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