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,bool)),this,SLOT(AddLink(QString,QString,bool)));
 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 = QDir::current().absoluteFilePath(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     int cols[3];
1244   }SplitterSize;
1245   SplitterSize sizes[4];
1246   sizes[0].splitter = OSplitter;
1247   sizes[0].size1.push_back(1);
1248   sizes[0].size1.push_back(0);
1249   sizes[0].size2.push_back(1);
1250   sizes[0].size2.push_back(0);
1251   sizes[0].cols[0] = 2;
1252   sizes[0].cols[1] = 3;
1253   sizes[0].cols[2] = 4;
1254
1255   sizes[1].splitter = ESplitter;
1256   sizes[1].size1.push_back(0);
1257   sizes[1].size1.push_back(1);
1258   sizes[1].size2.push_back(1);
1259   sizes[1].size2.push_back(0);
1260   sizes[1].cols[0] = 1;
1261   sizes[1].cols[1] = 3;
1262   sizes[1].cols[2] = 4;
1263
1264   sizes[2].splitter = OSplitter;
1265   sizes[2].size1.push_back(1);
1266   sizes[2].size1.push_back(0);
1267   sizes[2].size2.push_back(0);
1268   sizes[2].size2.push_back(1);
1269   sizes[2].cols[0] = 1;
1270   sizes[2].cols[1] = 2;
1271   sizes[2].cols[2] = 4;
1272
1273   sizes[3].splitter = ESplitter;
1274   sizes[3].size1.push_back(0);
1275   sizes[3].size1.push_back(1);
1276   sizes[3].size2.push_back(0);
1277   sizes[3].size2.push_back(1);
1278   sizes[3].cols[0] = 1;
1279   sizes[3].cols[1] = 2;
1280   sizes[3].cols[2] = 3;
1281
1282   int slicer = mSlicerManagers[mCurrentPickedImageIndex]->GetSelectedSlicer();
1283   if (viewMode == 1) {
1284     if (slicer >= 0) {
1285       viewMode = 0;
1286       splitter_3->setSizes(sizes[slicer].size1);
1287       sizes[slicer].splitter->setSizes(sizes[slicer].size2);
1288       DataTree->setColumnHidden(sizes[slicer].cols[0],1);
1289       DataTree->setColumnHidden(sizes[slicer].cols[1],1);
1290       DataTree->setColumnHidden(sizes[slicer].cols[2],1);
1291     }
1292   } else {
1293     QList<int> size;
1294     if (slicer >= 0) {
1295       viewMode = 1;
1296       size.push_back(1);
1297       size.push_back(1);
1298       splitter_3->setSizes(size);
1299       sizes[slicer].splitter->setSizes(size);
1300       DataTree->setColumnHidden(sizes[slicer].cols[0],0);
1301       DataTree->setColumnHidden(sizes[slicer].cols[1],0);
1302       DataTree->setColumnHidden(sizes[slicer].cols[2],0);
1303     }
1304   }
1305   UpdateRenderWindows();
1306   /*
1307   ** I don't know why but for both resized QVTKWidget we also need to render
1308   ** the associated Slicer to redraw crosses.
1309   */
1310   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
1311 //     if (DataTree->topLevelItem(i)->data(COLUMN_UL_VIEW,Qt::CheckStateRole).toInt() > 1)
1312       mSlicerManagers[i]->GetSlicer(0)->Render();
1313       mSlicerManagers[i]->GetSlicer(1)->Render();
1314 //     if (DataTree->topLevelItem(i)->data(COLUMN_DL_VIEW,Qt::CheckStateRole).toInt() > 1)
1315       mSlicerManagers[i]->GetSlicer(2)->Render();
1316       mSlicerManagers[i]->GetSlicer(3)->Render();
1317   }
1318 }
1319 //------------------------------------------------------------------------------
1320
1321 //------------------------------------------------------------------------------
1322 QString vvMainWindow::GetSizeInBytes(unsigned long size)
1323 {
1324   QString result = "";// QString::number(size);
1325   //result += " bytes (";
1326   if (size > 1000000000) {
1327     size /= 1000000000;
1328     result += QString::number(size);
1329     result += "Gb";//)";
1330   } else if (size > 1000000) {
1331     size /= 1000000;
1332     result += QString::number(size);
1333     result += "Mb";//)";
1334   } else if (size > 1000) {
1335     size /= 1000;
1336     result += QString::number(size);
1337     result += "kb";//)";
1338   }
1339   return result;
1340 }
1341 //------------------------------------------------------------------------------
1342
1343 //------------------------------------------------------------------------------
1344 QString vvMainWindow::Get4x4MatrixDoubleAsString(vtkSmartPointer<vtkMatrix4x4> matrix, const int precision)
1345 {
1346   std::ostringstream strmatrix;
1347
1348   // Figure out the number of digits of the integer part of the largest absolute value
1349   // for each column
1350   unsigned width[4];
1351   for (unsigned int j = 0; j < 4; j++){
1352     double absmax = 0.;
1353     for (unsigned int i = 0; i < 4; i++)
1354       absmax = std::max(absmax, vnl_math_abs(matrix->GetElement(i, j)));
1355     unsigned ndigits = (unsigned)std::max(0.,std::log10(absmax))+1;
1356     width[j] = precision+ndigits+3;
1357   }
1358
1359   // Output with correct width, aligned to the right
1360   for (unsigned int i = 0; i < 4; i++) {
1361     for (unsigned int j = 0; j < 4; j++) {
1362       strmatrix.setf(ios::fixed,ios::floatfield);
1363       strmatrix.precision(precision);
1364       strmatrix.fill(' ');
1365       strmatrix.width(width[j]);
1366       strmatrix << std::right << matrix->GetElement(i, j);
1367     }
1368     strmatrix << std::endl;
1369   }
1370   QString result = strmatrix.str().c_str();
1371   return result;
1372 }
1373 //------------------------------------------------------------------------------
1374
1375 //------------------------------------------------------------------------------
1376 QString vvMainWindow::GetVectorDoubleAsString(std::vector<double> vectorDouble)
1377 {
1378   QString result;
1379   for (unsigned int i= 0; i < vectorDouble.size(); i++) {
1380     if (i != 0)
1381       result += " ";
1382     result += QString::number(vectorDouble[i]);
1383   }
1384   return result;
1385 }
1386 //------------------------------------------------------------------------------
1387
1388 //------------------------------------------------------------------------------
1389 QString vvMainWindow::GetVectorIntAsString(std::vector<int> vectorInt)
1390 {
1391   QString result;
1392   for (unsigned int i= 0; i < vectorInt.size(); i++) {
1393     if (i != 0)
1394       result += " ";
1395     result += QString::number(vectorInt[i]);
1396   }
1397   return result;
1398 }
1399 //------------------------------------------------------------------------------
1400
1401 //------------------------------------------------------------------------------
1402 int vvMainWindow::GetSlicerIndexFromItem(QTreeWidgetItem* item)
1403 {
1404   QString id = item->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString();
1405   for (int i = 0; i < DataTree->topLevelItemCount(); i++) {
1406     if (DataTree->topLevelItem(i)->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString() == id)
1407       return i;
1408   }
1409   return -1;
1410 }
1411 //------------------------------------------------------------------------------
1412
1413 //------------------------------------------------------------------------------
1414 QTreeWidgetItem* vvMainWindow::GetItemFromSlicerManager(vvSlicerManager* sm)
1415 {
1416   QString id = sm->GetId().c_str();
1417   for (int i = 0; i < DataTree->topLevelItemCount(); i++) {
1418     if (DataTree->topLevelItem(i)->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString() == id)
1419       return DataTree->topLevelItem(i);
1420   }
1421   return NULL;
1422 }
1423 //------------------------------------------------------------------------------
1424
1425 //------------------------------------------------------------------------------
1426 void vvMainWindow::DisplayChanged(QTreeWidgetItem *clickedItem, int column)
1427 {
1428   if ( column >= COLUMN_CLOSE_IMAGE || column <= 0)
1429     return;
1430
1431   // Get parent information (might be the same item)
1432   int slicerManagerIndex = GetSlicerIndexFromItem(clickedItem);
1433   QTreeWidgetItem* clickedParentItem = DataTree->topLevelItem(slicerManagerIndex);
1434   vvSlicer* clickedSlicer = mSlicerManagers[slicerManagerIndex]->GetSlicer(column-1);
1435
1436   // Go over the complete item tree (only 2 levels, parents and children)
1437   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
1438     // Trick to avoid redoing twice the job for a key (sr)
1439     mSlicerManagers[i]->GetSlicer(column-1)->GetRenderWindow()->GetInteractor()->SetKeySym("Crap");
1440
1441     QTreeWidgetItem* currentParentItem = DataTree->topLevelItem(i);
1442     if(currentParentItem != clickedParentItem) {
1443       // Not the branch of the clicked item, uncheck all
1444
1445       // Parent
1446       currentParentItem->setData(column,Qt::CheckStateRole, 0);
1447       mSlicerManagers[i]->UpdateSlicer(column-1, false);
1448
1449       // Children
1450       for (int iChild = 0; iChild < currentParentItem->childCount(); iChild++) {
1451         currentParentItem->child(iChild)->setData(column,Qt::CheckStateRole, 0);
1452       }
1453     }
1454     else {
1455       // Branch of the clicked one: get check status from actor visibility in slicer
1456       // and toggle the clicked one
1457
1458       // Parent
1459       bool vis = clickedSlicer->GetActorVisibility("image", 0);
1460       bool draw = clickedSlicer->GetRenderer()->GetDraw();
1461
1462       // Update slicer (after getting visibility)
1463       mSlicerManagers[slicerManagerIndex]->UpdateSlicer(column-1, true);
1464       mSlicerManagers[slicerManagerIndex]->UpdateInfoOnCursorPosition(column-1);
1465       DisplaySliders(slicerManagerIndex, column-1);
1466       if(clickedParentItem == clickedItem) {
1467         // Toggle
1468         vis = !draw || !vis;
1469       }
1470       clickedSlicer->SetActorVisibility("image", 0, vis);
1471       clickedParentItem->setData(column, Qt::CheckStateRole, vis?2:0);
1472
1473       // Children
1474       std::map<std::string, int> actorTypeCounts;
1475       for (int iChild = 0; iChild < clickedParentItem->childCount(); iChild++) {
1476         QTreeWidgetItem* currentChildItem = clickedParentItem->child(iChild);
1477         std::string actorType = currentChildItem->data(1,Qt::UserRole).toString().toStdString();
1478         vis = clickedSlicer->GetActorVisibility(actorType, actorTypeCounts[actorType]);
1479         if(currentChildItem == clickedItem) {
1480           // Toggle or force visibility if it was not on this branch so far
1481           vis = !draw || !vis;
1482           clickedSlicer->SetActorVisibility(actorType, actorTypeCounts[actorType], vis);
1483         }
1484         currentChildItem->setData(column, Qt::CheckStateRole, vis?2:0);
1485         actorTypeCounts[actorType]++;
1486       }
1487     }
1488   }
1489
1490   clickedSlicer->Render();
1491 }
1492 //------------------------------------------------------------------------------
1493
1494 void vvMainWindow::InitSlicers()
1495 {
1496   if (mSlicerManagers.size()) {
1497     mSlicerManagers.back()->GenerateDefaultLookupTable();
1498
1499     mSlicerManagers.back()->SetSlicerWindow(0,NOViewWidget->GetRenderWindow());
1500     mSlicerManagers.back()->SetSlicerWindow(1,NEViewWidget->GetRenderWindow());
1501     mSlicerManagers.back()->SetSlicerWindow(2,SOViewWidget->GetRenderWindow());
1502     mSlicerManagers.back()->SetSlicerWindow(3,SEViewWidget->GetRenderWindow());
1503   }
1504 }
1505
1506 //------------------------------------------------------------------------------
1507 void vvMainWindow::InitDisplay()
1508 {
1509   if (mSlicerManagers.size()) {
1510     //BE CAREFUL : this is absolutely necessary to set the interactor style
