694     mSlicerManagers[index]->SetFusionSequenceFrameIndex(fusionSequenceFrameIndex);
2695
2696     //select the right frame of the US sequence
2697     mSlicerManagers[index]->SetFusionSequenceTSlice(fusionSequenceFrameIndex); //here, I should only update the overlayed sequence
2698     mSlicerManagers[secondaryIndex]->SetTSlice(fusionSequenceFrameIndex, false); //this should update the secondary sequence (individual version)
2699
2700     //update the horizontal sliders of the main window
2701     overlayPanel->updateFusionSequenceSliderValueFromWindow(fusionSequenceFrameIndex, false);
2702
2703     if (spatialSyncFlag) { //reslice the CT
2704
2705       if (temporalSyncFlag) { //do the temporal synchronisation
2706         int mainSequenceFrameIndex=0;
2707         //estimate the TSlice to set to the CT
2708         unsigned nbFramesMain = mSlicerManagers[index]->GetImage()->GetTransform().size();
2709         mainSequenceFrameIndex = mSlicerManagers[index]->GetFusionSequenceCorrespondances()[ nbFramesMain + fusionSequenceFrameIndex];
2710         //and set it!
2711         mSlicerManagers[index]->SetTSlice(mainSequenceFrameIndex, false);
2712         //warning, there is a loopback, and modification of the TSlice in main sequence forces an update of the TSlice in secondary, etc...
2713       }
2714
2715
2716       //Set the transform matrix of the parent sequence (typically CT / 4DCT)
2717       vtkSmartPointer<vtkMatrix4x4> tmpMat = vtkSmartPointer<vtkMatrix4x4>::New();
2718       vtkMatrix4x4::Invert( mSlicerManagers[index]->GetFusionSequenceInitialTransformMatrixAtFrame(fusionSequenceFrameIndex), tmpMat );
2719       for ( unsigned i=0 ; i<mSlicerManagers[index]->GetSlicer(0)->GetImage()->GetTransform().size() ; i++ ) {
2720         mSlicerManagers[index]->GetSlicer(0)->GetImage()->GetTransform()[i]->SetMatrix( mSlicerManagers[index]->GetFusionSequenceMainTransformMatrix() );
2721         mSlicerManagers[index]->GetSlicer(0)->GetImage()->GetTransform()[i]->PreMultiply();
2722         mSlicerManagers[index]->GetSlicer(0)->GetImage()->GetTransform()[i]->Concatenate( tmpMat );
2723         mSlicerManagers[index]->GetSlicer(0)->GetImage()->GetTransform()[i]->Update();
2724       }
2725
2726       for (int i=0; i<mSlicerManagers[index]->GetNumberOfSlicers(); i++) {
2727         mSlicerManagers[index]->GetSlicer(i)->ForceUpdateDisplayExtent();
2728         mSlicerManagers[index]->GetSlicer(i)->Render();
2729       }
2730
2731     }
2732
2733   }
2734 }
2735 //------------------------------------------------------------------------------
2736
2737
2738 //------------------------------------------------------------------------------
2739 void vvMainWindow::SaveAs()
2740 {
2741   if (DataTree->selectedItems()[0]->data(1,Qt::UserRole).toString() == "vector") {
2742     QMessageBox::warning(this,tr("Unsupported type"),tr("Sorry, saving a vector field is unsupported for the moment"));
2743     return;
2744   }
2745
2746   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2747   int dimension = mSlicerManagers[index]->GetDimension();
2748   QStringList OutputListeFormat;
2749   OutputListeFormat.clear();
2750   if (dimension == 1) {
2751     OutputListeFormat.push_back(".mhd");
2752     OutputListeFormat.push_back(".mha");
2753   }
2754   if (dimension == 2) {
2755     OutputListeFormat.push_back(".bmp");
2756     OutputListeFormat.push_back(".png");
2757     OutputListeFormat.push_back(".jpeg");
2758     OutputListeFormat.push_back(".tif");
2759     OutputListeFormat.push_back(".mhd");
2760     OutputListeFormat.push_back(".mha");
2761     OutputListeFormat.push_back(".hdr");
2762     OutputListeFormat.push_back(".vox");
2763   } else if (dimension == 3) {
2764     OutputListeFormat.push_back(".mhd");
2765     OutputListeFormat.push_back(".mha");
2766     OutputListeFormat.push_back(".nii");
2767     OutputListeFormat.push_back(".nrrd");
2768     OutputListeFormat.push_back(".nhdr");
2769     OutputListeFormat.push_back(".hdr");
2770     OutputListeFormat.push_back(".vox");
2771   } else if (dimension == 4) {
2772     OutputListeFormat.push_back(".mhd");
2773     OutputListeFormat.push_back(".mha");
2774     OutputListeFormat.push_back(".nii");
2775     OutputListeFormat.push_back(".nrrd");
2776     OutputListeFormat.push_back(".nhdr");
2777   }
2778   QString Extensions = "AllFiles(*.*)";
2779   for (int i = 0; i < OutputListeFormat.count(); i++) {
2780     Extensions += ";;Images ( *";
2781     Extensions += OutputListeFormat[i];
2782     Extensions += ")";
2783   }
2784   QString fileName = QFileDialog::getSaveFileName(this,
2785     tr("Save As"),
2786     mSlicerManagers[index]->GetFileName().c_str(),
2787     Extensions);
2788   if (!fileName.isEmpty()) {
2789     std::string fileformat = itksys::SystemTools::GetFilenameLastExtension(fileName.toStdString());
2790     if (OutputListeFormat.contains(
2791       fileformat.c_str())) {
2792         QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
2793         std::string action = "Saving";
2794         vvProgressDialog progress("Saving "+fileName.toStdString());
2795         qApp->processEvents();
2796         vvImageWriter::Pointer writer = vvImageWriter::New();
2797         writer->SetOutputFileName(fileName.toStdString());
2798         writer->SetInput(mSlicerManagers[index]->GetImage());
2799
2800         // Check on transform and prompt user
2801         writer->SetSaveTransform(false);
2802         bool bId = true;
2803         for(int i=0; i<4; i++)
2804           for(int j=0; j<4; j++) {
2805             // TODO SR and BP: check on the list of transforms and not the first only
2806             double elt = mSlicerManagers[index]->GetImage()->GetTransform()[0]->GetMatrix()->GetElement(i,j);
2807             if(i==j && elt!=1.)
