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 *.refscan *.usf)"
 105 #else
 106   #define EXTENSIONS "Images ( *.bmp *.png *.jpeg *.jpg *.tif *.mhd *.mha *.hdr *.vox *.his *.xdr *.SCAN *.nii *.nrrd *.nhdr *.refscan)"
 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     int tSlice = 0;
1104     vvImage::Pointer imageSelected;
1105     if (DataTree->topLevelItem(index) == DataTree->selectedItems()[0]) {
1106       imageSelected = mSlicerManagers[index]->GetSlicer(0)->GetImage();
1107       tSlice = mSlicerManagers[index]->GetSlicer(0)->GetTSlice();
1108     } else if (DataTree->selectedItems()[0]->data(1,Qt::UserRole).toString() == "vector") {
1109       imageSelected = mSlicerManagers[index]->GetSlicer(0)->GetVF();
1110       tSlice = mSlicerManagers[index]->GetSlicer(0)->GetOverlayTSlice();
1111     } else if (DataTree->selectedItems()[0]->data(1,Qt::UserRole).toString() == "overlay") {
1112       imageSelected = mSlicerManagers[index]->GetSlicer(0)->GetOverlay();
1113       tSlice = mSlicerManagers[index]->GetSlicer(0)->GetOverlayTSlice();
1114     } else if (DataTree->selectedItems()[0]->data(1,Qt::UserRole).toString() == "fusion") {
1115       imageSelected = mSlicerManagers[index]->GetSlicer(0)->GetFusion();
1116       tSlice = mSlicerManagers[index]->GetSlicer(0)->GetFusionTSlice();
1117     }
1118     else if (DataTree->selectedItems()[0]->data(1,Qt::UserRole).toString() == "contour") {
1119       imageSelected = mSlicerManagers[index]->GetSlicer(0)->GetImage();
1120       tSlice = mSlicerManagers[index]->GetSlicer(0)->GetTSlice();
1121     }
1122     else {
1123       imageSelected = mSlicerManagers[index]->GetSlicer(0)->GetImage();
1124       tSlice = mSlicerManagers[index]->GetSlicer(0)->GetTSlice();
1125     }
1126
1127     dimension = imageSelected->GetNumberOfDimensions();
1128     origin.resize(dimension);
1129     inputSpacing.resize(dimension);
1130     inputSize.resize(dimension);
1131     sizeMM.resize(dimension);
1132     pixelType = mSlicerManagers[index]->GetImage()->GetScalarTypeAsITKString().c_str();
1133     for (int i = 0; i < dimension; i++) {
1134       origin[i] = imageSelected->GetOrigin()[i];
1135       inputSpacing[i] = imageSelected->GetSpacing()[i];
1136       inputSize[i] = imageSelected->GetSize()[i];
1137       sizeMM[i] = inputSize[i]*inputSpacing[i];
1138       NPixel *= inputSize[i];
1139     }
1140     inputSizeInBytes = GetSizeInBytes(imageSelected->GetActualMemorySize()*1000);
1141
1142     QString dim = QString::number(dimension) + " (";
1143     dim += pixelType + ")";
1144
1145     infoPanel->setFileName(image);
1146     infoPanel->setDimension(dim);
1147     infoPanel->setSizePixel(GetVectorIntAsString(inputSize));
1148     infoPanel->setSizeMM(GetVectorDoubleAsString(sizeMM));
1149     infoPanel->setOrigin(GetVectorDoubleAsString(origin));
1150     infoPanel->setSpacing(GetVectorDoubleAsString(inputSpacing));
1151     infoPanel->setNPixel(QString::number(NPixel)+" ("+inputSizeInBytes+")");
1152     transformation = imageSelected->GetTransform()[tSlice]->GetMatrix();
1153     infoPanel->setTransformation(Get4x4MatrixDoubleAsString(transformation));
1154
1155     landmarksPanel->SetCurrentLandmarks(mSlicerManagers[index]->GetLandmarks(),
1156                                         mSlicerManagers[index]->GetSlicer(0)->GetImage()->GetVTKImages().size());
1157     landmarksPanel->SetCurrentPath(mInputPathName.toStdString());
1158     landmarksPanel->SetCurrentImage(mSlicerManagers[index]->GetFileName().c_str());
1159
1160     overlayPanel->getCurrentImageName(mSlicerManagers[index]->GetFileName().c_str());
1161     for (int i = 0; i < 4; i++) {
1162       if (DataTree->selectedItems()[0]->data(i+1,Qt::CheckStateRole).toInt() > 0 || i == 3) {
1163         mSlicerManagers[index]->UpdateInfoOnCursorPosition(i);
1164         break;
1165       }
1166     }
1167
1168     infoPanel->setFileName(image);
1169     infoPanel->setDimension(dim);
1170     infoPanel->setSizePixel(GetVectorIntAsString(inputSize));
1171     infoPanel->setSizeMM(GetVectorDoubleAsString(sizeMM));
1172     infoPanel->setOrigin(GetVectorDoubleAsString(origin));
1173     infoPanel->setSpacing(GetVectorDoubleAsString(inputSpacing));
1174     infoPanel->setNPixel(QString::number(NPixel)+" ("+inputSizeInBytes+")");
1175
1176     landmarksPanel->SetCurrentLandmarks(mSlicerManagers[index]->GetLandmarks(),
1177                                         mSlicerManagers[index]->GetSlicer(0)->GetImage()->GetVTKImages().size());
1178     landmarksPanel->SetCurrentPath(mInputPathName.toStdString());
1179     landmarksPanel->SetCurrentImage(mSlicerManagers[index]->GetFileName().c_str());
1180
1181     overlayPanel->getCurrentImageName(mSlicerManagers[index]->GetFileName().c_str());
1182     for (int i = 0; i < 4; i++) {
1183       if (DataTree->selectedItems()[0]->data(i+1,Qt::CheckStateRole).toInt() > 0 || i == 3) {
1184         mSlicerManagers[index]->UpdateInfoOnCursorPosition(i);
1185         break;
1186       }
1187     }
1188     WindowLevelChanged();
1189     slicingPresetComboBox->setCurrentIndex(mSlicerManagers[index]->GetSlicingPreset());
1190
1191     if (mSlicerManagers[index]->GetSlicer(0)->GetVF()) {
1192       overlayPanel->getVFName(mSlicerManagers[index]->GetVFName().c_str());
1193       overlayPanel->getVFProperty(mSlicerManagers[index]->GetSlicer(0)->GetVFSubSampling(),
1194                                   mSlicerManagers[index]->GetSlicer(0)->GetVFScale(),
1195                                   mSlicerManagers[index]->GetSlicer(0)->GetVFLog());
1196     } else {
1197       overlayPanel->getVFName(mSlicerManagers[index]->GetVFName().c_str());
1198       overlayPanel->getVFProperty(-1,-1,-1);
1199     }
1200     if (mSlicerManagers[index]->GetSlicer(0)->GetOverlay()) {
1201       overlayPanel->getOverlayName(mSlicerManagers[index]->GetOverlayName().c_str());
1202     } else {
1203       overlayPanel->getOverlayName(mSlicerManagers[index]->GetOverlayName().c_str());
1204     }
1205
1206     if (mSlicerManagers[index]->GetSlicer(0)->GetFusion()) {
1207       overlayPanel->getFusionName(mSlicerManagers[index]->GetFusionName().c_str());
1208     } else {
1209       overlayPanel->getFusionName(mSlicerManagers[index]->GetFusionName().c_str());
1210     }
1211   }
1212 }
1213 //------------------------------------------------------------------------------
1214
1215 //------------------------------------------------------------------------------
1216 void vvMainWindow::ShowDocumentation()
1217 {
1218   documentation->show();
1219 }
1220 //------------------------------------------------------------------------------
1221
1222 //------------------------------------------------------------------------------
1223 void vvMainWindow::PopupRegisterForm(bool checkCanPush)
1224 {
1225   vvRegisterForm* registerForm = new vvRegisterForm(QUrl("http://www.creatis.insa-lyon.fr/~dsarrut/vvregister/write.php"), getVVSettingsPath(), getSettingsOptionFormat());
1226   if(!checkCanPush) {
1227     registerForm->show();
1228   } else {
1229     if(registerForm->canPush()) {
1230       registerForm->show();
1231       registerForm->acquitPushed();//too bad if there is not internet connection anymore.
