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
  27 // VV include
  28 #include "vvMainWindow.h"
  29 #include "vvHelpDialog.h"
  30 #include "vvRegisterForm.h"
  31 #include "vvDocumentation.h"
  32 #include "vvProgressDialog.h"
  33 #include "vvQDicomSeriesSelector.h"
  34 #include "vvSlicerManager.h"
  35 #include "clitkImageCommon.h"
  36 #include "vvSlicer.h"
  37 #include "vvInteractorStyleNavigator.h"
  38 #include "vvImageWriter.h"
  39 #include "vvSegmentationDialog.h"
  40 #include "vvSurfaceViewerDialog.h"
  41 #include "vvDeformationDialog.h"
  42 #include "vvImageWarp.h"
  43 #include "vvUtils.h"
  44 #include "vvMidPosition.h"
  45 #include "vvMesh.h"
  46 #include "vvStructSelector.h"
  47 #include "vvMeshReader.h"
  48 #include "vvSaveState.h"
  49 #include "vvReadState.h"
  50 #include "clitkConfiguration.h"
  51
  52 // ITK include
  53 #include <itkImage.h>
  54 #include <itkImageFileReader.h>
  55 #include <itkByteSwapper.h>
  56 #include <itkCommand.h>
  57 #include <itkNumericSeriesFileNames.h>
  58
  59 // VTK include
  60 #include <vtkImageData.h>
  61 #include <vtkImageActor.h>
  62 #include <vtkCornerAnnotation.h>
  63 #include <vtkRenderWindow.h>
  64 #include <vtkRenderWindowInteractor.h>
  65 #include <vtkRenderer.h>
  66 #include <vtkRendererCollection.h>
  67 #include <vtkWindowToImageFilter.h>
  68 #include <vtkBMPWriter.h>
  69 #include <vtkTIFFWriter.h>
  70 #include <vtkPNMWriter.h>
  71 #include <vtkPNGWriter.h>
  72 #include <vtkJPEGWriter.h>
  73 #include <vtkGenericMovieWriter.h>
  74 #ifdef CLITK_EXPERIMENTAL
  75 #  include <vvAnimatedGIFWriter.h>
  76 #endif
  77 #ifdef VTK_USE_VIDEO_FOR_WINDOWS
  78 #  include <vtkAVIWriter.h>
  79 #endif
  80 #ifdef VTK_USE_FFMPEG_ENCODER
  81 #  include <vtkFFMPEGWriter.h>
  82 #endif
  83 #ifdef VTK_USE_MPEG2_ENCODER
  84 #  include <vtkMPEG2Writer.h>
  85 #endif
  86 #include <vtkMatrix4x4.h>
  87 #include <vtkTransform.h>
  88
  89 // Standard includes
  90 #include <iostream>
  91 #include <sstream>
  92 #include <iomanip>
  93
  94 #define COLUMN_TREE 0
  95 #define COLUMN_UL_VIEW 1
  96 #define COLUMN_UR_VIEW 2
  97 #define COLUMN_DL_VIEW 3
  98 #define COLUMN_DR_VIEW 4
  99 #define COLUMN_CLOSE_IMAGE 5
 100 #define COLUMN_RELOAD_IMAGE 6
 101 #define COLUMN_IMAGE_NAME 7
 102
 103 #ifdef CLITK_PRIVATE_FEATURES
 104 #define EXTENSIONS "Images ( *.bmp *.png *.jpeg *.jpg *.tif *.mhd *.mha *.hdr *.vox *.his *.xdr *.SCAN *.nii *.nrrd *.nhdr *.refscan *.nii.gz *.usf)"
 105 #else
 106 #define EXTENSIONS "Images ( *.bmp *.png *.jpeg *.jpg *.tif *.mhd *.mha *.hdr *.vox *.his *.xdr *.SCAN *.nii *.nrrd *.nhdr *.refscan *.nii.gz)"
 107 #endif
 108
 109
 110 /*Data Tree values
 111   0,Qt::UserRole full filename
 112   1,Qt::CheckStateRole checkbutton UL View
 113   1,Qt::UserRole overlay, fusion or vector
 114   2,Qt::CheckStateRole checkbutton UR View
 115   3,Qt::CheckStateRole checkbutton DL View
 116   4,Qt::CheckStateRole checkbutton DR View
 117   5,0  short filename
 118   5,Qt::UserRole mSlicerManager id*/
 119
 120 //------------------------------------------------------------------------------
 121 vvMainWindow::vvMainWindow():vvMainWindowBase()
 122 {
 123   setupUi(this); // this sets up the GUI
 124
 125   mInputPathName = "";
 126   mMenuTools = menuTools;
 127   //  mMenuSegmentation = menuSegmentation;
 128   mContextMenu = &contextMenu;
 129   mMenuExperimentalTools = menuExperimental;
 130   mMainWidget = this;
 131   mCurrentTime = -1;
 132   mCurrentSelectedImageId = "";
 133   mCurrentPickedImageId = "";
 134   mCurrentPickedImageIndex = 0;
 135
 136   //Init the contextMenu
 137   this->setContextMenuPolicy(Qt::CustomContextMenu);
 138   contextActions.resize(0);
 139   QAction* actionOpen_new_image = contextMenu.addAction(QIcon(QString::fromUtf8(":/common/icons/fileopen.png")),
 140                                   tr("O&pen new Image"));
 141   actionOpen_new_image->setShortcut(QKeySequence(tr("Ctrl+O")));
 142   connect(actionOpen_new_image,SIGNAL(triggered()),this,SLOT(OpenImages()));
 143   contextActions.push_back(actionOpen_new_image);
 144   contextMenu.addSeparator();
 145
 146   QAction* actionClose_Image = contextMenu.addAction(QIcon(QString::fromUtf8(":/common/icons/exit.png")),
 147                                tr("Close Current Image"));
 148   connect(actionClose_Image,SIGNAL(triggered()),this,SLOT(CloseImage()));
 149   contextActions.push_back(actionClose_Image);
 150
 151   QAction* actionReload_image = contextMenu.addAction(QIcon(QString::fromUtf8(":/common/icons/rotateright.png")),
 152                                 tr("Reload Current Image"));
 153   connect(actionReload_image,SIGNAL(triggered()),this,SLOT(ReloadImage()));
 154   contextActions.push_back(actionReload_image);
 155
 156   QAction* actionSave_image = contextMenu.addAction(QIcon(QString::fromUtf8(":/common/icons/filesave.png")),
 157                               tr("Save Current Image"));
 158   connect(actionSave_image,SIGNAL(triggered()),this,SLOT(SaveAs()));
 159   contextActions.push_back(actionSave_image);
 160
 161   QAction* actionSave_state = contextMenu.addAction(QIcon(QString::fromUtf8(":/common/icons/filesave.png")),
 162                               tr("Save Current State"));
 163   connect(actionSave_state,SIGNAL(triggered()),this,SLOT(SaveCurrentState()));
 164   contextActions.push_back(actionSave_state);
 165
 166   QAction* actionRead_state = contextMenu.addAction(QIcon(QString::fromUtf8(":/common/icons/filesave.png")),
 167                               tr("Read Saved State"));
 168   connect(actionRead_state,SIGNAL(triggered()),this,SLOT(ReadSavedState()));
 169   contextActions.push_back(actionRead_state);
 170
 171   contextMenu.addSeparator();
 172
 173   contextMenu.addAction(actionAdd_VF_to_current_Image);
 174   contextActions.push_back(actionAdd_VF_to_current_Image);
 175
 176   //QAction* actionAdd_Overlay_to_current_Image = menuOverlay->addAction(QIcon(QString::fromUtf8(":/common/icons/GPSup.png")),
 177   //    tr("Add overlay image to current image"));
 178   contextMenu.addAction(actionAdd_overlay_image_to_current_image);
 179   contextActions.push_back(actionAdd_overlay_image_to_current_image);
 180
 181   contextMenu.addAction(actionAdd_fusion_image);
 182   contextActions.push_back(actionAdd_fusion_image);
 183
 184   contextMenu.addSeparator();
 185   QAction* actionResetMatrix = contextMenu.addAction(QIcon(QString::fromUtf8(":/common/icons/identity.png")),
 186                                                       tr("Reset transformation to identity"));
 187   connect(actionResetMatrix, SIGNAL(triggered()), this,SLOT(ResetTransformationToIdentity()));
 188
 189   // TRIAL DS
 190   /*
 191   QMenu * m = new QMenu(menubar);
 192   m->setTitle("TOTO");
 193   //  m->setObjectName(QString::fromUtf8("TOTOTO"));
 194   contextMenu.addMenu(m);
 195   QAction * a = m->addAction(QIcon(QString::fromUtf8(":/common/icons/GPSup.png")),
 196                      tr("BIDON"));
 197   QAction * b = m->addAction(QIcon(QString::fromUtf8(":/common/icons/GPSup.png")),
 198                      tr("BIDON2"));
 199   m->addAction(a);
 200   m->addAction(b);
 201   connect(a,SIGNAL(triggered()),this,SLOT(AddFusionImage()));
 202   */
 203
 204   //init the DataTree
 205   mSlicerManagers.resize(0);
 206
 207   QStringList header;
 208   header.append("");
 209   header.append("TL");
 210   header.append("TR");
 211   header.append("BL");
 212   header.append("BR");
 213   header.append("");
 214   header.append("");
 215   header.append("Name");
 216
 217   DataTree->setHeaderLabels(header);
 218   DataTree->resizeColumnToContents(COLUMN_TREE);
 219   DataTree->resizeColumnToContents(COLUMN_UL_VIEW);
 220   DataTree->resizeColumnToContents(COLUMN_UR_VIEW);
 221   DataTree->resizeColumnToContents(COLUMN_DL_VIEW);
 222   DataTree->resizeColumnToContents(COLUMN_DR_VIEW);
 223   DataTree->resizeColumnToContents(COLUMN_CLOSE_IMAGE);
 224   DataTree->resizeColumnToContents(COLUMN_RELOAD_IMAGE);
 225   DataTree->resizeColumnToContents(COLUMN_IMAGE_NAME);
 226
 227   viewMode = 1;
 228   documentation = new vvDocumentation();
 229   help_dialog = new vvHelpDialog();
 230   dicomSeriesSelector = new vvDicomSeriesSelector();
 231
 232   inverseButton->setEnabled(0);
 233   actionAdd_overlay_image_to_current_image->setEnabled(0);
 234   actionSave_As->setEnabled(0);
 235   actionAdd_VF_to_current_Image->setEnabled(0);
 236   actionAdd_fusion_image->setEnabled(0);
 237
 238   //init the sliders
 239   verticalSliders.push_back(NOVerticalSlider);
 240   verticalSliders.push_back(NEVerticalSlider);
 241   verticalSliders.push_back(SOVerticalSlider);
 242   verticalSliders.push_back(SEVerticalSlider);
 243
 244   for (int i =0; i < 4; i++)
 245     verticalSliders[i]->hide();
 246
 247   horizontalSliders.push_back(NOHorizontalSlider);
 248   horizontalSliders.push_back(NEHorizontalSlider);
 249   horizontalSliders.push_back(SOHorizontalSlider);
 250   horizontalSliders.push_back(SEHorizontalSlider);
 251
 252   for (int i =0; i < 4; i++)
 253     horizontalSliders[i]->hide();
 254
 255
 256   connect(NOVerticalSlider,SIGNAL(valueChanged(int)),this,SLOT(NOVerticalSliderChanged()));
 257   connect(NEVerticalSlider,SIGNAL(valueChanged(int)),this,SLOT(NEVerticalSliderChanged()));
 258   connect(SOVerticalSlider,SIGNAL(valueChanged(int)),this,SLOT(SOVerticalSliderChanged()));
 259   connect(SEVerticalSlider,SIGNAL(valueChanged(int)),this,SLOT(SEVerticalSliderChanged()));
 260
 261   connect(NOHorizontalSlider,SIGNAL(valueChanged(int)),this,SLOT(NOHorizontalSliderMoved()));
 262   connect(NEHorizontalSlider,SIGNAL(valueChanged(int)),this,SLOT(NEHorizontalSliderMoved()));
 263   connect(SOHorizontalSlider,SIGNAL(valueChanged(int)),this,SLOT(SOHorizontalSliderMoved()));
 264   connect(SEHorizontalSlider,SIGNAL(valueChanged(int)),this,SLOT(SEHorizontalSliderMoved()));
 265
 266   //connect everything
 267   connect(actionCompute_mid_position_image,SIGNAL(triggered()),this,SLOT(ComputeMidPosition()));
 268   connect(actionDeformable_Registration,SIGNAL(triggered()),this,SLOT(ComputeDeformableRegistration()));
 269   connect(actionWarp_image_with_vector_field,SIGNAL(triggered()),this,SLOT(WarpImage()));
 270   connect(actionLoad_images,SIGNAL(triggered()),this,SLOT(OpenImages()));
 271   connect(actionOpen_Dicom,SIGNAL(triggered()),this,SLOT(OpenDicom()));
 272   connect(actionOpen_Dicom_Struct,SIGNAL(triggered()),this,SLOT(OpenDCStructContour()));
 273   connect(actionOpen_VTK_contour,SIGNAL(triggered()),this,SLOT(OpenVTKContour()));
 274   connect(actionOpen_Multiple_Images_As_One,SIGNAL(triggered()),this,SLOT(MergeImages()));
 275   connect(actionSlice_Image_As_Multiple_Images,SIGNAL(triggered()),this,SLOT(SliceImages()));
 276   connect(actionOpen_Image_With_Time,SIGNAL(triggered()),this,SLOT(OpenImageWithTime()));
 277   connect(actionMerge_images_as_n_dim_t, SIGNAL(triggered()), this, SLOT(MergeImagesWithTime()));
 278   connect(actionSave_As,SIGNAL(triggered()),this,SLOT(SaveAs()));
 279   connect(actionSave_current_state,SIGNAL(triggered()),this,SLOT(SaveCurrentState()));
 280   connect(actionRead_saved_state,SIGNAL(triggered()),this,SLOT(ReadSavedState()));
 281   connect(actionExit,SIGNAL(triggered()),this,SLOT(close()));
 282   connect(actionAdd_VF_to_current_Image,SIGNAL(triggered()),this,SLOT(OpenField()));
 283   connect(actionAdd_fusion_image,SIGNAL(triggered()),this,SLOT(SelectFusionImage()));
 284   connect(actionAdd_overlay_image_to_current_image,SIGNAL(triggered()), this,SLOT(SelectOverlayImage()));  connect(actionNavigation_Help,SIGNAL(triggered()),this,SLOT(ShowHelpDialog()));
 285   connect(actionDocumentation,SIGNAL(triggered()),this,SLOT(ShowDocumentation()));
 286   connect(actionRegister_vv,SIGNAL(triggered()),this,SLOT(PopupRegisterForm()));
 287
 288   ///////////////////////////////////////////////
 289   connect(actionSegmentation,SIGNAL(triggered()),this,SLOT(SegmentationOnCurrentImage()));
 290   connect(actionSurface_Viewer,SIGNAL(triggered()),this,SLOT(SurfaceViewerLaunch()));
 291   ///////////////////////////////////////////////
 292
 293   actionNorth_East_Window->setEnabled(0);
 294   actionNorth_West_Window->setEnabled(0);
 295   actionSouth_East_Window->setEnabled(0);
 296   actionSouth_West_Window->setEnabled(0);
 297
 298   connect(actionNorth_East_Window,SIGNAL(triggered()),this,SLOT(SaveNEScreenshot()));
 299   connect(actionNorth_West_Window,SIGNAL(triggered()),this,SLOT(SaveNOScreenshot()));
 300   connect(actionSouth_East_Window,SIGNAL(triggered()),this,SLOT(SaveSEScreenshot()));
 301   connect(actionSouth_West_Window,SIGNAL(triggered()),this,SLOT(SaveSOScreenshot()));
 302   connect(actionSave_all_slices,SIGNAL(triggered()),this,SLOT(SaveScreenshotAllSlices()));
 303
 304   connect(DataTree,SIGNAL(itemSelectionChanged()),this,SLOT(ImageInfoChanged()));
 305   connect(DataTree,SIGNAL(itemClicked(QTreeWidgetItem*, int)),this,
 306           SLOT(DisplayChanged(QTreeWidgetItem*, int)));
 307
 308   connect(viewButton,SIGNAL(clicked()),this, SLOT(ChangeViewMode()) );
 309   connect(windowSpinBox,SIGNAL(editingFinished()),this,SLOT(WindowLevelEdited()));
 310   connect(levelSpinBox,SIGNAL(editingFinished()),this,SLOT(WindowLevelEdited()));
 311   connect(colorMapComboBox,SIGNAL(currentIndexChanged(int)),this,SLOT(UpdateColorMap()));
 312   connect(presetComboBox,SIGNAL(currentIndexChanged(int)),this,SLOT(UpdateWindowLevel()));
 313   connect(slicingPresetComboBox, SIGNAL(currentIndexChanged(int)),this,SLOT(UpdateSlicingPreset()));
 314   connect(inverseButton,SIGNAL(clicked()),this,SLOT(SwitchWindowLevel()));
 315   connect(applyWindowLevelToAllButton,SIGNAL(clicked()),this,SLOT(ApplyWindowLevelToAllImages()));
 316
 317   connect(this,SIGNAL(customContextMenuRequested(QPoint)),this,SLOT(ShowContextMenu(QPoint)));
 318
 319   connect(linkPanel,SIGNAL(addLink(QString,QString,bool)),this,SLOT(AddLink(QString,QString,bool)));
 320   connect(linkPanel,SIGNAL(removeLink(QString,QString)),this,SLOT(RemoveLink(QString,QString)));
 321   connect(overlayPanel,SIGNAL(VFPropertyUpdated(int,int,int,int,double,double,double)),this,SLOT(SetVFProperty(int,int,int,int,double,double,double)));
 322   connect(overlayPanel,SIGNAL(OverlayPropertyUpdated(int,int,double,double)),
 323           this,SLOT(SetOverlayProperty(int,int,double,double)));
 324   connect(overlayPanel,SIGNAL(FusionPropertyUpdated(int,int,int,double,double, bool)),
 325           this,SLOT(SetFusionProperty(int,int,int,double,double, bool)));
 326   connect(landmarksPanel,SIGNAL(UpdateRenderWindows()),this,SLOT(UpdateRenderWindows()));
 327   connect(landmarksPanel,SIGNAL(SelectedPointChanged()),this,SLOT(GoToLandmark()));
 328
 329   playMode = 0;//pause
 330   mFrameRate = 10;
 331   playButton->setEnabled(0);
 332   frameRateLabel->setEnabled(0);
 333   frameRateSpinBox->setEnabled(0);
 334   connect(playButton, SIGNAL(clicked()),this,SLOT(PlayPause()));
 335   connect(frameRateSpinBox, SIGNAL(valueChanged(int)),this,SLOT(ChangeFrameRate(int)));
 336
 337   goToCursorPushButton->setEnabled(0);
 338   connect(goToCursorPushButton, SIGNAL(clicked()),this,SLOT(GoToCursor()));
 339
 340   NOViewWidget->hide();
 341   NEViewWidget->hide();
 342   SOViewWidget->hide();
 343   SEViewWidget->hide();
 344
 345   //Recently opened files
 346   std::list<std::string> recent_files = GetRecentlyOpenedImages();
 347   recentlyOpenedFilesMenu=NULL;
 348   if ( !recent_files.empty() ) {
 349     createRecentlyOpenedFilesMenu();
 350     updateRecentlyOpenedFilesMenu(recent_files);
 351   }
 352
 353   // Adding all new tools (insertion in the menu)
 354   vvToolManager::GetInstance()->InsertToolsInMenu(this);
 355   vvToolManager::GetInstance()->EnableToolsInMenu(this, false);
 356
 357   if (!CLITK_EXPERIMENTAL)
 358     menuExperimental->menuAction()->setVisible(false);
 359
 360
 361   QTimer * timerMemory = new QTimer(this);
 362   //timerMemory->setInterval(5);
 363   connect(timerMemory, SIGNAL(timeout()), this, SLOT(UpdateMemoryUsage()));
 364   timerMemory->start(2000);
 365 }
 366 //------------------------------------------------------------------------------
 367 void vvMainWindow::show()
 368 {
 369   vvMainWindowBase::show();
 370   PopupRegisterForm(true);
 371 }
 372 //------------------------------------------------------------------------------
 373 void vvMainWindow::UpdateMemoryUsage()
 374 {
 375   //  clitk::PrintMemory(true);
 376   if (clitk::GetMemoryUsageInMb() == 0) infoPanel->setMemoryInMb("NA");
 377   else infoPanel->setMemoryInMb(QString::number(clitk::GetMemoryUsageInMb())+" MiB");
 378 }
 379 //------------------------------------------------------------------------------
 380
 381
 382 //------------------------------------------------------------------------------
 383 void vvMainWindow::createRecentlyOpenedFilesMenu()
 384 {
 385   recentlyOpenedFilesMenu = new QMenu("Recently opened files...");
 386   recentlyOpenedFilesMenu->setIcon(QIcon(QString::fromUtf8(":/common/icons/open.png")));
 387   menuFile->insertMenu(actionOpen_Image_With_Time,recentlyOpenedFilesMenu);
 388   menuFile->insertSeparator(actionOpen_Image_With_Time);
 389 }
 390 //------------------------------------------------------------------------------
 391
 392
 393 //------------------------------------------------------------------------------
 394
 395 void vvMainWindow::updateRecentlyOpenedFilesMenu(const std::list<std::string> &recent_files)
 396 {
 397   if(recentlyOpenedFilesMenu==NULL) {
 398     createRecentlyOpenedFilesMenu();
 399   } else {
 400     recentlyOpenedFilesMenu->clear();
 401   }
 402   for (std::list<std::string>::const_iterator i = recent_files.begin(); i!=recent_files.end(); i++) {
 403     QAction* current=new QAction(QIcon(QString::fromUtf8(":/common/icons/open.png")), i->c_str(),this);
 404     recentlyOpenedFilesMenu->addAction(current);
 405     connect(current,SIGNAL(triggered()),this,SLOT(OpenRecentImage()));
 406   }
 407 }
 408 //------------------------------------------------------------------------------
 409
 410
 411 //------------------------------------------------------------------------------
 412 void vvMainWindow::ComputeMidPosition()
 413 {
 414   bool ok;
 415   int index=GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
 416   int ref = QInputDialog::getInteger(this,"Chose reference phase","Reference phase",0,0,\
 417                                      mSlicerManagers[index]->GetImage()->GetVTKImages().size()-1,1,&ok);
 418   if (ok) {
 419     vvMidPosition midp;