2808               bId = false;
2809             if(i!=j && elt!=0.)
2810               bId = false;
2811           }
2812           if( !bId ) {
2813             QString warning = "The image has an associated linear transform. Do you want to save it along?";
2814             QMessageBox msgBox(QMessageBox::Warning, tr("Save transform"), warning, 0, this);
2815             msgBox.addButton(tr("Yes"), QMessageBox::AcceptRole);
2816             msgBox.addButton(tr("No"), QMessageBox::RejectRole);
2817             if (msgBox.exec() == QMessageBox::AcceptRole)
2818               writer->SetSaveTransform(true);
2819           }
2820
2821           writer->Update();
2822           QApplication::restoreOverrideCursor();
2823           if (writer->GetLastError().size()) {
2824             QString error = "Saving did not succeed\n";
2825             error += writer->GetLastError().c_str();
2826             QMessageBox::information(this,tr("Saving Problem"),error);
2827             SaveAs();
2828           }
2829     } else {
2830       QString error = fileformat.c_str();
2831       if (error.isEmpty())
2832         error += "no file format specified !";
2833       else
2834         error += " format unknown !!!\n";
2835       QMessageBox::information(this,tr("Saving Problem"),error);
2836       SaveAs();
2837     }
2838   }
2839 }
2840 //------------------------------------------------------------------------------
2841
2842 //------------------------------------------------------------------------------
2843 void vvMainWindow::SaveCurrentState()
2844 {
2845   QString Extensions = "XML Files(*.xml)";
2846   QString fileName = QFileDialog::getSaveFileName(this,
2847     tr("Save Current Window State"),
2848     "",
2849     Extensions);
2850
2851   SaveCurrentStateAs(fileName.toStdString());
2852 }
2853 //------------------------------------------------------------------------------
2854
2855 //------------------------------------------------------------------------------
2856 void vvMainWindow::SaveCurrentStateAs(const std::string& stateFile)
2857 {
2858   vvSaveState save_state;
2859   save_state.Run(this, stateFile);
2860 }
2861
2862 //------------------------------------------------------------------------------
2863 void vvMainWindow::ReadSavedState()
2864 {
2865   QString Extensions = "XML Files(*.xml)";
2866   QString fileName = QFileDialog::getOpenFileName(this,
2867     tr("Load Window State"),
2868     "",
2869     Extensions);
2870
2871   ReadSavedStateFile(fileName.toStdString());
2872 }
2873 //------------------------------------------------------------------------------
2874
2875 //------------------------------------------------------------------------------
2876 void vvMainWindow::ReadSavedStateFile(const std::string& stateFile)
2877 {
2878   vvReadState read_state;
2879   read_state.Run(this, stateFile);
2880 }
2881 //------------------------------------------------------------------------------
2882
2883 //------------------------------------------------------------------------------
2884 void vvMainWindow::LinkAllImages()
2885 {
2886   linkPanel->linkAll();
2887 }
2888
2889 //------------------------------------------------------------------------------
2890 void vvMainWindow::AddLink(QString image1,QString image2,bool fromPanel)
2891 {
2892   if (!fromPanel) {
2893     // delegate to linkPanel if call came from elsewhere...
2894     linkPanel->addLinkFromIds(image1, image2);
2895     return;
2896   }
2897
2898   unsigned int sm1 = 0;
2899   unsigned int sm2 = 0;
2900
2901   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
2902     if (image1.toStdString() == mSlicerManagers[i]->GetId()) {
2903       mSlicerManagers[i]->AddLink(image2.toStdString());
2904       sm1 = i;
2905     }
2906     if (image2.toStdString() == mSlicerManagers[i]->GetId()) {
2907       mSlicerManagers[i]->AddLink(image1.toStdString());
2908       sm2 = i;
2909     }
2910   }
2911
2912   if (linkPanel->isLinkAll())   {
2913     emit UpdateLinkedNavigation(mSlicerManagers[sm1]->GetId(), mSlicerManagers[mCurrentPickedImageIndex], mSlicerManagers[mCurrentPickedImageIndex]->GetSlicer(0));
2914     emit UpdateLinkedNavigation(mSlicerManagers[sm2]->GetId(), mSlicerManagers[mCurrentPickedImageIndex], mSlicerManagers[mCurrentPickedImageIndex]->GetSlicer(0));
2915   } else {
2916     emit UpdateLinkedNavigation(mSlicerManagers[sm2]->GetId(), mSlicerManagers[sm1], mSlicerManagers[sm1]->GetSlicer(0));
2917   }
2918 }
2919
2920 //------------------------------------------------------------------------------
2921
2922
2923 //------------------------------------------------------------------------------
2924 void vvMainWindow::RemoveLink(QString image1,QString image2)
2925 {
2926   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
2927     if (image1.toStdString() == mSlicerManagers[i]->GetId()) {
2928       mSlicerManagers[i]->RemoveLink(image2.toStdString());
2929     }
2930     if (image2.toStdString() == mSlicerManagers[i]->GetId()) {
2931       mSlicerManagers[i]->RemoveLink(image1.toStdString());
2932     }
2933   }
2934 }
2935 //------------------------------------------------------------------------------
2936
2937 //------------------------------------------------------------------------------
2938 void vvMainWindow::ChangeImageWithIndexOffset(vvSlicerManager *sm, int slicer, int offset)
2939 {
2940   if(mSlicerManagers.size()==1)
2941     return;
2942
2943   int index = 0;
2944   while(sm != mSlicerManagers[index])
2945     index++;
2946   index = (index+offset+mSlicerManagers.size()) % mSlicerManagers.size();
2947
2948   QTreeWidgetItem* item = GetItemFromSlicerManager(mSlicerManagers[index]);
2949   item->setData(slicer+1,Qt::CheckStateRole,2);         //change checkbox
2950   CurrentImageChanged(mSlicerManagers[index]->GetId()); //select new image
2951   DisplayChanged(item,slicer+1);
2952 }
2953 //------------------------------------------------------------------------------
2954 void vvMainWindow::HorizontalSliderMoved(int value,int column, int slicer_index)
2955 {
2956   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
2957     if (DataTree->topLevelItem(i)->data(column,Qt::CheckStateRole).toInt() > 1) {
2958       //i is the SlicerManager that is in charge of this slicer.