1511     //in order to have the same style instanciation for all SlicerManagers in
1512     // a same window
1513     for (int j = 0; j < 4; j++) {
1514       vvInteractorStyleNavigator* style = vvInteractorStyleNavigator::New();
1515       style->SetAutoAdjustCameraClippingRange(1);
1516       bool AlreadySelected = false;
1517       for (int i = 0; i < DataTree->topLevelItemCount(); i++) {
1518         mSlicerManagers[i]->SetInteractorStyleNavigator(j,style);
1519
1520         //select the image only if previous are not selected
1521         if (DataTree->topLevelItem(i)->data(j+1,Qt::CheckStateRole).toInt() > 1) {
1522           mSlicerManagers[i]->UpdateSlicer(j,1);
1523           AlreadySelected = true;
1524         } else if (i == DataTree->topLevelItemCount()-1 && !AlreadySelected) {
1525           if (DataTree->selectedItems().size() == 0)
1526             DataTree->topLevelItem(i)->setSelected(1);
1527           DataTree->topLevelItem(i)->setData(j+1,Qt::CheckStateRole,2);
1528           mSlicerManagers[i]->UpdateSlicer(j,1);
1529           DisplaySliders(i,j);
1530         } else {
1531           DataTree->topLevelItem(i)->setData(j+1,Qt::CheckStateRole,0);
1532           mSlicerManagers[i]->UpdateSlicer(j,0);
1533         }
1534       }
1535       style->Delete();
1536     }
1537   }
1538 }
1539 //------------------------------------------------------------------------------
1540
1541 //------------------------------------------------------------------------------
1542 void vvMainWindow::DisplaySliders(int slicer, int window)
1543 {
1544   int range[2];
1545   mSlicerManagers[slicer]->GetSlicer(window)->GetSliceRange(range);
1546   int position = mSlicerManagers[slicer]->GetSlicer(window)->GetSlice();
1547
1548   int tRange[2];
1549   tRange[0] = 0;
1550   tRange[1] = mSlicerManagers[slicer]->GetSlicer(window)->GetTMax();
1551   int tPosition = mSlicerManagers[slicer]->GetSlicer(window)->GetMaxCurrentTSlice();
1552   bool showHorizontal = false;
1553   bool showVertical = false;
1554   if (range[1]>0)
1555     showVertical = true;
1556   if (tRange[1]>0)
1557     showHorizontal = true;
1558
1559   if (showVertical)
1560     verticalSliders[window]->show();
1561   else
1562     verticalSliders[window]->hide();
1563   verticalSliders[window]->setRange(range[0],range[1]);
1564   verticalSliders[window]->setValue(position);
1565
1566   if (showHorizontal)
1567     horizontalSliders[window]->show();
1568   else
1569     horizontalSliders[window]->hide();
1570   horizontalSliders[window]->setRange(tRange[0],tRange[1]);
1571   horizontalSliders[window]->setValue(tPosition);
1572 }
1573 //------------------------------------------------------------------------------
1574
1575 //------------------------------------------------------------------------------
1576 void vvMainWindow::CloseImage(QTreeWidgetItem* item, int column)
1577 {
1578   int index = GetSlicerIndexFromItem(item);
1579
1580   if (DataTree->topLevelItem(index) != item) {
1581     QString warning = "Do you really want to close the overlay : ";
1582     warning += item->data(COLUMN_IMAGE_NAME,Qt::DisplayRole).toString();
1583     QMessageBox msgBox(QMessageBox::Warning, tr("Close Overlay"),
1584                        warning, 0, this);
1585     msgBox.addButton(tr("Close"), QMessageBox::AcceptRole);
1586     msgBox.addButton(tr("Cancel"), QMessageBox::RejectRole);
1587     if (msgBox.exec() == QMessageBox::AcceptRole) {
1588       std::string overlay_type=item->data(1,Qt::UserRole).toString().toStdString();
1589       int overlay_index=0;
1590       for (int child = 0; child < DataTree->topLevelItem(index)->childCount(); child++) {
1591         if (DataTree->topLevelItem(index)->\
1592             child(child)->data(1,Qt::UserRole).toString().toStdString() == overlay_type)
1593           overlay_index++;
1594         if (DataTree->topLevelItem(index)->child(child) == item) break;
1595       }
1596       mSlicerManagers[index]->RemoveActor(overlay_type, overlay_index-1);
1597       mSlicerManagers[index]->SetColorMap(0);
1598       DataTree->topLevelItem(index)->takeChild(DataTree->topLevelItem(index)->indexOfChild(item));
1599       mSlicerManagers[index]->Render();
1600     }
1601   } else if (DataTree->topLevelItemCount() <= 1) {
1602     QString warning = "Do you really want to close the image : ";
1603     warning += item->data(COLUMN_IMAGE_NAME,Qt::DisplayRole).toString();
1604     warning += "\nThis is the last image, you're about to close vv !!!";
1605     QMessageBox msgBox(QMessageBox::Warning, tr("Close Image"),
1606                        warning, 0, this);
1607     msgBox.addButton(tr("Close vv"), QMessageBox::AcceptRole);
1608     msgBox.addButton(tr("Cancel"), QMessageBox::RejectRole);
1609     if (msgBox.exec() == QMessageBox::AcceptRole) {
1610       this->close();
1611     }
1612   } else {
1613     QString warning = "Do you really want to close the image : ";
1614     warning += item->data(COLUMN_IMAGE_NAME,Qt::DisplayRole).toString();
1615     QMessageBox msgBox(QMessageBox::Warning, tr("Close Image"),
1616                        warning, 0, this);
1617     msgBox.addButton(tr("Close"), QMessageBox::AcceptRole);
1618     msgBox.addButton(tr("Cancel"), QMessageBox::RejectRole);
1619     if (msgBox.exec() == QMessageBox::AcceptRole) {
1620
1621       // Tell tools that we close an image
1622       emit AnImageIsBeingClosed(mSlicerManagers[index]);
1623
1624       std::vector<vvSlicerManager*>::iterator Manageriter = mSlicerManagers.begin();
1625       DataTree->takeTopLevelItem(index);
1626       for (int i = 0; i < index; i++) {
1627         Manageriter++;
1628       }
1629       linkPanel->removeImage(index);
1630       mSlicerManagers[index]->RemoveActors();
1631       delete mSlicerManagers[index];
1632       mSlicerManagers.erase(Manageriter);
1633
1634       //
1635       InitDisplay();
1636     }
1637   }
1638   ImageInfoChanged();
1639 }
1640 //------------------------------------------------------------------------------
1641
1642 //------------------------------------------------------------------------------
1643 void vvMainWindow::ReloadImage(QTreeWidgetItem* item, int column)
1644 {
1645   // int index = GetSlicerIndexFromItem(item);
1646   //   QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
1647   //   if (item->data(1,Qt::UserRole).toString() == "vector")
1648   //     mSlicerManagers[index]->ReloadVF();
1649   //   else
1650   //     mSlicerManagers[index]->Reload();
1651
1652   //   QApplication::restoreOverrideCursor();
1653   int index = GetSlicerIndexFromItem(item);
1654   QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
1655   QString role=item->data(1,Qt::UserRole).toString();
1656   if ( role == "vector"){
1657     mSlicerManagers[index]->ReloadVF();
1658   }
1659   else if (role == "overlay"){
1660     mSlicerManagers[index]->ReloadOverlay();
1661   }
1662   else if (role == "fusion"){
1663     mSlicerManagers[index]->ReloadFusion();
1664   }
1665   else{
1666     mSlicerManagers[index]->Reload();
1667   }
1668   // Update view and info
1669   ImageInfoChanged();
1670   mSlicerManagers[index]->Render();
1671   QApplication::restoreOverrideCursor();
1672 }
1673 //------------------------------------------------------------------------------
1674
1675 //------------------------------------------------------------------------------
1676 void vvMainWindow::MousePositionChanged(int visibility,double x, double y, double z, double X, double Y, double Z , double value)
1677 {
1678   infoPanel->setCurrentInfo(visibility,x,y,z,X,Y,Z,value);
1679 }
1680 //------------------------------------------------------------------------------
1681
1682 //------------------------------------------------------------------------------
1683 void vvMainWindow::VectorChanged(int visibility,double x, double y, double z, double value)
1684 {
1685   overlayPanel->getCurrentVectorInfo(visibility,x,y,z,value);
1686 }
1687 //------------------------------------------------------------------------------
1688
1689 //------------------------------------------------------------------------------
1690 void vvMainWindow::OverlayChanged(int visibility, double valueOver, double valueRef)
1691 {
1692   overlayPanel->getCurrentOverlayInfo(visibility,valueOver, valueRef);
1693 }
1694 //------------------------------------------------------------------------------
1695
1696 //------------------------------------------------------------------------------
1697 void vvMainWindow::FusionChanged(int visibility, double value)
1698 {
1699   overlayPanel->getCurrentFusionInfo(visibility,value);
1700 }
1701 //------------------------------------------------------------------------------
1702
1703 //------------------------------------------------------------------------------
1704 void vvMainWindow::WindowLevelChanged()
1705 {
1706   // Base image
1707   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1708   if(index==-1) return;
1709   windowSpinBox->setValue(mSlicerManagers[index]->GetColorWindow());
1710   levelSpinBox->setValue(mSlicerManagers[index]->GetColorLevel());
1711   colorMapComboBox->setCurrentIndex(mSlicerManagers[index]->GetColorMap());
1712   presetComboBox->setCurrentIndex(mSlicerManagers[index]->GetPreset());
1713
1714   // Overlay image
1715   if (mSlicerManagers[index]->GetSlicer(0)->GetOverlay())
1716     overlayPanel->getOverlayProperty(mSlicerManagers[index]->GetOverlayColor(),
1717                                      mSlicerManagers[index]->GetLinkOverlayWindowLevel(),
1718                                      mSlicerManagers[index]->GetOverlayColorWindow(),
1719                                      mSlicerManagers[index]->GetOverlayColorLevel());
1720   else
1721     overlayPanel->getOverlayProperty(-1,0,0.,0.);
1722
1723   // Fusion image
1724   if (mSlicerManagers[index]->GetSlicer(0)->GetFusion())
1725     overlayPanel->getFusionProperty(mSlicerManagers[index]->GetFusionOpacity(),
1726                                     mSlicerManagers[index]->GetFusionThresholdOpacity(),
1727                                     mSlicerManagers[index]->GetFusionColorMap(),
1728                                     mSlicerManagers[index]->GetFusionWindow(),
1729                                     mSlicerManagers[index]->GetFusionLevel());
1730   else
1731     overlayPanel->getFusionProperty(-1, -1, -1, -1, -1);
1732 }
1733 //------------------------------------------------------------------------------
1734
1735 //------------------------------------------------------------------------------
1736 void vvMainWindow::WindowLevelEdited()
1737 {
1738   presetComboBox->setCurrentIndex(6);
1739   UpdateWindowLevel();
1740 }
1741 //------------------------------------------------------------------------------
1742
1743 //------------------------------------------------------------------------------
1744 void vvMainWindow::SetWindowLevel(double w, double l)
1745 {
1746   windowSpinBox->setValue(w);
1747   levelSpinBox->setValue(l);
1748   presetComboBox->setCurrentIndex(6);
1749   colorMapComboBox->setCurrentIndex(0);
1750   UpdateWindowLevel();
1751 }
1752 //------------------------------------------------------------------------------
1753
1754 //------------------------------------------------------------------------------
1755 void vvMainWindow::UpdateWindowLevel()