 420     midp.slicer_manager = mSlicerManagers[index];
 421     midp.reference_image_index = ref;
 422     QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
 423     midp.Update();
 424     if (midp.error)
 425       QMessageBox::warning(this, "Error computing midposition image",midp.error_message.c_str());
 426     else {
 427       QFileInfo info(midp.slicer_manager->GetFileName().c_str());
 428       AddImage(midp.output,info.path().toStdString()+"/"+info.completeBaseName().toStdString()+"_midposition.mhd");
 429     }
 430     QApplication::restoreOverrideCursor();
 431   }
 432 }
 433 //------------------------------------------------------------------------------
 434
 435
 436 //------------------------------------------------------------------------------
 437 void vvMainWindow::AddContour(int image_index, vvMesh::Pointer contour, bool propagation)
 438 {
 439   QTreeWidgetItem *item = new QTreeWidgetItem();
 440   item->setData(0,Qt::UserRole,"filename.vtk");
 441   item->setData(1,Qt::UserRole,tr("contour"));
 442   QBrush brush;
 443   brush.setColor(QColor(contour->r*255,contour->g*255,contour->b*255));
 444   brush.setStyle(Qt::SolidPattern);
 445   item->setData(COLUMN_IMAGE_NAME,Qt::BackgroundRole,brush);
 446   item->setData(COLUMN_IMAGE_NAME,Qt::DisplayRole,contour->structure_name.c_str());
 447
 448   for (int j = 1; j <= 4; j++)
 449     item->setData(j,Qt::CheckStateRole,DataTree->topLevelItem(image_index)->data(j,Qt::CheckStateRole));
 450
 451   QTreePushButton* cButton = new QTreePushButton;
 452   cButton->setItem(item);
 453   cButton->setColumn(COLUMN_CLOSE_IMAGE);
 454   cButton->setToolTip(tr("close image"));
 455   cButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/exit.png")));
 456   connect(cButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
 457           this,SLOT(CloseImage(QTreeWidgetItem*, int)));
 458
 459   QTreePushButton* rButton = new QTreePushButton;
 460   rButton->setItem(item);
 461   rButton->setColumn(COLUMN_RELOAD_IMAGE);
 462   rButton->setToolTip(tr("reload image"));
 463   rButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/rotateright.png")));
 464   rButton->setEnabled(false);
 465   //Not implemented
 466   //connect(rButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
 467   //this,SLOT(ReloadImage(QTreeWidgetItem*, int)));
 468
 469   DataTree->topLevelItem(image_index)->setExpanded(1);
 470   DataTree->topLevelItem(image_index)->addChild(item);
 471   DataTree->setItemWidget(item, COLUMN_CLOSE_IMAGE, cButton);
 472   DataTree->setItemWidget(item, COLUMN_RELOAD_IMAGE, rButton);
 473   QString id = DataTree->topLevelItem(image_index)->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString();
 474   item->setData(COLUMN_IMAGE_NAME,Qt::UserRole,id.toStdString().c_str());
 475
 476   UpdateTree();
 477   mSlicerManagers[image_index]->AddContour(contour,propagation);
 478   mSlicerManagers[image_index]->Render();
 479 }
 480 //------------------------------------------------------------------------------
 481
 482
 483 //------------------------------------------------------------------------------
 484 void vvMainWindow::OpenVTKContour()
 485 {
 486   if (mSlicerManagers.size() > 0) {
 487     QString Extensions = "Images ( *.vtk *.obj)";
 488     Extensions += ";;All Files (*)";
 489     QString file = QFileDialog::getOpenFileName(this,tr("Open vtkPolyData"),mInputPathName,Extensions);
 490     if (file.isNull())
 491       return;
 492     QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
 493     int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
 494     vvMeshReader reader;
 495     reader.SetImage(mSlicerManagers[index]->GetImage());
 496     reader.SetModeToVTK();
 497     reader.SetFilename(file.toStdString());
 498     reader.Update();
 499     AddContour(index,reader.GetOutput()[0],false);
 500     QApplication::restoreOverrideCursor();
 501   }
 502 }
 503 //------------------------------------------------------------------------------
 504
 505
 506 //------------------------------------------------------------------------------
 507 void vvMainWindow::AddDCStructContour(int index, QString file)
 508 {
 509     vvMeshReader reader;
 510     reader.SetFilename(file.toStdString());
 511     vvStructSelector selector;
 512     selector.SetStructures(reader.GetROINames());
 513     if (!mSlicerManagers[index]->GetVF().IsNull())
 514       selector.EnablePropagationCheckBox();
 515     if (selector.exec()) {
 516       QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
 517       reader.SetSelectedItems(selector.getSelectedItems());
 518       reader.SetImage(mSlicerManagers[index]->GetImage());
 519       if (selector.PropagationEnabled())
 520         reader.SetPropagationVF(mSlicerManagers[index]->GetVF());
 521       reader.Update();
 522       std::vector<vvMesh::Pointer> contours=reader.GetOutput();
 523       for (std::vector<vvMesh::Pointer>::iterator i=contours.begin();
 524            i!=contours.end(); i++)
 525         AddContour(index,*i,selector.PropagationEnabled());
 526       QApplication::restoreOverrideCursor();
 527     }
 528 }
 529
 530 //------------------------------------------------------------------------------
 531 void vvMainWindow::OpenDCStructContour()
 532 {
 533   if (mSlicerManagers.size() > 0) {
 534     QString Extensions = "Dicom Files ( *.dcm RS*)";
 535     Extensions += ";;All Files (*)";
 536     QString file = QFileDialog::getOpenFileName(this,tr("Merge Images"),mInputPathName,Extensions);
 537     if (file.isNull())
 538       return;
 539     int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
 540     AddDCStructContour(index, file);
 541   }
 542 }
 543 //------------------------------------------------------------------------------
 544
 545
 546 //------------------------------------------------------------------------------
 547 void vvMainWindow::ComputeDeformableRegistration()
 548 {
 549   if (mSlicerManagers.size() > 0) {
 550     int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
 551     vvDeformationDialog dialog(index,mSlicerManagers);
 552     if (dialog.exec()) {
 553       std::string base_name=itksys::SystemTools::GetFilenameWithoutExtension(mSlicerManagers[dialog.GetInputFileIndex()]->GetFileName());
 554       AddField(dialog.GetOutput(),dialog.getFieldFile(),dialog.GetInputFileIndex());
 555       WarpImage(dialog.GetSelectedSlicer(),dialog.GetReferenceFrameIndex());
 556     } else
 557       std::cout << "Error or user cancellation while computing deformation field..." << std::endl;
 558   } else QMessageBox::information(this, "Need to open image","You must open an image first.");
 559 }
 560 //------------------------------------------------------------------------------
 561
 562
 563 //------------------------------------------------------------------------------
 564 void vvMainWindow::WarpImage()
 565 {
 566   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
 567   if (!mSlicerManagers[index]->GetVF().IsNull()) {
 568     bool ok;
 569     int ref = QInputDialog::getInteger(this,"Chose reference phase","Reference phase",0,0,\
 570                                        mSlicerManagers[index]->GetImage()->GetVTKImages().size()-1,1,&ok);
 571     if (ok) {
 572       WarpImage(mSlicerManagers[index],ref);
 573     }
 574   } else
 575     QMessageBox::warning(this,tr("No vector field"),tr("Sorry, can't warp without a vector field"));
 576 }
 577 //------------------------------------------------------------------------------
 578
 579
 580 //------------------------------------------------------------------------------
 581 void vvMainWindow::WarpImage(vvSlicerManager* selected_slicer,int reference_phase)
 582 {
 583   if (!selected_slicer->GetVF().IsNull()) {
 584     QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
 585     QFileInfo info(selected_slicer->GetFileName().c_str());
 586     vvImageWarp warp(selected_slicer->GetImage(),selected_slicer->GetVF(),
 587                      reference_phase,this);
 588     if (warp.ComputeWarpedImage()) {
 589       AddImage(warp.GetWarpedImage(),info.path().toStdString()+"/"+info.completeBaseName().toStdString()+"_warped.mhd");
 590       AddImage(warp.GetDiffImage()  ,info.path().toStdString()+"/"+info.completeBaseName().toStdString()+"_diff.mhd");
 591       AddImage(warp.GetJacobianImage()  ,info.path().toStdString()+"/"+info.completeBaseName().toStdString()+"_jacobian.mhd");
 592       QApplication::restoreOverrideCursor();
 593     } else {
 594       QApplication::restoreOverrideCursor();
 595       QMessageBox::warning(this,tr("Different spacings"),tr("The vector field and image spacings must be the same in order to warp."));
 596     }
 597   } else
 598     QMessageBox::warning(this,tr("No vector field"),tr("Sorry, can't warp without a vector field."));
 599 }
 600 //------------------------------------------------------------------------------
 601
 602
 603 //------------------------------------------------------------------------------
 604 vvMainWindow::~vvMainWindow()
 605 {
 606   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
 607     if (mSlicerManagers[i] != NULL)
 608       delete mSlicerManagers[i];
 609   }
 610 }
 611 //------------------------------------------------------------------------------
 612
 613 //------------------------------------------------------------------------------
 614 QTabWidget * vvMainWindow::GetTab()
 615 {
 616   return tabWidget;
 617 }
 618 //------------------------------------------------------------------------------
 619
 620
 621 //------------------------------------------------------------------------------
 622 void vvMainWindow::MergeImages()
 623 {
 624   QString Extensions = EXTENSIONS;
 625   Extensions += ";;All Files (*)";
 626   QStringList files = QFileDialog::getOpenFileNames(this,tr("Merge Images"),mInputPathName,Extensions);
 627   if (files.isEmpty())
 628     return;
 629   mInputPathName = itksys::SystemTools::GetFilenamePath(files[0].toStdString()).c_str();
 630   std::vector<std::string> vector;
 631
 632   unsigned int currentDim = 0;
 633   std::vector<double> currentSpacing;
 634   std::vector<int> currentSize;
 635   std::vector<double> currentOrigin;
 636
 637   for (int i = 0; i < files.size(); i++) {
 638     itk::ImageIOBase::Pointer reader = itk::ImageIOFactory::CreateImageIO(
 639                                          files[i].toStdString().c_str(), itk::ImageIOFactory::ReadMode);
 640     reader->SetFileName(files[i].toStdString().c_str());
 641     reader->ReadImageInformation();
 642     if (reader)        {
 643       //NOViewWidget->hide();
 644       //NEViewWidget->hide();
 645       //SOViewWidget->hide();
 646       //SEViewWidget->hide();
 647       if (i == 0)
 648         currentDim = reader->GetNumberOfDimensions();
 649       bool IsOk = true;
 650       for (unsigned int j = 0; j < currentDim; j++) {
 651         if (i == 0) {
 652           if (j == 0) {
 653             currentSpacing.resize(currentDim);
 654             currentSize.resize(currentDim);
 655             currentOrigin.resize(currentDim);
 656           }
 657           currentOrigin[j] = reader->GetOrigin(j);
 658           currentSpacing[j] = reader->GetSpacing(j);
 659           currentSize[j] = reader->GetDimensions(j);
 660         } else if (currentDim != reader->GetNumberOfDimensions()
 661                    || currentSpacing[j] != reader->GetSpacing(j)
 662                    || currentSize[j] != (int)reader->GetDimensions(j)
 663                    || currentOrigin[j] != reader->GetOrigin(j)) {
 664           QString error = "Cannot read file (too different from others ";
 665           error += files[i].toStdString().c_str();
 666           QMessageBox::information(this,tr("Reading problem"),error);
 667           IsOk = false;
 668           break;
 669         }
 670       }
 671       if (IsOk)
 672         vector.push_back(files[i].toStdString());
 673     }
 674   }
 675   if (vector.size() > 0)
 676     LoadImages(vector, vvImageReader::MERGED);
 677 }
 678 //------------------------------------------------------------------------------
 679
 680 //------------------------------------------------------------------------------
 681 void vvMainWindow::SliceImages()
 682 {
 683   QString Extensions = EXTENSIONS;
 684   Extensions += ";;All Files (*)";
 685
 686   QStringList files = QFileDialog::getOpenFileNames(this,tr("Slice Images"),mInputPathName,Extensions);
 687   if (files.isEmpty())
 688     return;
 689   mInputPathName = itksys::SystemTools::GetFilenamePath(files[0].toStdString()).c_str();
 690   std::vector<std::string> vector;
 691   for (int i = 0; i < files.size(); i++)
 692     vector.push_back(files[i].toStdString());
 693   LoadImages(vector, vvImageReader::SLICED);
 694 }
 695 //------------------------------------------------------------------------------
 696
 697 //------------------------------------------------------------------------------
 698 void vvMainWindow::MergeImagesWithTime()
 699 {
 700   QString Extensions = EXTENSIONS;
 701   Extensions += ";;All Files (*)";
 702   QStringList files = QFileDialog::getOpenFileNames(this,tr("Merge Images With Time"),mInputPathName,Extensions);
 703   if (files.isEmpty())
 704     return;
 705   mInputPathName = itksys::SystemTools::GetFilenamePath(files[0].toStdString()).c_str();
 706   std::vector<std::string> vector;
 707
 708   for (int i = 0; i < files.size(); i++)
 709     vector.push_back(files[i].toStdString());
 710   sort(vector.begin(),vector.end());
 711   if (vector.size() > 1)
 712     LoadImages(vector, vvImageReader::MERGEDWITHTIME);
 713   else
 714     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.");
 715 }
 716 //------------------------------------------------------------------------------
 717
 718
 719 //------------------------------------------------------------------------------
 720 void vvMainWindow::OpenDicom()
 721 {
 722   std::vector<std::string> files;
 723
 724   std::cout << "dicomSeriesSelector " << std::endl;
 725   if (dicomSeriesSelector->exec() == QDialog::Accepted) {
 726     files = *(dicomSeriesSelector->GetFilenames());
 727     LoadImages(files, vvImageReader::DICOM);
 728   }
 729 }
 730 //------------------------------------------------------------------------------
 731
 732 //------------------------------------------------------------------------------
 733 void vvMainWindow::OpenImages()
 734 {
 735   QString Extensions = EXTENSIONS;
 736   Extensions += ";;All Files (*)";
 737
 738   QStringList files = QFileDialog::getOpenFileNames(this,tr("Load Images"),mInputPathName,Extensions);
 739   if (files.isEmpty())
 740     return;
 741   mInputPathName = itksys::SystemTools::GetFilenamePath(files[0].toStdString()).c_str();
 742   std::vector<std::string> vector;
 743   for (int i = 0; i < files.size(); i++)
 744     vector.push_back(files[i].toStdString());
 745   LoadImages(vector, vvImageReader::IMAGE);
 746 }
 747 //------------------------------------------------------------------------------
 748 void vvMainWindow::OpenRecentImage()
 749 {
 750   QAction * caller = qobject_cast<QAction*>(sender());
 751   std::vector<std::string> images;
 752   images.push_back(caller->text().toStdString());
 753   mInputPathName = itksys::SystemTools::GetFilenamePath(images[0]).c_str();
 754   LoadImages(images, vvImageReader::IMAGE);
 755 }
 756 //------------------------------------------------------------------------------
 757
 758
 759 //------------------------------------------------------------------------------
 760 void vvMainWindow::OpenImageWithTime()
 761 {
 762   QString Extensions = EXTENSIONS;
 763   Extensions += ";;All Files (*)";
 764
 765   QStringList files = QFileDialog::getOpenFileNames(this,tr("Load Images With Time"),mInputPathName,Extensions);
 766   if (files.isEmpty())
 767     return;
 768   mInputPathName = itksys::SystemTools::GetFilenamePath(files[0].toStdString()).c_str();
 769   std::vector<std::string> vector;
 770   for (int i = 0; i < files.size(); i++) {
 771     vector.push_back(files[i].toStdString());
 772   }
 773   LoadImages(vector, vvImageReader::IMAGEWITHTIME);
 774 }
 775 //------------------------------------------------------------------------------
 776
 777
 778 //------------------------------------------------------------------------------
 779 void vvMainWindow::LoadImages(std::vector<std::string> files, vvImageReader::LoadedImageType filetype)
 780 {
 781   //Separate the way to open images and dicoms
 782   int fileSize;
 783   if (filetype == vvImageReader::IMAGE || filetype == vvImageReader::IMAGEWITHTIME)
 784     fileSize = files.size();
 785   else
 786     fileSize = 1;
 787
 788   // For SLICED, we need the number of slices (ndim and #slices)
 789   std::vector<unsigned int> nSlices;
 790   nSlices.resize(files.size());
 791   std::fill(nSlices.begin(), nSlices.end(), 1);
 792   if (filetype == vvImageReader::SLICED) {
 793     for (int i = 0; i < fileSize; i++) {
 794       itk::ImageIOBase::Pointer header = clitk::readImageHeader(files[i]);
 795       QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
 796       if (!header) {
 797         nSlices[i] = 0;
 798         QString error = "Cannot open file \n";
 799         error += files[i].c_str();
 800         QMessageBox::information(this,tr("Reading problem"),error);
 801         return;
 802       }
 803       if (header->GetNumberOfDimensions() < 3) {
 804         nSlices[i] = 0;
 805         QString error = "Dimension problem. Cannot slice \n";
 806         error += files[i].c_str();
 807         QMessageBox::information(this,tr("Reading problem"),error);
 808         return;
 809       }
 810       nSlices[i] = header->GetDimensions( header->GetNumberOfDimensions()-1 );
 811     }
 812   }
 813
 814   //Only add to the list of recently opened files when a single file is opened,
 815   //to avoid polluting the list of recently opened files
 816   if (files.size() == 1) {
 817     QFileInfo finfo=tr(files[0].c_str());
 818     AddToRecentlyOpenedImages(finfo.absoluteFilePath().toStdString());
 819     updateRecentlyOpenedFilesMenu(GetRecentlyOpenedImages());
 820   }
 821   //init the progress events
 822   QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
 823   vvProgressDialog progress("Opening " + files[0],fileSize>1);
 824   qApp->processEvents();
 825
 826   int numberofsuccesulreads=0;
 827   //open images as 1 or multiples
 828   for (int i = 0; i < fileSize; i++) {
 829
 830     progress.SetText("Opening " + files[i]);
 831     progress.SetProgress(i,fileSize);