2959       if (mSlicerManagers[i]->IsInvolvedInFusionSequence()) {
2960         //if the slicerManager is involved in a fusionSequence as the secondary sequence, then update the slider position in the overlay panel and everything accordingly
2961         if (mSlicerManagers[i]->IsSecondarySequenceOfFusionSequence()) {
2962           overlayPanel->updateFusionSequenceSliderValueFromWindow(value, true);
2963         }
2964         else { //if this is the primary sequence that has been modified
2965           if (mSlicerManagers[i]->GetFusionSequenceTemporalSyncFlag()) {
2966             //WARNING: for some obscure reason, there are problems when accessing mSlicerManagers[mSlicerManagers[i]->GetFusionSequenceIndexOfLinkedManager()]->GetFusionSequenceFrameIndex();
2967
2968             int estimatedValue=0;
2969             //estimate a corresponding time index for the secondary (US) sequence, and update it accordingly.
2970             estimatedValue = mSlicerManagers[i]->GetFusionSequenceCorrespondances()[ value ];
2971             //TODO: at the moment, there is a loop in TSlice modifications
2972             //modifying sequence 1 causes seq 2 to update, which in turns update seq1...
2973             //I disable control on seq1 at the moment.
2974             //overlayPanel->updateFusionSequenceSliderValueFromWindow(estimatedValue, true);
2975           }
2976         }
2977       }
2978
2979       for (int j = 0; j < 4; j++) {
2980         mSlicerManagers[i]->SetTSliceInSlicer(value,j);
2981       }
2982       mSlicerManagers[i]->GetSlicer(slicer_index)->Render();
2983       break;
2984     }
2985   }
2986 }
2987 //------------------------------------------------------------------------------
2988
2989
2990 //------------------------------------------------------------------------------
2991 void vvMainWindow::NOHorizontalSliderMoved()
2992 {
2993   // if (mCurrentTime == NOHorizontalSlider->value()) return;
2994   HorizontalSliderMoved(NOHorizontalSlider->value(),COLUMN_UL_VIEW,0);
2995   //  mCurrentTime = NOHorizontalSlider->value();
2996 }
2997 //------------------------------------------------------------------------------
2998
2999
3000 //------------------------------------------------------------------------------
3001 void vvMainWindow::NEHorizontalSliderMoved()
3002 {
3003   // if (mCurrentTime == NEHorizontalSlider->value()) return;
3004   HorizontalSliderMoved(NEHorizontalSlider->value(),COLUMN_UR_VIEW,1);
3005   //  mCurrentTime = NEHorizontalSlider->value();
3006 }
3007 //------------------------------------------------------------------------------
3008
3009
3010 //------------------------------------------------------------------------------
3011 void vvMainWindow::SOHorizontalSliderMoved()
3012 {
3013   // if (mCurrentTime == SOHorizontalSlider->value()) return;
3014   HorizontalSliderMoved(SOHorizontalSlider->value(),COLUMN_DL_VIEW,2);
3015   // mCurrentTime = SOHorizontalSlider->value();
3016 }
3017 //------------------------------------------------------------------------------
3018
3019
3020 //------------------------------------------------------------------------------
3021 void vvMainWindow::SEHorizontalSliderMoved()
3022 {
3023   // if (mCurrentTime == SEHorizontalSlider->value()) return;
3024   HorizontalSliderMoved(SEHorizontalSlider->value(),COLUMN_DR_VIEW,3);
3025   // mCurrentTime = SEHorizontalSlider->value();
3026 }
3027 //------------------------------------------------------------------------------
3028
3029 //------------------------------------------------------------------------------
3030 void vvMainWindow::NOVerticalSliderChanged()
3031 {
3032   static int value=-1;
3033   if (value == NOVerticalSlider->value()) return;
3034   else value = NOVerticalSlider->value();
3035   //  int value = NOVerticalSlider->value();
3036   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
3037     if (DataTree->topLevelItem(i)->data(COLUMN_UL_VIEW,Qt::CheckStateRole).toInt() > 1) {
3038       if (mSlicerManagers[i]->GetSlicer(0)->GetSlice() != value) {
3039         mSlicerManagers[i]->GetSlicer(0)->SetSlice(value);
3040         mSlicerManagers[i]->VerticalSliderHasChanged(0, value);
3041
3042         // If nor Update/Render -> slider not work
3043         // only render = ok navigation, but for contour Update needed but slower ?
3044
3045         mSlicerManagers[i]->UpdateSlice(0);  // <-- DS add this. Not too much update ? YES. but needed for ImageContour ...
3046         //mSlicerManagers[i]->GetSlicer(0)->Render(); // <-- DS add this, needed for contour, seems ok ? not too slow ?
3047       }
3048       break;
3049     }
3050   }
3051 }
3052 //------------------------------------------------------------------------------
3053
3054
3055 //------------------------------------------------------------------------------
3056 void vvMainWindow::NEVerticalSliderChanged()
3057 {
3058   static int value=-1;
3059   if (value == NEVerticalSlider->value()) return;
3060   else value = NEVerticalSlider->value();
3061   //  int value = NEVerticalSlider->value();
3062   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
3063     if (DataTree->topLevelItem(i)->data(COLUMN_UR_VIEW,Qt::CheckStateRole).toInt() > 1) {
3064       if (mSlicerManagers[i]->GetSlicer(1)->GetSlice() != value) {
3065         mSlicerManagers[i]->GetSlicer(1)->SetSlice(value);
3066         mSlicerManagers[i]->VerticalSliderHasChanged(1, value);
3067         mSlicerManagers[i]->UpdateSlice(1);
3068         //mSlicerManagers[i]->GetSlicer(1)->Render(); // <-- DS add this, needed for contour, seems ok ? not too slow ?