1756 {
1757   if (DataTree->selectedItems().size()) {
1758     if (presetComboBox->currentIndex() == 7) //For ventilation
1759       colorMapComboBox->setCurrentIndex(5);
1760     int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1761     mSlicerManagers[index]->SetColorWindow(windowSpinBox->value());
1762     mSlicerManagers[index]->SetColorLevel(levelSpinBox->value());
1763     mSlicerManagers[index]->SetPreset(presetComboBox->currentIndex());
1764     mSlicerManagers[index]->Render();
1765     WindowLevelChanged();
1766   }
1767 }
1768 //------------------------------------------------------------------------------
1769
1770 //------------------------------------------------------------------------------
1771 void vvMainWindow::UpdateSlicingPreset()
1772 {
1773   if (DataTree->selectedItems().size()) {
1774     int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1775     mSlicerManagers[index]->SetSlicingPreset(vvSlicerManager::SlicingPresetType(slicingPresetComboBox->currentIndex()));
1776   }
1777 }
1778 //------------------------------------------------------------------------------
1779
1780 //------------------------------------------------------------------------------
1781 void vvMainWindow::UpdateColorMap()
1782 {
1783   if (DataTree->selectedItems().size()) {
1784     int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1785     mSlicerManagers[index]->SetColorMap(colorMapComboBox->currentIndex());
1786     mSlicerManagers[index]->Render();
1787   }
1788 }
1789 //------------------------------------------------------------------------------
1790 void vvMainWindow::SwitchWindowLevel()
1791 {
1792   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1793   int window = mSlicerManagers[index]->GetColorWindow();
1794   presetComboBox->setCurrentIndex(6);
1795   windowSpinBox->setValue(-window);
1796   UpdateWindowLevel();
1797 }
1798 //------------------------------------------------------------------------------
1799
1800 //------------------------------------------------------------------------------
1801 void vvMainWindow::ApplyWindowLevelToAllImages()
1802 {
1803   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1804   if(index==-1) return;
1805   double window = mSlicerManagers[index]->GetColorWindow();
1806   double level = mSlicerManagers[index]->GetColorLevel();
1807
1808   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
1809     if (mSlicerManagers[i] == NULL)
1810       continue;
1811     mSlicerManagers[i]->SetColorWindow(window);
1812     mSlicerManagers[i]->SetColorLevel(level);
1813     mSlicerManagers[i]->SetPreset(6);
1814     mSlicerManagers[i]->Render();
1815   }
1816 }
1817 //------------------------------------------------------------------------------
1818
1819 //------------------------------------------------------------------------------
1820 void vvMainWindow::ApplyWindowToSetOfImages(double window, 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]->SetColorWindow(window);
1826     mSlicerManagers[i]->SetPreset(6);
1827     mSlicerManagers[i]->Render();
1828   }
1829 }
1830 //------------------------------------------------------------------------------
1831
1832 //------------------------------------------------------------------------------
1833 void vvMainWindow::ApplyLevelToSetOfImages(double level, unsigned int indexMin, unsigned int indexMax)
1834 {
1835   for (unsigned int i = indexMin; i <= indexMax && i < mSlicerManagers.size(); i++) {
1836     if (mSlicerManagers[i] == NULL)
1837       continue;
1838     mSlicerManagers[i]->SetColorLevel(level);
1839     mSlicerManagers[i]->SetPreset(6);
1840     mSlicerManagers[i]->Render();
1841   }
1842 }
1843 //------------------------------------------------------------------------------
1844
1845 //------------------------------------------------------------------------------
1846 void vvMainWindow::UpdateLinkManager(std::string id, int slicer, double x, double y, double z, int temps)
1847 {
1848   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
1849     if (mSlicerManagers[i]->GetId() == id) {
1850       //mSlicerManagers[i]->SetTSlice(temps);
1851       mSlicerManagers[i]->GetSlicer(slicer)->SetCurrentPosition(x,y,z,temps);
1852       mSlicerManagers[i]->UpdateViews(0,slicer);
1853       break;
1854     }
1855   }
1856 }
1857 //------------------------------------------------------------------------------
1858
1859 //------------------------------------------------------------------------------
1860 void vvMainWindow::UpdateLinkedNavigation(std::string id, vvSlicerManager * sm, vvSlicer* refSlicer)
1861 {
1862   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
1863     if (id == mSlicerManagers[i]->GetId()) {
1864       mSlicerManagers[i]->UpdateLinkedNavigation(refSlicer);
1865     }
1866   }
1867 }
1868 //------------------------------------------------------------------------------
1869
1870 //------------------------------------------------------------------------------
1871 void vvMainWindow::ShowContextMenu(QPoint point)
1872 {
1873   if (!DataTree->selectedItems().size()) {
1874     contextActions[1]->setEnabled(0);
1875     contextActions[2]->setEnabled(0);
1876     contextActions[3]->setEnabled(0);
1877     contextActions[4]->setEnabled(0);
1878     contextActions[5]->setEnabled(0);
1879     contextActions[6]->setEnabled(0);
1880   } else {
1881     int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1882     contextActions[1]->setEnabled(1);
1883     contextActions[2]->setEnabled(
1884       DataTree->itemWidget(DataTree->selectedItems()[0],
1885                            COLUMN_RELOAD_IMAGE)->isEnabled());
1886     contextActions[3]->setEnabled(1);
1887     contextActions[5]->setEnabled(1);
1888     contextActions[6]->setEnabled(1);
1889
1890     if (mSlicerManagers[index]->GetDimension() < 3)
1891       contextActions[4]->setEnabled(0);
1892     else
1893       contextActions[4]->setEnabled(1);
1894   }
1895   contextMenu.exec(QCursor::pos());
1896 }
1897 //------------------------------------------------------------------------------
1898
1899 //------------------------------------------------------------------------------
1900 void vvMainWindow::CloseImage()
1901 {
1902   CloseImage(DataTree->selectedItems()[0],0);
1903 }
1904 //------------------------------------------------------------------------------
1905
1906 //------------------------------------------------------------------------------
1907 void vvMainWindow::ReloadImage()
1908 {
1909   ReloadImage(DataTree->selectedItems()[0],0);
1910 }
1911 //------------------------------------------------------------------------------
1912
1913 //------------------------------------------------------------------------------
1914 void vvMainWindow::SelectOverlayImage()
1915 {
1916   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1917
1918   //check if one overlay image is added
1919   for (int child = 0; child < DataTree->topLevelItem(index)->childCount(); child++)
1920     if (DataTree->topLevelItem(index)->child(child)->data(1,Qt::UserRole).toString() == "overlay") {
1921       QString error = "Cannot add more than one compared image\n";
1922       error += "Please remove first ";
1923       error += DataTree->topLevelItem(index)->child(child)->data(COLUMN_IMAGE_NAME,Qt::DisplayRole).toString();
1924       QMessageBox::information(this,tr("Problem adding compared image !"),error);
1925       return;
1926     }
1927
1928   QString Extensions = EXTENSIONS;
1929   Extensions += ";;All Files (*)";
1930   QStringList files = QFileDialog::getOpenFileNames(this,tr("Load Overlay image"),mInputPathName,Extensions);
1931   if (files.isEmpty())
1932     return;
1933
1934   std::vector<std::string> vecFileNames;
1935   for (int i = 0; i < files.size(); i++) {
1936     vecFileNames.push_back(files[i].toStdString());
1937   }
1938   AddOverlayImage(index,vecFileNames,vvImageReader::IMAGE);
1939 }
1940 //------------------------------------------------------------------------------
1941
1942 //------------------------------------------------------------------------------
1943 void vvMainWindow::AddOverlayImage(int index, std::vector<std::string> fileNames, vvImageReader::LoadedImageType type)
1944 {
1945   QString file(fileNames[0].c_str());
1946   if (QFile::exists(file))
1947   {
1948     mInputPathName = itksys::SystemTools::GetFilenamePath(file.toStdString()).c_str();
1949     itk::ImageIOBase::Pointer reader = itk::ImageIOFactory::CreateImageIO(
1950         file.toStdString().c_str(), itk::ImageIOFactory::ReadMode);
1951     reader->SetFileName(fileNames[0].c_str());
1952     reader->ReadImageInformation();
1953     std::string component = reader->GetComponentTypeAsString(reader->GetComponentType());
1954     int dimension = reader->GetNumberOfDimensions();
1955     QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
1956     vvProgressDialog progress("Opening " + file.toStdString());
1957     qApp->processEvents();
1958
1959     std::string filename = itksys::SystemTools::GetFilenameWithoutExtension(file.toStdString()).c_str();
1960     if (mSlicerManagers[index]->SetOverlay(fileNames,dimension, component,type)) {
1961       //create an item in the tree with good settings
1962       QTreeWidgetItem *item = new QTreeWidgetItem();
1963       item->setData(0,Qt::UserRole,file.toStdString().c_str());
1964       item->setData(1,Qt::UserRole,tr("overlay"));
1965       QFileInfo fileinfo(file); //Do not show the path
1966       item->setData(COLUMN_IMAGE_NAME,Qt::DisplayRole,fileinfo.fileName());
1967       item->setToolTip(COLUMN_IMAGE_NAME, mSlicerManagers[index]->GetListOfAbsoluteFilePathInOneString("overlay").c_str());
1968       qApp->processEvents();
1969
1970       for (int j = 1; j <= 4; j++) {
1971         item->setData(j,Qt::CheckStateRole,DataTree->topLevelItem(index)->data(j,Qt::CheckStateRole));
1972       }
1973
1974       //Create the buttons for reload and close
1975       qApp->processEvents();
1976       QTreePushButton* cButton = new QTreePushButton;
1977       cButton->setItem(item);
1978       cButton->setColumn(COLUMN_CLOSE_IMAGE);
1979       cButton->setToolTip(tr("close image"));
1980       cButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/exit.png")));
1981       connect(cButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
1982           this,SLOT(CloseImage(QTreeWidgetItem*, int)));
1983
1984       QTreePushButton* rButton = new QTreePushButton;
1985       rButton->setItem(item);
1986       rButton->setColumn(COLUMN_RELOAD_IMAGE);
1987       rButton->setToolTip(tr("reload image"));
1988       rButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/rotateright.png")));
1989       connect(rButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
1990           this,SLOT(ReloadImage(QTreeWidgetItem*, int)));
1991
1992       DataTree->topLevelItem(index)->setExpanded(1);
1993       DataTree->topLevelItem(index)->addChild(item);
1994       DataTree->setItemWidget(item, COLUMN_CLOSE_IMAGE, cButton);
1995       DataTree->setItemWidget(item, COLUMN_RELOAD_IMAGE, rButton);
1996
1997       //set the id of the image
1998       QString id = DataTree->topLevelItem(index)->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString();
1999       item->setData(COLUMN_IMAGE_NAME,Qt::UserRole,id.toStdString().c_str());
2000       UpdateTree();