 832     qApp->processEvents();
 833
 834     for (unsigned int j = 0; j < nSlices[i]; j++) {
 835       //read the image and put it in mSlicerManagers
 836       vvSlicerManager* imageManager = new vvSlicerManager(4);
 837       qApp->processEvents();
 838
 839       bool SetImageSucceed=false;
 840
 841       // Change filename if an image with the same already exist
 842       int number = GetImageDuplicateFilenameNumber(files[i] + std::string("_slice"));
 843
 844       if (filetype == vvImageReader::IMAGE || filetype == vvImageReader::IMAGEWITHTIME || filetype == vvImageReader::SLICED)
 845         SetImageSucceed = imageManager->SetImage(files[i],filetype, number, j);
 846       else {
 847         SetImageSucceed = imageManager->SetImages(files,filetype, number);
 848       }
 849       if (!SetImageSucceed) {
 850         QApplication::restoreOverrideCursor();
 851         QString error = "Cannot open file \n";
 852         error += imageManager->GetLastError().c_str();
 853         QMessageBox::information(this,tr("Reading problem"),error);
 854         delete imageManager;
 855       } else {
 856         mSlicerManagers.push_back(imageManager);
 857
 858         //create an item in the tree with good settings
 859         QTreeWidgetItem *item = new QTreeWidgetItem();
 860         item->setData(0,Qt::UserRole,files[i].c_str());
 861         QFileInfo fileinfo(imageManager->GetFileName().c_str()); //Do not show the path
 862         item->setData(COLUMN_IMAGE_NAME,Qt::DisplayRole,fileinfo.fileName());
 863         item->setData(1,Qt::UserRole,tr("image"));
 864         item->setToolTip(COLUMN_IMAGE_NAME, imageManager->GetListOfAbsoluteFilePathInOneString("image").c_str());
 865         qApp->processEvents();
 866
 867         //Create the buttons for reload and close
 868         qApp->processEvents();
 869         QTreePushButton* cButton = new QTreePushButton;
 870         cButton->setItem(item);
 871         cButton->setColumn(COLUMN_CLOSE_IMAGE);
 872         cButton->setToolTip(tr("close image"));
 873         cButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/exit.png")));
 874         connect(cButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
 875                 this,SLOT(CloseImage(QTreeWidgetItem*, int)));
 876
 877         QTreePushButton* rButton = new QTreePushButton;
 878         rButton->setItem(item);
 879         rButton->setColumn(COLUMN_RELOAD_IMAGE);
 880         rButton->setToolTip(tr("reload image"));
 881         rButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/rotateright.png")));
 882         connect(rButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
 883                 this,SLOT(ReloadImage(QTreeWidgetItem*, int)));
 884
 885         DataTree->addTopLevelItem(item);
 886         DataTree->setItemWidget(item, COLUMN_CLOSE_IMAGE, cButton);
 887         DataTree->setItemWidget(item, COLUMN_RELOAD_IMAGE, rButton);
 888
 889         //set the id of the image
 890         QString id = QDir::current().absoluteFilePath(files[i].c_str()) + QString::number(mSlicerManagers.size()-1);
 891         item->setData(COLUMN_IMAGE_NAME,Qt::UserRole,id.toStdString().c_str());
 892         mSlicerManagers.back()->SetId(id.toStdString());
 893
 894         linkPanel->addImage(imageManager->GetFileName(), id.toStdString());
 895
 896         connect(mSlicerManagers.back(), SIGNAL(currentImageChanged(std::string)),
 897                 this,SLOT(CurrentImageChanged(std::string)));
 898         connect(mSlicerManagers.back(), SIGNAL(currentPickedImageChanged(std::string)),
 899                 this, SLOT(CurrentPickedImageChanged(std::string)));
 900         connect(mSlicerManagers.back(), SIGNAL(UpdatePosition(int, double, double, double, double, double, double, double)),
 901                 this,SLOT(MousePositionChanged(int,double, double, double, double, double, double, double)));
 902         connect(mSlicerManagers.back(), SIGNAL(UpdateVector(int, double, double, double, double)),
 903                 this, SLOT(VectorChanged(int,double,double,double, double)));
 904         connect(mSlicerManagers.back(), SIGNAL(UpdateOverlay(int, double, double)),
 905                 this, SLOT(OverlayChanged(int,double,double)));
 906         connect(mSlicerManagers.back(), SIGNAL(UpdateFusion(int, double)),
 907                 this, SLOT(FusionChanged(int,double)));
 908         connect(mSlicerManagers.back(), SIGNAL(WindowLevelChanged()),
 909                 this,SLOT(WindowLevelChanged()));
 910         connect(mSlicerManagers.back(), SIGNAL(UpdateSlice(int,int)),
 911                 this,SLOT(UpdateSlice(int,int)));
 912         connect(mSlicerManagers.back(), SIGNAL(UpdateTSlice(int, int)),
 913                 this,SLOT(UpdateTSlice(int, int)));
 914         connect(mSlicerManagers.back(), SIGNAL(UpdateTSlice(int, int)),
 915                 this,SLOT(ImageInfoChanged()));
 916         connect(mSlicerManagers.back(), SIGNAL(UpdateSliceRange(int,int,int,int,int)),
 917                 this,SLOT(UpdateSliceRange(int,int,int,int,int)));
 918         connect(mSlicerManagers.back(), SIGNAL(UpdateLinkManager(std::string,int,double,double,double,int)),
 919                 this,SLOT(UpdateLinkManager(std::string,int,double,double,double,int)));
 920         connect(mSlicerManagers.back(), SIGNAL(UpdateLinkedNavigation(std::string,vvSlicerManager*,vvSlicer*)),
 921                 this,SLOT(UpdateLinkedNavigation(std::string,vvSlicerManager*,vvSlicer*)));
 922         connect(mSlicerManagers.back(), SIGNAL(ChangeImageWithIndexOffset(vvSlicerManager*,int,int)),
 923                 this,SLOT(ChangeImageWithIndexOffset(vvSlicerManager*,int,int)));
 924         connect(mSlicerManagers.back(),SIGNAL(LandmarkAdded()),landmarksPanel,SLOT(AddPoint()));
 925         InitSlicers();
 926         numberofsuccesulreads++;
 927       }
 928     }
 929   }
 930   if (numberofsuccesulreads) {
 931     NOViewWidget->show();
 932     NEViewWidget->show();
 933     SOViewWidget->show();
 934     SEViewWidget->show();
 935     UpdateTree();
 936     InitDisplay();
 937     ShowLastImage();
 938
 939     // Try to guess default WindowLevel
 940     double range[2];
 941     mSlicerManagers.back()->GetImage()->GetFirstVTKImageData()->GetScalarRange(range);
 942     if ((range[0] == 0) && (range[1] == 1)) {
 943       presetComboBox->setCurrentIndex(5);// binary
 944     } else {
 945       // TODO
 946     }
 947   }
 948   QApplication::restoreOverrideCursor();
 949 }
 950 //------------------------------------------------------------------------------
 951
 952 //------------------------------------------------------------------------------
 953 void vvMainWindow::UpdateTree()
 954 {
 955   DataTree->resizeColumnToContents(COLUMN_TREE);
 956   DataTree->resizeColumnToContents(COLUMN_UL_VIEW);
 957   DataTree->resizeColumnToContents(COLUMN_UR_VIEW);
 958   DataTree->resizeColumnToContents(COLUMN_DL_VIEW);
 959   DataTree->resizeColumnToContents(COLUMN_DR_VIEW);
 960   DataTree->resizeColumnToContents(COLUMN_IMAGE_NAME);
 961   DataTree->resizeColumnToContents(COLUMN_CLOSE_IMAGE);
 962   DataTree->resizeColumnToContents(COLUMN_RELOAD_IMAGE);
 963 }
 964 //------------------------------------------------------------------------------
 965
 966 //------------------------------------------------------------------------------
 967 void vvMainWindow::CurrentImageChanged(std::string id)
 968 {
 969   if (id == mCurrentSelectedImageId) return; // Do nothing
 970   int selected = 0;
 971   for (int i = 0; i < DataTree->topLevelItemCount(); i++) {
 972     if (DataTree->topLevelItem(i)->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString().toStdString() == id) {
 973       selected = i;
 974     } else {
 975       DataTree->topLevelItem(i)->setSelected(0);
 976     }
 977     for (int child = 0; child < DataTree->topLevelItem(i)->childCount(); child++)
 978       DataTree->topLevelItem(i)->child(child)->setSelected(0);
 979
 980   }
 981   DataTree->topLevelItem(selected)->setSelected(1);
 982   mCurrentSelectedImageId = id;
 983
 984   landmarksPanel->SetCurrentLandmarks(mSlicerManagers[selected]->GetLandmarks(),
 985                                       mSlicerManagers[selected]->GetTSlice());
 986   landmarksPanel->SetCurrentPath(mInputPathName.toStdString());
 987   landmarksPanel->SetCurrentImage(mSlicerManagers[selected]->GetFileName().c_str());
 988
 989   emit SelectedImageHasChanged(mSlicerManagers[selected]);
 990 }
 991 //------------------------------------------------------------------------------
 992
 993 //------------------------------------------------------------------------------
 994 void vvMainWindow::CurrentPickedImageChanged(std::string id)
 995 {
 996   if (id == mCurrentPickedImageId) return; // Do nothing
 997   int selected = 0;
 998   for (int i = 0; i < DataTree->topLevelItemCount(); i++) {
 999     if (DataTree->topLevelItem(i)->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString().toStdString() == id) {
1000       selected = i;
1001     } else {
1002       DataTree->topLevelItem(i)->setSelected(0);
1003     }
1004     for (int child = 0; child < DataTree->topLevelItem(i)->childCount(); child++)
1005       DataTree->topLevelItem(i)->child(child)->setSelected(0);
1006
1007   }
1008   DataTree->topLevelItem(selected)->setSelected(1);
1009   mCurrentPickedImageId = id;
1010   mCurrentPickedImageIndex = selected;
1011 }
1012 //------------------------------------------------------------------------------
1013
1014 //------------------------------------------------------------------------------
1015 void vvMainWindow::ImageInfoChanged()
1016 {
1017   contextActions[6]->setEnabled(1);
1018   contextActions[5]->setEnabled(1);
1019   actionSave_As->setEnabled(1);
1020   actionAdd_VF_to_current_Image->setEnabled(1);
1021   actionAdd_fusion_image->setEnabled(1);
1022   actionAdd_overlay_image_to_current_image->setEnabled(1);
1023   actionNorth_East_Window->setEnabled(1);
1024   actionNorth_West_Window->setEnabled(1);
1025   actionSouth_East_Window->setEnabled(1);
1026   actionSouth_West_Window->setEnabled(1);
1027   vvToolManager::GetInstance()->EnableToolsInMenu(this, true);
1028   inverseButton->setEnabled(1);
1029
1030   goToCursorPushButton->setEnabled(1);
1031
1032   if (DataTree->selectedItems().size()) {
1033     int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1034
1035     colorMapComboBox->setEnabled(1);
1036     for (int i = 0; i < DataTree->topLevelItem(index)->childCount(); i++) {
1037       if (DataTree->topLevelItem(index)->child(i)->data(1,Qt::UserRole).toString() == "overlay" ||
1038           DataTree->topLevelItem(index)->child(i)->data(1,Qt::UserRole).toString() == "fusion") {
1039         colorMapComboBox->setEnabled(0);
1040         break;
1041       }
1042     }
1043
1044     std::vector<double> origin;
1045     std::vector<double> inputSpacing;
1046     std::vector<int> inputSize;
1047     std::vector<double> sizeMM;
1048     vtkSmartPointer<vtkMatrix4x4> transformation;
1049     int dimension=0;
1050     QString pixelType;
1051     QString inputSizeInBytes;
1052     QString image = DataTree->selectedItems()[0]->data(COLUMN_IMAGE_NAME,Qt::DisplayRole).toString();
1053
1054     int nframes = mSlicerManagers[index]->GetSlicer(0)->GetTMax();
1055     if (nframes > 1 || playMode == 1) {
1056       playButton->setEnabled(1);
1057       frameRateLabel->setEnabled(1);
1058       frameRateSpinBox->setEnabled(1);
1059     } else {
1060       playButton->setEnabled(0);
1061       frameRateLabel->setEnabled(0);
1062       frameRateSpinBox->setEnabled(0);
1063     }
1064
1065     //read image header
1066     int NPixel = 1;
1067
1068     int tSlice = 0;
1069     vvImage::Pointer imageSelected;
1070     if (DataTree->topLevelItem(index) == DataTree->selectedItems()[0]) {
1071       imageSelected = mSlicerManagers[index]->GetSlicer(0)->GetImage();
1072       tSlice = mSlicerManagers[index]->GetSlicer(0)->GetTSlice();
1073     } else if (DataTree->selectedItems()[0]->data(1,Qt::UserRole).toString() == "vector") {
1074       imageSelected = mSlicerManagers[index]->GetSlicer(0)->GetVF();
1075       tSlice = mSlicerManagers[index]->GetSlicer(0)->GetOverlayTSlice();
1076     } else if (DataTree->selectedItems()[0]->data(1,Qt::UserRole).toString() == "overlay") {
1077       imageSelected = mSlicerManagers[index]->GetSlicer(0)->GetOverlay();
1078       tSlice = mSlicerManagers[index]->GetSlicer(0)->GetOverlayTSlice();
1079     } else if (DataTree->selectedItems()[0]->data(1,Qt::UserRole).toString() == "fusion") {
1080       imageSelected = mSlicerManagers[index]->GetSlicer(0)->GetFusion();
1081       tSlice = mSlicerManagers[index]->GetSlicer(0)->GetFusionTSlice();
1082     }
1083     else if (DataTree->selectedItems()[0]->data(1,Qt::UserRole).toString() == "contour") {
1084       imageSelected = mSlicerManagers[index]->GetSlicer(0)->GetImage();
1085       tSlice = mSlicerManagers[index]->GetSlicer(0)->GetTSlice();
1086     }
1087     else {
1088       imageSelected = mSlicerManagers[index]->GetSlicer(0)->GetImage();
1089       tSlice = mSlicerManagers[index]->GetSlicer(0)->GetTSlice();
1090     }
1091
1092     dimension = imageSelected->GetNumberOfDimensions();
1093     origin.resize(dimension);
1094     inputSpacing.resize(dimension);
1095     inputSize.resize(dimension);
1096     sizeMM.resize(dimension);
1097     pixelType = mSlicerManagers[index]->GetImage()->GetScalarTypeAsITKString().c_str();
1098     for (int i = 0; i < dimension; i++) {
1099       origin[i] = imageSelected->GetOrigin()[i];
1100       inputSpacing[i] = imageSelected->GetSpacing()[i];
1101       inputSize[i] = imageSelected->GetSize()[i];
1102       sizeMM[i] = inputSize[i]*inputSpacing[i];
1103       NPixel *= inputSize[i];
1104     }
1105     inputSizeInBytes = GetSizeInBytes(imageSelected->GetActualMemorySize()*1000);
1106
1107     QString dim = QString::number(dimension) + " (";
1108     dim += pixelType + ")";
1109
1110     infoPanel->setFileName(image);
1111     infoPanel->setDimension(dim);
1112     infoPanel->setSizePixel(GetVectorIntAsString(inputSize));
1113     infoPanel->setSizeMM(GetVectorDoubleAsString(sizeMM));
1114     infoPanel->setOrigin(GetVectorDoubleAsString(origin));
1115     infoPanel->setSpacing(GetVectorDoubleAsString(inputSpacing));
1116     infoPanel->setNPixel(QString::number(NPixel)+" ("+inputSizeInBytes+")");
1117     transformation = imageSelected->GetTransform()[tSlice]->GetMatrix();
1118     infoPanel->setTransformation(Get4x4MatrixDoubleAsString(transformation));
1119
1120     landmarksPanel->SetCurrentLandmarks(mSlicerManagers[index]->GetLandmarks(),
1121                                         mSlicerManagers[index]->GetTSlice());
1122     landmarksPanel->SetCurrentPath(mInputPathName.toStdString());
1123     landmarksPanel->SetCurrentImage(mSlicerManagers[index]->GetFileName().c_str());
1124
1125     overlayPanel->getCurrentImageName(mSlicerManagers[index]->GetFileName().c_str());
1126     for (int i = 0; i < 4; i++) {
1127       if (DataTree->selectedItems()[0]->data(i+1,Qt::CheckStateRole).toInt() > 0 || i == 3) {
1128         mSlicerManagers[index]->UpdateInfoOnCursorPosition(i);
1129         break;
1130       }
1131     }
1132
1133 //     infoPanel->setFileName(image);
1134 //     infoPanel->setDimension(dim);
1135 //     infoPanel->setSizePixel(GetVectorIntAsString(inputSize));
1136 //     infoPanel->setSizeMM(GetVectorDoubleAsString(sizeMM));
1137 //     infoPanel->setOrigin(GetVectorDoubleAsString(origin));
1138 //     infoPanel->setSpacing(GetVectorDoubleAsString(inputSpacing));
1139 //     infoPanel->setNPixel(QString::number(NPixel)+" ("+inputSizeInBytes+")");
1140 //
1141 //     landmarksPanel->SetCurrentLandmarks(mSlicerManagers[index]->GetLandmarks(),
1142 //                                         mSlicerManagers[index]->GetTSlice());
1143 //     landmarksPanel->SetCurrentPath(mInputPathName.toStdString());
1144 //     landmarksPanel->SetCurrentImage(mSlicerManagers[index]->GetFileName().c_str());
1145 //
1146 //     overlayPanel->getCurrentImageName(mSlicerManagers[index]->GetFileName().c_str());
1147 //     for (int i = 0; i < 4; i++) {
1148 //       if (DataTree->selectedItems()[0]->data(i+1,Qt::CheckStateRole).toInt() > 0 || i == 3) {
1149 //         mSlicerManagers[index]->UpdateInfoOnCursorPosition(i);
1150 //         break;
1151 //       }
1152 //     }
1153     WindowLevelChanged();
1154     slicingPresetComboBox->setCurrentIndex(mSlicerManagers[index]->GetSlicingPreset());
1155
1156     if (mSlicerManagers[index]->GetSlicer(0)->GetVF()) {
1157       overlayPanel->getVFName(mSlicerManagers[index]->GetVFName().c_str());
1158       overlayPanel->getVFProperty(mSlicerManagers[index]->GetSlicer(0)->GetVFSubSampling(),
1159                                   mSlicerManagers[index]->GetSlicer(0)->GetVFScale(),
1160                                   mSlicerManagers[index]->GetSlicer(0)->GetVFLog());
1161     } else {
1162       overlayPanel->getVFName(mSlicerManagers[index]->GetVFName().c_str());
1163       overlayPanel->getVFProperty(-1,-1,-1);
1164     }
1165     if (mSlicerManagers[index]->GetSlicer(0)->GetOverlay()) {
1166       overlayPanel->getOverlayName(mSlicerManagers[index]->GetOverlayName().c_str());
1167     } else {
1168       overlayPanel->getOverlayName(mSlicerManagers[index]->GetOverlayName().c_str());
1169     }
1170
1171     if (mSlicerManagers[index]->GetSlicer(0)->GetFusion()) {
1172       overlayPanel->getFusionName(mSlicerManagers[index]->GetFusionName().c_str());
1173     } else {
1174       overlayPanel->getFusionName(mSlicerManagers[index]->GetFusionName().c_str());
1175     }
1176   }
1177 }
1178 //------------------------------------------------------------------------------
1179
1180 //------------------------------------------------------------------------------
1181 void vvMainWindow::ShowDocumentation()
1182 {
1183   documentation->show();
1184 }
1185 //------------------------------------------------------------------------------
1186
1187 //------------------------------------------------------------------------------
1188 void vvMainWindow::PopupRegisterForm(bool checkCanPush)
1189 {
1190   vvRegisterForm* registerForm = new vvRegisterForm(QUrl("http://www.creatis.insa-lyon.fr/~dsarrut/vvregister/write.php"), getVVSettingsPath(), getSettingsOptionFormat());
1191   if(!checkCanPush) {
1192     registerForm->show();
1193   } else {
1194     if(registerForm->canPush()) {
1195       registerForm->show();
1196       registerForm->acquitPushed();//too bad if there is not internet connection anymore.