1232     }
1233   }
1234 }
1235 //------------------------------------------------------------------------------
1236
1237 //------------------------------------------------------------------------------
1238 void vvMainWindow::ShowHelpDialog()
1239 {
1240   help_dialog->show();
1241 }
1242 //------------------------------------------------------------------------------
1243
1244 //------------------------------------------------------------------------------
1245 void vvMainWindow::ChangeViewMode()
1246 {
1247   typedef struct _SIZE{
1248     QSplitter* splitter;
1249     QList<int> size1, size2;
1250     int cols[3];
1251   }SplitterSize;
1252   SplitterSize sizes[4];
1253   sizes[0].splitter = OSplitter;
1254   sizes[0].size1.push_back(1);
1255   sizes[0].size1.push_back(0);
1256   sizes[0].size2.push_back(1);
1257   sizes[0].size2.push_back(0);
1258   sizes[0].cols[0] = 2;
1259   sizes[0].cols[1] = 3;
1260   sizes[0].cols[2] = 4;
1261
1262   sizes[1].splitter = ESplitter;
1263   sizes[1].size1.push_back(0);
1264   sizes[1].size1.push_back(1);
1265   sizes[1].size2.push_back(1);
1266   sizes[1].size2.push_back(0);
1267   sizes[1].cols[0] = 1;
1268   sizes[1].cols[1] = 3;
1269   sizes[1].cols[2] = 4;
1270
1271   sizes[2].splitter = OSplitter;
1272   sizes[2].size1.push_back(1);
1273   sizes[2].size1.push_back(0);
1274   sizes[2].size2.push_back(0);
1275   sizes[2].size2.push_back(1);
1276   sizes[2].cols[0] = 1;
1277   sizes[2].cols[1] = 2;
1278   sizes[2].cols[2] = 4;
1279
1280   sizes[3].splitter = ESplitter;
1281   sizes[3].size1.push_back(0);
1282   sizes[3].size1.push_back(1);
1283   sizes[3].size2.push_back(0);
1284   sizes[3].size2.push_back(1);
1285   sizes[3].cols[0] = 1;
1286   sizes[3].cols[1] = 2;
1287   sizes[3].cols[2] = 3;
1288
1289   int slicer = mSlicerManagers[mCurrentPickedImageIndex]->GetSelectedSlicer();
1290   if (viewMode == 1) {
1291     if (slicer >= 0) {
1292       viewMode = 0;
1293       splitter_3->setSizes(sizes[slicer].size1);
1294       sizes[slicer].splitter->setSizes(sizes[slicer].size2);
1295       DataTree->setColumnHidden(sizes[slicer].cols[0],1);
1296       DataTree->setColumnHidden(sizes[slicer].cols[1],1);
1297       DataTree->setColumnHidden(sizes[slicer].cols[2],1);
1298     }
1299   } else {
1300     QList<int> size;
1301     if (slicer >= 0) {
1302       viewMode = 1;
1303       size.push_back(1);
1304       size.push_back(1);
1305       splitter_3->setSizes(size);
1306       sizes[slicer].splitter->setSizes(size);
1307       DataTree->setColumnHidden(sizes[slicer].cols[0],0);
1308       DataTree->setColumnHidden(sizes[slicer].cols[1],0);
1309       DataTree->setColumnHidden(sizes[slicer].cols[2],0);
1310     }
1311   }
1312   UpdateRenderWindows();
1313   /*
1314   ** I don't know why but for both resized QVTKWidget we also need to render
1315   ** the associated Slicer to redraw crosses.
1316   */
1317   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
1318 //     if (DataTree->topLevelItem(i)->data(COLUMN_UL_VIEW,Qt::CheckStateRole).toInt() > 1)
1319       mSlicerManagers[i]->GetSlicer(0)->Render();
1320       mSlicerManagers[i]->GetSlicer(1)->Render();
1321 //     if (DataTree->topLevelItem(i)->data(COLUMN_DL_VIEW,Qt::CheckStateRole).toInt() > 1)
1322       mSlicerManagers[i]->GetSlicer(2)->Render();
1323       mSlicerManagers[i]->GetSlicer(3)->Render();
1324   }
1325 }
1326 //------------------------------------------------------------------------------
1327
1328 //------------------------------------------------------------------------------
1329 QString vvMainWindow::GetSizeInBytes(unsigned long size)
1330 {
1331   QString result = "";// QString::number(size);
1332   //result += " bytes (";
1333   if (size > 1000000000) {
1334     size /= 1000000000;
1335     result += QString::number(size);
1336     result += "Gb";//)";
1337   } else if (size > 1000000) {
1338     size /= 1000000;
1339     result += QString::number(size);
1340     result += "Mb";//)";
1341   } else if (size > 1000) {
1342     size /= 1000;
1343     result += QString::number(size);
1344     result += "kb";//)";
1345   }
1346   return result;
1347 }
1348 //------------------------------------------------------------------------------
1349
1350 //------------------------------------------------------------------------------
1351 QString vvMainWindow::Get4x4MatrixDoubleAsString(vtkSmartPointer<vtkMatrix4x4> matrix, const int precision)
1352 {
1353   std::ostringstream strmatrix;
1354
1355   // Figure out the number of digits of the integer part of the largest absolute value
1356   // for each column
1357   unsigned width[4];
1358   for (unsigned int j = 0; j < 4; j++){
1359     double absmax = 0.;
1360     for (unsigned int i = 0; i < 4; i++)
1361       absmax = std::max(absmax, vnl_math_abs(matrix->GetElement(i, j)));
1362     unsigned ndigits = (unsigned)std::max(0.,std::log10(absmax))+1;
1363     width[j] = precision+ndigits+3;
1364   }
1365
1366   // Output with correct width, aligned to the right
1367   for (unsigned int i = 0; i < 4; i++) {
1368     for (unsigned int j = 0; j < 4; j++) {
1369       strmatrix.setf(ios::fixed,ios::floatfield);
1370       strmatrix.precision(precision);
1371       strmatrix.fill(' ');
1372       strmatrix.width(width[j]);
1373       strmatrix << std::right << matrix->GetElement(i, j);
1374     }
1375     strmatrix << std::endl;
1376   }
1377   QString result = strmatrix.str().c_str();
1378   return result;
1379 }
1380 //------------------------------------------------------------------------------
1381
1382 //------------------------------------------------------------------------------
1383 QString vvMainWindow::GetVectorDoubleAsString(std::vector<double> vectorDouble)
1384 {
1385   QString result;
1386   for (unsigned int i= 0; i < vectorDouble.size(); i++) {
1387     if (i != 0)
1388       result += " ";
1389     result += QString::number(vectorDouble[i]);
1390   }
1391   return result;
1392 }
1393 //------------------------------------------------------------------------------
1394
1395 //------------------------------------------------------------------------------
1396 QString vvMainWindow::GetVectorIntAsString(std::vector<int> vectorInt)
1397 {
1398   QString result;
1399   for (unsigned int i= 0; i < vectorInt.size(); i++) {
1400     if (i != 0)
1401       result += " ";
1402     result += QString::number(vectorInt[i]);
1403   }
1404   return result;
1405 }
1406 //------------------------------------------------------------------------------
1407
1408 //------------------------------------------------------------------------------
1409 int vvMainWindow::GetSlicerIndexFromItem(QTreeWidgetItem* item)
1410 {
1411   QString id = item->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString();
1412   for (int i = 0; i < DataTree->topLevelItemCount(); i++) {
1413     if (DataTree->topLevelItem(i)->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString() == id)
1414       return i;
1415   }
1416   return -1;
1417 }
1418 //------------------------------------------------------------------------------
1419
1420 //------------------------------------------------------------------------------
1421 QTreeWidgetItem* vvMainWindow::GetItemFromSlicerManager(vvSlicerManager* sm)
1422 {
1423   QString id = sm->GetId().c_str();
1424   for (int i = 0; i < DataTree->topLevelItemCount(); i++) {
1425     if (DataTree->topLevelItem(i)->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString() == id)
1426       return DataTree->topLevelItem(i);
1427   }
1428   return NULL;
1429 }
1430 //------------------------------------------------------------------------------
1431
1432 //------------------------------------------------------------------------------
1433 void vvMainWindow::DisplayChanged(QTreeWidgetItem *clickedItem, int column)
1434 {
1435   if ( column >= COLUMN_CLOSE_IMAGE || column <= 0)
1436     return;
1437
1438   // Get parent information (might be the same item)
1439   int slicerManagerIndex = GetSlicerIndexFromItem(clickedItem);
1440   QTreeWidgetItem* clickedParentItem = DataTree->topLevelItem(slicerManagerIndex);
1441   vvSlicer* clickedSlicer = mSlicerManagers[slicerManagerIndex]->GetSlicer(column-1);
1442
1443   // Go over the complete item tree (only 2 levels, parents and children)
1444   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
1445     // Trick to avoid redoing twice the job for a key (sr)
1446     mSlicerManagers[i]->GetSlicer(column-1)->GetRenderWindow()->GetInteractor()->SetKeySym("Crap");
1447
1448     QTreeWidgetItem* currentParentItem = DataTree->topLevelItem(i);
1449     if(currentParentItem != clickedParentItem) {
1450       // Not the branch of the clicked item, uncheck all
1451
1452       // Parent
1453       currentParentItem->setData(column,Qt::CheckStateRole, 0);
1454       mSlicerManagers[i]->UpdateSlicer(column-1, false);
1455
1456       // Children
1457       for (int iChild = 0; iChild < currentParentItem->childCount(); iChild++) {
1458         currentParentItem->child(iChild)->setData(column,Qt::CheckStateRole, 0);
1459       }
1460     }
1461     else {
1462       // Branch of the clicked one: get check status from actor visibility in slicer
1463       // and toggle the clicked one
1464
1465       // Parent
1466       bool vis = clickedSlicer->GetActorVisibility("image", 0);
1467       bool draw = clickedSlicer->GetRenderer()->GetDraw();
1468
1469       // Update slicer (after getting visibility)
1470       mSlicerManagers[slicerManagerIndex]->UpdateSlicer(column-1, true);