3069       }
3070       break;
3071     }
3072   }
3073 }
3074 //------------------------------------------------------------------------------
3075
3076
3077 //------------------------------------------------------------------------------
3078 void vvMainWindow::SOVerticalSliderChanged()
3079 {
3080   static int value=-1;
3081   if (value == SOVerticalSlider->value()) return;
3082   else value = SOVerticalSlider->value();
3083   //int value = SOVerticalSlider->value();
3084   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
3085     if (DataTree->topLevelItem(i)->data(COLUMN_DL_VIEW,Qt::CheckStateRole).toInt() > 1) {
3086       if (mSlicerManagers[i]->GetSlicer(2)->GetSlice() != value) {
3087         mSlicerManagers[i]->GetSlicer(2)->SetSlice(value);
3088         mSlicerManagers[i]->VerticalSliderHasChanged(2, value);
3089         mSlicerManagers[i]->UpdateSlice(2);
3090         //mSlicerManagers[i]->GetSlicer(2)->Render(); // <-- DS add this, needed for contour, seems ok ? not too slow ?
3091       }
3092       // else { DD("avoid SOVerticalSlider slicer update"); }
3093       break;
3094     }
3095   }
3096 }
3097 //------------------------------------------------------------------------------
3098
3099
3100 //------------------------------------------------------------------------------
3101 void vvMainWindow::SEVerticalSliderChanged()
3102 {
3103   static int value=-1;
3104   if (value == SEVerticalSlider->value()) return;
3105   else value = SEVerticalSlider->value();
3106   // int value = SEVerticalSlider->value();
3107   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
3108     if (DataTree->topLevelItem(i)->data(COLUMN_DR_VIEW,Qt::CheckStateRole).toInt() > 1) {
3109       if (mSlicerManagers[i]->GetSlicer(3)->GetSlice() != value) {
3110         mSlicerManagers[i]->GetSlicer(3)->SetSlice(value);
3111         mSlicerManagers[i]->VerticalSliderHasChanged(3, value);
3112         mSlicerManagers[i]->UpdateSlice(3);
3113         //mSlicerManagers[i]->GetSlicer(3)->Render(); // <-- DS add this, needed for contour, seems ok ? not too slow ?
3114       }
3115       break;
3116     }
3117   }
3118 }
3119 //------------------------------------------------------------------------------
3120
3121
3122 //------------------------------------------------------------------------------
3123 void vvMainWindow::UpdateSlice(int slicer, int slice)
3124 {
3125   // DD("vvMainWindow::UpdateSlice");
3126   //   DD(slicer);
3127   //   DD(slice);
3128   if (slicer == 0) {
3129     //    if (slice != NOVerticalSlider->value())
3130     NOVerticalSlider->setValue(slice);
3131   } else {
3132     if (slicer == 1)
3133       NEVerticalSlider->setValue(slice);
3134     else {
3135       if (slicer == 2)
3136         SOVerticalSlider->setValue(slice);
3137       else {
3138         if (slicer == 3)
3139           SEVerticalSlider->setValue(slice);
3140       }
3141     }
3142   }
3143   // DD("vvMainWindow:UpdateSlice END");
3144 }
3145 //------------------------------------------------------------------------------
3146
3147
3148 //------------------------------------------------------------------------------
3149 void vvMainWindow::UpdateTSlice(int slicer, int slice, int code)
3150 {
3151   //FusionSequence: the slider value should be updated for slicers which show the same sequence as requested
3152   bool doUpdate=false;
3153   if (code==-1) doUpdate=true;
3154   else {
3155     for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
3156       if (DataTree->topLevelItem(i)->data(slicer+1,Qt::CheckStateRole).toInt() > 1) {
3157         //i is the active SlicerManager
3158         if (mSlicerManagers[i]->GetFusionSequenceInvolvmentCode()==code) doUpdate=true;
3159         break;
3160       }
3161     }
3162   }
3163   if (!doUpdate) return;
3164
3165   switch (slicer) {
3166   case 0:
3167     if (NOHorizontalSlider->value()==slice) return;
3168     NOHorizontalSlider->setValue(slice);
3169     break;
3170   case 1:
3171     if (NEHorizontalSlider->value()==slice) return;
3172     NEHorizontalSlider->setValue(slice);
3173     break;
3174   case 2:
3175     if (SOHorizontalSlider->value()==slice) return;
3176     SOHorizontalSlider->setValue(slice);
3177     break;
3178   case 3:
3179     if (SEHorizontalSlider->value()==slice) return;
3180     SEHorizontalSlider->setValue(slice);
3181     break;
3182   }
3183 }
3184 //------------------------------------------------------------------------------
3185
3186
3187 //------------------------------------------------------------------------------
3188 void vvMainWindow::UpdateSliceRange(int slicer, int min, int max, int tmin, int tmax)
3189 {
3190   //int position = int((min+max)/2);
3191   int position = mSlicerManagers[mCurrentPickedImageIndex]->GetSlicer(slicer)->GetSlice();
3192   if (slicer == 0) {
3193     NOVerticalSlider->setRange(min,max);
3194     NOHorizontalSlider->setRange(tmin,tmax);
3195     NOVerticalSlider->setValue(position);
3196   } else if (slicer == 1) {
3197     NEVerticalSlider->setRange(min,max);
3198     NEHorizontalSlider->setRange(tmin,tmax);
3199     NEVerticalSlider->setValue(position);
3200   } else if (slicer == 2) {
3201     SOVerticalSlider->setRange(min,max);
3202     SOHorizontalSlider->setRange(tmin,tmax);
3203     SOVerticalSlider->setValue(position);