2001       qApp->processEvents();
2002       ImageInfoChanged();
2003       QApplication::restoreOverrideCursor();
2004
2005       // Update the display to update, e.g., the sliders
2006       for(int i=0; i<4; i++)
2007         DisplaySliders(index, i);
2008     } else {
2009       QApplication::restoreOverrideCursor();
2010       QString error = "Cannot import the new image.\n";
2011       error += mSlicerManagers[index]->GetLastError().c_str();
2012       QMessageBox::information(this,tr("Problem reading image !"),error);
2013     }
2014     WindowLevelChanged();
2015   }
2016   else
2017     QMessageBox::information(this,tr("Problem reading Overlay !"),"File doesn't exist!");
2018 }
2019 //------------------------------------------------------------------------------
2020
2021
2022 //------------------------------------------------------------------------------
2023 void vvMainWindow::AddROI(int index, QString file)
2024 {
2025   /*
2026   // Get slice manager
2027
2028   // Load image
2029
2030   vvImageReader * mReader = new vvImageReader;
2031   mReader->SetInputFilename(filename.toStdString());
2032   mReader->Update(IMAGE);
2033   if (mReader->GetLastError().size() != 0) {
2034     std::cerr << "Error while reading " << filename.toStdString() << std::endl;
2035     QString error = "Cannot open file \n";
2036     error += mReader->GetLastError().c_str();
2037     QMessageBox::information(this,tr("Reading problem"),error);
2038     delete mReader;
2039     return;
2040   }
2041   vvImage::Pointer roi = mReader->GetOutput();
2042
2043   // Create roi in new tool
2044   vvToolStructureSetManager::AddImage(mCurrentSlicerManager, roi);
2045   */
2046 }
2047 //------------------------------------------------------------------------------
2048
2049 //------------------------------------------------------------------------------
2050 void vvMainWindow::SelectFusionImage()
2051 {
2052   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2053
2054   //check if one fusion image is added
2055   for (int child = 0; child < DataTree->topLevelItem(index)->childCount(); child++)
2056     if (DataTree->topLevelItem(index)->child(child)->data(1,Qt::UserRole).toString() == "fusion") {
2057       QString error = "Cannot add more than one fusion image\n";
2058       error += "Please remove first ";
2059       error += DataTree->topLevelItem(index)->child(child)->data(COLUMN_IMAGE_NAME,Qt::DisplayRole).toString();
2060       QMessageBox::information(this,tr("Problem adding fusion image !"),error);
2061       return;
2062     }
2063
2064   QString Extensions = EXTENSIONS;
2065   Extensions += ";;All Files (*)";
2066   QString file = QFileDialog::getOpenFileName(this,tr("Load Fusion image"),mInputPathName,Extensions);
2067   if (!file.isEmpty())
2068     AddFusionImage(index,file);
2069 }
2070 //------------------------------------------------------------------------------
2071
2072 //------------------------------------------------------------------------------
2073 void vvMainWindow::ResetTransformationToIdentity()
2074 {
2075   std::string actorType = DataTree->selectedItems()[0]->data(1,Qt::UserRole).toString().toStdString();
2076   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2077   mSlicerManagers[index]->ResetTransformationToIdentity(actorType);
2078   ImageInfoChanged();
2079 }
2080 //------------------------------------------------------------------------------
2081
2082 //------------------------------------------------------------------------------
2083 void vvMainWindow::AddFusionImage(int index, QString file)
2084 {
2085   if (QFile::exists(file))
2086   {
2087     mInputPathName = itksys::SystemTools::GetFilenamePath(file.toStdString()).c_str();
2088     itk::ImageIOBase::Pointer reader = itk::ImageIOFactory::CreateImageIO(
2089         file.toStdString().c_str(), itk::ImageIOFactory::ReadMode);
2090     reader->SetFileName(file.toStdString().c_str());
2091     reader->ReadImageInformation();
2092     std::string component = reader->GetComponentTypeAsString(reader->GetComponentType());
2093     if (reader) {
2094       QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
2095       vvProgressDialog progress("Opening fusion");
2096       qApp->processEvents();
2097
2098       std::string filename = itksys::SystemTools::GetFilenameWithoutExtension(file.toStdString()).c_str();
2099       if (mSlicerManagers[index]->SetFusion(file.toStdString(),
2100             reader->GetNumberOfDimensions(), component)) {
2101         //create an item in the tree with good settings
2102         QTreeWidgetItem *item = new QTreeWidgetItem();
2103         item->setData(0,Qt::UserRole,file.toStdString().c_str());
2104         item->setData(1,Qt::UserRole,tr("fusion"));
2105         QFileInfo fileinfo(filename.c_str()); //Do not show the path
2106         item->setData(COLUMN_IMAGE_NAME,Qt::DisplayRole,fileinfo.fileName());
2107         item->setToolTip(COLUMN_IMAGE_NAME, mSlicerManagers[index]->GetListOfAbsoluteFilePathInOneString("fusion").c_str());
2108         qApp->processEvents();
2109
2110         for (int j = 1; j <= 4; j++) {
2111           item->setData(j,Qt::CheckStateRole,DataTree->topLevelItem(index)->data(j,Qt::CheckStateRole));
2112         }
2113
2114         //Create the buttons for reload and close
2115         qApp->processEvents();
2116         QTreePushButton* cButton = new QTreePushButton;
2117         cButton->setItem(item);
2118         cButton->setColumn(COLUMN_CLOSE_IMAGE);
2119         cButton->setToolTip(tr("close image"));
2120         cButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/exit.png")));
2121         connect(cButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
2122             this,SLOT(CloseImage(QTreeWidgetItem*, int)));
2123
2124         QTreePushButton* rButton = new QTreePushButton;
2125         rButton->setItem(item);
2126         rButton->setColumn(COLUMN_RELOAD_IMAGE);
2127         rButton->setToolTip(tr("reload image"));
2128         rButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/rotateright.png")));
2129         connect(rButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
2130             this,SLOT(ReloadImage(QTreeWidgetItem*, int)));
2131
2132         DataTree->topLevelItem(index)->setExpanded(1);
2133         DataTree->topLevelItem(index)->addChild(item);
2134         DataTree->setItemWidget(item, COLUMN_CLOSE_IMAGE, cButton);
2135         DataTree->setItemWidget(item, COLUMN_RELOAD_IMAGE, rButton);
2136
2137         //set the id of the image
2138         QString id = DataTree->topLevelItem(index)->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString();
2139         item->setData(COLUMN_IMAGE_NAME,Qt::UserRole,id.toStdString().c_str());
2140         UpdateTree();
2141         qApp->processEvents();
2142         ImageInfoChanged();
2143         QApplication::restoreOverrideCursor();
2144       } else {
2145         QApplication::restoreOverrideCursor();
2146         QString error = "Cannot import the new image.\n";
2147         error += mSlicerManagers[index]->GetLastError().c_str();
2148         QMessageBox::information(this,tr("Problem reading image !"),error);
2149       }
2150     } else {
2151       QString error = "Cannot import the new image.\n";
2152       QMessageBox::information(this,tr("Problem reading image !"),error);
2153     }
2154   }
2155   else
2156     QMessageBox::information(this,tr("Problem reading Fusion !"),"File doesn't exist!");
2157 }
2158 //------------------------------------------------------------------------------
2159
2160
2161 //------------------------------------------------------------------------------
2162 void vvMainWindow::OpenField()
2163 {
2164   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2165   //check if a vector field has already been added
2166   for (int child = 0; child < DataTree->topLevelItem(index)->childCount(); child++)
2167     if (DataTree->topLevelItem(index)->child(child)->data(1,Qt::UserRole).toString() == "vector") {
2168       QString error = "Cannot add more than one vector field\n";
2169       error += "Please remove first ";
2170       error += DataTree->topLevelItem(index)->child(child)->data(COLUMN_IMAGE_NAME,Qt::DisplayRole).toString();
2171       QMessageBox::information(this,tr("Problem adding vector field!"),error);
2172       return;
2173     }
2174
2175   QString Extensions = "Images ( *.mhd)";
2176   Extensions += ";;Images ( *.mha)";
2177   Extensions += ";;Images ( *.vf)";
2178   QString file = QFileDialog::getOpenFileName(this,tr("Load deformation field"),mInputPathName,Extensions);
2179   if (!file.isEmpty())
2180     AddField(file,index);
2181 }
2182 //------------------------------------------------------------------------------
2183
2184
2185 //------------------------------------------------------------------------------
2186 void vvMainWindow::AddFieldEntry(QString filename,int index,bool from_disk)
2187 {
2188   //create an item in the tree with good settings
2189   QTreeWidgetItem *item = new QTreeWidgetItem();
2190   item->setData(0,Qt::UserRole,filename.toStdString().c_str());
2191   item->setData(1,Qt::UserRole,tr("vector"));
2192   QFileInfo fileinfo(filename); //Do not show the path
2193   item->setData(COLUMN_IMAGE_NAME,Qt::DisplayRole,fileinfo.fileName());
2194   item->setToolTip(COLUMN_IMAGE_NAME, mSlicerManagers[index]->GetListOfAbsoluteFilePathInOneString("vector").c_str());
2195   qApp->processEvents();
2196
2197   for (int j = 1; j <= 4; j++) {
2198     item->setData(j,Qt::CheckStateRole,DataTree->topLevelItem(index)->data(j,Qt::CheckStateRole));
2199   }
2200
2201   //Create the buttons for reload and close
2202   qApp->processEvents();
2203   QTreePushButton* cButton = new QTreePushButton;
2204   cButton->setItem(item);
2205   cButton->setColumn(COLUMN_CLOSE_IMAGE);
2206   cButton->setToolTip(tr("close vector field"));
2207   cButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/exit.png")));
2208   connect(cButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
2209           this,SLOT(CloseImage(QTreeWidgetItem*, int)));
2210
2211   QTreePushButton* rButton = new QTreePushButton;
2212   rButton->setItem(item);
2213   rButton->setColumn(COLUMN_RELOAD_IMAGE);
2214   rButton->setToolTip(tr("reload vector field"));
2215   rButton->setEnabled(from_disk);
2216   rButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/rotateright.png")));
2217   connect(rButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
2218           this,SLOT(ReloadImage(QTreeWidgetItem*, int)));
2219
2220   DataTree->topLevelItem(index)->setExpanded(1);
2221   DataTree->topLevelItem(index)->addChild(item);
2222   DataTree->setItemWidget(item, COLUMN_RELOAD_IMAGE, rButton);
2223   DataTree->setItemWidget(item, COLUMN_CLOSE_IMAGE, cButton);
2224
2225   //set the id of the image
2226   QString id = DataTree->topLevelItem(index)->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString();
2227   item->setData(COLUMN_IMAGE_NAME,Qt::UserRole,id.toStdString().c_str());
2228   UpdateTree();
2229   qApp->processEvents();
2230   ImageInfoChanged();
2231   QApplication::restoreOverrideCursor();
2232 }
2233 //------------------------------------------------------------------------------
2234
2235
2236 //------------------------------------------------------------------------------