1197     }
1198   }
1199 }
1200 //------------------------------------------------------------------------------
1201
1202 //------------------------------------------------------------------------------
1203 void vvMainWindow::ShowHelpDialog()
1204 {
1205   help_dialog->show();
1206 }
1207 //------------------------------------------------------------------------------
1208
1209 //------------------------------------------------------------------------------
1210 void vvMainWindow::ChangeViewMode()
1211 {
1212   typedef struct _SIZE{
1213     QSplitter* splitter;
1214     QList<int> size1, size2;
1215     int cols[3];
1216   }SplitterSize;
1217   SplitterSize sizes[4];
1218   sizes[0].splitter = OSplitter;
1219   sizes[0].size1.push_back(1);
1220   sizes[0].size1.push_back(0);
1221   sizes[0].size2.push_back(1);
1222   sizes[0].size2.push_back(0);
1223   sizes[0].cols[0] = 2;
1224   sizes[0].cols[1] = 3;
1225   sizes[0].cols[2] = 4;
1226
1227   sizes[1].splitter = ESplitter;
1228   sizes[1].size1.push_back(0);
1229   sizes[1].size1.push_back(1);
1230   sizes[1].size2.push_back(1);
1231   sizes[1].size2.push_back(0);
1232   sizes[1].cols[0] = 1;
1233   sizes[1].cols[1] = 3;
1234   sizes[1].cols[2] = 4;
1235
1236   sizes[2].splitter = OSplitter;
1237   sizes[2].size1.push_back(1);
1238   sizes[2].size1.push_back(0);
1239   sizes[2].size2.push_back(0);
1240   sizes[2].size2.push_back(1);
1241   sizes[2].cols[0] = 1;
1242   sizes[2].cols[1] = 2;
1243   sizes[2].cols[2] = 4;
1244
1245   sizes[3].splitter = ESplitter;
1246   sizes[3].size1.push_back(0);
1247   sizes[3].size1.push_back(1);
1248   sizes[3].size2.push_back(0);
1249   sizes[3].size2.push_back(1);
1250   sizes[3].cols[0] = 1;
1251   sizes[3].cols[1] = 2;
1252   sizes[3].cols[2] = 3;
1253
1254   int slicer = mSlicerManagers[mCurrentPickedImageIndex]->GetSelectedSlicer();
1255   if (viewMode == 1) {
1256     if (slicer >= 0) {
1257       viewMode = 0;
1258       splitter_3->setSizes(sizes[slicer].size1);
1259       sizes[slicer].splitter->setSizes(sizes[slicer].size2);
1260       DataTree->setColumnHidden(sizes[slicer].cols[0],1);
1261       DataTree->setColumnHidden(sizes[slicer].cols[1],1);
1262       DataTree->setColumnHidden(sizes[slicer].cols[2],1);
1263     }
1264   } else {
1265     QList<int> size;
1266     if (slicer >= 0) {
1267       viewMode = 1;
1268       size.push_back(1);
1269       size.push_back(1);
1270       splitter_3->setSizes(size);
1271       sizes[slicer].splitter->setSizes(size);
1272       DataTree->setColumnHidden(sizes[slicer].cols[0],0);
1273       DataTree->setColumnHidden(sizes[slicer].cols[1],0);
1274       DataTree->setColumnHidden(sizes[slicer].cols[2],0);
1275     }
1276   }
1277   UpdateRenderWindows();
1278   /*
1279   ** I don't know why but for both resized QVTKWidget we also need to render
1280   ** the associated Slicer to redraw crosses.
1281   */
1282   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
1283 //     if (DataTree->topLevelItem(i)->data(COLUMN_UL_VIEW,Qt::CheckStateRole).toInt() > 1)
1284       mSlicerManagers[i]->GetSlicer(0)->Render();
1285       mSlicerManagers[i]->GetSlicer(1)->Render();
1286 //     if (DataTree->topLevelItem(i)->data(COLUMN_DL_VIEW,Qt::CheckStateRole).toInt() > 1)
1287       mSlicerManagers[i]->GetSlicer(2)->Render();
1288       mSlicerManagers[i]->GetSlicer(3)->Render();
1289   }
1290 }
1291 //------------------------------------------------------------------------------
1292
1293 //------------------------------------------------------------------------------
1294 QString vvMainWindow::GetSizeInBytes(unsigned long size)
1295 {
1296   QString result = "";// QString::number(size);
1297   //result += " bytes (";
1298   if (size > 1000000000) {
1299     size /= 1000000000;
1300     result += QString::number(size);
1301     result += "Gb";//)";
1302   } else if (size > 1000000) {
1303     size /= 1000000;
1304     result += QString::number(size);
1305     result += "Mb";//)";
1306   } else if (size > 1000) {
1307     size /= 1000;
1308     result += QString::number(size);
1309     result += "kb";//)";
1310   }
1311   return result;
1312 }
1313 //------------------------------------------------------------------------------
1314
1315 //------------------------------------------------------------------------------
1316 QString vvMainWindow::Get4x4MatrixDoubleAsString(vtkSmartPointer<vtkMatrix4x4> matrix, const int precision)
1317 {
1318   std::ostringstream strmatrix;
1319
1320   // Figure out the number of digits of the integer part of the largest absolute value
1321   // for each column
1322   unsigned width[4];
1323   for (unsigned int j = 0; j < 4; j++){
1324     double absmax = 0.;
1325     for (unsigned int i = 0; i < 4; i++)
1326       absmax = std::max(absmax, vnl_math_abs(matrix->GetElement(i, j)));
1327     unsigned ndigits = (unsigned)std::max(0.,std::log10(absmax))+1;
1328     width[j] = precision+ndigits+3;
1329   }
1330
1331   // Output with correct width, aligned to the right
1332   for (unsigned int i = 0; i < 4; i++) {
1333     for (unsigned int j = 0; j < 4; j++) {
1334       strmatrix.setf(ios::fixed,ios::floatfield);
1335       strmatrix.precision(precision);
1336       strmatrix.fill(' ');
1337       strmatrix.width(width[j]);
1338       strmatrix << std::right << matrix->GetElement(i, j);
1339     }
1340     strmatrix << std::endl;
1341   }
1342   QString result = strmatrix.str().c_str();
1343   return result;
1344 }
1345 //------------------------------------------------------------------------------
1346
1347 //------------------------------------------------------------------------------
1348 QString vvMainWindow::GetVectorDoubleAsString(std::vector<double> vectorDouble)
1349 {
1350   QString result;
1351   for (unsigned int i= 0; i < vectorDouble.size(); i++) {
1352     if (i != 0)
1353       result += " ";
1354     result += QString::number(vectorDouble[i]);
1355   }
1356   return result;
1357 }
1358 //------------------------------------------------------------------------------
1359
1360 //------------------------------------------------------------------------------
1361 QString vvMainWindow::GetVectorIntAsString(std::vector<int> vectorInt)
1362 {
1363   QString result;
1364   for (unsigned int i= 0; i < vectorInt.size(); i++) {
1365     if (i != 0)
1366       result += " ";
1367     result += QString::number(vectorInt[i]);
1368   }
1369   return result;
1370 }
1371 //------------------------------------------------------------------------------
1372
1373 //------------------------------------------------------------------------------
1374 int vvMainWindow::GetSlicerIndexFromItem(QTreeWidgetItem* item)
1375 {
1376   QString id = item->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString();
1377   for (int i = 0; i < DataTree->topLevelItemCount(); i++) {
1378     if (DataTree->topLevelItem(i)->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString() == id)
1379       return i;
1380   }
1381   return -1;
1382 }
1383 //------------------------------------------------------------------------------
1384
1385 //------------------------------------------------------------------------------
1386 QTreeWidgetItem* vvMainWindow::GetItemFromSlicerManager(vvSlicerManager* sm)
1387 {
1388   QString id = sm->GetId().c_str();
1389   for (int i = 0; i < DataTree->topLevelItemCount(); i++) {
1390     if (DataTree->topLevelItem(i)->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString() == id)
1391       return DataTree->topLevelItem(i);
1392   }
1393   return NULL;
1394 }
1395 //------------------------------------------------------------------------------
1396
1397 //------------------------------------------------------------------------------
1398 void vvMainWindow::DisplayChanged(QTreeWidgetItem *clickedItem, int column)
1399 {
1400   if ( column >= COLUMN_CLOSE_IMAGE || column <= 0)
1401     return;
1402
1403   // Get parent information (might be the same item)
1404   int slicerManagerIndex = GetSlicerIndexFromItem(clickedItem);
1405   QTreeWidgetItem* clickedParentItem = DataTree->topLevelItem(slicerManagerIndex);
1406   vvSlicer* clickedSlicer = mSlicerManagers[slicerManagerIndex]->GetSlicer(column-1);
1407
1408   // Go over the complete item tree (only 2 levels, parents and children)
1409   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
1410     // Trick to avoid redoing twice the job for a key (sr)
1411     mSlicerManagers[i]->GetSlicer(column-1)->GetRenderWindow()->GetInteractor()->SetKeySym("Crap");
1412
1413     QTreeWidgetItem* currentParentItem = DataTree->topLevelItem(i);
1414     if(currentParentItem != clickedParentItem) {
1415       // Not the branch of the clicked item, uncheck all
1416
1417       // Parent
1418       currentParentItem->setData(column,Qt::CheckStateRole, 0);
1419       mSlicerManagers[i]->UpdateSlicer(column-1, false);
1420
1421       // Children
1422       for (int iChild = 0; iChild < currentParentItem->childCount(); iChild++) {
1423         currentParentItem->child(iChild)->setData(column,Qt::CheckStateRole, 0);
1424       }
1425     }
1426     else {
1427       // Branch of the clicked one: get check status from actor visibility in slicer
1428       // and toggle the clicked one
1429
1430       // Parent
1431       bool vis = clickedSlicer->GetActorVisibility("image", 0);
1432       bool draw = clickedSlicer->GetRenderer()->GetDraw();
1433
1434       // Update slicer (after getting visibility)
1435       mSlicerManagers[slicerManagerIndex]->UpdateSlicer(column-1, true);
1436       mSlicerManagers[slicerManagerIndex]->UpdateInfoOnCursorPosition(column-1);
1437       DisplaySliders(slicerManagerIndex, column-1);
1438       if(clickedParentItem == clickedItem) {
1439         // Toggle
1440         vis = !draw || !vis;
1441       }
1442       clickedSlicer->SetActorVisibility("image", 0, vis);
1443       clickedParentItem->setData(column, Qt::CheckStateRole, vis?2:0);
1444
1445       // Children
1446       std::map<std::string, int> actorTypeCounts;
1447       for (int iChild = 0; iChild < clickedParentItem->childCount(); iChild++) {
1448         QTreeWidgetItem* currentChildItem = clickedParentItem->child(iChild);
1449         std::string actorType = currentChildItem->data(1,Qt::UserRole).toString().toStdString();
1450         vis = clickedSlicer->GetActorVisibility(actorType, actorTypeCounts[actorType]);
1451         if(currentChildItem == clickedItem) {
1452           // Toggle or force visibility if it was not on this branch so far
1453           vis = !draw || !vis;
1454           clickedSlicer->SetActorVisibility(actorType, actorTypeCounts[actorType], vis);
1455         }
1456         currentChildItem->setData(column, Qt::CheckStateRole, vis?2:0);
1457         actorTypeCounts[actorType]++;
1458       }
1459     }
1460   }
1461
1462   clickedSlicer->Render();
1463 }
1464 //------------------------------------------------------------------------------
1465
1466 void vvMainWindow::InitSlicers()
1467 {
1468   if (mSlicerManagers.size()) {
1469     mSlicerManagers.back()->GenerateDefaultLookupTable();
1470
1471     mSlicerManagers.back()->SetSlicerWindow(0,NOViewWidget->GetRenderWindow());
1472     mSlicerManagers.back()->SetSlicerWindow(1,NEViewWidget->GetRenderWindow());
1473     mSlicerManagers.back()->SetSlicerWindow(2,SOViewWidget->GetRenderWindow());
1474     mSlicerManagers.back()->SetSlicerWindow(3,SEViewWidget->GetRenderWindow());
1475   }
1476 }
1477
1478 //------------------------------------------------------------------------------
1479 void vvMainWindow::InitDisplay()
1480 {
1481   if (mSlicerManagers.size()) {
1482     //BE CAREFUL : this is absolutely necessary to set the interactor style
1483     //in order to have the same style instanciation for all SlicerManagers in
1484     // a same window
1485     for (int j = 0; j < 4; j++) {
1486       vvInteractorStyleNavigator* style = vvInteractorStyleNavigator::New();
1487       style->SetAutoAdjustCameraClippingRange(1);
1488       bool AlreadySelected = false;
1489       for (int i = 0; i < DataTree->topLevelItemCount(); i++) {
1490         mSlicerManagers[i]->SetInteractorStyleNavigator(j,style);
1491
1492         //select the image only if previous are not selected
1493         if (DataTree->topLevelItem(i)->data(j+1,Qt::CheckStateRole).toInt() > 1) {
1494           mSlicerManagers[i]->UpdateSlicer(j,1);
1495           AlreadySelected = true;
1496         } else if (i == DataTree->topLevelItemCount()-1 && !AlreadySelected) {
1497           if (DataTree->selectedItems().size() == 0)
1498             DataTree->topLevelItem(i)->setSelected(1);
1499           DataTree->topLevelItem(i)->setData(j+1,Qt::CheckStateRole,2);
1500           mSlicerManagers[i]->UpdateSlicer(j,1);
1501           DisplaySliders(i,j);
1502         } else {
1503           DataTree->topLevelItem(i)->setData(j+1,Qt::CheckStateRole,0);
1504           mSlicerManagers[i]->UpdateSlicer(j,0);
1505         }
1506       }
1507       style->Delete();
1508     }
1509   }
1510 }
1511 //------------------------------------------------------------------------------
1512
1513 //------------------------------------------------------------------------------
1514 void vvMainWindow::DisplaySliders(int slicer, int window)
1515 {
1516   if(!mSlicerManagers[slicer]->GetSlicer(window)->GetRenderer()->GetDraw())
1517     return;
1518
1519   int range[2];
1520   mSlicerManagers[slicer]->GetSlicer(window)->GetSliceRange(range);
1521   int position = mSlicerManagers[slicer]->GetSlicer(window)->GetSlice();
1522   if (range[1]>0)
1523     verticalSliders[window]->show();
1524   else
1525     verticalSliders[window]->hide();
1526   verticalSliders[window]->setRange(range[0],range[1]);
1527   verticalSliders[window]->setValue(position);
1528
1529   int tRange[2];
1530   tRange[0] = 0;
1531   tRange[1] = mSlicerManagers[slicer]->GetSlicer(window)->GetTMax();
1532   if (tRange[1]>0)
1533     horizontalSliders[window]->show();
1534   else
1535     horizontalSliders[window]->hide();
1536   horizontalSliders[window]->setRange(tRange[0],tRange[1]);
1537   int tPosition = mSlicerManagers[slicer]->GetSlicer(window)->GetMaxCurrentTSlice();
1538   horizontalSliders[window]->setValue(tPosition);
1539 }
1540 //------------------------------------------------------------------------------
1541
1542 //------------------------------------------------------------------------------
1543 void vvMainWindow::CloseImage(QTreeWidgetItem* item, int column)
1544 {
1545   int index = GetSlicerIndexFromItem(item);
1546
1547   if (DataTree->topLevelItem(index) != item) {
1548     QString warning = "Do you really want to close the overlay : ";
1549     warning += item->data(COLUMN_IMAGE_NAME,Qt::DisplayRole).toString();
1550     QMessageBox msgBox(QMessageBox::Warning, tr("Close Overlay"),
1551                        warning, 0, this);
1552     msgBox.addButton(tr("Close"), QMessageBox::AcceptRole);
1553     msgBox.addButton(tr("Cancel"), QMessageBox::RejectRole);
1554     if (msgBox.exec() == QMessageBox::AcceptRole) {
1555       std::string overlay_type=item->data(1,Qt::UserRole).toString().toStdString();
1556       int overlay_index=0;
1557       for (int child = 0; child < DataTree->topLevelItem(index)->childCount(); child++) {
1558         if (DataTree->topLevelItem(index)->\
1559             child(child)->data(1,Qt::UserRole).toString().toStdString() == overlay_type)
1560           overlay_index++;
1561         if (DataTree->topLevelItem(index)->child(child) == item) break;
1562       }
1563       mSlicerManagers[index]->RemoveActor(overlay_type, overlay_index-1);
1564       mSlicerManagers[index]->SetColorMap(0);
1565       DataTree->topLevelItem(index)->takeChild(DataTree->topLevelItem(index)->indexOfChild(item));
1566       mSlicerManagers[index]->Render();
1567     }
1568   } else if (DataTree->topLevelItemCount() <= 1) {
1569     QString warning = "Do you really want to close the image : ";
1570     warning += item->data(COLUMN_IMAGE_NAME,Qt::DisplayRole).toString();
1571     warning += "\nThis is the last image, you're about to close vv !!!";
1572     QMessageBox msgBox(QMessageBox::Warning, tr("Close Image"),
1573                        warning, 0, this);
1574     msgBox.addButton(tr("Close vv"), QMessageBox::AcceptRole);
1575     msgBox.addButton(tr("Cancel"), QMessageBox::RejectRole);
1576     if (msgBox.exec() == QMessageBox::AcceptRole) {
1577       this->close();
1578     }
1579   } else {
1580     QString warning = "Do you really want to close the image : ";
1581     warning += item->data(COLUMN_IMAGE_NAME,Qt::DisplayRole).toString();
1582     QMessageBox msgBox(QMessageBox::Warning, tr("Close Image"),
1583                        warning, 0, this);
1584     msgBox.addButton(tr("Close"), QMessageBox::AcceptRole);
1585     msgBox.addButton(tr("Cancel"), QMessageBox::RejectRole);
1586     if (msgBox.exec() == QMessageBox::AcceptRole) {
1587
1588       // Tell tools that we close an image
1589       emit AnImageIsBeingClosed(mSlicerManagers[index]);
1590
1591       std::vector<vvSlicerManager*>::iterator Manageriter = mSlicerManagers.begin();
1592       DataTree->takeTopLevelItem(index);
1593       for (int i = 0; i < index; i++) {
1594         Manageriter++;
1595       }
1596       linkPanel->removeImage(index);
1597       mSlicerManagers[index]->RemoveActors();
1598       delete mSlicerManagers[index];
1599       mSlicerManagers.erase(Manageriter);
1600
1601       //
1602       InitDisplay();
1603     }
1604   }
1605   ImageInfoChanged();
1606 }
1607 //------------------------------------------------------------------------------
1608
1609 //------------------------------------------------------------------------------
1610 void vvMainWindow::ReloadImage(QTreeWidgetItem* item, int column)
1611 {
1612   // int index = GetSlicerIndexFromItem(item);
1613   //   QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
1614   //   if (item->data(1,Qt::UserRole).toString() == "vector")
1615   //     mSlicerManagers[index]->ReloadVF();
1616   //   else
1617   //     mSlicerManagers[index]->Reload();
1618
1619   //   QApplication::restoreOverrideCursor();