1471       mSlicerManagers[slicerManagerIndex]->UpdateInfoOnCursorPosition(column-1);
1472       DisplaySliders(slicerManagerIndex, column-1);
1473       if(clickedParentItem == clickedItem) {
1474         // Toggle
1475         vis = !draw || !vis;
1476       }
1477       clickedSlicer->SetActorVisibility("image", 0, vis);
1478       clickedParentItem->setData(column, Qt::CheckStateRole, vis?2:0);
1479
1480       // Children
1481       std::map<std::string, int> actorTypeCounts;
1482       for (int iChild = 0; iChild < clickedParentItem->childCount(); iChild++) {
1483         QTreeWidgetItem* currentChildItem = clickedParentItem->child(iChild);
1484         std::string actorType = currentChildItem->data(1,Qt::UserRole).toString().toStdString();
1485         vis = clickedSlicer->GetActorVisibility(actorType, actorTypeCounts[actorType]);
1486         if(currentChildItem == clickedItem) {
1487           // Toggle or force visibility if it was not on this branch so far
1488           vis = !draw || !vis;
1489           clickedSlicer->SetActorVisibility(actorType, actorTypeCounts[actorType], vis);
1490         }
1491         currentChildItem->setData(column, Qt::CheckStateRole, vis?2:0);
1492         actorTypeCounts[actorType]++;
1493       }
1494     }
1495   }
1496
1497   clickedSlicer->Render();
1498 }
1499 //------------------------------------------------------------------------------
1500
1501 void vvMainWindow::InitSlicers()
1502 {
1503   if (mSlicerManagers.size()) {
1504     mSlicerManagers.back()->GenerateDefaultLookupTable();
1505
1506     mSlicerManagers.back()->SetSlicerWindow(0,NOViewWidget->GetRenderWindow());
1507     mSlicerManagers.back()->SetSlicerWindow(1,NEViewWidget->GetRenderWindow());
1508     mSlicerManagers.back()->SetSlicerWindow(2,SOViewWidget->GetRenderWindow());
1509     mSlicerManagers.back()->SetSlicerWindow(3,SEViewWidget->GetRenderWindow());
1510   }
1511 }
1512
1513 //------------------------------------------------------------------------------
1514 void vvMainWindow::InitDisplay()
1515 {
1516   if (mSlicerManagers.size()) {
1517     //BE CAREFUL : this is absolutely necessary to set the interactor style
1518     //in order to have the same style instanciation for all SlicerManagers in
1519     // a same window
1520     for (int j = 0; j < 4; j++) {
1521       vvInteractorStyleNavigator* style = vvInteractorStyleNavigator::New();
1522       style->SetAutoAdjustCameraClippingRange(1);
1523       bool AlreadySelected = false;
1524       for (int i = 0; i < DataTree->topLevelItemCount(); i++) {
1525         mSlicerManagers[i]->SetInteractorStyleNavigator(j,style);
1526
1527         //select the image only if previous are not selected
1528         if (DataTree->topLevelItem(i)->data(j+1,Qt::CheckStateRole).toInt() > 1) {
1529           mSlicerManagers[i]->UpdateSlicer(j,1);
1530           AlreadySelected = true;
1531         } else if (i == DataTree->topLevelItemCount()-1 && !AlreadySelected) {
1532           if (DataTree->selectedItems().size() == 0)
1533             DataTree->topLevelItem(i)->setSelected(1);
1534           DataTree->topLevelItem(i)->setData(j+1,Qt::CheckStateRole,2);
1535           mSlicerManagers[i]->UpdateSlicer(j,1);
1536           DisplaySliders(i,j);
1537         } else {
1538           DataTree->topLevelItem(i)->setData(j+1,Qt::CheckStateRole,0);
1539           mSlicerManagers[i]->UpdateSlicer(j,0);
1540         }
1541       }
1542       style->Delete();
1543     }
1544   }
1545 }
1546 //------------------------------------------------------------------------------
1547
1548 //------------------------------------------------------------------------------
1549 void vvMainWindow::DisplaySliders(int slicer, int window)
1550 {
1551   if(!mSlicerManagers[slicer]->GetSlicer(window)->GetRenderer()->GetDraw())
1552     return;
1553
1554   int range[2];
1555   mSlicerManagers[slicer]->GetSlicer(window)->GetSliceRange(range);
1556   int position = mSlicerManagers[slicer]->GetSlicer(window)->GetSlice();
1557   if (range[1]>0)
1558     verticalSliders[window]->show();
1559   else
1560     verticalSliders[window]->hide();
1561   verticalSliders[window]->setRange(range[0],range[1]);
1562   verticalSliders[window]->setValue(position);
1563
1564   int tRange[2];
1565   tRange[0] = 0;
1566   tRange[1] = mSlicerManagers[slicer]->GetSlicer(window)->GetTMax();
1567   if (tRange[1]>0)
1568     horizontalSliders[window]->show();
1569   else
1570     horizontalSliders[window]->hide();
1571   horizontalSliders[window]->setRange(tRange[0],tRange[1]);
1572   int tPosition = mSlicerManagers[slicer]->GetSlicer(window)->GetMaxCurrentTSlice();
1573   horizontalSliders[window]->setValue(tPosition);
1574 }
1575 //------------------------------------------------------------------------------
1576
1577 //------------------------------------------------------------------------------
1578 void vvMainWindow::CloseImage(QTreeWidgetItem* item, int column)
1579 {
1580   int index = GetSlicerIndexFromItem(item);
1581
1582   if (DataTree->topLevelItem(index) != item) {
1583     QString warning = "Do you really want to close the overlay : ";
1584     warning += item->data(COLUMN_IMAGE_NAME,Qt::DisplayRole).toString();
1585     QMessageBox msgBox(QMessageBox::Warning, tr("Close Overlay"),
1586                        warning, 0, this);
1587     msgBox.addButton(tr("Close"), QMessageBox::AcceptRole);
1588     msgBox.addButton(tr("Cancel"), QMessageBox::RejectRole);
1589     if (msgBox.exec() == QMessageBox::AcceptRole) {
1590       std::string overlay_type=item->data(1,Qt::UserRole).toString().toStdString();
1591       int overlay_index=0;
1592       for (int child = 0; child < DataTree->topLevelItem(index)->childCount(); child++) {
1593         if (DataTree->topLevelItem(index)->\
1594             child(child)->data(1,Qt::UserRole).toString().toStdString() == overlay_type)
1595           overlay_index++;
1596         if (DataTree->topLevelItem(index)->child(child) == item) break;
1597       }
1598       mSlicerManagers[index]->RemoveActor(overlay_type, overlay_index-1);
1599       mSlicerManagers[index]->SetColorMap(0);
1600       DataTree->topLevelItem(index)->takeChild(DataTree->topLevelItem(index)->indexOfChild(item));
1601       mSlicerManagers[index]->Render();
1602     }
1603   } else if (DataTree->topLevelItemCount() <= 1) {
1604     QString warning = "Do you really want to close the image : ";
1605     warning += item->data(COLUMN_IMAGE_NAME,Qt::DisplayRole).toString();
1606     warning += "\nThis is the last image, you're about to close vv !!!";
1607     QMessageBox msgBox(QMessageBox::Warning, tr("Close Image"),
1608                        warning, 0, this);
1609     msgBox.addButton(tr("Close vv"), QMessageBox::AcceptRole);
1610     msgBox.addButton(tr("Cancel"), QMessageBox::RejectRole);
1611     if (msgBox.exec() == QMessageBox::AcceptRole) {
1612       this->close();
1613     }
1614   } else {
1615     QString warning = "Do you really want to close the image : ";
1616     warning += item->data(COLUMN_IMAGE_NAME,Qt::DisplayRole).toString();
1617     QMessageBox msgBox(QMessageBox::Warning, tr("Close Image"),
1618                        warning, 0, this);
1619     msgBox.addButton(tr("Close"), QMessageBox::AcceptRole);
1620     msgBox.addButton(tr("Cancel"), QMessageBox::RejectRole);
1621     if (msgBox.exec() == QMessageBox::AcceptRole) {
1622
1623       // Tell tools that we close an image
1624       emit AnImageIsBeingClosed(mSlicerManagers[index]);
1625
1626       std::vector<vvSlicerManager*>::iterator Manageriter = mSlicerManagers.begin();
1627       DataTree->takeTopLevelItem(index);
1628       for (int i = 0; i < index; i++) {
1629         Manageriter++;
1630       }
1631       linkPanel->removeImage(index);
1632       mSlicerManagers[index]->RemoveActors();
1633       delete mSlicerManagers[index];
1634       mSlicerManagers.erase(Manageriter);
1635
1636       //
1637       InitDisplay();
1638     }
1639   }
1640   ImageInfoChanged();
1641 }
1642 //------------------------------------------------------------------------------
1643
1644 //------------------------------------------------------------------------------
1645 void vvMainWindow::ReloadImage(QTreeWidgetItem* item, int column)
1646 {
1647   // int index = GetSlicerIndexFromItem(item);
1648   //   QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
1649   //   if (item->data(1,Qt::UserRole).toString() == "vector")
1650   //     mSlicerManagers[index]->ReloadVF();
1651   //   else
1652   //     mSlicerManagers[index]->Reload();
1653
1654   //   QApplication::restoreOverrideCursor();
1655   int index = GetSlicerIndexFromItem(item);
1656   QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
1657   QString role=item->data(1,Qt::UserRole).toString();
1658   if ( role == "vector"){
1659     mSlicerManagers[index]->ReloadVF();
1660   }
1661   else if (role == "overlay"){
1662     mSlicerManagers[index]->ReloadOverlay();
1663   }
1664   else if (role == "fusion"){
1665     mSlicerManagers[index]->ReloadFusion();
1666   }
1667   else{
1668     mSlicerManagers[index]->Reload();
1669   }
1670   // Update view and info
1671   ImageInfoChanged();
1672   mSlicerManagers[index]->Render();
1673   QApplication::restoreOverrideCursor();
1674 }
1675 //------------------------------------------------------------------------------
1676
1677 //------------------------------------------------------------------------------