2237 void vvMainWindow::AddField(vvImage::Pointer vf,QString file,int index)
2238 {
2239   QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
2240   vvSlicerManager* imageManager = mSlicerManagers[index];
2241   if (imageManager->SetVF(vf,file.toStdString())) {
2242     AddFieldEntry(file,index,false);
2243   } else {
2244     QString error = "Cannot import the vector field for this image.\n";
2245     error += imageManager->GetLastError().c_str();
2246     QMessageBox::information(this,tr("Problem reading VF !"),error);
2247   }
2248   QApplication::restoreOverrideCursor();
2249 }
2250 //------------------------------------------------------------------------------
2251
2252
2253 //------------------------------------------------------------------------------
2254 void vvMainWindow::AddField(QString file,int index)
2255 {
2256   if (QFile::exists(file)) {
2257     mInputPathName = itksys::SystemTools::GetFilenamePath(file.toStdString()).c_str();
2258
2259     //init the progress events
2260     QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
2261     vvProgressDialog progress("Opening " + file.toStdString());
2262     qApp->processEvents();
2263
2264     //read the vector and put it in the current mSlicerManager
2265     vvSlicerManager* imageManager = mSlicerManagers[index];
2266     qApp->processEvents();
2267
2268     std::string filename = itksys::SystemTools::GetFilenameWithoutExtension(file.toStdString()).c_str();
2269     if (imageManager->SetVF(file.toStdString())) {
2270       imageManager->Render();
2271       AddFieldEntry(file,index,true);
2272     } else {
2273       QApplication::restoreOverrideCursor();
2274       QString error = "Cannot import the vector field for this image.\n";
2275       error += imageManager->GetLastError().c_str();
2276       QMessageBox::information(this,tr("Problem reading VF !"),error);
2277     }
2278   } else
2279     QMessageBox::information(this,tr("Problem reading VF !"),"File doesn't exist!");
2280
2281 }
2282 //------------------------------------------------------------------------------
2283
2284
2285 //------------------------------------------------------------------------------
2286 void vvMainWindow::SetVFProperty(int subsampling, int scale, int log, int width, double r, double g, double b)
2287 {
2288   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2289   if (mSlicerManagers[index]->GetSlicer(0)->GetVF()) {
2290     for (int i = 0; i < 4; i++) {
2291       mSlicerManagers[index]->GetSlicer(i)->SetVFSubSampling(subsampling);
2292       mSlicerManagers[index]->GetSlicer(i)->SetVFScale(scale);
2293       mSlicerManagers[index]->GetSlicer(i)->SetVFWidth(width);
2294       mSlicerManagers[index]->GetSlicer(i)->SetVFColor(r,g,b);
2295       if (log > 0)
2296         mSlicerManagers[index]->GetSlicer(i)->SetVFLog(1);
2297       else
2298         mSlicerManagers[index]->GetSlicer(i)->SetVFLog(0);
2299     }
2300   }
2301 }
2302 //------------------------------------------------------------------------------
2303
2304
2305 //------------------------------------------------------------------------------
2306 void vvMainWindow::SetOverlayProperty(int color, int linked, double window, double level)
2307 {
2308   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2309   if (mSlicerManagers[index]->GetSlicer(0)->GetOverlay()) {
2310     mSlicerManagers[index]->SetOverlayColor(color);
2311     mSlicerManagers[index]->SetColorMap(0);
2312     mSlicerManagers[index]->SetLinkOverlayWindowLevel(linked);
2313     mSlicerManagers[index]->SetOverlayColorWindow(window);
2314     mSlicerManagers[index]->SetOverlayColorLevel(level);
2315     mSlicerManagers[index]->Render();
2316   }
2317 }
2318 //------------------------------------------------------------------------------
2319
2320 //------------------------------------------------------------------------------
2321 void vvMainWindow::SetFusionProperty(int opacity, int thresOpacity, int colormap,double window, double level, bool showLegend)
2322 {
2323   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2324   if (mSlicerManagers[index]->GetSlicer(0)->GetFusion()) {
2325     mSlicerManagers[index]->SetFusionColorMap(colormap);
2326     mSlicerManagers[index]->SetFusionOpacity(opacity);
2327     mSlicerManagers[index]->SetFusionThresholdOpacity(thresOpacity);
2328     mSlicerManagers[index]->SetFusionWindow(window);
2329     mSlicerManagers[index]->SetFusionLevel(level);
2330     mSlicerManagers[index]->SetFusionShowLegend(showLegend);
2331     mSlicerManagers[index]->SetColorMap(0);
2332     mSlicerManagers[index]->Render();
2333   }
2334 }
2335 //------------------------------------------------------------------------------
2336
2337 //------------------------------------------------------------------------------
2338 void vvMainWindow::SaveAs()
2339 {
2340   if (DataTree->selectedItems()[0]->data(1,Qt::UserRole).toString() == "vector") {
2341     QMessageBox::warning(this,tr("Unsupported type"),tr("Sorry, saving a vector field is unsupported for the moment"));
2342     return;
2343   }
2344
2345   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2346   int dimension = mSlicerManagers[index]->GetDimension();
2347   QStringList OutputListeFormat;
2348   OutputListeFormat.clear();
2349   if (dimension == 1) {
2350     OutputListeFormat.push_back(".mhd");
2351     OutputListeFormat.push_back(".mha");
2352   }
2353   if (dimension == 2) {
2354     OutputListeFormat.push_back(".bmp");
2355     OutputListeFormat.push_back(".png");
2356     OutputListeFormat.push_back(".jpeg");
2357     OutputListeFormat.push_back(".tif");
2358     OutputListeFormat.push_back(".mhd");
2359     OutputListeFormat.push_back(".mha");
2360     OutputListeFormat.push_back(".hdr");
2361     OutputListeFormat.push_back(".vox");
2362   } else if (dimension == 3) {
2363     OutputListeFormat.push_back(".mhd");
2364     OutputListeFormat.push_back(".mha");
2365     OutputListeFormat.push_back(".nii");
2366     OutputListeFormat.push_back(".nrrd");
2367     OutputListeFormat.push_back(".nhdr");
2368     OutputListeFormat.push_back(".hdr");
2369     OutputListeFormat.push_back(".vox");
2370   } else if (dimension == 4) {
2371     OutputListeFormat.push_back(".mhd");
2372     OutputListeFormat.push_back(".mha");
2373     OutputListeFormat.push_back(".nii");
2374     OutputListeFormat.push_back(".nrrd");
2375     OutputListeFormat.push_back(".nhdr");
2376   }
2377   QString Extensions = "AllFiles(*.*)";
2378   for (int i = 0; i < OutputListeFormat.count(); i++) {
2379     Extensions += ";;Images ( *";
2380     Extensions += OutputListeFormat[i];
2381     Extensions += ")";
2382   }
2383   QString fileName = QFileDialog::getSaveFileName(this,
2384                      tr("Save As"),
2385                      mSlicerManagers[index]->GetFileName().c_str(),
2386                      Extensions);
2387   if (!fileName.isEmpty()) {
2388     std::string fileformat = itksys::SystemTools::GetFilenameLastExtension(fileName.toStdString());
2389     if (OutputListeFormat.contains(
2390           fileformat.c_str())) {
2391       QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
2392       std::string action = "Saving";
2393       vvProgressDialog progress("Saving "+fileName.toStdString());
2394       qApp->processEvents();
2395       vvImageWriter::Pointer writer = vvImageWriter::New();
2396       writer->SetOutputFileName(fileName.toStdString());
2397       writer->SetInput(mSlicerManagers[index]->GetImage());
2398
2399       // Check on transform and prompt user
2400       writer->SetSaveTransform(false);
2401       bool bId = true;
2402       for(int i=0; i<4; i++)
2403         for(int j=0; j<4; j++) {
2404           // TODO SR and BP: check on the list of transforms and not the first only
2405           double elt = mSlicerManagers[index]->GetImage()->GetTransform()[0]->GetMatrix()->GetElement(i,j);
2406           if(i==j && elt!=1.)
2407             bId = false;
2408           if(i!=j && elt!=0.)
2409             bId = false;
2410         }
2411       if( !bId ) {
2412         QString warning = "The image has an associated linear transform. Do you want to save it along?";
2413         QMessageBox msgBox(QMessageBox::Warning, tr("Save transform"), warning, 0, this);
2414         msgBox.addButton(tr("Yes"), QMessageBox::AcceptRole);
2415         msgBox.addButton(tr("No"), QMessageBox::RejectRole);
2416         if (msgBox.exec() == QMessageBox::AcceptRole)
2417           writer->SetSaveTransform(true);
2418       }
2419
2420       writer->Update();
2421       QApplication::restoreOverrideCursor();
2422       if (writer->GetLastError().size()) {
2423         QString error = "Saving did not succeed\n";
2424         error += writer->GetLastError().c_str();
2425         QMessageBox::information(this,tr("Saving Problem"),error);
2426         SaveAs();
2427       }
2428     } else {
2429       QString error = fileformat.c_str();
2430       if (error.isEmpty())
2431         error += "no file format specified !";
2432       else
2433         error += " format unknown !!!\n";
2434       QMessageBox::information(this,tr("Saving Problem"),error);
2435       SaveAs();
2436     }
2437   }
2438 }
2439 //------------------------------------------------------------------------------
2440
2441 //------------------------------------------------------------------------------
2442 void vvMainWindow::SaveCurrentState()
2443 {
2444   QString Extensions = "XML Files(*.xml)";
2445   QString fileName = QFileDialog::getSaveFileName(this,
2446                      tr("Save Current Window State"),
2447                      "",
2448                      Extensions);
2449
2450   SaveCurrentStateAs(fileName.toStdString());
2451 }
2452 //------------------------------------------------------------------------------
2453
2454 //------------------------------------------------------------------------------
2455 void vvMainWindow::SaveCurrentStateAs(const std::string& stateFile)
2456 {
2457   vvSaveState save_state;
2458   save_state.Run(this, stateFile);
2459 }
2460
2461 //------------------------------------------------------------------------------
2462 void vvMainWindow::ReadSavedState()
2463 {
2464   QString Extensions = "XML Files(*.xml)";
2465   QString fileName = QFileDialog::getOpenFileName(this,
2466                      tr("Load Window State"),
2467                      "",
2468                      Extensions);
2469
2470   ReadSavedStateFile(fileName.toStdString());
2471 }
2472 //------------------------------------------------------------------------------
2473
2474 //------------------------------------------------------------------------------
2475 void vvMainWindow::ReadSavedStateFile(const std::string& stateFile)
2476 {
2477   vvReadState read_state;
2478   read_state.Run(this, stateFile);
2479 }
2480 //------------------------------------------------------------------------------
2481
2482 //------------------------------------------------------------------------------
2483 void vvMainWindow::LinkAllImages()
2484 {
2485         linkPanel->linkAll();
2486 }
2487
2488 //------------------------------------------------------------------------------
2489 void vvMainWindow::AddLink(QString image1,QString image2,bool fromPanel)
2490 {
2491   if (!fromPanel) {
2492     // delegate to linkPanel if call came from elsewhere...