3204   } else if (slicer == 3) {
3205     SEVerticalSlider->setRange(min,max);
3206     SEHorizontalSlider->setRange(tmin,tmax);
3207     SEVerticalSlider->setValue(position);
3208   }
3209 }
3210 //------------------------------------------------------------------------------
3211
3212
3213 //------------------------------------------------------------------------------
3214 void vvMainWindow::SaveNOScreenshot()
3215 {
3216   SaveScreenshot(NOViewWidget);
3217 }
3218 //------------------------------------------------------------------------------
3219
3220
3221 //------------------------------------------------------------------------------
3222 void vvMainWindow::SaveNEScreenshot()
3223 {
3224   SaveScreenshot(NEViewWidget);
3225 }
3226 //------------------------------------------------------------------------------
3227
3228
3229 //------------------------------------------------------------------------------
3230 void vvMainWindow::SaveSOScreenshot()
3231 {
3232   SaveScreenshot(SOViewWidget);
3233 }
3234 //------------------------------------------------------------------------------
3235
3236
3237 //------------------------------------------------------------------------------
3238 void vvMainWindow::SaveSEScreenshot()
3239 {
3240   SaveScreenshot(SEViewWidget);
3241 }
3242 //------------------------------------------------------------------------------
3243
3244
3245 //------------------------------------------------------------------------------
3246 void vvMainWindow::SaveScreenshotAllSlices()
3247 {
3248   QVTKWidget *widget = NOViewWidget;
3249
3250   int index = 0;// GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
3251   vvSlicerManager * SM = mSlicerManagers[index];
3252   vvImage * image = SM->GetImage();
3253   vvSlicer * slicer = SM->GetSlicer(0);
3254   int orientation = slicer->GetOrientation();
3255   int nbSlices = image->GetSize()[orientation];
3256   vtkSmartPointer<vtkRenderWindow>  renderWindow = widget->GetRenderWindow();
3257
3258   // Select filename base
3259   QString filename = QFileDialog::getSaveFileName(this,
3260     tr("Save As (filename will be completed by slice number)"),
3261     itksys::SystemTools::GetFilenamePath(mSlicerManagers[index]->GetFileName()).c_str(),
3262     "Images( *.png);;Images( *.jpg)");
3263
3264   // Loop on slices
3265   for(int i=0; i<nbSlices; i++) {
3266     // Change the slice
3267     slicer->SetSlice(i); // -> change the slice of the current slicer
3268     SM->UpdateSlice(0); // --> this one emit UpdateSlice
3269     QCoreApplication::flush(); // -> needed to force display of contours
3270
3271     // Screenshot
3272     vtkSmartPointer<vtkWindowToImageFilter> windowToImageFilter = vtkSmartPointer<vtkWindowToImageFilter>::New();
3273     windowToImageFilter->SetInput(renderWindow);
3274     windowToImageFilter->SetMagnification(1);
3275     windowToImageFilter->SetInputBufferTypeToRGBA(); //also record the alpha (transparency) channel
3276     windowToImageFilter->Update();
3277
3278     vtkSmartPointer<vtkPNGWriter> writer = vtkSmartPointer<vtkPNGWriter>::New();
3279     std::string fn = itksys::SystemTools::GetFilenameWithoutLastExtension(filename.toStdString());
3280     std::string num = clitk::toString(i);
3281     if (i<10) num = "0"+num;
3282     if (i<100) num = "0"+num;
3283     if (i<1000) num = "0"+num;
3284
3285     fn = itksys::SystemTools::GetFilenamePath(filename.toStdString()) + "/"+ fn
3286       + "_" + num + itksys::SystemTools::GetFilenameLastExtension(filename.toStdString());
3287     writer->SetFileName(fn.c_str());
3288 #if VTK_MAJOR_VERSION <= 5
3289     writer->SetInput(windowToImageFilter->GetOutput());
3290 #else
3291     writer->SetInputConnection(windowToImageFilter->GetOutputPort());
3292 #endif
3293     writer->Write();
3294   }
3295 }
3296 //------------------------------------------------------------------------------
3297
3298
3299 //------------------------------------------------------------------------------
3300 void vvMainWindow::SaveScreenshot(QVTKWidget *widget)
3301 {
3302   QString Extensions = "Images( *.png);;";
3303   Extensions += "Images( *.jpg);;";
3304   Extensions += "Images( *.bmp);;";
3305   Extensions += "Images( *.tif);;";
3306   Extensions += "Images( *.ppm)";
3307 #if defined(VTK_USE_FFMPEG_ENCODER) || defined(VTK_USE_VIDEO_FOR_WINDOWS)
3308   Extensions += ";;Video( *.avi)";
3309 #endif
3310 #ifdef VTK_USE_MPEG2_ENCODER
3311   Extensions += ";;Video( *.mpg)";
3312 #endif
3313 #ifdef CLITK_EXPERIMENTAL
3314   Extensions += ";;Video( *.gif)";
3315 #endif
3316
3317   int smIndex=GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
3318   QString fileName = QFileDialog::getSaveFileName(this,
3319     tr("Save As"),
3320     itksys::SystemTools::GetFilenamePath(mSlicerManagers[smIndex]->GetFileName()).c_str(),
3321     Extensions);
3322
3323   if (!fileName.isEmpty()) {
3324     vtkSmartPointer<vtkWindowToImageFilter> w2i = vtkSmartPointer<vtkWindowToImageFilter>::New();
3325     w2i->SetInput(widget->GetRenderWindow());
3326     w2i->SetMagnification(1);
3327     w2i->SetInputBufferTypeToRGBA(); //also record the alpha (transparency) channel
3328     w2i->Update();
3329     vtkImageData *image = w2i->GetOutput();
3330
3331     std::string ext(itksys::SystemTools::GetFilenameLastExtension(fileName.toStdString()));
3332