1678 void vvMainWindow::MousePositionChanged(int visibility,double x, double y, double z, double X, double Y, double Z , double value)
1679 {
1680   infoPanel->setCurrentInfo(visibility,x,y,z,X,Y,Z,value);
1681 }
1682 //------------------------------------------------------------------------------
1683
1684 //------------------------------------------------------------------------------
1685 void vvMainWindow::VectorChanged(int visibility,double x, double y, double z, double value)
1686 {
1687   overlayPanel->getCurrentVectorInfo(visibility,x,y,z,value);
1688 }
1689 //------------------------------------------------------------------------------
1690
1691 //------------------------------------------------------------------------------
1692 void vvMainWindow::OverlayChanged(int visibility, double valueOver, double valueRef)
1693 {
1694   overlayPanel->getCurrentOverlayInfo(visibility,valueOver, valueRef);
1695 }
1696 //------------------------------------------------------------------------------
1697
1698 //------------------------------------------------------------------------------
1699 void vvMainWindow::FusionChanged(int visibility, double value)
1700 {
1701   overlayPanel->getCurrentFusionInfo(visibility,value);
1702 }
1703 //------------------------------------------------------------------------------
1704
1705 //------------------------------------------------------------------------------
1706 void vvMainWindow::WindowLevelChanged()
1707 {
1708   // Base image
1709   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1710   if(index==-1) return;
1711   windowSpinBox->setValue(mSlicerManagers[index]->GetColorWindow());
1712   levelSpinBox->setValue(mSlicerManagers[index]->GetColorLevel());
1713   colorMapComboBox->setCurrentIndex(mSlicerManagers[index]->GetColorMap());
1714   presetComboBox->setCurrentIndex(mSlicerManagers[index]->GetPreset());
1715
1716   // Overlay image
1717   if (mSlicerManagers[index]->GetSlicer(0)->GetOverlay())
1718     overlayPanel->getOverlayProperty(mSlicerManagers[index]->GetOverlayColor(),
1719                                      mSlicerManagers[index]->GetLinkOverlayWindowLevel(),
1720                                      mSlicerManagers[index]->GetOverlayColorWindow(),
1721                                      mSlicerManagers[index]->GetOverlayColorLevel());
1722   else
1723     overlayPanel->getOverlayProperty(-1,0,0.,0.);
1724
1725   // Fusion image
1726   if (mSlicerManagers[index]->GetSlicer(0)->GetFusion())
1727     overlayPanel->getFusionProperty(mSlicerManagers[index]->GetFusionOpacity(),
1728                                     mSlicerManagers[index]->GetFusionThresholdOpacity(),
1729                                     mSlicerManagers[index]->GetFusionColorMap(),
1730                                     mSlicerManagers[index]->GetFusionWindow(),
1731                                     mSlicerManagers[index]->GetFusionLevel());
1732   else
1733     overlayPanel->getFusionProperty(-1, -1, -1, -1, -1);
1734 }
1735 //------------------------------------------------------------------------------
1736
1737 //------------------------------------------------------------------------------
1738 void vvMainWindow::WindowLevelEdited()
1739 {
1740   presetComboBox->setCurrentIndex(6);
1741   UpdateWindowLevel();
1742 }
1743 //------------------------------------------------------------------------------
1744
1745 //------------------------------------------------------------------------------
1746 void vvMainWindow::SetWindowLevel(double w, double l)
1747 {
1748   windowSpinBox->setValue(w);
1749   levelSpinBox->setValue(l);
1750   presetComboBox->setCurrentIndex(6);
1751   colorMapComboBox->setCurrentIndex(0);
1752   UpdateWindowLevel();
1753 }
1754 //------------------------------------------------------------------------------
1755
1756 //------------------------------------------------------------------------------
1757 void vvMainWindow::UpdateWindowLevel()
1758 {
1759   if (DataTree->selectedItems().size()) {
1760     if (presetComboBox->currentIndex() == 7) //For ventilation
1761       colorMapComboBox->setCurrentIndex(5);
1762     int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1763     mSlicerManagers[index]->SetColorWindow(windowSpinBox->value());
1764     mSlicerManagers[index]->SetColorLevel(levelSpinBox->value());
1765     mSlicerManagers[index]->SetPreset(presetComboBox->currentIndex());
1766     mSlicerManagers[index]->Render();
1767     WindowLevelChanged();
1768   }
1769 }
1770 //------------------------------------------------------------------------------
1771
1772 //------------------------------------------------------------------------------
1773 void vvMainWindow::UpdateSlicingPreset()
1774 {
1775   if (DataTree->selectedItems().size()) {
1776     int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1777     mSlicerManagers[index]->SetSlicingPreset(vvSlicerManager::SlicingPresetType(slicingPresetComboBox->currentIndex()));
1778   }
1779 }
1780 //------------------------------------------------------------------------------
1781
1782 //------------------------------------------------------------------------------
1783 void vvMainWindow::UpdateColorMap()
1784 {
1785   if (DataTree->selectedItems().size()) {
1786     int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1787     mSlicerManagers[index]->SetColorMap(colorMapComboBox->currentIndex());
1788     mSlicerManagers[index]->Render();
1789   }
1790 }
1791 //------------------------------------------------------------------------------
1792 void vvMainWindow::SwitchWindowLevel()
1793 {
1794   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1795   int window = mSlicerManagers[index]->GetColorWindow();
1796   presetComboBox->setCurrentIndex(6);
1797   windowSpinBox->setValue(-window);
1798   UpdateWindowLevel();
1799 }
1800 //------------------------------------------------------------------------------
1801
1802 //------------------------------------------------------------------------------
1803 void vvMainWindow::ApplyWindowLevelToAllImages()
1804 {
1805   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1806   if(index==-1) return;
1807   double window = mSlicerManagers[index]->GetColorWindow();
1808   double level = mSlicerManagers[index]->GetColorLevel();
1809
1810   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
1811     if (mSlicerManagers[i] == NULL)
1812       continue;
1813     mSlicerManagers[i]->SetColorWindow(window);
1814     mSlicerManagers[i]->SetColorLevel(level);
1815     mSlicerManagers[i]->SetPreset(6);
1816     mSlicerManagers[i]->Render();
1817   }
1818 }
1819 //------------------------------------------------------------------------------
1820
1821 //------------------------------------------------------------------------------
1822 void vvMainWindow::ApplyWindowToSetOfImages(double window, unsigned int indexMin, unsigned int indexMax)
1823 {
1824   for (unsigned int i = indexMin; i <= indexMax && i < mSlicerManagers.size(); i++) {
1825     if (mSlicerManagers[i] == NULL)
1826       continue;
1827     mSlicerManagers[i]->SetColorWindow(window);
1828     mSlicerManagers[i]->SetPreset(6);
1829     mSlicerManagers[i]->Render();
1830   }
1831 }
1832 //------------------------------------------------------------------------------
1833
1834 //------------------------------------------------------------------------------
1835 void vvMainWindow::ApplyLevelToSetOfImages(double level, unsigned int indexMin, unsigned int indexMax)
1836 {
1837   for (unsigned int i = indexMin; i <= indexMax && i < mSlicerManagers.size(); i++) {
1838     if (mSlicerManagers[i] == NULL)
1839       continue;
1840     mSlicerManagers[i]->SetColorLevel(level);
1841     mSlicerManagers[i]->SetPreset(6);
1842     mSlicerManagers[i]->Render();
1843   }
1844 }
1845 //------------------------------------------------------------------------------
1846
1847 //------------------------------------------------------------------------------
1848 void vvMainWindow::UpdateLinkManager(std::string id, int slicer, double x, double y, double z, int temps)
1849 {
1850   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
1851     if (mSlicerManagers[i]->GetId() == id) {
1852       //mSlicerManagers[i]->SetTSlice(temps);
1853       mSlicerManagers[i]->GetSlicer(slicer)->SetCurrentPosition(x,y,z,temps);
1854       mSlicerManagers[i]->UpdateViews(0,slicer);
1855       break;
1856     }
1857   }
1858 }
1859 //------------------------------------------------------------------------------
1860
1861 //------------------------------------------------------------------------------
1862 void vvMainWindow::UpdateLinkedNavigation(std::string id, vvSlicerManager * sm, vvSlicer* refSlicer)
1863 {
1864   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
1865     if (id == mSlicerManagers[i]->GetId()) {
1866       mSlicerManagers[i]->UpdateLinkedNavigation(refSlicer);
1867     }
1868   }
1869 }
1870 //------------------------------------------------------------------------------
1871
1872 //------------------------------------------------------------------------------
1873 void vvMainWindow::ShowContextMenu(QPoint point)
1874 {
1875   if (!DataTree->selectedItems().size()) {
1876     contextActions[1]->setEnabled(0);
1877     contextActions[2]->setEnabled(0);
1878     contextActions[3]->setEnabled(0);
1879     contextActions[4]->setEnabled(0);
1880     contextActions[5]->setEnabled(0);
1881     contextActions[6]->setEnabled(0);
1882   } else {
1883     int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1884     contextActions[1]->setEnabled(1);