1620   int index = GetSlicerIndexFromItem(item);
1621   QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
1622   QString role=item->data(1,Qt::UserRole).toString();
1623   if ( role == "vector"){
1624     mSlicerManagers[index]->ReloadVF();
1625   }
1626   else if (role == "overlay"){
1627     mSlicerManagers[index]->ReloadOverlay();
1628   }
1629   else if (role == "fusion"){
1630     mSlicerManagers[index]->ReloadFusion();
1631   }
1632   else{
1633     mSlicerManagers[index]->Reload();
1634   }
1635   // Update view and info
1636   ImageInfoChanged();
1637   mSlicerManagers[index]->Render();
1638   QApplication::restoreOverrideCursor();
1639 }
1640 //------------------------------------------------------------------------------
1641
1642 //------------------------------------------------------------------------------
1643 void vvMainWindow::MousePositionChanged(int visibility,double x, double y, double z, double X, double Y, double Z , double value)
1644 {
1645   infoPanel->setCurrentInfo(visibility,x,y,z,X,Y,Z,value);
1646 }
1647 //------------------------------------------------------------------------------
1648
1649 //------------------------------------------------------------------------------
1650 void vvMainWindow::VectorChanged(int visibility,double x, double y, double z, double value)
1651 {
1652   overlayPanel->getCurrentVectorInfo(visibility,x,y,z,value);
1653 }
1654 //------------------------------------------------------------------------------
1655
1656 //------------------------------------------------------------------------------
1657 void vvMainWindow::OverlayChanged(int visibility, double valueOver, double valueRef)
1658 {
1659   overlayPanel->getCurrentOverlayInfo(visibility,valueOver, valueRef);
1660 }
1661 //------------------------------------------------------------------------------
1662
1663 //------------------------------------------------------------------------------
1664 void vvMainWindow::FusionChanged(int visibility, double value)
1665 {
1666   overlayPanel->getCurrentFusionInfo(visibility,value);
1667 }
1668 //------------------------------------------------------------------------------
1669
1670 //------------------------------------------------------------------------------
1671 void vvMainWindow::WindowLevelChanged()
1672 {
1673   // Base image
1674   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1675   if(index==-1) return;
1676   windowSpinBox->setValue(mSlicerManagers[index]->GetColorWindow());
1677   levelSpinBox->setValue(mSlicerManagers[index]->GetColorLevel());
1678   colorMapComboBox->setCurrentIndex(mSlicerManagers[index]->GetColorMap());
1679   presetComboBox->setCurrentIndex(mSlicerManagers[index]->GetPreset());
1680
1681   // Overlay image
1682   if (mSlicerManagers[index]->GetSlicer(0)->GetOverlay())
1683     overlayPanel->getOverlayProperty(mSlicerManagers[index]->GetOverlayColor(),
1684                                      mSlicerManagers[index]->GetLinkOverlayWindowLevel(),
1685                                      mSlicerManagers[index]->GetOverlayColorWindow(),
1686                                      mSlicerManagers[index]->GetOverlayColorLevel());
1687   else
1688     overlayPanel->getOverlayProperty(-1,0,0.,0.);
1689
1690   // Fusion image
1691   if (mSlicerManagers[index]->GetSlicer(0)->GetFusion())
1692     overlayPanel->getFusionProperty(mSlicerManagers[index]->GetFusionOpacity(),
1693                                     mSlicerManagers[index]->GetFusionThresholdOpacity(),
1694                                     mSlicerManagers[index]->GetFusionColorMap(),
1695                                     mSlicerManagers[index]->GetFusionWindow(),
1696                                     mSlicerManagers[index]->GetFusionLevel());
1697   else
1698     overlayPanel->getFusionProperty(-1, -1, -1, -1, -1);
1699 }
1700 //------------------------------------------------------------------------------
1701
1702 //------------------------------------------------------------------------------
1703 void vvMainWindow::WindowLevelEdited()
1704 {
1705   presetComboBox->setCurrentIndex(6);
1706   UpdateWindowLevel();
1707 }
1708 //------------------------------------------------------------------------------
1709
1710 //------------------------------------------------------------------------------
1711 void vvMainWindow::SetWindowLevel(double w, double l)
1712 {
1713   windowSpinBox->setValue(w);
1714   levelSpinBox->setValue(l);
1715   presetComboBox->setCurrentIndex(6);
1716   colorMapComboBox->setCurrentIndex(0);
1717   UpdateWindowLevel();
1718 }
1719 //------------------------------------------------------------------------------
1720
1721 //------------------------------------------------------------------------------
1722 void vvMainWindow::UpdateWindowLevel()
1723 {
1724   if (DataTree->selectedItems().size()) {
1725     if (presetComboBox->currentIndex() == 7) //For ventilation
1726       colorMapComboBox->setCurrentIndex(5);
1727     int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1728     mSlicerManagers[index]->SetColorWindow(windowSpinBox->value());
1729     mSlicerManagers[index]->SetColorLevel(levelSpinBox->value());
1730     mSlicerManagers[index]->SetPreset(presetComboBox->currentIndex());
1731     mSlicerManagers[index]->Render();
1732     WindowLevelChanged();
1733   }
1734 }
1735 //------------------------------------------------------------------------------
1736
1737 //------------------------------------------------------------------------------
1738 void vvMainWindow::UpdateSlicingPreset()
1739 {
1740   if (DataTree->selectedItems().size()) {
1741     int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1742     mSlicerManagers[index]->SetSlicingPreset(vvSlicerManager::SlicingPresetType(slicingPresetComboBox->currentIndex()));
1743   }
1744 }
1745 //------------------------------------------------------------------------------
1746
1747 //------------------------------------------------------------------------------
1748 void vvMainWindow::UpdateColorMap()
1749 {
1750   if (DataTree->selectedItems().size()) {
1751     int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1752     mSlicerManagers[index]->SetColorMap(colorMapComboBox->currentIndex());
1753     mSlicerManagers[index]->Render();
1754   }
1755 }
1756 //------------------------------------------------------------------------------
1757 void vvMainWindow::SwitchWindowLevel()
1758 {
1759   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1760   int window = mSlicerManagers[index]->GetColorWindow();
1761   presetComboBox->setCurrentIndex(6);
1762   windowSpinBox->setValue(-window);
1763   UpdateWindowLevel();
1764 }
1765 //------------------------------------------------------------------------------
1766
1767 //------------------------------------------------------------------------------
1768 void vvMainWindow::ApplyWindowLevelToAllImages()
1769 {
1770   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1771   if(index==-1) return;
1772   double window = mSlicerManagers[index]->GetColorWindow();
1773   double level = mSlicerManagers[index]->GetColorLevel();
1774
1775   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
1776     if (mSlicerManagers[i] == NULL)
1777       continue;
1778     mSlicerManagers[i]->SetColorWindow(window);
1779     mSlicerManagers[i]->SetColorLevel(level);
1780     mSlicerManagers[i]->SetPreset(6);
1781     mSlicerManagers[i]->Render();
1782   }
1783 }
1784 //------------------------------------------------------------------------------
1785
1786 //------------------------------------------------------------------------------
1787 void vvMainWindow::ApplyWindowToSetOfImages(double window, unsigned int indexMin, unsigned int indexMax)
1788 {
1789   for (unsigned int i = indexMin; i <= indexMax && i < mSlicerManagers.size(); i++) {
1790     if (mSlicerManagers[i] == NULL)
1791       continue;
1792     mSlicerManagers[i]->SetColorWindow(window);
1793     mSlicerManagers[i]->SetPreset(6);
1794     mSlicerManagers[i]->Render();
1795   }
1796 }
1797 //------------------------------------------------------------------------------
1798
1799 //------------------------------------------------------------------------------
1800 void vvMainWindow::ApplyLevelToSetOfImages(double level, unsigned int indexMin, unsigned int indexMax)
1801 {
1802   for (unsigned int i = indexMin; i <= indexMax && i < mSlicerManagers.size(); i++) {
1803     if (mSlicerManagers[i] == NULL)
1804       continue;
1805     mSlicerManagers[i]->SetColorLevel(level);
1806     mSlicerManagers[i]->SetPreset(6);
1807     mSlicerManagers[i]->Render();
1808   }
1809 }
1810 //------------------------------------------------------------------------------
1811
1812 //------------------------------------------------------------------------------
1813 void vvMainWindow::UpdateLinkManager(std::string id, int slicer, double x, double y, double z, int temps)
1814 {
1815   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
1816     if (mSlicerManagers[i]->GetId() == id) {
1817       //mSlicerManagers[i]->SetTSlice(temps);
1818       mSlicerManagers[i]->GetSlicer(slicer)->SetCurrentPosition(x,y,z,temps);
1819       mSlicerManagers[i]->UpdateViews(0,slicer);
1820       break;
1821     }
1822   }
1823 }
1824 //------------------------------------------------------------------------------
1825
1826 //------------------------------------------------------------------------------
1827 void vvMainWindow::UpdateLinkedNavigation(std::string id, vvSlicerManager * sm, vvSlicer* refSlicer)
1828 {
1829   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
1830     if (id == mSlicerManagers[i]->GetId()) {
1831       mSlicerManagers[i]->UpdateLinkedNavigation(refSlicer);
1832     }
1833   }
1834 }
1835 //------------------------------------------------------------------------------
1836
1837 //------------------------------------------------------------------------------
1838 void vvMainWindow::ShowContextMenu(QPoint point)
1839 {
1840   if (!DataTree->selectedItems().size()) {
1841     contextActions[1]->setEnabled(0);
1842     contextActions[2]->setEnabled(0);
1843     contextActions[3]->setEnabled(0);
1844     contextActions[4]->setEnabled(0);
1845     contextActions[5]->setEnabled(0);
1846     contextActions[6]->setEnabled(0);
1847   } else {
1848     int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1849     contextActions[1]->setEnabled(1);
1850     contextActions[2]->setEnabled(
1851       DataTree->itemWidget(DataTree->selectedItems()[0],
1852                            COLUMN_RELOAD_IMAGE)->isEnabled());
1853     contextActions[3]->setEnabled(1);
1854     contextActions[5]->setEnabled(1);
1855     contextActions[6]->setEnabled(1);
1856
1857     if (mSlicerManagers[index]->GetDimension() < 3)
1858       contextActions[4]->setEnabled(0);
1859     else
1860       contextActions[4]->setEnabled(1);
1861   }
1862   contextMenu.exec(QCursor::pos());
1863 }
1864 //------------------------------------------------------------------------------
1865
1866 //------------------------------------------------------------------------------
1867 void vvMainWindow::CloseImage()
1868 {
1869   CloseImage(DataTree->selectedItems()[0],0);
1870 }
1871 //------------------------------------------------------------------------------
1872
1873 //------------------------------------------------------------------------------
1874 void vvMainWindow::ReloadImage()
1875 {
1876   ReloadImage(DataTree->selectedItems()[0],0);
1877 }
1878 //------------------------------------------------------------------------------
1879
1880 //------------------------------------------------------------------------------
1881 void vvMainWindow::SelectOverlayImage()
1882 {
1883   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1884
1885   //check if one overlay image is added
1886   for (int child = 0; child < DataTree->topLevelItem(index)->childCount(); child++)
1887     if (DataTree->topLevelItem(index)->child(child)->data(1,Qt::UserRole).toString() == "overlay") {
1888       QString error = "Cannot add more than one compared image\n";
1889       error += "Please remove first ";
1890       error += DataTree->topLevelItem(index)->child(child)->data(COLUMN_IMAGE_NAME,Qt::DisplayRole).toString();
1891       QMessageBox::information(this,tr("Problem adding compared image !"),error);
1892       return;
1893     }
1894
1895   QString Extensions = EXTENSIONS;
1896   Extensions += ";;All Files (*)";
1897   QStringList files = QFileDialog::getOpenFileNames(this,tr("Load Overlay image"),mInputPathName,Extensions);
1898   if (files.isEmpty())
1899     return;
1900
1901   std::vector<std::string> vecFileNames;
1902   for (int i = 0; i < files.size(); i++) {
1903     vecFileNames.push_back(files[i].toStdString());
1904   }
1905   AddOverlayImage(index,vecFileNames,vvImageReader::IMAGE);
1906 }
1907 //------------------------------------------------------------------------------
1908
1909 //------------------------------------------------------------------------------
1910 void vvMainWindow::AddOverlayImage(int index, std::vector<std::string> fileNames, vvImageReader::LoadedImageType type)
1911 {
1912   QString file(fileNames[0].c_str());
1913   if (QFile::exists(file))
1914   {
1915     mInputPathName = itksys::SystemTools::GetFilenamePath(file.toStdString()).c_str();
1916     itk::ImageIOBase::Pointer reader = itk::ImageIOFactory::CreateImageIO(
1917         file.toStdString().c_str(), itk::ImageIOFactory::ReadMode);
1918     reader->SetFileName(fileNames[0].c_str());
1919     reader->ReadImageInformation();
1920     std::string component = reader->GetComponentTypeAsString(reader->GetComponentType());
1921     int dimension = reader->GetNumberOfDimensions();
1922     QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
1923     vvProgressDialog progress("Opening " + file.toStdString());
1924     qApp->processEvents();
1925
1926     std::string filename = itksys::SystemTools::GetFilenameWithoutExtension(file.toStdString()).c_str();
1927     if (mSlicerManagers[index]->SetOverlay(fileNames,dimension, component,type)) {
1928       //create an item in the tree with good settings
1929       QTreeWidgetItem *item = new QTreeWidgetItem();
1930       item->setData(0,Qt::UserRole,file.toStdString().c_str());
1931       item->setData(1,Qt::UserRole,tr("overlay"));
1932       QFileInfo fileinfo(file); //Do not show the path
1933       item->setData(COLUMN_IMAGE_NAME,Qt::DisplayRole,fileinfo.fileName());
1934       item->setToolTip(COLUMN_IMAGE_NAME, mSlicerManagers[index]->GetListOfAbsoluteFilePathInOneString("overlay").c_str());
1935       qApp->processEvents();
1936
1937       for (int j = 1; j <= 4; j++) {
1938         item->setData(j,Qt::CheckStateRole,DataTree->topLevelItem(index)->data(j,Qt::CheckStateRole));
1939       }
1940
1941       //Create the buttons for reload and close
1942       qApp->processEvents();
1943       QTreePushButton* cButton = new QTreePushButton;
1944       cButton->setItem(item);
1945       cButton->setColumn(COLUMN_CLOSE_IMAGE);
1946       cButton->setToolTip(tr("close image"));
1947       cButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/exit.png")));
1948       connect(cButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
1949           this,SLOT(CloseImage(QTreeWidgetItem*, int)));
1950
1951       QTreePushButton* rButton = new QTreePushButton;
1952       rButton->setItem(item);
1953       rButton->setColumn(COLUMN_RELOAD_IMAGE);
1954       rButton->setToolTip(tr("reload image"));
1955       rButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/rotateright.png")));
1956       connect(rButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
1957           this,SLOT(ReloadImage(QTreeWidgetItem*, int)));
1958
1959       DataTree->topLevelItem(index)->setExpanded(1);
1960       DataTree->topLevelItem(index)->addChild(item);
1961       DataTree->setItemWidget(item, COLUMN_CLOSE_IMAGE, cButton);
1962       DataTree->setItemWidget(item, COLUMN_RELOAD_IMAGE, rButton);
1963
1964       //set the id of the image
1965       QString id = DataTree->topLevelItem(index)->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString();
1966       item->setData(COLUMN_IMAGE_NAME,Qt::UserRole,id.toStdString().c_str());
1967       UpdateTree();
1968       qApp->processEvents();
1969       ImageInfoChanged();
1970       QApplication::restoreOverrideCursor();
1971
1972       // Update the display to update, e.g., the sliders
1973       for(int i=0; i<4; i++)
1974         DisplaySliders(index, i);
1975     } else {
1976       QApplication::restoreOverrideCursor();
1977       QString error = "Cannot import the new image.\n";
1978       error += mSlicerManagers[index]->GetLastError().c_str();
1979       QMessageBox::information(this,tr("Problem reading image !"),error);
1980     }
1981     WindowLevelChanged();
1982   }
1983   else
1984     QMessageBox::information(this,tr("Problem reading Overlay !"),"File doesn't exist!");
1985 }
1986 //------------------------------------------------------------------------------
1987
1988
1989 //------------------------------------------------------------------------------
1990 void vvMainWindow::AddROI(int index, QString file)
1991 {
1992   /*
1993   // Get slice manager
1994
1995   // Load image
1996
1997   vvImageReader * mReader = new vvImageReader;
1998   mReader->SetInputFilename(filename.toStdString());
1999   mReader->Update(IMAGE);
2000   if (mReader->GetLastError().size() != 0) {
2001     std::cerr << "Error while reading " << filename.toStdString() << std::endl;
2002     QString error = "Cannot open file \n";
2003     error += mReader->GetLastError().c_str();
2004     QMessageBox::information(this,tr("Reading problem"),error);
2005     delete mReader;
2006     return;
2007   }
2008   vvImage::Pointer roi = mReader->GetOutput();
2009
2010   // Create roi in new tool
2011   vvToolStructureSetManager::AddImage(mCurrentSlicerManager, roi);
2012   */
2013 }
2014 //------------------------------------------------------------------------------
2015