3333     // Image
3334     vtkImageWriter *imgwriter = NULL;
3335     if (ext==".bmp")
3336       imgwriter = vtkBMPWriter::New();
3337     else if (ext==".tif")
3338       imgwriter = vtkTIFFWriter::New();
3339     else if (ext==".ppm")
3340       imgwriter = vtkPNMWriter::New();
3341     else if (ext==".png")
3342       imgwriter = vtkPNGWriter::New();
3343     else if (ext==".jpg")
3344       imgwriter = vtkJPEGWriter::New();
3345
3346     // Snapshot image if not null
3347     if(imgwriter!=NULL) {
3348 #if VTK_MAJOR_VERSION <= 5
3349       imgwriter->SetInput(image);
3350 #else
3351       imgwriter->SetInputConnection(w2i->GetOutputPort());
3352 #endif
3353       imgwriter->SetFileName(fileName.toStdString().c_str());
3354       imgwriter->Write();
3355       return;
3356     }
3357
3358     // Video
3359     vtkGenericMovieWriter *vidwriter = NULL;
3360 #if CLITK_EXPERIMENTAL == 1
3361     if (ext==".gif") {
3362       vvAnimatedGIFWriter *gif = vvAnimatedGIFWriter::New();
3363       vidwriter = gif;
3364
3365       // FPS
3366       bool ok;
3367       int fps = QInputDialog::getInt(this, tr("Number of frames per second"),
3368         tr("FPS:"), 5, 0, 1000, 1, &ok);
3369       if(ok)
3370         gif->SetRate(fps);
3371
3372       // Loops
3373       int loops = QInputDialog::getInt(this, tr("Loops"),
3374         tr("Number of loops (0 means infinite):"), 0, 0, 1000000000, 1, &ok);
3375       if(ok)
3376         gif->SetLoops(loops);
3377
3378       // Dithering
3379       QString msg = "Would you like to activate dithering?";
3380       QMessageBox msgBox(QMessageBox::Question, tr("Dithering"),msg, 0, this);
3381       msgBox.addButton(tr("Yes"), QMessageBox::AcceptRole);
3382       msgBox.addButton(tr("No"), QMessageBox::RejectRole);
3383       gif->SetDither(msgBox.exec() == QMessageBox::AcceptRole);
3384     }
3385 #endif
3386 #ifdef VTK_USE_VIDEO_FOR_WINDOWS
3387     if (ext==".avi") {
3388       vtkAVIWriter *mpg = vtkAVIWriter::New();
3389       vidwriter = mpg;
3390       mpg->SetQuality(2);
3391       bool ok;
3392       int fps = QInputDialog::getInt(this, tr("Number of frames per second"),
3393         tr("FPS:"), 5, 0, 1024, 1, &ok);
3394       if(!ok)
3395         fps = 5;
3396       mpg->SetRate(fps);
3397     }
3398 #endif
3399 #ifdef VTK_USE_FFMPEG_ENCODER
3400     if (ext==".avi") {
3401       vtkFFMPEGWriter *mpg = vtkFFMPEGWriter::New();
3402       vidwriter = mpg;
3403       mpg->SetQuality(2);
3404       bool ok;
3405       int fps = QInputDialog::getInt(this, tr("Number of frames per second"),
3406         tr("FPS:"), 5, 0, 1024, 1, &ok);
3407       if(!ok)
3408         fps = 5;
3409       mpg->SetRate(fps);
3410       mpg->SetBitRateTolerance(int(ceil(12.0*1024*1024/fps)));
3411     }
3412 #endif
3413 #ifdef VTK_USE_MPEG2_ENCODER
3414     if (ext==".mpg") {
3415       vtkMPEG2Writer *mpg = vtkMPEG2Writer::New();
3416       vidwriter = mpg;
3417     }
3418 #endif
3419
3420     // Take video if not null
3421     if(vidwriter!=NULL){
3422 #if VTK_MAJOR_VERSION <= 5
3423       vidwriter->SetInput(image);
3424 #else
3425       vidwriter->SetInputConnection(w2i->GetOutputPort());
3426 #endif
3427       vidwriter->SetFileName(fileName.toStdString().c_str());
3428       vidwriter->Start();
3429       int nSlice = mSlicerManagers[smIndex]->GetSlicer(0)->GetTMax();
3430       for(int i=0; i<=nSlice; i++) {
3431         mSlicerManagers[smIndex]->SetNextTSlice(0);
3432         vtkSmartPointer<vtkWindowToImageFilter> w2i = vtkSmartPointer<vtkWindowToImageFilter>::New();
3433         w2i->SetInput(widget->GetRenderWindow());
3434         w2i->Update();
3435 #if VTK_MAJOR_VERSION <= 5
3436         vidwriter->SetInput(w2i->GetOutput());
3437 #else
3438         vidwriter->SetInputConnection(w2i->GetOutputPort());
3439 #endif
3440         vidwriter->Write();
3441       }
3442       vidwriter->End();
3443       vidwriter->Delete();
3444       return;
3445     }
3446
3447     QMessageBox::information(this,tr("Problem saving screenshot !"),tr("Cannot save image.\nPlease set a file extension !!!"));
3448   }
3449 }
3450 //------------------------------------------------------------------------------
3451
3452
3453 //------------------------------------------------------------------------------
3454 void vvMainWindow::GoToCursor()
3455 {
3456   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
3457   for (int column = 1; column < 5; column++) {
3458     if (DataTree->selectedItems()[0]->data(column,Qt::CheckStateRole).toInt() > 1) {
3459       double* cursorPos = mSlicerManagers[index]->GetSlicer(column-1)->GetCursorPosition();
3460       mSlicerManagers[index]->GetSlicer(column-1)->SetCurrentPosition(
3461         cursorPos[0],cursorPos[1],cursorPos[2],cursorPos[3]);
3462       mSlicerManagers[index]->UpdateViews(1,column-1);
3463       mSlicerManagers[index]->UpdateLinked(column-1);
3464       break;
3465     }
3466   }
3467 }
3468 //------------------------------------------------------------------------------
3469
3470 //------------------------------------------------------------------------------
3471 void vvMainWindow::GoToLandmark()
3472 {
3473   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
3474   for (int column = 1; column < 5; column++) {
3475     if (DataTree->selectedItems()[0]->data(column,Qt::CheckStateRole).toInt() > 1) {