1885     contextActions[2]->setEnabled(
1886       DataTree->itemWidget(DataTree->selectedItems()[0],
1887                            COLUMN_RELOAD_IMAGE)->isEnabled());
1888     contextActions[3]->setEnabled(1);
1889     contextActions[5]->setEnabled(1);
1890     contextActions[6]->setEnabled(1);
1891
1892     if (mSlicerManagers[index]->GetDimension() < 3)
1893       contextActions[4]->setEnabled(0);
1894     else
1895       contextActions[4]->setEnabled(1);
1896   }
1897   contextMenu.exec(QCursor::pos());
1898 }
1899 //------------------------------------------------------------------------------
1900
1901 //------------------------------------------------------------------------------
1902 void vvMainWindow::CloseImage()
1903 {
1904   CloseImage(DataTree->selectedItems()[0],0);
1905 }
1906 //------------------------------------------------------------------------------
1907
1908 //------------------------------------------------------------------------------
1909 void vvMainWindow::ReloadImage()
1910 {
1911   ReloadImage(DataTree->selectedItems()[0],0);
1912 }
1913 //------------------------------------------------------------------------------
1914
1915 //------------------------------------------------------------------------------
1916 void vvMainWindow::SelectOverlayImage()
1917 {
1918   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1919
1920   //check if one overlay image is added
1921   for (int child = 0; child < DataTree->topLevelItem(index)->childCount(); child++)
1922     if (DataTree->topLevelItem(index)->child(child)->data(1,Qt::UserRole).toString() == "overlay") {
1923       QString error = "Cannot add more than one compared image\n";
1924       error += "Please remove first ";
1925       error += DataTree->topLevelItem(index)->child(child)->data(COLUMN_IMAGE_NAME,Qt::DisplayRole).toString();
1926       QMessageBox::information(this,tr("Problem adding compared image !"),error);
1927       return;
1928     }
1929
1930   QString Extensions = EXTENSIONS;
1931   Extensions += ";;All Files (*)";
1932   QStringList files = QFileDialog::getOpenFileNames(this,tr("Load Overlay image"),mInputPathName,Extensions);
1933   if (files.isEmpty())
1934     return;
1935
1936   std::vector<std::string> vecFileNames;
1937   for (int i = 0; i < files.size(); i++) {
1938     vecFileNames.push_back(files[i].toStdString());
1939   }
1940   AddOverlayImage(index,vecFileNames,vvImageReader::IMAGE);
1941 }
1942 //------------------------------------------------------------------------------
1943
1944 //------------------------------------------------------------------------------
1945 void vvMainWindow::AddOverlayImage(int index, std::vector<std::string> fileNames, vvImageReader::LoadedImageType type)
1946 {
1947   QString file(fileNames[0].c_str());
1948   if (QFile::exists(file))
1949   {
1950     mInputPathName = itksys::SystemTools::GetFilenamePath(file.toStdString()).c_str();
1951     itk::ImageIOBase::Pointer reader = itk::ImageIOFactory::CreateImageIO(
1952         file.toStdString().c_str(), itk::ImageIOFactory::ReadMode);
1953     reader->SetFileName(fileNames[0].c_str());
1954     reader->ReadImageInformation();
1955     std::string component = reader->GetComponentTypeAsString(reader->GetComponentType());
1956     int dimension = reader->GetNumberOfDimensions();
1957     QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
1958     vvProgressDialog progress("Opening " + file.toStdString());
1959     qApp->processEvents();
1960
1961     std::string filename = itksys::SystemTools::GetFilenameWithoutExtension(file.toStdString()).c_str();
1962     if (mSlicerManagers[index]->SetOverlay(fileNames,dimension, component,type)) {
1963       //create an item in the tree with good settings
1964       QTreeWidgetItem *item = new QTreeWidgetItem();
1965       item->setData(0,Qt::UserRole,file.toStdString().c_str());
1966       item->setData(1,Qt::UserRole,tr("overlay"));
1967       QFileInfo fileinfo(file); //Do not show the path
1968       item->setData(COLUMN_IMAGE_NAME,Qt::DisplayRole,fileinfo.fileName());
1969       item->setToolTip(COLUMN_IMAGE_NAME, mSlicerManagers[index]->GetListOfAbsoluteFilePathInOneString("overlay").c_str());
1970       qApp->processEvents();
1971
1972       for (int j = 1; j <= 4; j++) {
1973         item->setData(j,Qt::CheckStateRole,DataTree->topLevelItem(index)->data(j,Qt::CheckStateRole));
1974       }
1975
1976       //Create the buttons for reload and close
1977       qApp->processEvents();
1978       QTreePushButton* cButton = new QTreePushButton;
1979       cButton->setItem(item);
1980       cButton->setColumn(COLUMN_CLOSE_IMAGE);
1981       cButton->setToolTip(tr("close image"));
1982       cButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/exit.png")));
1983       connect(cButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
1984           this,SLOT(CloseImage(QTreeWidgetItem*, int)));
1985
1986       QTreePushButton* rButton = new QTreePushButton;
1987       rButton->setItem(item);
1988       rButton->setColumn(COLUMN_RELOAD_IMAGE);
1989       rButton->setToolTip(tr("reload image"));
1990       rButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/rotateright.png")));
1991       connect(rButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
1992           this,SLOT(ReloadImage(QTreeWidgetItem*, int)));
1993
1994       DataTree->topLevelItem(index)->setExpanded(1);
1995       DataTree->topLevelItem(index)->addChild(item);
1996       DataTree->setItemWidget(item, COLUMN_CLOSE_IMAGE, cButton);
1997       DataTree->setItemWidget(item, COLUMN_RELOAD_IMAGE, rButton);
1998
1999       //set the id of the image
2000       QString id = DataTree->topLevelItem(index)->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString();
2001       item->setData(COLUMN_IMAGE_NAME,Qt::UserRole,id.toStdString().c_str());
2002       UpdateTree();
2003       qApp->processEvents();
2004       ImageInfoChanged();
2005       QApplication::restoreOverrideCursor();
2006
2007       // Update the display to update, e.g., the sliders
2008       for(int i=0; i<4; i++)
2009         DisplaySliders(index, i);
2010     } else {
2011       QApplication::restoreOverrideCursor();
2012       QString error = "Cannot import the new image.\n";
2013       error += mSlicerManagers[index]->GetLastError().c_str();
2014       QMessageBox::information(this,tr("Problem reading image !"),error);
2015     }
2016     WindowLevelChanged();
2017   }
2018   else
2019     QMessageBox::information(this,tr("Problem reading Overlay !"),"File doesn't exist!");
2020 }
2021 //------------------------------------------------------------------------------
2022
2023
2024 //------------------------------------------------------------------------------
2025 void vvMainWindow::AddROI(int index, QString file)
2026 {
2027   /*
2028   // Get slice manager
2029
2030   // Load image
2031
2032   vvImageReader * mReader = new vvImageReader;
2033   mReader->SetInputFilename(filename.toStdString());
2034   mReader->Update(IMAGE);
2035   if (mReader->GetLastError().size() != 0) {
2036     std::cerr << "Error while reading " << filename.toStdString() << std::endl;
2037     QString error = "Cannot open file \n";
2038     error += mReader->GetLastError().c_str();
2039     QMessageBox::information(this,tr("Reading problem"),error);
2040     delete mReader;
2041     return;
2042   }
2043   vvImage::Pointer roi = mReader->GetOutput();
2044
2045   // Create roi in new tool
2046   vvToolStructureSetManager::AddImage(mCurrentSlicerManager, roi);
2047   */
2048 }
2049 //------------------------------------------------------------------------------
2050
2051 //------------------------------------------------------------------------------
2052 void vvMainWindow::SelectFusionImage()
2053 {
2054   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2055
2056   //check if one fusion image is added
2057   for (int child = 0; child < DataTree->topLevelItem(index)->childCount(); child++)
2058     if (DataTree->topLevelItem(index)->child(child)->data(1,Qt::UserRole).toString() == "fusion") {
2059       QString error = "Cannot add more than one fusion image\n";
2060       error += "Please remove first ";
2061       error += DataTree->topLevelItem(index)->child(child)->data(COLUMN_IMAGE_NAME,Qt::DisplayRole).toString();
2062       QMessageBox::information(this,tr("Problem adding fusion image !"),error);
2063       return;
2064     }
2065
2066   QString Extensions = EXTENSIONS;
2067   Extensions += ";;All Files (*)";
2068   QString file = QFileDialog::getOpenFileName(this,tr("Load Fusion image"),mInputPathName,Extensions);
2069   if (!file.isEmpty())
2070     AddFusionImage(index,file);
2071 }
2072 //------------------------------------------------------------------------------
2073
2074 //------------------------------------------------------------------------------
2075 void vvMainWindow::ResetTransformationToIdentity()
2076 {
2077   std::string actorType = DataTree->selectedItems()[0]->data(1,Qt::UserRole).toString().toStdString();
2078   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2079   mSlicerManagers[index]->ResetTransformationToIdentity(actorType);
2080   ImageInfoChanged();
2081 }
2082 //------------------------------------------------------------------------------
2083
2084 //------------------------------------------------------------------------------
2085 void vvMainWindow::AddFusionImage(int index, QString file)
2086 {
2087   if (QFile::exists(file))
2088   {