2016 //------------------------------------------------------------------------------
2017 void vvMainWindow::SelectFusionImage()
2018 {
2019   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2020
2021   //check if one fusion image is added
2022   for (int child = 0; child < DataTree->topLevelItem(index)->childCount(); child++)
2023     if (DataTree->topLevelItem(index)->child(child)->data(1,Qt::UserRole).toString() == "fusion") {
2024       QString error = "Cannot add more than one fusion image\n";
2025       error += "Please remove first ";
2026       error += DataTree->topLevelItem(index)->child(child)->data(COLUMN_IMAGE_NAME,Qt::DisplayRole).toString();
2027       QMessageBox::information(this,tr("Problem adding fusion image !"),error);
2028       return;
2029     }
2030
2031   QString Extensions = EXTENSIONS;
2032   Extensions += ";;All Files (*)";
2033   QString file = QFileDialog::getOpenFileName(this,tr("Load Fusion image"),mInputPathName,Extensions);
2034   if (!file.isEmpty())
2035     AddFusionImage(index,file);
2036 }
2037 //------------------------------------------------------------------------------
2038
2039 //------------------------------------------------------------------------------
2040 void vvMainWindow::ResetTransformationToIdentity()
2041 {
2042   std::string actorType = DataTree->selectedItems()[0]->data(1,Qt::UserRole).toString().toStdString();
2043   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2044   mSlicerManagers[index]->ResetTransformationToIdentity(actorType);
2045   ImageInfoChanged();
2046 }
2047 //------------------------------------------------------------------------------
2048
2049 //------------------------------------------------------------------------------
2050 void vvMainWindow::AddFusionImage(int index, QString file)
2051 {
2052   if (QFile::exists(file))
2053   {
2054     mInputPathName = itksys::SystemTools::GetFilenamePath(file.toStdString()).c_str();
2055     itk::ImageIOBase::Pointer reader = itk::ImageIOFactory::CreateImageIO(
2056         file.toStdString().c_str(), itk::ImageIOFactory::ReadMode);
2057     reader->SetFileName(file.toStdString().c_str());
2058     reader->ReadImageInformation();
2059     std::string component = reader->GetComponentTypeAsString(reader->GetComponentType());
2060     if (reader) {
2061       QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
2062       vvProgressDialog progress("Opening fusion");
2063       qApp->processEvents();
2064
2065       std::string filename = itksys::SystemTools::GetFilenameWithoutExtension(file.toStdString()).c_str();
2066       if (mSlicerManagers[index]->SetFusion(file.toStdString(),
2067             reader->GetNumberOfDimensions(), component)) {
2068         //create an item in the tree with good settings
2069         QTreeWidgetItem *item = new QTreeWidgetItem();
2070         item->setData(0,Qt::UserRole,file.toStdString().c_str());
2071         item->setData(1,Qt::UserRole,tr("fusion"));
2072         QFileInfo fileinfo(filename.c_str()); //Do not show the path
2073         item->setData(COLUMN_IMAGE_NAME,Qt::DisplayRole,fileinfo.fileName());
2074         item->setToolTip(COLUMN_IMAGE_NAME, mSlicerManagers[index]->GetListOfAbsoluteFilePathInOneString("fusion").c_str());
2075         qApp->processEvents();
2076
2077         for (int j = 1; j <= 4; j++) {
2078           item->setData(j,Qt::CheckStateRole,DataTree->topLevelItem(index)->data(j,Qt::CheckStateRole));
2079         }
2080
2081         //Create the buttons for reload and close
2082         qApp->processEvents();
2083         QTreePushButton* cButton = new QTreePushButton;
2084         cButton->setItem(item);
2085         cButton->setColumn(COLUMN_CLOSE_IMAGE);
2086         cButton->setToolTip(tr("close image"));
2087         cButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/exit.png")));
2088         connect(cButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
2089             this,SLOT(CloseImage(QTreeWidgetItem*, int)));
2090
2091         QTreePushButton* rButton = new QTreePushButton;
2092         rButton->setItem(item);
2093         rButton->setColumn(COLUMN_RELOAD_IMAGE);
2094         rButton->setToolTip(tr("reload image"));
2095         rButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/rotateright.png")));
2096         connect(rButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
2097             this,SLOT(ReloadImage(QTreeWidgetItem*, int)));
2098
2099         DataTree->topLevelItem(index)->setExpanded(1);
2100         DataTree->topLevelItem(index)->addChild(item);
2101         DataTree->setItemWidget(item, COLUMN_CLOSE_IMAGE, cButton);
2102         DataTree->setItemWidget(item, COLUMN_RELOAD_IMAGE, rButton);
2103
2104         //set the id of the image
2105         QString id = DataTree->topLevelItem(index)->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString();
2106         item->setData(COLUMN_IMAGE_NAME,Qt::UserRole,id.toStdString().c_str());
2107         UpdateTree();
2108         qApp->processEvents();
2109         ImageInfoChanged();
2110         QApplication::restoreOverrideCursor();
2111       } else {
2112         QApplication::restoreOverrideCursor();
2113         QString error = "Cannot import the new image.\n";
2114         error += mSlicerManagers[index]->GetLastError().c_str();
2115         QMessageBox::information(this,tr("Problem reading image !"),error);
2116       }
2117     } else {
2118       QString error = "Cannot import the new image.\n";
2119       QMessageBox::information(this,tr("Problem reading image !"),error);
2120     }
2121   }
2122   else
2123     QMessageBox::information(this,tr("Problem reading Fusion !"),"File doesn't exist!");
2124 }
2125 //------------------------------------------------------------------------------
2126 //------------------------------------------------------------------------------
2127 void vvMainWindow::AddLandmarks(int index, std::vector<std::string> files)
2128 {
2129     if (!landmarksPanel->LoadFromFile(files))
2130       QMessageBox::information(this,tr("Problem reading Landmarks !"),"File doesn't exist!");
2131
2132     landmarksPanel->SetCurrentPath(mInputPathName.toStdString());
2133     landmarksPanel->SetCurrentImage(mSlicerManagers[index]->GetFileName().c_str());
2134 }
2135
2136 //------------------------------------------------------------------------------
2137 void vvMainWindow::OpenField()
2138 {
2139   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2140   //check if a vector field has already been added
2141   for (int child = 0; child < DataTree->topLevelItem(index)->childCount(); child++)
2142     if (DataTree->topLevelItem(index)->child(child)->data(1,Qt::UserRole).toString() == "vector") {
2143       QString error = "Cannot add more than one vector field\n";
2144       error += "Please remove first ";
2145       error += DataTree->topLevelItem(index)->child(child)->data(COLUMN_IMAGE_NAME,Qt::DisplayRole).toString();
2146       QMessageBox::information(this,tr("Problem adding vector field!"),error);
2147       return;
2148     }
2149
2150   QString Extensions = "Images ( *.mhd)";
2151   Extensions += ";;Images ( *.mha)";
2152   Extensions += ";;VF Images ( *.vf)";
2153   Extensions += ";;nii Images ( *.nii)";
2154   Extensions += ";;nrrd Images ( *.nrrd)";
2155   Extensions += ";;nhdr Images ( *.nhdr)";
2156   Extensions += ";;All Files (*)";
2157   QString file = QFileDialog::getOpenFileName(this,tr("Load deformation field"),mInputPathName,Extensions);
2158   if (!file.isEmpty())
2159     AddField(file,index);
2160 }
2161 //------------------------------------------------------------------------------
2162
2163
2164 //------------------------------------------------------------------------------
2165 void vvMainWindow::AddFieldEntry(QString filename,int index,bool from_disk)
2166 {
2167   //create an item in the tree with good settings
2168   QTreeWidgetItem *item = new QTreeWidgetItem();
2169   item->setData(0,Qt::UserRole,filename.toStdString().c_str());
2170   item->setData(1,Qt::UserRole,tr("vector"));
2171   QFileInfo fileinfo(filename); //Do not show the path
2172   item->setData(COLUMN_IMAGE_NAME,Qt::DisplayRole,fileinfo.fileName());
2173   item->setToolTip(COLUMN_IMAGE_NAME, mSlicerManagers[index]->GetListOfAbsoluteFilePathInOneString("vector").c_str());
2174   qApp->processEvents();
2175
2176   for (int j = 1; j <= 4; j++) {
2177     item->setData(j,Qt::CheckStateRole,DataTree->topLevelItem(index)->data(j,Qt::CheckStateRole));
2178   }
2179
2180   //Create the buttons for reload and close
2181   qApp->processEvents();
2182   QTreePushButton* cButton = new QTreePushButton;
2183   cButton->setItem(item);
2184   cButton->setColumn(COLUMN_CLOSE_IMAGE);
2185   cButton->setToolTip(tr("close vector field"));
2186   cButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/exit.png")));
2187   connect(cButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
2188           this,SLOT(CloseImage(QTreeWidgetItem*, int)));
2189
2190   QTreePushButton* rButton = new QTreePushButton;
2191   rButton->setItem(item);
2192   rButton->setColumn(COLUMN_RELOAD_IMAGE);
2193   rButton->setToolTip(tr("reload vector field"));
2194   rButton->setEnabled(from_disk);
2195   rButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/rotateright.png")));
2196   connect(rButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
2197           this,SLOT(ReloadImage(QTreeWidgetItem*, int)));
2198
2199   DataTree->topLevelItem(index)->setExpanded(1);
2200   DataTree->topLevelItem(index)->addChild(item);
2201   DataTree->setItemWidget(item, COLUMN_RELOAD_IMAGE, rButton);
2202   DataTree->setItemWidget(item, COLUMN_CLOSE_IMAGE, cButton);
2203
2204   //set the id of the image
2205   QString id = DataTree->topLevelItem(index)->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString();
2206   item->setData(COLUMN_IMAGE_NAME,Qt::UserRole,id.toStdString().c_str());
2207   UpdateTree();
2208   qApp->processEvents();
2209   ImageInfoChanged();
2210   QApplication::restoreOverrideCursor();
2211 }
2212 //------------------------------------------------------------------------------
2213
2214
2215 //------------------------------------------------------------------------------
2216 void vvMainWindow::AddField(vvImage::Pointer vf,QString file,int index)
2217 {
2218   QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
2219   vvSlicerManager* imageManager = mSlicerManagers[index];
2220   if (imageManager->SetVF(vf,file.toStdString())) {
2221     AddFieldEntry(file,index,false);
2222   } else {
2223     QString error = "Cannot import the vector field for this image.\n";
2224     error += imageManager->GetLastError().c_str();
2225     QMessageBox::information(this,tr("Problem reading VF !"),error);
2226   }
2227   QApplication::restoreOverrideCursor();
2228 }
2229 //------------------------------------------------------------------------------
2230
2231
2232 //------------------------------------------------------------------------------
2233 void vvMainWindow::AddField(QString file,int index)
2234 {
2235   if (QFile::exists(file)) {
2236     mInputPathName = itksys::SystemTools::GetFilenamePath(file.toStdString()).c_str();
2237
2238     //init the progress events
2239     QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
2240     vvProgressDialog progress("Opening " + file.toStdString());
2241     qApp->processEvents();
2242
2243     //read the vector and put it in the current mSlicerManager
2244     vvSlicerManager* imageManager = mSlicerManagers[index];
2245     qApp->processEvents();
2246
2247     std::string filename = itksys::SystemTools::GetFilenameWithoutExtension(file.toStdString()).c_str();
2248     if (imageManager->SetVF(file.toStdString())) {
2249       imageManager->Render();
2250       AddFieldEntry(file,index,true);
2251     } else {
2252       QApplication::restoreOverrideCursor();
2253       QString error = "Cannot import the vector field for this image.\n";
2254       error += imageManager->GetLastError().c_str();
2255       QMessageBox::information(this,tr("Problem reading VF !"),error);
2256     }
2257   } else
2258     QMessageBox::information(this,tr("Problem reading VF !"),"File doesn't exist!");
2259
2260 }
2261 //------------------------------------------------------------------------------
2262
2263
2264 //------------------------------------------------------------------------------
2265 void vvMainWindow::SetVFProperty(int subsampling, int scale, int log, int width, double r, double g, double b)
2266 {
2267   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2268   if (mSlicerManagers[index]->GetSlicer(0)->GetVF()) {
2269     for (int i = 0; i < 4; i++) {
2270       mSlicerManagers[index]->GetSlicer(i)->SetVFSubSampling(subsampling);
2271       mSlicerManagers[index]->GetSlicer(i)->SetVFScale(scale);
2272       mSlicerManagers[index]->GetSlicer(i)->SetVFWidth(width);
2273       mSlicerManagers[index]->GetSlicer(i)->SetVFColor(r,g,b);
2274       if (log > 0)
2275         mSlicerManagers[index]->GetSlicer(i)->SetVFLog(1);
2276       else
2277         mSlicerManagers[index]->GetSlicer(i)->SetVFLog(0);
2278     }
2279   }
2280 }
2281 //------------------------------------------------------------------------------
2282
2283
2284 //------------------------------------------------------------------------------
2285 void vvMainWindow::SetOverlayProperty(int color, int linked, double window, double level)
2286 {
2287   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2288   if (mSlicerManagers[index]->GetSlicer(0)->GetOverlay()) {
2289     mSlicerManagers[index]->SetOverlayColor(color);
2290     mSlicerManagers[index]->SetColorMap(0);
2291     mSlicerManagers[index]->SetLinkOverlayWindowLevel(linked);
2292     mSlicerManagers[index]->SetOverlayColorWindow(window);
2293     mSlicerManagers[index]->SetOverlayColorLevel(level);
2294     mSlicerManagers[index]->Render();
2295   }
2296 }
2297 //------------------------------------------------------------------------------
2298
2299 //------------------------------------------------------------------------------
2300 void vvMainWindow::SetFusionProperty(int opacity, int thresOpacity, int colormap,double window, double level, bool showLegend)
2301 {
2302   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2303   if (mSlicerManagers[index]->GetSlicer(0)->GetFusion()) {
2304     mSlicerManagers[index]->SetFusionColorMap(colormap);
2305     mSlicerManagers[index]->SetFusionOpacity(opacity);
2306     mSlicerManagers[index]->SetFusionThresholdOpacity(thresOpacity);
2307     mSlicerManagers[index]->SetFusionWindow(window);
2308     mSlicerManagers[index]->SetFusionLevel(level);
2309     mSlicerManagers[index]->SetFusionShowLegend(showLegend);
2310     mSlicerManagers[index]->SetColorMap(0);
2311     mSlicerManagers[index]->Render();
2312   }
2313 }
2314 //------------------------------------------------------------------------------
2315
2316 //------------------------------------------------------------------------------
2317 void vvMainWindow::SaveAs()
2318 {
2319   if (DataTree->selectedItems()[0]->data(1,Qt::UserRole).toString() == "vector") {
2320     QMessageBox::warning(this,tr("Unsupported type"),tr("Sorry, saving a vector field is unsupported for the moment"));
2321     return;
2322   }
2323
2324   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2325   int dimension = mSlicerManagers[index]->GetDimension();
2326   QStringList OutputListeFormat;
2327   OutputListeFormat.clear();
2328   if (dimension == 1) {
2329     OutputListeFormat.push_back(".mhd");
2330     OutputListeFormat.push_back(".mha");
2331   }
2332   if (dimension == 2) {
2333     OutputListeFormat.push_back(".bmp");
2334     OutputListeFormat.push_back(".png");
2335     OutputListeFormat.push_back(".jpeg");
2336     OutputListeFormat.push_back(".tif");
2337     OutputListeFormat.push_back(".mhd");
2338     OutputListeFormat.push_back(".mha");
2339     OutputListeFormat.push_back(".hdr");
2340     OutputListeFormat.push_back(".vox");
2341   } else if (dimension == 3) {
2342     OutputListeFormat.push_back(".mhd");
2343     OutputListeFormat.push_back(".mha");
2344     OutputListeFormat.push_back(".nii");
2345     OutputListeFormat.push_back(".nrrd");
2346     OutputListeFormat.push_back(".nhdr");
2347     OutputListeFormat.push_back(".hdr");
2348     OutputListeFormat.push_back(".vox");
2349   } else if (dimension == 4) {
2350     OutputListeFormat.push_back(".mhd");
2351     OutputListeFormat.push_back(".mha");
2352     OutputListeFormat.push_back(".nii");
2353     OutputListeFormat.push_back(".nrrd");
2354     OutputListeFormat.push_back(".nhdr");
2355   }
2356   QString Extensions = "AllFiles(*.*)";
2357   for (int i = 0; i < OutputListeFormat.count(); i++) {
2358     Extensions += ";;Images ( *";
2359     Extensions += OutputListeFormat[i];
2360     Extensions += ")";
2361   }
2362   QString fileName = QFileDialog::getSaveFileName(this,
2363                      tr("Save As"),
2364                      mSlicerManagers[index]->GetFileName().c_str(),
2365                      Extensions);
2366   if (!fileName.isEmpty()) {
2367     std::string fileformat = itksys::SystemTools::GetFilenameLastExtension(fileName.toStdString());
2368     if (OutputListeFormat.contains(
2369           fileformat.c_str())) {
2370       QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
2371       std::string action = "Saving";
2372       vvProgressDialog progress("Saving "+fileName.toStdString());
2373       qApp->processEvents();
2374       vvImageWriter::Pointer writer = vvImageWriter::New();
2375       writer->SetOutputFileName(fileName.toStdString());
2376       writer->SetInput(mSlicerManagers[index]->GetImage());
2377
2378       // Check on transform and prompt user
2379       writer->SetSaveTransform(false);
2380       bool bId = true;
2381       for(int i=0; i<4; i++)
2382         for(int j=0; j<4; j++) {
2383           // TODO SR and BP: check on the list of transforms and not the first only
2384           double elt = mSlicerManagers[index]->GetImage()->GetTransform()[0]->GetMatrix()->GetElement(i,j);
2385           if(i==j && elt!=1.)