3476       double* cursorPos = landmarksPanel->GetSelectedPoint();
3477       mSlicerManagers[index]->GetSlicer(column-1)->SetCurrentPosition(
3478         cursorPos[0],cursorPos[1],cursorPos[2],cursorPos[3]);
3479       mSlicerManagers[index]->UpdateViews(1,column-1);
3480       mSlicerManagers[index]->UpdateLinked(column-1);
3481       break;
3482     }
3483   }
3484 }
3485 //------------------------------------------------------------------------------
3486
3487 //------------------------------------------------------------------------------
3488 void vvMainWindow::PlayPause()
3489 {
3490   if (playMode) {
3491     playMode = 0;
3492     playButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/player_play.png")));
3493     ImageInfoChanged();
3494     return;
3495   } else {
3496     int image_number=DataTree->topLevelItemCount();
3497     bool has_temporal;
3498     for (int i=0; i<image_number; i++)
3499       if (mSlicerManagers[i]->GetSlicer(0)->GetTMax() > 0) {
3500         has_temporal=true;
3501         break;
3502       }
3503       if (has_temporal) {
3504         playMode = 1;
3505         playButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/player_pause.png")));
3506         QTimer::singleShot(1000/mFrameRate, this, SLOT(PlayNext()));
3507       }
3508   }
3509 }
3510 //------------------------------------------------------------------------------
3511
3512 //------------------------------------------------------------------------------
3513 void vvMainWindow::PlayNext()
3514 {
3515   if (playMode && !this->isHidden()) {
3516     int image_number=DataTree->topLevelItemCount();
3517     ///Only play one slicer per SM, and only if the SM is being displayed
3518     for (int i=0; i<image_number; i++)
3519       for (int j=0; j<4; j++)
3520         if (mSlicerManagers[i]->GetSlicer(0)->GetTMax() > 0 &&
3521           DataTree->topLevelItem(i)->data(j+1,Qt::CheckStateRole).toInt() > 0) {
3522             mSlicerManagers[i]->SetNextTSlice(j);
3523             break;
3524         }
3525         QTimer::singleShot(1000/mFrameRate, this, SLOT(PlayNext()));
3526   }
3527 }
3528 //------------------------------------------------------------------------------
3529
3530 void vvMainWindow::ShowLastImage()
3531 {
3532   if (mSlicerManagers.size() > 1) {
3533     QTreeWidgetItem * item=DataTree->topLevelItem(DataTree->topLevelItemCount()-1);
3534     CurrentImageChanged(mSlicerManagers.back()->GetId()); //select new image
3535     item->setData(1,Qt::CheckStateRole,2); //show the new image in the first panel
3536     //mSlicerManagers[GetSlicerIndexFromItem(item)]->GetSlicer(0)->SetActorVisibility("image", 0, 1); //Set the Last Image visibles
3537     DisplayChanged(item,1);
3538   }
3539 }
3540
3541 //------------------------------------------------------------------------------
3542 void vvMainWindow::UpdateRenderWindows()
3543 {
3544   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
3545       for (unsigned int j = 0; j < 4; ++j) {
3546         mSlicerManagers[i]->GetSlicer(j)->RemoveLandmarks();
3547         mSlicerManagers[i]->GetSlicer(j)->DisplayLandmarks();
3548       }
3549   }
3550   if (NOViewWidget->GetRenderWindow()) NOViewWidget->GetRenderWindow()->Render();
3551   if (NEViewWidget->GetRenderWindow()) NEViewWidget->GetRenderWindow()->Render();
3552   if (SOViewWidget->GetRenderWindow()) SOViewWidget->GetRenderWindow()->Render();
3553   if (SEViewWidget->GetRenderWindow()) SEViewWidget->GetRenderWindow()->Render();
3554 }
3555 //------------------------------------------------------------------------------
3556
3557 //------------------------------------------------------------------------------
3558 void vvMainWindow::SegmentationOnCurrentImage()
3559 {
3560   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
3561
3562   vvSegmentationDialog segmentation;
3563   segmentation.SetImage(mSlicerManagers[index]->GetSlicer(0)->GetImage());
3564   segmentation.exec();
3565 }
3566 //------------------------------------------------------------------------------
3567
3568 void vvMainWindow::SurfaceViewerLaunch()
3569 {
3570   vvSurfaceViewerDialog surfaceViewer;
3571   surfaceViewer.exec();
3572 }
3573 //------------------------------------------------------------------------------
3574
3575
3576 //------------------------------------------------------------------------------
3577 int vvMainWindow::GetImageDuplicateFilenameNumber(std::string filename)
3578 {
3579   int number=0;
3580   for(unsigned int l=0; l<mSlicerManagers.size(); l++) {
3581     vvSlicerManager * v = mSlicerManagers[l];
3582     if (v->GetBaseFileName() ==
3583       vtksys::SystemTools::GetFilenameName(vtksys::SystemTools::GetFilenameWithoutLastExtension(filename))) {
3584         number = std::max(number, v->GetBaseFileNameNumber()+1);
3585     }
3586   }
3587   return number;
3588 }
3589 //------------------------------------------------------------------------------
3590
3591
3592 //------------------------------------------------------------------------------
3593 vvSlicerManager* vvMainWindow::AddImage(vvImage::Pointer image,std::string filename)
3594 {
3595   // Change filename if another image exist with the same name
3596   int number = GetImageDuplicateFilenameNumber(filename);
3597
3598   // Create new SliceManager