2089     mInputPathName = itksys::SystemTools::GetFilenamePath(file.toStdString()).c_str();
2090     itk::ImageIOBase::Pointer reader = itk::ImageIOFactory::CreateImageIO(
2091         file.toStdString().c_str(), itk::ImageIOFactory::ReadMode);
2092     reader->SetFileName(file.toStdString().c_str());
2093     reader->ReadImageInformation();
2094     std::string component = reader->GetComponentTypeAsString(reader->GetComponentType());
2095     if (reader) {
2096       QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
2097       vvProgressDialog progress("Opening fusion");
2098       qApp->processEvents();
2099
2100       std::string filename = itksys::SystemTools::GetFilenameWithoutExtension(file.toStdString()).c_str();
2101       if (mSlicerManagers[index]->SetFusion(file.toStdString(),
2102             reader->GetNumberOfDimensions(), component)) {
2103         //create an item in the tree with good settings
2104         QTreeWidgetItem *item = new QTreeWidgetItem();
2105         item->setData(0,Qt::UserRole,file.toStdString().c_str());
2106         item->setData(1,Qt::UserRole,tr("fusion"));
2107         QFileInfo fileinfo(filename.c_str()); //Do not show the path
2108         item->setData(COLUMN_IMAGE_NAME,Qt::DisplayRole,fileinfo.fileName());
2109         item->setToolTip(COLUMN_IMAGE_NAME, mSlicerManagers[index]->GetListOfAbsoluteFilePathInOneString("fusion").c_str());
2110         qApp->processEvents();
2111
2112         for (int j = 1; j <= 4; j++) {
2113           item->setData(j,Qt::CheckStateRole,DataTree->topLevelItem(index)->data(j,Qt::CheckStateRole));
2114         }
2115
2116         //Create the buttons for reload and close
2117         qApp->processEvents();
2118         QTreePushButton* cButton = new QTreePushButton;
2119         cButton->setItem(item);
2120         cButton->setColumn(COLUMN_CLOSE_IMAGE);
2121         cButton->setToolTip(tr("close image"));
2122         cButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/exit.png")));
2123         connect(cButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
2124             this,SLOT(CloseImage(QTreeWidgetItem*, int)));
2125
2126         QTreePushButton* rButton = new QTreePushButton;
2127         rButton->setItem(item);
2128         rButton->setColumn(COLUMN_RELOAD_IMAGE);
2129         rButton->setToolTip(tr("reload image"));
2130         rButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/rotateright.png")));
2131         connect(rButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
2132             this,SLOT(ReloadImage(QTreeWidgetItem*, int)));
2133
2134         DataTree->topLevelItem(index)->setExpanded(1);
2135         DataTree->topLevelItem(index)->addChild(item);
2136         DataTree->setItemWidget(item, COLUMN_CLOSE_IMAGE, cButton);
2137         DataTree->setItemWidget(item, COLUMN_RELOAD_IMAGE, rButton);
2138
2139         //set the id of the image
2140         QString id = DataTree->topLevelItem(index)->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString();
2141         item->setData(COLUMN_IMAGE_NAME,Qt::UserRole,id.toStdString().c_str());
2142         UpdateTree();
2143         qApp->processEvents();
2144         ImageInfoChanged();
2145         QApplication::restoreOverrideCursor();
2146       } else {
2147         QApplication::restoreOverrideCursor();
2148         QString error = "Cannot import the new image.\n";
2149         error += mSlicerManagers[index]->GetLastError().c_str();
2150         QMessageBox::information(this,tr("Problem reading image !"),error);
2151       }
2152     } else {
2153       QString error = "Cannot import the new image.\n";
2154       QMessageBox::information(this,tr("Problem reading image !"),error);
2155     }
2156   }
2157   else
2158     QMessageBox::information(this,tr("Problem reading Fusion !"),"File doesn't exist!");
2159 }
2160 //------------------------------------------------------------------------------
2161
2162
2163 //------------------------------------------------------------------------------
2164 void vvMainWindow::OpenField()
2165 {
2166   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2167   //check if a vector field has already been added
2168   for (int child = 0; child < DataTree->topLevelItem(index)->childCount(); child++)
2169     if (DataTree->topLevelItem(index)->child(child)->data(1,Qt::UserRole).toString() == "vector") {
2170       QString error = "Cannot add more than one vector field\n";
2171       error += "Please remove first ";
2172       error += DataTree->topLevelItem(index)->child(child)->data(COLUMN_IMAGE_NAME,Qt::DisplayRole).toString();
2173       QMessageBox::information(this,tr("Problem adding vector field!"),error);
2174       return;
2175     }
2176
2177   QString Extensions = "Images ( *.mhd)";
2178   Extensions += ";;Images ( *.mha)";
2179   Extensions += ";;Images ( *.vf)";
2180   QString file = QFileDialog::getOpenFileName(this,tr("Load deformation field"),mInputPathName,Extensions);
2181   if (!file.isEmpty())
2182     AddField(file,index);
2183 }
2184 //------------------------------------------------------------------------------
2185
2186
2187 //------------------------------------------------------------------------------
2188 void vvMainWindow::AddFieldEntry(QString filename,int index,bool from_disk)
2189 {
2190   //create an item in the tree with good settings
2191   QTreeWidgetItem *item = new QTreeWidgetItem();
2192   item->setData(0,Qt::UserRole,filename.toStdString().c_str());
2193   item->setData(1,Qt::UserRole,tr("vector"));
2194   QFileInfo fileinfo(filename); //Do not show the path
2195   item->setData(COLUMN_IMAGE_NAME,Qt::DisplayRole,fileinfo.fileName());
2196   item->setToolTip(COLUMN_IMAGE_NAME, mSlicerManagers[index]->GetListOfAbsoluteFilePathInOneString("vector").c_str());
2197   qApp->processEvents();
2198
2199   for (int j = 1; j <= 4; j++) {
2200     item->setData(j,Qt::CheckStateRole,DataTree->topLevelItem(index)->data(j,Qt::CheckStateRole));
2201   }
2202
2203   //Create the buttons for reload and close
2204   qApp->processEvents();
2205   QTreePushButton* cButton = new QTreePushButton;
2206   cButton->setItem(item);
2207   cButton->setColumn(COLUMN_CLOSE_IMAGE);
2208   cButton->setToolTip(tr("close vector field"));
2209   cButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/exit.png")));
2210   connect(cButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
2211           this,SLOT(CloseImage(QTreeWidgetItem*, int)));
2212
2213   QTreePushButton* rButton = new QTreePushButton;
2214   rButton->setItem(item);
2215   rButton->setColumn(COLUMN_RELOAD_IMAGE);
2216   rButton->setToolTip(tr("reload vector field"));
2217   rButton->setEnabled(from_disk);
2218   rButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/rotateright.png")));
2219   connect(rButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
2220           this,SLOT(ReloadImage(QTreeWidgetItem*, int)));
2221
2222   DataTree->topLevelItem(index)->setExpanded(1);
2223   DataTree->topLevelItem(index)->addChild(item);
2224   DataTree->setItemWidget(item, COLUMN_RELOAD_IMAGE, rButton);
2225   DataTree->setItemWidget(item, COLUMN_CLOSE_IMAGE, cButton);
2226
2227   //set the id of the image
2228   QString id = DataTree->topLevelItem(index)->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString();
2229   item->setData(COLUMN_IMAGE_NAME,Qt::UserRole,id.toStdString().c_str());
2230   UpdateTree();
2231   qApp->processEvents();
2232   ImageInfoChanged();
2233   QApplication::restoreOverrideCursor();
2234 }
2235 //------------------------------------------------------------------------------
2236
2237
2238 //------------------------------------------------------------------------------
2239 void vvMainWindow::AddField(vvImage::Pointer vf,QString file,int index)
2240 {
2241   QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
2242   vvSlicerManager* imageManager = mSlicerManagers[index];
2243   if (imageManager->SetVF(vf,file.toStdString())) {
2244     AddFieldEntry(file,index,false);
2245   } else {
2246     QString error = "Cannot import the vector field for this image.\n";
2247     error += imageManager->GetLastError().c_str();
2248     QMessageBox::information(this,tr("Problem reading VF !"),error);
2249   }
2250   QApplication::restoreOverrideCursor();
2251 }
2252 //------------------------------------------------------------------------------
2253
2254
2255 //------------------------------------------------------------------------------
2256 void vvMainWindow::AddField(QString file,int index)
2257 {
2258   if (QFile::exists(file)) {
2259     mInputPathName = itksys::SystemTools::GetFilenamePath(file.toStdString()).c_str();
2260
2261     //init the progress events
2262     QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
2263     vvProgressDialog progress("Opening " + file.toStdString());
2264     qApp->processEvents();
2265
2266     //read the vector and put it in the current mSlicerManager
2267     vvSlicerManager* imageManager = mSlicerManagers[index];
2268     qApp->processEvents();
2269
2270     std::string filename = itksys::SystemTools::GetFilenameWithoutExtension(file.toStdString()).c_str();
2271     if (imageManager->SetVF(file.toStdString())) {
2272       imageManager->Render();
2273       AddFieldEntry(file,index,true);
2274     } else {
2275       QApplication::restoreOverrideCursor();
2276       QString error = "Cannot import the vector field for this image.\n";
2277       error += imageManager->GetLastError().c_str();
2278       QMessageBox::information(this,tr("Problem reading VF !"),error);