2386             bId = false;
2387           if(i!=j && elt!=0.)
2388             bId = false;
2389         }
2390       if( !bId ) {
2391         QString warning = "The image has an associated linear transform. Do you want to save it along?";
2392         QMessageBox msgBox(QMessageBox::Warning, tr("Save transform"), warning, 0, this);
2393         msgBox.addButton(tr("Yes"), QMessageBox::AcceptRole);
2394         msgBox.addButton(tr("No"), QMessageBox::RejectRole);
2395         if (msgBox.exec() == QMessageBox::AcceptRole)
2396           writer->SetSaveTransform(true);
2397       }
2398
2399       writer->Update();
2400       QApplication::restoreOverrideCursor();
2401       if (writer->GetLastError().size()) {
2402         QString error = "Saving did not succeed\n";
2403         error += writer->GetLastError().c_str();
2404         QMessageBox::information(this,tr("Saving Problem"),error);
2405         SaveAs();
2406       }
2407     } else {
2408       QString error = fileformat.c_str();
2409       if (error.isEmpty())
2410         error += "no file format specified !";
2411       else
2412         error += " format unknown !!!\n";
2413       QMessageBox::information(this,tr("Saving Problem"),error);
2414       SaveAs();
2415     }
2416   }
2417 }
2418 //------------------------------------------------------------------------------
2419
2420 //------------------------------------------------------------------------------
2421 void vvMainWindow::SaveCurrentState()
2422 {
2423   QString Extensions = "XML Files(*.xml)";
2424   QString fileName = QFileDialog::getSaveFileName(this,
2425                      tr("Save Current Window State"),
2426                      "",
2427                      Extensions);
2428
2429   SaveCurrentStateAs(fileName.toStdString());
2430 }
2431 //------------------------------------------------------------------------------
2432
2433 //------------------------------------------------------------------------------
2434 void vvMainWindow::SaveCurrentStateAs(const std::string& stateFile)
2435 {
2436   vvSaveState save_state;
2437   save_state.Run(this, stateFile);
2438 }
2439
2440 //------------------------------------------------------------------------------
2441 void vvMainWindow::ReadSavedState()
2442 {
2443   QString Extensions = "XML Files(*.xml)";
2444   QString fileName = QFileDialog::getOpenFileName(this,
2445                      tr("Load Window State"),
2446                      "",
2447                      Extensions);
2448
2449   ReadSavedStateFile(fileName.toStdString());
2450 }
2451 //------------------------------------------------------------------------------
2452
2453 //------------------------------------------------------------------------------
2454 void vvMainWindow::ReadSavedStateFile(const std::string& stateFile)
2455 {
2456   vvReadState read_state;
2457   read_state.Run(this, stateFile);
2458 }
2459 //------------------------------------------------------------------------------
2460
2461 //------------------------------------------------------------------------------
2462 void vvMainWindow::LinkAllImages()
2463 {
2464         linkPanel->linkAll();
2465 }
2466
2467 //------------------------------------------------------------------------------
2468 void vvMainWindow::AddLink(QString image1,QString image2,bool fromPanel)
2469 {
2470   if (!fromPanel) {
2471     // delegate to linkPanel if call came from elsewhere...
2472     linkPanel->addLinkFromIds(image1, image2);
2473     return;
2474   }
2475
2476   unsigned int sm1 = 0;
2477   unsigned int sm2 = 0;
2478
2479   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
2480     if (image1.toStdString() == mSlicerManagers[i]->GetId()) {
2481       mSlicerManagers[i]->AddLink(image2.toStdString());
2482       sm1 = i;
2483     }
2484     if (image2.toStdString() == mSlicerManagers[i]->GetId()) {
2485       mSlicerManagers[i]->AddLink(image1.toStdString());
2486       sm2 = i;
2487     }
2488   }
2489
2490   if (linkPanel->isLinkAll())   {
2491     emit UpdateLinkedNavigation(mSlicerManagers[sm1]->GetId(), mSlicerManagers[mCurrentPickedImageIndex], mSlicerManagers[mCurrentPickedImageIndex]->GetSlicer(0));
2492     emit UpdateLinkedNavigation(mSlicerManagers[sm2]->GetId(), mSlicerManagers[mCurrentPickedImageIndex], mSlicerManagers[mCurrentPickedImageIndex]->GetSlicer(0));
2493   } else {
2494     emit UpdateLinkedNavigation(mSlicerManagers[sm2]->GetId(), mSlicerManagers[sm1], mSlicerManagers[sm1]->GetSlicer(0));
2495   }
2496 }
2497
2498 //------------------------------------------------------------------------------
2499
2500
2501 //------------------------------------------------------------------------------
2502 void vvMainWindow::RemoveLink(QString image1,QString image2)
2503 {
2504   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
2505     if (image1.toStdString() == mSlicerManagers[i]->GetId()) {
2506       mSlicerManagers[i]->RemoveLink(image2.toStdString());
2507     }
2508     if (image2.toStdString() == mSlicerManagers[i]->GetId()) {
2509       mSlicerManagers[i]->RemoveLink(image1.toStdString());
2510     }
2511   }
2512 }
2513 //------------------------------------------------------------------------------
2514
2515 //------------------------------------------------------------------------------
2516 void vvMainWindow::ChangeImageWithIndexOffset(vvSlicerManager *sm, int slicer, int offset)
2517 {
2518   if(mSlicerManagers.size()==1)
2519     return;
2520
2521   int index = 0;
2522   while(sm != mSlicerManagers[index])
2523     index++;
2524   index = (index+offset+mSlicerManagers.size()) % mSlicerManagers.size();
2525
2526   QTreeWidgetItem* item = GetItemFromSlicerManager(mSlicerManagers[index]);
2527   item->setData(slicer+1,Qt::CheckStateRole,2);         //change checkbox
2528   CurrentImageChanged(mSlicerManagers[index]->GetId()); //select new image
2529   DisplayChanged(item,slicer+1);
2530 }
2531 //------------------------------------------------------------------------------
2532
2533 void vvMainWindow::HorizontalSliderMoved(int value,int column, int slicer_index)
2534 {
2535   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
2536     if (DataTree->topLevelItem(i)->data(column,Qt::CheckStateRole).toInt() > 1) {
2537       for (int j = 0; j < 4; j++) {
2538         mSlicerManagers[i]->SetTSliceInSlicer(value,j);
2539         //if (mSlicerManagers[i]->GetSlicer(j)->GetImageActor()->GetVisibility())
2540         //UpdateTSlice(j,value);
2541       }
2542       mSlicerManagers[i]->GetSlicer(slicer_index)->Render();
2543       break;
2544     }
2545   }
2546 }
2547 //------------------------------------------------------------------------------
2548
2549
2550 //------------------------------------------------------------------------------
2551 void vvMainWindow::NOHorizontalSliderMoved()
2552 {
2553   // if (mCurrentTime == NOHorizontalSlider->value()) return;
2554   HorizontalSliderMoved(NOHorizontalSlider->value(),COLUMN_UL_VIEW,0);
2555 //  mCurrentTime = NOHorizontalSlider->value();
2556 }
2557 //------------------------------------------------------------------------------
2558
2559
2560 //------------------------------------------------------------------------------
2561 void vvMainWindow::NEHorizontalSliderMoved()
2562 {
2563   // if (mCurrentTime == NEHorizontalSlider->value()) return;
2564   HorizontalSliderMoved(NEHorizontalSlider->value(),COLUMN_UR_VIEW,1);
2565 //  mCurrentTime = NEHorizontalSlider->value();
2566 }
2567 //------------------------------------------------------------------------------
2568
2569
2570 //------------------------------------------------------------------------------
2571 void vvMainWindow::SOHorizontalSliderMoved()
2572 {
2573   // if (mCurrentTime == SOHorizontalSlider->value()) return;
2574   HorizontalSliderMoved(SOHorizontalSlider->value(),COLUMN_DL_VIEW,2);
2575   // mCurrentTime = SOHorizontalSlider->value();
2576 }
2577 //------------------------------------------------------------------------------
2578
2579
2580 //------------------------------------------------------------------------------
2581 void vvMainWindow::SEHorizontalSliderMoved()
2582 {
2583   // if (mCurrentTime == SEHorizontalSlider->value()) return;
2584   HorizontalSliderMoved(SEHorizontalSlider->value(),COLUMN_DR_VIEW,3);
2585   // mCurrentTime = SEHorizontalSlider->value();
2586 }
2587 //------------------------------------------------------------------------------
2588
2589 //------------------------------------------------------------------------------
2590 void vvMainWindow::NOVerticalSliderChanged()
2591 {
2592   static int value=-1;
2593   if (value == NOVerticalSlider->value()) return;
2594   else value = NOVerticalSlider->value();
2595   //  int value = NOVerticalSlider->value();
2596   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
2597     if (DataTree->topLevelItem(i)->data(COLUMN_UL_VIEW,Qt::CheckStateRole).toInt() > 1) {
2598       if (mSlicerManagers[i]->GetSlicer(0)->GetSlice() != value) {
2599         mSlicerManagers[i]->GetSlicer(0)->SetSlice(value);
2600         mSlicerManagers[i]->VerticalSliderHasChanged(0, value);
2601
2602         // If nor Update/Render -> slider not work
2603         // only render = ok navigation, but for contour Update needed but slower ?
2604
2605         mSlicerManagers[i]->UpdateSlice(0);  // <-- DS add this. Not too much update ? YES. but needed for ImageContour ...
2606         //mSlicerManagers[i]->GetSlicer(0)->Render(); // <-- DS add this, needed for contour, seems ok ? not too slow ?
2607       }
2608       break;
2609     }
2610   }
2611 }
2612 //------------------------------------------------------------------------------
2613
2614
2615 //------------------------------------------------------------------------------
2616 void vvMainWindow::NEVerticalSliderChanged()
2617 {
2618   static int value=-1;
2619   if (value == NEVerticalSlider->value()) return;
2620   else value = NEVerticalSlider->value();
2621   //  int value = NEVerticalSlider->value();
2622   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
2623     if (DataTree->topLevelItem(i)->data(COLUMN_UR_VIEW,Qt::CheckStateRole).toInt() > 1) {
2624       if (mSlicerManagers[i]->GetSlicer(1)->GetSlice() != value) {
2625         mSlicerManagers[i]->GetSlicer(1)->SetSlice(value);
2626         mSlicerManagers[i]->VerticalSliderHasChanged(1, value);
2627         mSlicerManagers[i]->UpdateSlice(1);
2628         //mSlicerManagers[i]->GetSlicer(1)->Render(); // <-- DS add this, needed for contour, seems ok ? not too slow ?
2629       }
2630       break;
2631     }
2632   }
2633 }
2634 //------------------------------------------------------------------------------
2635
2636
2637 //------------------------------------------------------------------------------
2638 void vvMainWindow::SOVerticalSliderChanged()
2639 {
2640   static int value=-1;
2641   if (value == SOVerticalSlider->value()) return;
2642   else value = SOVerticalSlider->value();
2643   //int value = SOVerticalSlider->value();
2644   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
2645     if (DataTree->topLevelItem(i)->data(COLUMN_DL_VIEW,Qt::CheckStateRole).toInt() > 1) {
2646       if (mSlicerManagers[i]->GetSlicer(2)->GetSlice() != value) {
2647         mSlicerManagers[i]->GetSlicer(2)->SetSlice(value);
2648         mSlicerManagers[i]->VerticalSliderHasChanged(2, value);
2649         mSlicerManagers[i]->UpdateSlice(2);
2650         //mSlicerManagers[i]->GetSlicer(2)->Render(); // <-- DS add this, needed for contour, seems ok ? not too slow ?
2651       }
2652       // else { DD("avoid SOVerticalSlider slicer update"); }
2653       break;
2654     }
2655   }
2656 }
2657 //------------------------------------------------------------------------------
2658
2659
2660 //------------------------------------------------------------------------------
2661 void vvMainWindow::SEVerticalSliderChanged()
2662 {
2663   static int value=-1;
2664   if (value == SEVerticalSlider->value()) return;
2665   else value = SEVerticalSlider->value();
2666   // int value = SEVerticalSlider->value();
2667   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
2668     if (DataTree->topLevelItem(i)->data(COLUMN_DR_VIEW,Qt::CheckStateRole).toInt() > 1) {
2669       if (mSlicerManagers[i]->GetSlicer(3)->GetSlice() != value) {
2670         mSlicerManagers[i]->GetSlicer(3)->SetSlice(value);
2671         mSlicerManagers[i]->VerticalSliderHasChanged(3, value);
2672         mSlicerManagers[i]->UpdateSlice(3);
2673         //mSlicerManagers[i]->GetSlicer(3)->Render(); // <-- DS add this, needed for contour, seems ok ? not too slow ?