3599   vvSlicerManager* slicer_manager = new vvSlicerManager(4);
3600   slicer_manager->SetImage(image);//, IMAGE, number);
3601   //  filename = filename+"_"+clitk::toString(number);
3602   slicer_manager->SetFilename(filename, number);
3603   mSlicerManagers.push_back(slicer_manager);
3604
3605   //create an item in the tree with good settings
3606   QTreeWidgetItem *item = new QTreeWidgetItem();
3607   item->setData(0,Qt::UserRole,slicer_manager->GetFileName().c_str());//files[i].c_str());
3608   item->setData(1,Qt::UserRole,tr("image"));
3609   item->setData(COLUMN_IMAGE_NAME,Qt::DisplayRole,slicer_manager->GetFileName().c_str());//filename.c_str());
3610   qApp->processEvents();
3611
3612   for (int j = 1; j <= 4; j++) item->setData(j,Qt::CheckStateRole,1);
3613
3614   //Create the buttons for reload and close
3615   qApp->processEvents();
3616   QTreePushButton* cButton = new QTreePushButton;
3617   cButton->setItem(item);
3618   cButton->setColumn(COLUMN_CLOSE_IMAGE);
3619   cButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/exit.png")));
3620   connect(cButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
3621     this,SLOT(CloseImage(QTreeWidgetItem*, int)));
3622
3623   QTreePushButton* rButton = new QTreePushButton;
3624   rButton->setItem(item);
3625   rButton->setColumn(COLUMN_RELOAD_IMAGE);
3626   rButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/rotateright.png")));
3627   rButton->setEnabled(0);
3628   connect(rButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
3629     this,SLOT(ReloadImage(QTreeWidgetItem*, int)));
3630
3631   DataTree->addTopLevelItem(item);
3632   DataTree->setItemWidget(item, COLUMN_CLOSE_IMAGE, cButton);
3633   DataTree->setItemWidget(item, COLUMN_RELOAD_IMAGE, rButton);
3634
3635   //set the id of the image
3636   QString id = QDir::current().absoluteFilePath(slicer_manager->GetFileName().c_str()) + QString::number(mSlicerManagers.size()-1);
3637   item->setData(COLUMN_IMAGE_NAME,Qt::UserRole,id.toStdString().c_str());
3638   mSlicerManagers.back()->SetId(id.toStdString());
3639
3640   linkPanel->addImage(slicer_manager->GetFileName().c_str()// filename
3641     , id.toStdString());
3642
3643   connect(mSlicerManagers.back(), SIGNAL(currentImageChanged(std::string)),
3644     this, SLOT(CurrentImageChanged(std::string)));
3645   connect(mSlicerManagers.back(), SIGNAL(currentPickedImageChanged(std::string)),
3646     this, SLOT(CurrentPickedImageChanged(std::string)));
3647   connect(mSlicerManagers.back(), SIGNAL(UpdatePosition(int, double, double, double, double, double, double, double)),
3648     this, SLOT(MousePositionChanged(int,double, double, double, double, double, double, double)));
3649   connect(mSlicerManagers.back(), SIGNAL(UpdateVector(int, double, double, double, double)),
3650     this, SLOT(VectorChanged(int,double,double,double, double)));
3651   connect(mSlicerManagers.back(), SIGNAL(UpdateOverlay(int, double, double)),
3652     this, SLOT(OverlayChanged(int,double,double)));
3653   connect(mSlicerManagers.back(), SIGNAL(UpdateFusion(int, double)),
3654     this, SLOT(FusionChanged(int,double)));
3655   //connect(mSlicerManagers.back(), SIGNAL(UpdateFusionSequence(int, bool, unsigned int)),
3656   //  this, SLOT(FusionSequenceChanged(int, bool, unsigned int)));
3657   connect(mSlicerManagers.back(), SIGNAL(WindowLevelChanged()),
3658     this,SLOT(WindowLevelChanged()));
3659   connect(mSlicerManagers.back(), SIGNAL(UpdateSlice(int,int)),
3660     this,SLOT(UpdateSlice(int,int)));
3661   connect(mSlicerManagers.back(), SIGNAL(UpdateTSlice(int, int, int)),
3662     this,SLOT(UpdateTSlice(int, int, int)));
3663   connect(mSlicerManagers.back(), SIGNAL(UpdateTSlice(int, int, int)),
3664     this,SLOT(ImageInfoChanged()));
3665   connect(mSlicerManagers.back(), SIGNAL(UpdateSliceRange(int,int,int,int,int)),
3666     this,SLOT(UpdateSliceRange(int,int,int,int,int)));
3667   connect(mSlicerManagers.back(), SIGNAL(UpdateLinkManager(std::string,int,double,double,double,int)),
3668     this,SLOT(UpdateLinkManager(std::string,int,double,double,double,int)));
3669   connect(mSlicerManagers.back(), SIGNAL(UpdateLinkedNavigation(std::string,vvSlicerManager*,vvSlicer*)),
3670     this,SLOT(UpdateLinkedNavigation(std::string,vvSlicerManager*,vvSlicer*)));
3671   connect(mSlicerManagers.back(), SIGNAL(ChangeImageWithIndexOffset(vvSlicerManager*,int,int)),
3672     this,SLOT(ChangeImageWithIndexOffset(vvSlicerManager*,int,int)));
3673   connect(mSlicerManagers.back(), SIGNAL(LandmarkAdded()),landmarksPanel,SLOT(AddPoint()));
3674
3675
3676
3677   InitSlicers();
3678   UpdateTree();
3679   qApp->processEvents();
3680   InitDisplay();
3681   ShowLastImage();
3682   qApp->processEvents();
3683   // End
3684   ImageInfoChanged();
3685   return slicer_manager;
3686 }
3687 //------------------------------------------------------------------------------
3688
3689
3690 //------------------------------------------------------------------------------
3691 void vvMainWindow::UpdateCurrentSlicer()
3692 {
3693   int index = -1;
3694   if (DataTree->selectedItems().size() > 0) {
3695     index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
3696   }
3697   mSlicerManagerCurrentIndex = index;
3698 }
3699 //------------------------------------------------------------------------------