2279     }
2280   } else
2281     QMessageBox::information(this,tr("Problem reading VF !"),"File doesn't exist!");
2282
2283 }
2284 //------------------------------------------------------------------------------
2285
2286
2287 //------------------------------------------------------------------------------
2288 void vvMainWindow::SetVFProperty(int subsampling, int scale, int log, int width, double r, double g, double b)
2289 {
2290   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2291   if (mSlicerManagers[index]->GetSlicer(0)->GetVF()) {
2292     for (int i = 0; i < 4; i++) {
2293       mSlicerManagers[index]->GetSlicer(i)->SetVFSubSampling(subsampling);
2294       mSlicerManagers[index]->GetSlicer(i)->SetVFScale(scale);
2295       mSlicerManagers[index]->GetSlicer(i)->SetVFWidth(width);
2296       mSlicerManagers[index]->GetSlicer(i)->SetVFColor(r,g,b);
2297       if (log > 0)
2298         mSlicerManagers[index]->GetSlicer(i)->SetVFLog(1);
2299       else
2300         mSlicerManagers[index]->GetSlicer(i)->SetVFLog(0);
2301     }
2302   }
2303 }
2304 //------------------------------------------------------------------------------
2305
2306
2307 //------------------------------------------------------------------------------
2308 void vvMainWindow::SetOverlayProperty(int color, int linked, double window, double level)
2309 {
2310   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2311   if (mSlicerManagers[index]->GetSlicer(0)->GetOverlay()) {
2312     mSlicerManagers[index]->SetOverlayColor(color);
2313     mSlicerManagers[index]->SetColorMap(0);
2314     mSlicerManagers[index]->SetLinkOverlayWindowLevel(linked);
2315     mSlicerManagers[index]->SetOverlayColorWindow(window);
2316     mSlicerManagers[index]->SetOverlayColorLevel(level);
2317     mSlicerManagers[index]->Render();
2318   }
2319 }
2320 //------------------------------------------------------------------------------
2321
2322 //------------------------------------------------------------------------------
2323 void vvMainWindow::SetFusionProperty(int opacity, int thresOpacity, int colormap,double window, double level, bool showLegend)
2324 {
2325   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2326   if (mSlicerManagers[index]->GetSlicer(0)->GetFusion()) {
2327     mSlicerManagers[index]->SetFusionColorMap(colormap);
2328     mSlicerManagers[index]->SetFusionOpacity(opacity);
2329     mSlicerManagers[index]->SetFusionThresholdOpacity(thresOpacity);
2330     mSlicerManagers[index]->SetFusionWindow(window);
2331     mSlicerManagers[index]->SetFusionLevel(level);
2332     mSlicerManagers[index]->SetFusionShowLegend(showLegend);
2333     mSlicerManagers[index]->SetColorMap(0);
2334     mSlicerManagers[index]->Render();
2335   }
2336 }
2337 //------------------------------------------------------------------------------
2338
2339 //------------------------------------------------------------------------------
2340 void vvMainWindow::SaveAs()
2341 {
2342   if (DataTree->selectedItems()[0]->data(1,Qt::UserRole).toString() == "vector") {
2343     QMessageBox::warning(this,tr("Unsupported type"),tr("Sorry, saving a vector field is unsupported for the moment"));
2344     return;
2345   }
2346
2347   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2348   int dimension = mSlicerManagers[index]->GetDimension();
2349   QStringList OutputListeFormat;
2350   OutputListeFormat.clear();
2351   if (dimension == 1) {
2352     OutputListeFormat.push_back(".mhd");
2353     OutputListeFormat.push_back(".mha");
2354   }
2355   if (dimension == 2) {
2356     OutputListeFormat.push_back(".bmp");
2357     OutputListeFormat.push_back(".png");
2358     OutputListeFormat.push_back(".jpeg");
2359     OutputListeFormat.push_back(".tif");
2360     OutputListeFormat.push_back(".mhd");
2361     OutputListeFormat.push_back(".mha");
2362     OutputListeFormat.push_back(".hdr");
2363     OutputListeFormat.push_back(".vox");
2364   } else if (dimension == 3) {
2365     OutputListeFormat.push_back(".mhd");
2366     OutputListeFormat.push_back(".mha");
2367     OutputListeFormat.push_back(".nii");
2368     OutputListeFormat.push_back(".nrrd");
2369     OutputListeFormat.push_back(".nhdr");
2370     OutputListeFormat.push_back(".hdr");
2371     OutputListeFormat.push_back(".vox");
2372   } else if (dimension == 4) {
2373     OutputListeFormat.push_back(".mhd");
2374     OutputListeFormat.push_back(".mha");
2375     OutputListeFormat.push_back(".nii");
2376     OutputListeFormat.push_back(".nrrd");
2377     OutputListeFormat.push_back(".nhdr");
2378   }
2379   QString Extensions = "AllFiles(*.*)";
2380   for (int i = 0; i < OutputListeFormat.count(); i++) {
2381     Extensions += ";;Images ( *";
2382     Extensions += OutputListeFormat[i];
2383     Extensions += ")";
2384   }
2385   QString fileName = QFileDialog::getSaveFileName(this,
2386                      tr("Save As"),
2387                      mSlicerManagers[index]->GetFileName().c_str(),
2388                      Extensions);
2389   if (!fileName.isEmpty()) {
2390     std::string fileformat = itksys::SystemTools::GetFilenameLastExtension(fileName.toStdString());
2391     if (OutputListeFormat.contains(
2392           fileformat.c_str())) {
2393       QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
2394       std::string action = "Saving";
2395       vvProgressDialog progress("Saving "+fileName.toStdString());
2396       qApp->processEvents();
2397       vvImageWriter::Pointer writer = vvImageWriter::New();
2398       writer->SetOutputFileName(fileName.toStdString());
2399       writer->SetInput(mSlicerManagers[index]->GetImage());
2400
2401       // Check on transform and prompt user
2402       writer->SetSaveTransform(false);
2403       bool bId = true;
2404       for(int i=0; i<4; i++)
2405         for(int j=0; j<4; j++) {
2406           // TODO SR and BP: check on the list of transforms and not the first only
2407           double elt = mSlicerManagers[index]->GetImage()->GetTransform()[0]->GetMatrix()->GetElement(i,j);
2408           if(i==j && elt!=1.)
2409             bId = false;
2410           if(i!=j && elt!=0.)
2411             bId = false;
2412         }
2413       if( !bId ) {
2414         QString warning = "The image has an associated linear transform. Do you want to save it along?";
2415         QMessageBox msgBox(QMessageBox::Warning, tr("Save transform"), warning, 0, this);
2416         msgBox.addButton(tr("Yes"), QMessageBox::AcceptRole);
2417         msgBox.addButton(tr("No"), QMessageBox::RejectRole);
2418         if (msgBox.exec() == QMessageBox::AcceptRole)
2419           writer->SetSaveTransform(true);
2420       }
2421
2422       writer->Update();
2423       QApplication::restoreOverrideCursor();
2424       if (writer->GetLastError().size()) {
2425         QString error = "Saving did not succeed\n";
2426         error += writer->GetLastError().c_str();
2427         QMessageBox::information(this,tr("Saving Problem"),error);
2428         SaveAs();
2429       }
2430     } else {
2431       QString error = fileformat.c_str();
2432       if (error.isEmpty())
2433         error += "no file format specified !";
2434       else
2435         error += " format unknown !!!\n";
2436       QMessageBox::information(this,tr("Saving Problem"),error);
2437       SaveAs();
2438     }
2439   }
2440 }
2441 //------------------------------------------------------------------------------
2442
2443 //------------------------------------------------------------------------------
2444 void vvMainWindow::SaveCurrentState()
2445 {
2446   QString Extensions = "XML Files(*.xml)";
2447   QString fileName = QFileDialog::getSaveFileName(this,
2448                      tr("Save Current Window State"),
2449                      "",
2450                      Extensions);
2451
2452   SaveCurrentStateAs(fileName.toStdString());
2453 }
2454 //------------------------------------------------------------------------------
2455
2456 //------------------------------------------------------------------------------
2457 void vvMainWindow::SaveCurrentStateAs(const std::string& stateFile)
2458 {
2459   vvSaveState save_state;
2460   save_state.Run(this, stateFile);
2461 }
2462
2463 //------------------------------------------------------------------------------
2464 void vvMainWindow::ReadSavedState()
2465 {
2466   QString Extensions = "XML Files(*.xml)";
2467   QString fileName = QFileDialog::getOpenFileName(this,
2468                      tr("Load Window State"),
2469                      "",
2470                      Extensions);
2471
2472   ReadSavedStateFile(fileName.toStdString());
2473 }
2474 //------------------------------------------------------------------------------
2475
2476 //------------------------------------------------------------------------------
2477 void vvMainWindow::ReadSavedStateFile(const std::string& stateFile)
2478 {
2479   vvReadState read_state;
2480   read_state.Run(this, stateFile);
2481 }
2482 //------------------------------------------------------------------------------
2483
2484 //------------------------------------------------------------------------------
2485 void vvMainWindow::LinkAllImages()
2486 {
2487         linkPanel->linkAll();
2488 }
2489
2490 //------------------------------------------------------------------------------
2491 void vvMainWindow::AddLink(QString image1,QString image2,bool fromPanel)
2492 {
2493   if (!fromPanel) {
2494     // delegate to linkPanel if call came from elsewhere...