2493     linkPanel->addLinkFromIds(image1, image2);
2494     return;
2495   }
2496
2497   unsigned int sm1 = 0;
2498   unsigned int sm2 = 0;
2499
2500   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
2501     if (image1.toStdString() == mSlicerManagers[i]->GetId()) {
2502       mSlicerManagers[i]->AddLink(image2.toStdString());
2503       sm1 = i;
2504     }
2505     if (image2.toStdString() == mSlicerManagers[i]->GetId()) {
2506       mSlicerManagers[i]->AddLink(image1.toStdString());
2507       sm2 = i;
2508     }
2509   }
2510
2511   if (linkPanel->isLinkAll())   {
2512     emit UpdateLinkedNavigation(mSlicerManagers[sm1]->GetId(), mSlicerManagers[mCurrentPickedImageIndex], mSlicerManagers[mCurrentPickedImageIndex]->GetSlicer(0));
2513     emit UpdateLinkedNavigation(mSlicerManagers[sm2]->GetId(), mSlicerManagers[mCurrentPickedImageIndex], mSlicerManagers[mCurrentPickedImageIndex]->GetSlicer(0));
2514   } else {
2515     emit UpdateLinkedNavigation(mSlicerManagers[sm2]->GetId(), mSlicerManagers[sm1], mSlicerManagers[sm1]->GetSlicer(0));
2516   }
2517 }
2518
2519 //------------------------------------------------------------------------------
2520
2521
2522 //------------------------------------------------------------------------------
2523 void vvMainWindow::RemoveLink(QString image1,QString image2)
2524 {
2525   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
2526     if (image1.toStdString() == mSlicerManagers[i]->GetId()) {
2527       mSlicerManagers[i]->RemoveLink(image2.toStdString());
2528     }
2529     if (image2.toStdString() == mSlicerManagers[i]->GetId()) {
2530       mSlicerManagers[i]->RemoveLink(image1.toStdString());
2531     }
2532   }
2533 }
2534 //------------------------------------------------------------------------------
2535
2536 //------------------------------------------------------------------------------
2537 void vvMainWindow::ChangeImageWithIndexOffset(vvSlicerManager *sm, int slicer, int offset)
2538 {
2539   if(mSlicerManagers.size()==1)
2540     return;
2541
2542   int index = 0;
2543   while(sm != mSlicerManagers[index])
2544     index++;
2545   index = (index+offset+mSlicerManagers.size()) % mSlicerManagers.size();
2546
2547   QTreeWidgetItem* item = GetItemFromSlicerManager(mSlicerManagers[index]);
2548   item->setData(slicer+1,Qt::CheckStateRole,2);         //change checkbox
2549   CurrentImageChanged(mSlicerManagers[index]->GetId()); //select new image
2550   DisplayChanged(item,slicer+1);
2551 }
2552 //------------------------------------------------------------------------------
2553
2554 void vvMainWindow::HorizontalSliderMoved(int value,int column, int slicer_index)
2555 {
2556   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
2557     if (DataTree->topLevelItem(i)->data(column,Qt::CheckStateRole).toInt() > 1) {
2558       for (int j = 0; j < 4; j++) {
2559         mSlicerManagers[i]->SetTSliceInSlicer(value,j);
2560         //if (mSlicerManagers[i]->GetSlicer(j)->GetImageActor()->GetVisibility())
2561         //UpdateTSlice(j,value);
2562       }
2563       mSlicerManagers[i]->GetSlicer(slicer_index)->Render();
2564       break;
2565     }
2566   }
2567 }
2568 //------------------------------------------------------------------------------
2569
2570
2571 //------------------------------------------------------------------------------
2572 void vvMainWindow::NOHorizontalSliderMoved()
2573 {
2574   // if (mCurrentTime == NOHorizontalSlider->value()) return;
2575   HorizontalSliderMoved(NOHorizontalSlider->value(),COLUMN_UL_VIEW,0);
2576 //  mCurrentTime = NOHorizontalSlider->value();
2577 }
2578 //------------------------------------------------------------------------------
2579
2580
2581 //------------------------------------------------------------------------------
2582 void vvMainWindow::NEHorizontalSliderMoved()
2583 {
2584   // if (mCurrentTime == NEHorizontalSlider->value()) return;
2585   HorizontalSliderMoved(NEHorizontalSlider->value(),COLUMN_UR_VIEW,1);
2586 //  mCurrentTime = NEHorizontalSlider->value();
2587 }
2588 //------------------------------------------------------------------------------
2589
2590
2591 //------------------------------------------------------------------------------
2592 void vvMainWindow::SOHorizontalSliderMoved()
2593 {
2594   // if (mCurrentTime == SOHorizontalSlider->value()) return;
2595   HorizontalSliderMoved(SOHorizontalSlider->value(),COLUMN_DL_VIEW,2);
2596   // mCurrentTime = SOHorizontalSlider->value();
2597 }
2598 //------------------------------------------------------------------------------
2599
2600
2601 //------------------------------------------------------------------------------
2602 void vvMainWindow::SEHorizontalSliderMoved()
2603 {
2604   // if (mCurrentTime == SEHorizontalSlider->value()) return;
2605   HorizontalSliderMoved(SEHorizontalSlider->value(),COLUMN_DR_VIEW,3);
2606   // mCurrentTime = SEHorizontalSlider->value();
2607 }
2608 //------------------------------------------------------------------------------
2609
2610 //------------------------------------------------------------------------------
2611 void vvMainWindow::NOVerticalSliderChanged()
2612 {
2613   static int value=-1;
2614   if (value == NOVerticalSlider->value()) return;
2615   else value = NOVerticalSlider->value();
2616   //  int value = NOVerticalSlider->value();
2617   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
2618     if (DataTree->topLevelItem(i)->data(COLUMN_UL_VIEW,Qt::CheckStateRole).toInt() > 1) {
2619       if (mSlicerManagers[i]->GetSlicer(0)->GetSlice() != value) {
2620         mSlicerManagers[i]->GetSlicer(0)->SetSlice(value);
2621         mSlicerManagers[i]->VerticalSliderHasChanged(0, value);
2622
2623         // If nor Update/Render -> slider not work
2624         // only render = ok navigation, but for contour Update needed but slower ?
2625
2626         mSlicerManagers[i]->UpdateSlice(0);  // <-- DS add this. Not too much update ? YES. but needed for ImageContour ...
2627         //mSlicerManagers[i]->GetSlicer(0)->Render(); // <-- DS add this, needed for contour, seems ok ? not too slow ?
2628       }
2629       break;
2630     }
2631   }
2632 }
2633 //------------------------------------------------------------------------------
2634
2635
2636 //------------------------------------------------------------------------------
2637 void vvMainWindow::NEVerticalSliderChanged()
2638 {
2639   static int value=-1;
2640   if (value == NEVerticalSlider->value()) return;
2641   else value = NEVerticalSlider->value();
2642   //  int value = NEVerticalSlider->value();
2643   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
2644     if (DataTree->topLevelItem(i)->data(COLUMN_UR_VIEW,Qt::CheckStateRole).toInt() > 1) {
2645       if (mSlicerManagers[i]->GetSlicer(1)->GetSlice() != value) {
2646         mSlicerManagers[i]->GetSlicer(1)->SetSlice(value);
2647         mSlicerManagers[i]->VerticalSliderHasChanged(1, value);
2648         mSlicerManagers[i]->UpdateSlice(1);
2649         //mSlicerManagers[i]->GetSlicer(1)->Render(); // <-- DS add this, needed for contour, seems ok ? not too slow ?
2650       }
2651       break;
2652     }
2653   }
2654 }
2655 //------------------------------------------------------------------------------
2656
2657
2658 //------------------------------------------------------------------------------
2659 void vvMainWindow::SOVerticalSliderChanged()
2660 {
2661   static int value=-1;
2662   if (value == SOVerticalSlider->value()) return;
2663   else value = SOVerticalSlider->value();
2664   //int value = SOVerticalSlider->value();
2665   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
2666     if (DataTree->topLevelItem(i)->data(COLUMN_DL_VIEW,Qt::CheckStateRole).toInt() > 1) {
2667       if (mSlicerManagers[i]->GetSlicer(2)->GetSlice() != value) {
2668         mSlicerManagers[i]->GetSlicer(2)->SetSlice(value);
2669         mSlicerManagers[i]->VerticalSliderHasChanged(2, value);
2670         mSlicerManagers[i]->UpdateSlice(2);
2671         //mSlicerManagers[i]->GetSlicer(2)->Render(); // <-- DS add this, needed for contour, seems ok ? not too slow ?
2672       }
2673       // else { DD("avoid SOVerticalSlider slicer update"); }
2674       break;
2675     }
2676   }
2677 }
2678 //------------------------------------------------------------------------------
2679
2680
2681 //------------------------------------------------------------------------------
2682 void vvMainWindow::SEVerticalSliderChanged()
2683 {
2684   static int value=-1;
2685   if (value == SEVerticalSlider->value()) return;
2686   else value = SEVerticalSlider->value();
2687   // int value = SEVerticalSlider->value();
2688   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
2689     if (DataTree->topLevelItem(i)->data(COLUMN_DR_VIEW,Qt::CheckStateRole).toInt() > 1) {
2690       if (mSlicerManagers[i]->GetSlicer(3)->GetSlice() != value) {
2691         mSlicerManagers[i]->GetSlicer(3)->SetSlice(value);
2692         mSlicerManagers[i]->VerticalSliderHasChanged(3, value);
2693         mSlicerManagers[i]->UpdateSlice(3);
2694         //mSlicerManagers[i]->GetSlicer(3)->Render(); // <-- DS add this, needed for contour, seems ok ? not too slow ?