2674       }
2675       break;
2676     }
2677   }
2678 }
2679 //------------------------------------------------------------------------------
2680
2681
2682 //------------------------------------------------------------------------------
2683 void vvMainWindow::UpdateSlice(int slicer, int slice)
2684 {
2685   // DD("vvMainWindow::UpdateSlice");
2686 //   DD(slicer);
2687 //   DD(slice);
2688   if (slicer == 0) {
2689     //    if (slice != NOVerticalSlider->value())
2690     NOVerticalSlider->setValue(slice);
2691   } else {
2692     if (slicer == 1)
2693       NEVerticalSlider->setValue(slice);
2694     else {
2695       if (slicer == 2)
2696         SOVerticalSlider->setValue(slice);
2697       else {
2698         if (slicer == 3)
2699           SEVerticalSlider->setValue(slice);
2700       }
2701     }
2702   }
2703   // DD("vvMainWindow:UpdateSlice END");
2704 }
2705 //------------------------------------------------------------------------------
2706
2707
2708 //------------------------------------------------------------------------------
2709 void vvMainWindow::UpdateTSlice(int slicer, int slice)
2710 {
2711   switch (slicer) {
2712   case 0:
2713     NOHorizontalSlider->setValue(slice);
2714     break;
2715   case 1:
2716     NEHorizontalSlider->setValue(slice);
2717     break;
2718   case 2:
2719     SOHorizontalSlider->setValue(slice);
2720     break;
2721   case 3:
2722     SEHorizontalSlider->setValue(slice);
2723     break;
2724   }
2725 }
2726 //------------------------------------------------------------------------------
2727
2728
2729 //------------------------------------------------------------------------------
2730 void vvMainWindow::UpdateSliceRange(int slicer, int min, int max, int tmin, int tmax)
2731 {
2732   //int position = int((min+max)/2);
2733   int position = mSlicerManagers[mCurrentPickedImageIndex]->GetSlicer(slicer)->GetSlice();
2734   if (slicer == 0) {
2735     NOVerticalSlider->setRange(min,max);
2736     NOHorizontalSlider->setRange(tmin,tmax);
2737     NOVerticalSlider->setValue(position);
2738   } else if (slicer == 1) {
2739     NEVerticalSlider->setRange(min,max);
2740     NEHorizontalSlider->setRange(tmin,tmax);
2741     NEVerticalSlider->setValue(position);
2742   } else if (slicer == 2) {
2743     SOVerticalSlider->setRange(min,max);
2744     SOHorizontalSlider->setRange(tmin,tmax);
2745     SOVerticalSlider->setValue(position);
2746   } else if (slicer == 3) {
2747     SEVerticalSlider->setRange(min,max);
2748     SEHorizontalSlider->setRange(tmin,tmax);
2749     SEVerticalSlider->setValue(position);
2750   }
2751 }
2752 //------------------------------------------------------------------------------
2753
2754
2755 //------------------------------------------------------------------------------
2756 void vvMainWindow::SaveNOScreenshot()
2757 {
2758   SaveScreenshot(NOViewWidget);
2759 }
2760 //------------------------------------------------------------------------------
2761
2762
2763 //------------------------------------------------------------------------------
2764 void vvMainWindow::SaveNEScreenshot()
2765 {
2766   SaveScreenshot(NEViewWidget);
2767 }
2768 //------------------------------------------------------------------------------
2769
2770
2771 //------------------------------------------------------------------------------
2772 void vvMainWindow::SaveSOScreenshot()
2773 {
2774   SaveScreenshot(SOViewWidget);
2775 }
2776 //------------------------------------------------------------------------------
2777
2778
2779 //------------------------------------------------------------------------------
2780 void vvMainWindow::SaveSEScreenshot()
2781 {
2782   SaveScreenshot(SEViewWidget);
2783 }
2784 //------------------------------------------------------------------------------
2785
2786
2787 //------------------------------------------------------------------------------
2788 void vvMainWindow::SaveScreenshotAllSlices()
2789 {
2790   QVTKWidget *widget = NOViewWidget;
2791
2792   int index = 0;// GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2793   vvSlicerManager * SM = mSlicerManagers[index];
2794   vvImage * image = SM->GetImage();
2795   vvSlicer * slicer = SM->GetSlicer(0);
2796   int orientation = slicer->GetOrientation();
2797   int nbSlices = image->GetSize()[orientation];
2798   vtkSmartPointer<vtkRenderWindow>  renderWindow = widget->GetRenderWindow();
2799
2800   // Select filename base
2801   QString filename = QFileDialog::getSaveFileName(this,
2802                                                   tr("Save As (filename will be completed by slice number)"),
2803                                                   itksys::SystemTools::GetFilenamePath(mSlicerManagers[index]->GetFileName()).c_str(),
2804                                                   "Images( *.png);;Images( *.jpg)");
2805
2806   // Loop on slices
2807   for(int i=0; i<nbSlices; i++) {
2808     // Change the slice
2809     slicer->SetSlice(i); // -> change the slice of the current slicer
2810     SM->UpdateSlice(0); // --> this one emit UpdateSlice
2811     QCoreApplication::flush(); // -> needed to force display of contours
2812
2813     // Screenshot
2814     vtkSmartPointer<vtkWindowToImageFilter> windowToImageFilter = vtkSmartPointer<vtkWindowToImageFilter>::New();
2815     windowToImageFilter->SetInput(renderWindow);
2816     windowToImageFilter->SetMagnification(1);
2817     windowToImageFilter->SetInputBufferTypeToRGBA(); //also record the alpha (transparency) channel
2818     windowToImageFilter->Update();
2819
2820     vtkSmartPointer<vtkPNGWriter> writer = vtkSmartPointer<vtkPNGWriter>::New();
2821     std::string fn = itksys::SystemTools::GetFilenameWithoutLastExtension(filename.toStdString());
2822     std::string num = clitk::toString(i);
2823     if (i<10) num = "0"+num;
2824     if (i<100) num = "0"+num;
2825     if (i<1000) num = "0"+num;
2826
2827     fn = itksys::SystemTools::GetFilenamePath(filename.toStdString()) + "/"+ fn
2828       + "_" + num + itksys::SystemTools::GetFilenameLastExtension(filename.toStdString());
2829     writer->SetFileName(fn.c_str());
2830     writer->SetInput(windowToImageFilter->GetOutput());
2831     writer->Write();
2832   }
2833 }
2834 //------------------------------------------------------------------------------
2835
2836
2837 //------------------------------------------------------------------------------
2838 void vvMainWindow::SaveScreenshot(QVTKWidget *widget)
2839 {
2840   QString Extensions = "Images( *.png);;";
2841   Extensions += "Images( *.jpg);;";
2842   Extensions += "Images( *.bmp);;";
2843   Extensions += "Images( *.tif);;";
2844   Extensions += "Images( *.ppm)";
2845 #if defined(VTK_USE_FFMPEG_ENCODER) || defined(VTK_USE_VIDEO_FOR_WINDOWS)
2846   Extensions += ";;Video( *.avi)";
2847 #endif
2848 #ifdef VTK_USE_MPEG2_ENCODER
2849   Extensions += ";;Video( *.mpg)";
2850 #endif
2851 #ifdef CLITK_EXPERIMENTAL
2852   Extensions += ";;Video( *.gif)";
2853 #endif
2854
2855   int smIndex=GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2856   QString fileName = QFileDialog::getSaveFileName(this,
2857                      tr("Save As"),
2858                      itksys::SystemTools::GetFilenamePath(mSlicerManagers[smIndex]->GetFileName()).c_str(),
2859                      Extensions);
2860
2861   if (!fileName.isEmpty()) {
2862     vtkSmartPointer<vtkWindowToImageFilter> w2i = vtkSmartPointer<vtkWindowToImageFilter>::New();
2863     w2i->SetInput(widget->GetRenderWindow());
2864     w2i->Update();
2865     vtkImageData *image = w2i->GetOutput();
2866
2867     std::string ext(itksys::SystemTools::GetFilenameLastExtension(fileName.toStdString()));
2868
2869     // Image
2870     vtkImageWriter *imgwriter = NULL;
2871     if (ext==".bmp")
2872       imgwriter = vtkBMPWriter::New();
2873     else if (ext==".tif")
2874       imgwriter = vtkTIFFWriter::New();
2875     else if (ext==".ppm")
2876       imgwriter = vtkPNMWriter::New();
2877     else if (ext==".png")
2878       imgwriter = vtkPNGWriter::New();
2879     else if (ext==".jpg")
2880       imgwriter = vtkJPEGWriter::New();
2881
2882     // Snapshot image if not null
2883     if(imgwriter!=NULL) {
2884       imgwriter->SetInput(image);
2885       imgwriter->SetFileName(fileName.toStdString().c_str());
2886       imgwriter->Write();
2887       return;
2888     }
2889
2890     // Video
2891     vtkGenericMovieWriter *vidwriter = NULL;
2892 #if CLITK_EXPERIMENTAL == 1
2893     if (ext==".gif") {
2894       vvAnimatedGIFWriter *gif = vvAnimatedGIFWriter::New();
2895       vidwriter = gif;
2896
2897       // FPS
2898       bool ok;
2899       int fps = QInputDialog::getInteger(this, tr("Number of frames per second"),
2900                                      tr("FPS:"), 5, 0, 1000, 1, &ok);
2901       if(ok)
2902         gif->SetRate(fps);
2903
2904       // Loops
2905       int loops = QInputDialog::getInteger(this, tr("Loops"),
2906                                      tr("Number of loops (0 means infinite):"), 0, 0, 1000000000, 1, &ok);
2907       if(ok)
2908         gif->SetLoops(loops);
2909
2910       // Dithering
2911       QString msg = "Would you like to activate dithering?";
2912       QMessageBox msgBox(QMessageBox::Question, tr("Dithering"),msg, 0, this);
2913       msgBox.addButton(tr("Yes"), QMessageBox::AcceptRole);
2914       msgBox.addButton(tr("No"), QMessageBox::RejectRole);
2915       gif->SetDither(msgBox.exec() == QMessageBox::AcceptRole);
2916     }
2917 #endif
2918 #ifdef VTK_USE_VIDEO_FOR_WINDOWS
2919     if (ext==".avi") {
2920       vtkAVIWriter *mpg = vtkAVIWriter::New();
2921       vidwriter = mpg;
2922       mpg->SetQuality(2);
2923       bool ok;
2924       int fps = QInputDialog::getInteger(this, tr("Number of frames per second"),
2925                                      tr("FPS:"), 5, 0, 1024, 1, &ok);
2926       if(!ok)
2927         fps = 5;
2928       mpg->SetRate(fps);
2929     }
2930 #endif
2931 #ifdef VTK_USE_FFMPEG_ENCODER
2932     if (ext==".avi") {
2933       vtkFFMPEGWriter *mpg = vtkFFMPEGWriter::New();
2934       vidwriter = mpg;
2935       mpg->SetQuality(2);
2936       bool ok;
2937       int fps = QInputDialog::getInteger(this, tr("Number of frames per second"),
2938                                      tr("FPS:"), 5, 0, 1024, 1, &ok);
2939       if(!ok)
2940         fps = 5;
2941       mpg->SetRate(fps);
2942       mpg->SetBitRateTolerance(int(ceil(12.0*1024*1024/fps)));
2943     }
2944 #endif
2945 #ifdef VTK_USE_MPEG2_ENCODER
2946     if (ext==".mpg") {
2947       vtkMPEG2Writer *mpg = vtkMPEG2Writer::New();
2948       vidwriter = mpg;
2949     }
2950 #endif
2951
2952     // Take video if not null
2953     if(vidwriter!=NULL){
2954       vidwriter->SetInput(image);
2955       vidwriter->SetFileName(fileName.toStdString().c_str());
2956       vidwriter->Start();
2957       int nSlice = mSlicerManagers[smIndex]->GetSlicer(0)->GetTMax();
2958       for(int i=0; i<=nSlice; i++) {
2959         mSlicerManagers[smIndex]->SetNextTSlice(0);
2960         vtkSmartPointer<vtkWindowToImageFilter> w2i = vtkSmartPointer<vtkWindowToImageFilter>::New();
2961         w2i->SetInput(widget->GetRenderWindow());
2962         w2i->Update();
2963         vidwriter->SetInput(w2i->GetOutput());
2964         vidwriter->Write();
2965       }
2966       vidwriter->End();
2967       vidwriter->Delete();
2968       return;
2969     }
2970
2971     QMessageBox::information(this,tr("Problem saving screenshot !"),tr("Cannot save image.\nPlease set a file extension !!!"));
2972   }
2973 }
2974 //------------------------------------------------------------------------------
2975
2976
2977 //------------------------------------------------------------------------------
2978 void vvMainWindow::GoToCursor()
2979 {
2980   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2981   for (int column = 1; column < 5; column++) {
2982     if (DataTree->selectedItems()[0]->data(column,Qt::CheckStateRole).toInt() > 1) {
2983       double* cursorPos = mSlicerManagers[index]->GetSlicer(column-1)->GetCursorPosition();
2984       mSlicerManagers[index]->GetSlicer(column-1)->SetCurrentPosition(
2985         cursorPos[0],cursorPos[1],cursorPos[2],cursorPos[3]);
2986       mSlicerManagers[index]->UpdateViews(1,column-1);
2987       mSlicerManagers[index]->UpdateLinked(column-1);
2988       break;
2989     }
2990   }
2991 }
2992 //------------------------------------------------------------------------------
2993
2994 //------------------------------------------------------------------------------
2995 void vvMainWindow::GoToLandmark()
2996 {
2997   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2998   for (int column = 1; column < 5; column++) {
2999     if (DataTree->selectedItems()[0]->data(column,Qt::CheckStateRole).toInt() > 1) {
3000       double* cursorPos = landmarksPanel->GetSelectedPoint();
3001       mSlicerManagers[index]->GetSlicer(column-1)->SetCurrentPosition(
3002         cursorPos[0],cursorPos[1],cursorPos[2],cursorPos[3]);
3003       mSlicerManagers[index]->UpdateViews(1,column-1);
3004       mSlicerManagers[index]->UpdateLinked(column-1);
3005       break;
3006     }
3007   }
3008 }
3009 //------------------------------------------------------------------------------
3010
3011 //------------------------------------------------------------------------------
3012 void vvMainWindow::PlayPause()
3013 {
3014   if (playMode) {
3015     playMode = 0;
3016     playButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/player_play.png")));
3017     ImageInfoChanged();
3018     return;
3019   } else {
3020     int image_number=DataTree->topLevelItemCount();
3021     bool has_temporal;
3022     for (int i=0; i<image_number; i++)
3023       if (mSlicerManagers[i]->GetSlicer(0)->GetTMax() > 0) {
3024         has_temporal=true;
3025         break;
3026       }
3027     if (has_temporal) {
3028       playMode = 1;
3029       playButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/player_pause.png")));
3030       QTimer::singleShot(1000/mFrameRate, this, SLOT(PlayNext()));
3031     }
3032   }
3033 }
3034 //------------------------------------------------------------------------------
3035
3036 //------------------------------------------------------------------------------
3037 void vvMainWindow::PlayNext()
3038 {
3039   if (playMode && !this->isHidden()) {
3040     int image_number=DataTree->topLevelItemCount();
3041     ///Only play one slicer per SM, and only if the SM is being displayed
3042     for (int i=0; i<image_number; i++)
3043       for (int j=0; j<4; j++)
3044         if (mSlicerManagers[i]->GetSlicer(0)->GetTMax() > 0 &&
3045             DataTree->topLevelItem(i)->data(j+1,Qt::CheckStateRole).toInt() > 0) {
3046           mSlicerManagers[i]->SetNextTSlice(j);
3047           break;
3048         }
3049     QTimer::singleShot(1000/mFrameRate, this, SLOT(PlayNext()));
3050   }
3051 }
3052 //------------------------------------------------------------------------------
3053
3054 void vvMainWindow::ShowLastImage()
3055 {
3056   if (mSlicerManagers.size() > 1) {
3057     QTreeWidgetItem * item=DataTree->topLevelItem(DataTree->topLevelItemCount()-1);
3058     CurrentImageChanged(mSlicerManagers.back()->GetId()); //select new image
3059     item->setData(1,Qt::CheckStateRole,2); //show the new image in the first panel
3060     DisplayChanged(item,1);
3061   }
3062 }
3063
3064 //------------------------------------------------------------------------------
3065 void vvMainWindow::UpdateRenderWindows()
3066 {
3067   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
3068     mSlicerManagers[i]->GetSlicer(0)->UpdateLandmarks();
3069     mSlicerManagers[i]->GetSlicer(1)->UpdateLandmarks();
3070     mSlicerManagers[i]->GetSlicer(2)->UpdateLandmarks();
3071     mSlicerManagers[i]->GetSlicer(3)->UpdateLandmarks();
3072   }
3073   if (NOViewWidget->GetRenderWindow()) NOViewWidget->GetRenderWindow()->Render();
3074   if (NEViewWidget->GetRenderWindow()) NEViewWidget->GetRenderWindow()->Render();
3075   if (SOViewWidget->GetRenderWindow()) SOViewWidget->GetRenderWindow()->Render();
3076   if (SEViewWidget->GetRenderWindow()) SEViewWidget->GetRenderWindow()->Render();
3077 }
3078 //------------------------------------------------------------------------------
3079
3080 //------------------------------------------------------------------------------
3081 void vvMainWindow::SegmentationOnCurrentImage()
3082 {
3083   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
3084
3085   vvSegmentationDialog segmentation;
3086   segmentation.SetImage(mSlicerManagers[index]->GetSlicer(0)->GetImage());
3087   segmentation.exec();
3088 }
3089 //------------------------------------------------------------------------------
3090
3091 void vvMainWindow::SurfaceViewerLaunch()
3092 {
3093   vvSurfaceViewerDialog surfaceViewer;
3094   surfaceViewer.exec();
3095 }
3096 //------------------------------------------------------------------------------
3097
3098
3099 //------------------------------------------------------------------------------
3100 int vvMainWindow::GetImageDuplicateFilenameNumber(std::string filename)
3101 {
3102   int number=0;
3103   for(unsigned int l=0; l<mSlicerManagers.size(); l++) {
3104     vvSlicerManager * v = mSlicerManagers[l];
3105     if (v->GetBaseFileName() ==
3106         vtksys::SystemTools::GetFilenameName(vtksys::SystemTools::GetFilenameWithoutLastExtension(filename))) {
3107       number = std::max(number, v->GetBaseFileNameNumber()+1);
3108     }
3109   }
3110   return number;
3111 }
3112 //------------------------------------------------------------------------------
3113
3114
3115 //------------------------------------------------------------------------------
3116 vvSlicerManager* vvMainWindow::AddImage(vvImage::Pointer image,std::string filename)
3117 {
3118   // Change filename if another image exist with the same name
3119   int number = GetImageDuplicateFilenameNumber(filename);
3120
3121   // Create new SliceManager
3122   vvSlicerManager* slicer_manager = new vvSlicerManager(4);
3123   slicer_manager->SetImage(image);//, IMAGE, number);
3124   //  filename = filename+"_"+clitk::toString(number);
3125   slicer_manager->SetFilename(filename, number);
3126   mSlicerManagers.push_back(slicer_manager);
3127
3128   //create an item in the tree with good settings
3129   QTreeWidgetItem *item = new QTreeWidgetItem();
3130   item->setData(0,Qt::UserRole,slicer_manager->GetFileName().c_str());//files[i].c_str());
3131   item->setData(1,Qt::UserRole,tr("image"));
3132   item->setData(COLUMN_IMAGE_NAME,Qt::DisplayRole,slicer_manager->GetFileName().c_str());//filename.c_str());
3133   qApp->processEvents();
3134
3135   for (int j = 1; j <= 4; j++) item->setData(j,Qt::CheckStateRole,1);
3136
3137   //Create the buttons for reload and close
3138   qApp->processEvents();
3139   QTreePushButton* cButton = new QTreePushButton;
3140   cButton->setItem(item);
3141   cButton->setColumn(COLUMN_CLOSE_IMAGE);
3142   cButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/exit.png")));
3143   connect(cButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
3144           this,SLOT(CloseImage(QTreeWidgetItem*, int)));
3145
3146   QTreePushButton* rButton = new QTreePushButton;
3147   rButton->setItem(item);
3148   rButton->setColumn(COLUMN_RELOAD_IMAGE);
3149   rButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/rotateright.png")));
3150   rButton->setEnabled(0);
3151   connect(rButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
3152           this,SLOT(ReloadImage(QTreeWidgetItem*, int)));
3153
3154   DataTree->addTopLevelItem(item);
3155   DataTree->setItemWidget(item, COLUMN_CLOSE_IMAGE, cButton);
3156   DataTree->setItemWidget(item, COLUMN_RELOAD_IMAGE, rButton);
3157
3158   //set the id of the image
3159   QString id = QDir::current().absoluteFilePath(slicer_manager->GetFileName().c_str()) + QString::number(mSlicerManagers.size()-1);
3160   item->setData(COLUMN_IMAGE_NAME,Qt::UserRole,id.toStdString().c_str());
3161   mSlicerManagers.back()->SetId(id.toStdString());
3162
3163   linkPanel->addImage(slicer_manager->GetFileName().c_str()// filename
3164                       , id.toStdString());
3165
3166   connect(mSlicerManagers.back(), SIGNAL(currentImageChanged(std::string)),
3167           this, SLOT(CurrentImageChanged(std::string)));
3168   connect(mSlicerManagers.back(), SIGNAL(currentPickedImageChanged(std::string)),
3169           this, SLOT(CurrentPickedImageChanged(std::string)));
3170   connect(mSlicerManagers.back(), SIGNAL(UpdatePosition(int, double, double, double, double, double, double, double)),
3171           this, SLOT(MousePositionChanged(int,double, double, double, double, double, double, double)));
3172   connect(mSlicerManagers.back(), SIGNAL(UpdateVector(int, double, double, double, double)),
3173           this, SLOT(VectorChanged(int,double,double,double, double)));
3174   connect(mSlicerManagers.back(), SIGNAL(UpdateOverlay(int, double, double)),
3175           this, SLOT(OverlayChanged(int,double,double)));
3176   connect(mSlicerManagers.back(), SIGNAL(UpdateFusion(int, double)),
3177           this, SLOT(FusionChanged(int,double)));
3178   connect(mSlicerManagers.back(), SIGNAL(WindowLevelChanged()),
3179           this,SLOT(WindowLevelChanged()));
3180   connect(mSlicerManagers.back(), SIGNAL(UpdateSlice(int,int)),
3181           this,SLOT(UpdateSlice(int,int)));
3182   connect(mSlicerManagers.back(), SIGNAL(UpdateTSlice(int, int)),
3183           this,SLOT(UpdateTSlice(int, int)));
3184   connect(mSlicerManagers.back(), SIGNAL(UpdateTSlice(int, int)),
3185           this,SLOT(ImageInfoChanged()));
3186   connect(mSlicerManagers.back(), SIGNAL(UpdateSliceRange(int,int,int,int,int)),
3187           this,SLOT(UpdateSliceRange(int,int,int,int,int)));
3188   connect(mSlicerManagers.back(), SIGNAL(UpdateLinkManager(std::string,int,double,double,double,int)),
3189           this,SLOT(UpdateLinkManager(std::string,int,double,double,double,int)));
3190   connect(mSlicerManagers.back(), SIGNAL(UpdateLinkedNavigation(std::string,vvSlicerManager*,vvSlicer*)),
3191           this,SLOT(UpdateLinkedNavigation(std::string,vvSlicerManager*,vvSlicer*)));
3192   connect(mSlicerManagers.back(), SIGNAL(ChangeImageWithIndexOffset(vvSlicerManager*,int,int)),
3193           this,SLOT(ChangeImageWithIndexOffset(vvSlicerManager*,int,int)));
3194   connect(mSlicerManagers.back(), SIGNAL(LandmarkAdded()),landmarksPanel,SLOT(AddPoint()));
3195   UpdateTree();
3196   qApp->processEvents();
3197   InitSlicers();
3198   ShowLastImage();
3199   InitDisplay();
3200   qApp->processEvents();
3201
3202   // End
3203   ImageInfoChanged();
3204   return slicer_manager;
3205 }
3206 //------------------------------------------------------------------------------
3207
3208
3209 //------------------------------------------------------------------------------
3210 void vvMainWindow::UpdateCurrentSlicer()
3211 {
3212   int index = -1;
3213   if (DataTree->selectedItems().size() > 0) {
3214     index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
3215   }
3216   mSlicerManagerCurrentIndex = index;
3217 }
3218 //------------------------------------------------------------------------------
3219