2695       }
2696       break;
2697     }
2698   }
2699 }
2700 //------------------------------------------------------------------------------
2701
2702
2703 //------------------------------------------------------------------------------
2704 void vvMainWindow::UpdateSlice(int slicer, int slice)
2705 {
2706   // DD("vvMainWindow::UpdateSlice");
2707 //   DD(slicer);
2708 //   DD(slice);
2709   if (slicer == 0) {
2710     //    if (slice != NOVerticalSlider->value())
2711     NOVerticalSlider->setValue(slice);
2712   } else {
2713     if (slicer == 1)
2714       NEVerticalSlider->setValue(slice);
2715     else {
2716       if (slicer == 2)
2717         SOVerticalSlider->setValue(slice);
2718       else {
2719         if (slicer == 3)
2720           SEVerticalSlider->setValue(slice);
2721       }
2722     }
2723   }
2724   // DD("vvMainWindow:UpdateSlice END");
2725 }
2726 //------------------------------------------------------------------------------
2727
2728
2729 //------------------------------------------------------------------------------
2730 void vvMainWindow::UpdateTSlice(int slicer, int slice)
2731 {
2732   switch (slicer) {
2733   case 0:
2734     NOHorizontalSlider->setValue(slice);
2735     break;
2736   case 1:
2737     NEHorizontalSlider->setValue(slice);
2738     break;
2739   case 2:
2740     SOHorizontalSlider->setValue(slice);
2741     break;
2742   case 3:
2743     SEHorizontalSlider->setValue(slice);
2744     break;
2745   }
2746 }
2747 //------------------------------------------------------------------------------
2748
2749
2750 //------------------------------------------------------------------------------
2751 void vvMainWindow::UpdateSliceRange(int slicer, int min, int max, int tmin, int tmax)
2752 {
2753   //int position = int((min+max)/2);
2754   int position = mSlicerManagers[mCurrentPickedImageIndex]->GetSlicer(slicer)->GetSlice();
2755   if (slicer == 0) {
2756     NOVerticalSlider->setRange(min,max);
2757     NOHorizontalSlider->setRange(tmin,tmax);
2758     NOVerticalSlider->setValue(position);
2759   } else if (slicer == 1) {
2760     NEVerticalSlider->setRange(min,max);
2761     NEHorizontalSlider->setRange(tmin,tmax);
2762     NEVerticalSlider->setValue(position);
2763   } else if (slicer == 2) {
2764     SOVerticalSlider->setRange(min,max);
2765     SOHorizontalSlider->setRange(tmin,tmax);
2766     SOVerticalSlider->setValue(position);
2767   } else if (slicer == 3) {
2768     SEVerticalSlider->setRange(min,max);
2769     SEHorizontalSlider->setRange(tmin,tmax);
2770     SEVerticalSlider->setValue(position);
2771   }
2772 }
2773 //------------------------------------------------------------------------------
2774
2775
2776 //------------------------------------------------------------------------------
2777 void vvMainWindow::SaveNOScreenshot()
2778 {
2779   SaveScreenshot(NOViewWidget);
2780 }
2781 //------------------------------------------------------------------------------
2782
2783
2784 //------------------------------------------------------------------------------
2785 void vvMainWindow::SaveNEScreenshot()
2786 {
2787   SaveScreenshot(NEViewWidget);
2788 }
2789 //------------------------------------------------------------------------------
2790
2791
2792 //------------------------------------------------------------------------------
2793 void vvMainWindow::SaveSOScreenshot()
2794 {
2795   SaveScreenshot(SOViewWidget);
2796 }
2797 //------------------------------------------------------------------------------
2798
2799
2800 //------------------------------------------------------------------------------
2801 void vvMainWindow::SaveSEScreenshot()
2802 {
2803   SaveScreenshot(SEViewWidget);
2804 }
2805 //------------------------------------------------------------------------------
2806
2807
2808 //------------------------------------------------------------------------------
2809 void vvMainWindow::SaveScreenshotAllSlices()
2810 {
2811   QVTKWidget *widget = NOViewWidget;
2812
2813   int index = 0;// GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2814   vvSlicerManager * SM = mSlicerManagers[index];
2815   vvImage * image = SM->GetImage();
2816   vvSlicer * slicer = SM->GetSlicer(0);
2817   int orientation = slicer->GetOrientation();
2818   int nbSlices = image->GetSize()[orientation];
2819   vtkSmartPointer<vtkRenderWindow>  renderWindow = widget->GetRenderWindow();
2820
2821   // Select filename base
2822   QString filename = QFileDialog::getSaveFileName(this,
2823                                                   tr("Save As (filename will be completed by slice number)"),
2824                                                   itksys::SystemTools::GetFilenamePath(mSlicerManagers[index]->GetFileName()).c_str(),
2825                                                   "Images( *.png);;Images( *.jpg)");
2826
2827   // Loop on slices
2828   for(int i=0; i<nbSlices; i++) {
2829     // Change the slice
2830     slicer->SetSlice(i); // -> change the slice of the current slicer
2831     SM->UpdateSlice(0); // --> this one emit UpdateSlice
2832     QCoreApplication::flush(); // -> needed to force display of contours
2833
2834     // Screenshot
2835     vtkSmartPointer<vtkWindowToImageFilter> windowToImageFilter = vtkSmartPointer<vtkWindowToImageFilter>::New();
2836     windowToImageFilter->SetInput(renderWindow);
2837     windowToImageFilter->SetMagnification(1);
2838     windowToImageFilter->SetInputBufferTypeToRGBA(); //also record the alpha (transparency) channel
2839     windowToImageFilter->Update();
2840
2841     vtkSmartPointer<vtkPNGWriter> writer = vtkSmartPointer<vtkPNGWriter>::New();
2842     std::string fn = itksys::SystemTools::GetFilenameWithoutLastExtension(filename.toStdString());
2843     std::string num = clitk::toString(i);
2844     if (i<10) num = "0"+num;
2845     if (i<100) num = "0"+num;
2846     if (i<1000) num = "0"+num;
2847
2848     fn = itksys::SystemTools::GetFilenamePath(filename.toStdString()) + "/"+ fn
2849       + "_" + num + itksys::SystemTools::GetFilenameLastExtension(filename.toStdString());
2850     writer->SetFileName(fn.c_str());
2851     writer->SetInput(windowToImageFilter->GetOutput());
2852     writer->Write();
2853   }
2854 }
2855 //------------------------------------------------------------------------------
2856
2857
2858 //------------------------------------------------------------------------------
2859 void vvMainWindow::SaveScreenshot(QVTKWidget *widget)
2860 {
2861   QString Extensions = "Images( *.png);;";
2862   Extensions += "Images( *.jpg);;";
2863   Extensions += "Images( *.bmp);;";
2864   Extensions += "Images( *.tif);;";
2865   Extensions += "Images( *.ppm)";
2866 #if defined(VTK_USE_FFMPEG_ENCODER) || defined(VTK_USE_VIDEO_FOR_WINDOWS)
2867   Extensions += ";;Video( *.avi)";
2868 #endif
2869 #ifdef VTK_USE_MPEG2_ENCODER
2870   Extensions += ";;Video( *.mpg)";
2871 #endif
2872 #ifdef CLITK_EXPERIMENTAL
2873   Extensions += ";;Video( *.gif)";
2874 #endif
2875
2876   int smIndex=GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2877   QString fileName = QFileDialog::getSaveFileName(this,
2878                      tr("Save As"),
2879                      itksys::SystemTools::GetFilenamePath(mSlicerManagers[smIndex]->GetFileName()).c_str(),
2880                      Extensions);
2881
2882   if (!fileName.isEmpty()) {
2883     vtkSmartPointer<vtkWindowToImageFilter> w2i = vtkSmartPointer<vtkWindowToImageFilter>::New();
2884     w2i->SetInput(widget->GetRenderWindow());
2885     w2i->Update();
2886     vtkImageData *image = w2i->GetOutput();
2887
2888     std::string ext(itksys::SystemTools::GetFilenameLastExtension(fileName.toStdString()));
2889
2890     // Image
2891     vtkImageWriter *imgwriter = NULL;
2892     if (ext==".bmp")
2893       imgwriter = vtkBMPWriter::New();
2894     else if (ext==".tif")
2895       imgwriter = vtkTIFFWriter::New();
2896     else if (ext==".ppm")
2897       imgwriter = vtkPNMWriter::New();
2898     else if (ext==".png")
2899       imgwriter = vtkPNGWriter::New();
2900     else if (ext==".jpg")
2901       imgwriter = vtkJPEGWriter::New();
2902
2903     // Snapshot image if not null
2904     if(imgwriter!=NULL) {
2905       imgwriter->SetInput(image);
2906       imgwriter->SetFileName(fileName.toStdString().c_str());
2907       imgwriter->Write();
2908       return;
2909     }
2910
2911     // Video
2912     vtkGenericMovieWriter *vidwriter = NULL;
2913 #if CLITK_EXPERIMENTAL == 1
2914     if (ext==".gif") {
2915       vvAnimatedGIFWriter *gif = vvAnimatedGIFWriter::New();
2916       vidwriter = gif;
2917
2918       // FPS
2919       bool ok;
2920       int fps = QInputDialog::getInteger(this, tr("Number of frames per second"),
2921                                      tr("FPS:"), 5, 0, 1000, 1, &ok);
2922       if(ok)
2923         gif->SetRate(fps);
2924
2925       // Loops
2926       int loops = QInputDialog::getInteger(this, tr("Loops"),
2927                                      tr("Number of loops (0 means infinite):"), 0, 0, 1000000000, 1, &ok);
2928       if(ok)
2929         gif->SetLoops(loops);
2930
2931       // Dithering
2932       QString msg = "Would you like to activate dithering?";
2933       QMessageBox msgBox(QMessageBox::Question, tr("Dithering"),msg, 0, this);
2934       msgBox.addButton(tr("Yes"), QMessageBox::AcceptRole);
2935       msgBox.addButton(tr("No"), QMessageBox::RejectRole);
2936       gif->SetDither(msgBox.exec() == QMessageBox::AcceptRole);
2937     }
2938 #endif
2939 #ifdef VTK_USE_VIDEO_FOR_WINDOWS
2940     if (ext==".avi") {
2941       vtkAVIWriter *mpg = vtkAVIWriter::New();
2942       vidwriter = mpg;
2943       mpg->SetQuality(2);
2944       bool ok;
2945       int fps = QInputDialog::getInteger(this, tr("Number of frames per second"),
2946                                      tr("FPS:"), 5, 0, 1024, 1, &ok);
2947       if(!ok)
2948         fps = 5;
2949       mpg->SetRate(fps);
2950     }
2951 #endif
2952 #ifdef VTK_USE_FFMPEG_ENCODER
2953     if (ext==".avi") {
2954       vtkFFMPEGWriter *mpg = vtkFFMPEGWriter::New();
2955       vidwriter = mpg;
2956       mpg->SetQuality(2);
2957       bool ok;
2958       int fps = QInputDialog::getInteger(this, tr("Number of frames per second"),
2959                                      tr("FPS:"), 5, 0, 1024, 1, &ok);
2960       if(!ok)
2961         fps = 5;
2962       mpg->SetRate(fps);
2963       mpg->SetBitRateTolerance(int(ceil(12.0*1024*1024/fps)));
2964     }
2965 #endif
2966 #ifdef VTK_USE_MPEG2_ENCODER
2967     if (ext==".mpg") {
2968       vtkMPEG2Writer *mpg = vtkMPEG2Writer::New();
2969       vidwriter = mpg;
2970     }
2971 #endif
2972
2973     // Take video if not null
2974     if(vidwriter!=NULL){
2975       vidwriter->SetInput(image);
2976       vidwriter->SetFileName(fileName.toStdString().c_str());
2977       vidwriter->Start();
2978       int nSlice = mSlicerManagers[smIndex]->GetSlicer(0)->GetTMax();
2979       for(int i=0; i<=nSlice; i++) {
2980         mSlicerManagers[smIndex]->SetNextTSlice(0);
2981         vtkSmartPointer<vtkWindowToImageFilter> w2i = vtkSmartPointer<vtkWindowToImageFilter>::New();
2982         w2i->SetInput(widget->GetRenderWindow());
2983         w2i->Update();
2984         vidwriter->SetInput(w2i->GetOutput());
2985         vidwriter->Write();
2986       }
2987       vidwriter->End();
2988       vidwriter->Delete();
2989       return;
2990     }
2991
2992     QMessageBox::information(this,tr("Problem saving screenshot !"),tr("Cannot save image.\nPlease set a file extension !!!"));
2993   }
2994 }
2995 //------------------------------------------------------------------------------
2996
2997
2998 //------------------------------------------------------------------------------
2999 void vvMainWindow::GoToCursor()
3000 {
3001   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
3002   for (int column = 1; column < 5; column++) {
3003     if (DataTree->selectedItems()[0]->data(column,Qt::CheckStateRole).toInt() > 1) {
3004       double* cursorPos = mSlicerManagers[index]->GetSlicer(column-1)->GetCursorPosition();
3005       mSlicerManagers[index]->GetSlicer(column-1)->SetCurrentPosition(
3006         cursorPos[0],cursorPos[1],cursorPos[2],cursorPos[3]);
3007       mSlicerManagers[index]->UpdateViews(1,column-1);
3008       mSlicerManagers[index]->UpdateLinked(column-1);
3009       break;
3010     }
3011   }
3012 }
3013 //------------------------------------------------------------------------------
3014
3015 //------------------------------------------------------------------------------
3016 void vvMainWindow::PlayPause()
3017 {
3018   if (playMode) {
3019     playMode = 0;
3020     playButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/player_play.png")));
3021     ImageInfoChanged();
3022     return;
3023   } else {
3024     int image_number=DataTree->topLevelItemCount();
3025     bool has_temporal;
3026     for (int i=0; i<image_number; i++)
3027       if (mSlicerManagers[i]->GetSlicer(0)->GetTMax() > 0) {
3028         has_temporal=true;
3029         break;
3030       }
3031     if (has_temporal) {
3032       playMode = 1;
3033       playButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/player_pause.png")));
3034       QTimer::singleShot(1000/mFrameRate, this, SLOT(PlayNext()));
3035     }
3036   }
3037 }
3038 //------------------------------------------------------------------------------
3039
3040 //------------------------------------------------------------------------------
3041 void vvMainWindow::PlayNext()
3042 {
3043   if (playMode && !this->isHidden()) {
3044     int image_number=DataTree->topLevelItemCount();
3045     ///Only play one slicer per SM, and only if the SM is being displayed
3046     for (int i=0; i<image_number; i++)
3047       for (int j=0; j<4; j++)
3048         if (mSlicerManagers[i]->GetSlicer(0)->GetTMax() > 0 &&
3049             DataTree->topLevelItem(i)->data(j+1,Qt::CheckStateRole).toInt() > 0) {
3050           mSlicerManagers[i]->SetNextTSlice(j);
3051           break;
3052         }
3053     QTimer::singleShot(1000/mFrameRate, this, SLOT(PlayNext()));
3054   }
3055 }
3056 //------------------------------------------------------------------------------
3057
3058 void vvMainWindow::ShowLastImage()
3059 {
3060   if (mSlicerManagers.size() > 1) {
3061     QTreeWidgetItem * item=DataTree->topLevelItem(DataTree->topLevelItemCount()-1);
3062     CurrentImageChanged(mSlicerManagers.back()->GetId()); //select new image
3063     item->setData(1,Qt::CheckStateRole,2); //show the new image in the first panel
3064     DisplayChanged(item,1);
3065   }
3066 }
3067
3068 //------------------------------------------------------------------------------
3069 void vvMainWindow::UpdateRenderWindows()
3070 {
3071   if (NOViewWidget->GetRenderWindow()) NOViewWidget->GetRenderWindow()->Render();
3072   if (NEViewWidget->GetRenderWindow()) NEViewWidget->GetRenderWindow()->Render();
3073   if (SOViewWidget->GetRenderWindow()) SOViewWidget->GetRenderWindow()->Render();
3074   if (SEViewWidget->GetRenderWindow()) SEViewWidget->GetRenderWindow()->Render();
3075 }
3076 //------------------------------------------------------------------------------
3077
3078 //------------------------------------------------------------------------------
3079 void vvMainWindow::SegmentationOnCurrentImage()
3080 {
3081   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
3082
3083   vvSegmentationDialog segmentation;
3084   segmentation.SetImage(mSlicerManagers[index]->GetSlicer(0)->GetImage());
3085   segmentation.exec();
3086 }
3087 //------------------------------------------------------------------------------
3088
3089 void vvMainWindow::SurfaceViewerLaunch()
3090 {
3091   vvSurfaceViewerDialog surfaceViewer;
3092   surfaceViewer.exec();
3093 }
3094 //------------------------------------------------------------------------------
3095
3096
3097 //------------------------------------------------------------------------------
3098 int vvMainWindow::GetImageDuplicateFilenameNumber(std::string filename)
3099 {
3100   int number=0;
3101   for(unsigned int l=0; l<mSlicerManagers.size(); l++) {
3102     vvSlicerManager * v = mSlicerManagers[l];
3103     if (v->GetBaseFileName() ==
3104         vtksys::SystemTools::GetFilenameName(vtksys::SystemTools::GetFilenameWithoutLastExtension(filename))) {
3105       number = std::max(number, v->GetBaseFileNameNumber()+1);
3106     }
3107   }
3108   return number;
3109 }
3110 //------------------------------------------------------------------------------
3111
3112
3113 //------------------------------------------------------------------------------
3114 vvSlicerManager* vvMainWindow::AddImage(vvImage::Pointer image,std::string filename)
3115 {
3116   // Change filename if another image exist with the same name
3117   int number = GetImageDuplicateFilenameNumber(filename);
3118
3119   // Create new SliceManager
3120   vvSlicerManager* slicer_manager = new vvSlicerManager(4);
3121   slicer_manager->SetImage(image);//, IMAGE, number);
3122   //  filename = filename+"_"+clitk::toString(number);
3123   slicer_manager->SetFilename(filename, number);
3124   mSlicerManagers.push_back(slicer_manager);
3125
3126   //create an item in the tree with good settings
3127   QTreeWidgetItem *item = new QTreeWidgetItem();
3128   item->setData(0,Qt::UserRole,slicer_manager->GetFileName().c_str());//files[i].c_str());
3129   item->setData(1,Qt::UserRole,tr("image"));
3130   item->setData(COLUMN_IMAGE_NAME,Qt::DisplayRole,slicer_manager->GetFileName().c_str());//filename.c_str());
3131   qApp->processEvents();
3132
3133   for (int j = 1; j <= 4; j++) item->setData(j,Qt::CheckStateRole,1);
3134
3135   //Create the buttons for reload and close
3136   qApp->processEvents();
3137   QTreePushButton* cButton = new QTreePushButton;
3138   cButton->setItem(item);
3139   cButton->setColumn(COLUMN_CLOSE_IMAGE);
3140   cButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/exit.png")));
3141   connect(cButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
3142           this,SLOT(CloseImage(QTreeWidgetItem*, int)));
3143
3144   QTreePushButton* rButton = new QTreePushButton;
3145   rButton->setItem(item);
3146   rButton->setColumn(COLUMN_RELOAD_IMAGE);
3147   rButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/rotateright.png")));
3148   rButton->setEnabled(0);
3149   connect(rButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
3150           this,SLOT(ReloadImage(QTreeWidgetItem*, int)));
3151
3152   DataTree->addTopLevelItem(item);
3153   DataTree->setItemWidget(item, COLUMN_CLOSE_IMAGE, cButton);
3154   DataTree->setItemWidget(item, COLUMN_RELOAD_IMAGE, rButton);
3155
3156   //set the id of the image
3157   QString id = QDir::current().absoluteFilePath(slicer_manager->GetFileName().c_str()) + QString::number(mSlicerManagers.size()-1);
3158   item->setData(COLUMN_IMAGE_NAME,Qt::UserRole,id.toStdString().c_str());
3159   mSlicerManagers.back()->SetId(id.toStdString());
3160
3161   linkPanel->addImage(slicer_manager->GetFileName().c_str()// filename
3162                       , id.toStdString());
3163
3164   connect(mSlicerManagers.back(), SIGNAL(currentImageChanged(std::string)),
3165           this, SLOT(CurrentImageChanged(std::string)));
3166   connect(mSlicerManagers.back(), SIGNAL(currentPickedImageChanged(std::string)),
3167           this, SLOT(CurrentPickedImageChanged(std::string)));
3168   connect(mSlicerManagers.back(), SIGNAL(UpdatePosition(int, double, double, double, double, double, double, double)),
3169           this, SLOT(MousePositionChanged(int,double, double, double, double, double, double, double)));
3170   connect(mSlicerManagers.back(), SIGNAL(UpdateVector(int, double, double, double, double)),
3171           this, SLOT(VectorChanged(int,double,double,double, double)));
3172   connect(mSlicerManagers.back(), SIGNAL(UpdateOverlay(int, double, double)),
3173           this, SLOT(OverlayChanged(int,double,double)));
3174   connect(mSlicerManagers.back(), SIGNAL(UpdateFusion(int, double)),
3175           this, SLOT(FusionChanged(int,double)));
3176   connect(mSlicerManagers.back(), SIGNAL(WindowLevelChanged()),
3177           this,SLOT(WindowLevelChanged()));
3178   connect(mSlicerManagers.back(), SIGNAL(UpdateSlice(int,int)),
3179           this,SLOT(UpdateSlice(int,int)));
3180   connect(mSlicerManagers.back(), SIGNAL(UpdateTSlice(int, int)),
3181           this,SLOT(UpdateTSlice(int, int)));
3182   connect(mSlicerManagers.back(), SIGNAL(UpdateTSlice(int, int)),
3183           this,SLOT(ImageInfoChanged()));
3184   connect(mSlicerManagers.back(), SIGNAL(UpdateSliceRange(int,int,int,int,int)),
3185           this,SLOT(UpdateSliceRange(int,int,int,int,int)));
3186   connect(mSlicerManagers.back(), SIGNAL(UpdateLinkManager(std::string,int,double,double,double,int)),
3187           this,SLOT(UpdateLinkManager(std::string,int,double,double,double,int)));
3188   connect(mSlicerManagers.back(), SIGNAL(UpdateLinkedNavigation(std::string,vvSlicerManager*,vvSlicer*)),
3189           this,SLOT(UpdateLinkedNavigation(std::string,vvSlicerManager*,vvSlicer*)));
3190   connect(mSlicerManagers.back(), SIGNAL(ChangeImageWithIndexOffset(vvSlicerManager*,int,int)),
3191           this,SLOT(ChangeImageWithIndexOffset(vvSlicerManager*,int,int)));
3192   connect(mSlicerManagers.back(), SIGNAL(LandmarkAdded()),landmarksPanel,SLOT(AddPoint()));
3193   UpdateTree();
3194   qApp->processEvents();
3195   InitSlicers();
3196   ShowLastImage();
3197   InitDisplay();
3198   qApp->processEvents();
3199
3200   // End
3201   ImageInfoChanged();
3202   return slicer_manager;
3203 }
3204 //------------------------------------------------------------------------------
3205
3206
3207 //------------------------------------------------------------------------------
3208 void vvMainWindow::UpdateCurrentSlicer()
3209 {
3210   int index = -1;
3211   if (DataTree->selectedItems().size() > 0) {
3212     index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
3213   }
3214   mSlicerManagerCurrentIndex = index;
3215 }
3216 //------------------------------------------------------------------------------
3217