2495     linkPanel->addLinkFromIds(image1, image2);
2496     return;
2497   }
2498
2499   unsigned int sm1 = 0;
2500   unsigned int sm2 = 0;
2501
2502   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
2503     if (image1.toStdString() == mSlicerManagers[i]->GetId()) {
2504       mSlicerManagers[i]->AddLink(image2.toStdString());
2505       sm1 = i;
2506     }
2507     if (image2.toStdString() == mSlicerManagers[i]->GetId()) {
2508       mSlicerManagers[i]->AddLink(image1.toStdString());
2509       sm2 = i;
2510     }
2511   }
2512
2513   if (linkPanel->isLinkAll())   {
2514     emit UpdateLinkedNavigation(mSlicerManagers[sm1]->GetId(), mSlicerManagers[mCurrentPickedImageIndex], mSlicerManagers[mCurrentPickedImageIndex]->GetSlicer(0));
2515     emit UpdateLinkedNavigation(mSlicerManagers[sm2]->GetId(), mSlicerManagers[mCurrentPickedImageIndex], mSlicerManagers[mCurrentPickedImageIndex]->GetSlicer(0));
2516   } else {
2517     emit UpdateLinkedNavigation(mSlicerManagers[sm2]->GetId(), mSlicerManagers[sm1], mSlicerManagers[sm1]->GetSlicer(0));
2518   }
2519 }
2520
2521 //------------------------------------------------------------------------------
2522
2523
2524 //------------------------------------------------------------------------------
2525 void vvMainWindow::RemoveLink(QString image1,QString image2)
2526 {
2527   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
2528     if (image1.toStdString() == mSlicerManagers[i]->GetId()) {
2529       mSlicerManagers[i]->RemoveLink(image2.toStdString());
2530     }
2531     if (image2.toStdString() == mSlicerManagers[i]->GetId()) {
2532       mSlicerManagers[i]->RemoveLink(image1.toStdString());
2533     }
2534   }
2535 }
2536 //------------------------------------------------------------------------------
2537
2538 //------------------------------------------------------------------------------
2539 void vvMainWindow::ChangeImageWithIndexOffset(vvSlicerManager *sm, int slicer, int offset)
2540 {
2541   if(mSlicerManagers.size()==1)
2542     return;
2543
2544   int index = 0;
2545   while(sm != mSlicerManagers[index])
2546     index++;
2547   index = (index+offset+mSlicerManagers.size()) % mSlicerManagers.size();
2548
2549   QTreeWidgetItem* item = GetItemFromSlicerManager(mSlicerManagers[index]);
2550   item->setData(slicer+1,Qt::CheckStateRole,2);         //change checkbox
2551   CurrentImageChanged(mSlicerManagers[index]->GetId()); //select new image
2552   DisplayChanged(item,slicer+1);
2553 }
2554 //------------------------------------------------------------------------------
2555
2556 void vvMainWindow::HorizontalSliderMoved(int value,int column, int slicer_index)
2557 {
2558   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
2559     if (DataTree->topLevelItem(i)->data(column,Qt::CheckStateRole).toInt() > 1) {
2560       for (int j = 0; j < 4; j++) {
2561         mSlicerManagers[i]->SetTSliceInSlicer(value,j);
2562         //if (mSlicerManagers[i]->GetSlicer(j)->GetImageActor()->GetVisibility())
2563         //UpdateTSlice(j,value);
2564       }
2565       mSlicerManagers[i]->GetSlicer(slicer_index)->Render();
2566       break;
2567     }
2568   }
2569 }
2570 //------------------------------------------------------------------------------
2571
2572
2573 //------------------------------------------------------------------------------
2574 void vvMainWindow::NOHorizontalSliderMoved()
2575 {
2576   // if (mCurrentTime == NOHorizontalSlider->value()) return;
2577   HorizontalSliderMoved(NOHorizontalSlider->value(),COLUMN_UL_VIEW,0);
2578 //  mCurrentTime = NOHorizontalSlider->value();
2579 }
2580 //------------------------------------------------------------------------------
2581
2582
2583 //------------------------------------------------------------------------------
2584 void vvMainWindow::NEHorizontalSliderMoved()
2585 {
2586   // if (mCurrentTime == NEHorizontalSlider->value()) return;
2587   HorizontalSliderMoved(NEHorizontalSlider->value(),COLUMN_UR_VIEW,1);
2588 //  mCurrentTime = NEHorizontalSlider->value();
2589 }
2590 //------------------------------------------------------------------------------
2591
2592
2593 //------------------------------------------------------------------------------
2594 void vvMainWindow::SOHorizontalSliderMoved()
2595 {
2596   // if (mCurrentTime == SOHorizontalSlider->value()) return;
2597   HorizontalSliderMoved(SOHorizontalSlider->value(),COLUMN_DL_VIEW,2);
2598   // mCurrentTime = SOHorizontalSlider->value();
2599 }
2600 //------------------------------------------------------------------------------
2601
2602
2603 //------------------------------------------------------------------------------
2604 void vvMainWindow::SEHorizontalSliderMoved()
2605 {
2606   // if (mCurrentTime == SEHorizontalSlider->value()) return;
2607   HorizontalSliderMoved(SEHorizontalSlider->value(),COLUMN_DR_VIEW,3);
2608   // mCurrentTime = SEHorizontalSlider->value();
2609 }
2610 //------------------------------------------------------------------------------
2611
2612 //------------------------------------------------------------------------------
2613 void vvMainWindow::NOVerticalSliderChanged()
2614 {
2615   static int value=-1;
2616   if (value == NOVerticalSlider->value()) return;
2617   else value = NOVerticalSlider->value();
2618   //  int value = NOVerticalSlider->value();
2619   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
2620     if (DataTree->topLevelItem(i)->data(COLUMN_UL_VIEW,Qt::CheckStateRole).toInt() > 1) {
2621       if (mSlicerManagers[i]->GetSlicer(0)->GetSlice() != value) {
2622         mSlicerManagers[i]->GetSlicer(0)->SetSlice(value);
2623         mSlicerManagers[i]->VerticalSliderHasChanged(0, value);
2624
2625         // If nor Update/Render -> slider not work
2626         // only render = ok navigation, but for contour Update needed but slower ?
2627
2628         mSlicerManagers[i]->UpdateSlice(0);  // <-- DS add this. Not too much update ? YES. but needed for ImageContour ...
2629         //mSlicerManagers[i]->GetSlicer(0)->Render(); // <-- DS add this, needed for contour, seems ok ? not too slow ?
2630       }
2631       break;
2632     }
2633   }
2634 }
2635 //------------------------------------------------------------------------------
2636
2637
2638 //------------------------------------------------------------------------------
2639 void vvMainWindow::NEVerticalSliderChanged()
2640 {
2641   static int value=-1;
2642   if (value == NEVerticalSlider->value()) return;
2643   else value = NEVerticalSlider->value();
2644   //  int value = NEVerticalSlider->value();
2645   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
2646     if (DataTree->topLevelItem(i)->data(COLUMN_UR_VIEW,Qt::CheckStateRole).toInt() > 1) {
2647       if (mSlicerManagers[i]->GetSlicer(1)->GetSlice() != value) {
2648         mSlicerManagers[i]->GetSlicer(1)->SetSlice(value);
2649         mSlicerManagers[i]->VerticalSliderHasChanged(1, value);
2650         mSlicerManagers[i]->UpdateSlice(1);
2651         //mSlicerManagers[i]->GetSlicer(1)->Render(); // <-- DS add this, needed for contour, seems ok ? not too slow ?
2652       }
2653       break;
2654     }
2655   }
2656 }
2657 //------------------------------------------------------------------------------
2658
2659
2660 //------------------------------------------------------------------------------
2661 void vvMainWindow::SOVerticalSliderChanged()
2662 {
2663   static int value=-1;
2664   if (value == SOVerticalSlider->value()) return;
2665   else value = SOVerticalSlider->value();
2666   //int value = SOVerticalSlider->value();
2667   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
2668     if (DataTree->topLevelItem(i)->data(COLUMN_DL_VIEW,Qt::CheckStateRole).toInt() > 1) {
2669       if (mSlicerManagers[i]->GetSlicer(2)->GetSlice() != value) {
2670         mSlicerManagers[i]->GetSlicer(2)->SetSlice(value);
2671         mSlicerManagers[i]->VerticalSliderHasChanged(2, value);
2672         mSlicerManagers[i]->UpdateSlice(2);
2673         //mSlicerManagers[i]->GetSlicer(2)->Render(); // <-- DS add this, needed for contour, seems ok ? not too slow ?
2674       }
2675       // else { DD("avoid SOVerticalSlider slicer update"); }
2676       break;
2677     }
2678   }
2679 }
2680 //------------------------------------------------------------------------------
2681
2682
2683 //------------------------------------------------------------------------------
2684 void vvMainWindow::SEVerticalSliderChanged()
2685 {
2686   static int value=-1;
2687   if (value == SEVerticalSlider->value()) return;
2688   else value = SEVerticalSlider->value();
2689   // int value = SEVerticalSlider->value();
2690   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
2691     if (DataTree->topLevelItem(i)->data(COLUMN_DR_VIEW,Qt::CheckStateRole).toInt() > 1) {
2692       if (mSlicerManagers[i]->GetSlicer(3)->GetSlice() != value) {
2693         mSlicerManagers[i]->GetSlicer(3)->SetSlice(value);
2694         mSlicerManagers[i]->VerticalSliderHasChanged(3, value);
2695         mSlicerManagers[i]->UpdateSlice(3);
2696         //mSlicerManagers[i]->GetSlicer(3)->Render(); // <-- DS add this, needed for contour, seems ok ? not too slow ?
2697       }
2698       break;
2699     }
2700   }
2701 }
2702 //------------------------------------------------------------------------------
2703
2704
2705 //------------------------------------------------------------------------------
2706 void vvMainWindow::UpdateSlice(int slicer, int slice)
2707 {
2708   // DD("vvMainWindow::UpdateSlice");
2709 //   DD(slicer);
2710 //   DD(slice);
2711   if (slicer == 0) {
2712     //    if (slice != NOVerticalSlider->value())
2713     NOVerticalSlider->setValue(slice);
2714   } else {
2715     if (slicer == 1)
2716       NEVerticalSlider->setValue(slice);
2717     else {
2718       if (slicer == 2)
2719         SOVerticalSlider->setValue(slice);
2720       else {
2721         if (slicer == 3)
2722           SEVerticalSlider->setValue(slice);
2723       }
2724     }
2725   }
2726   // DD("vvMainWindow:UpdateSlice END");
2727 }
2728 //------------------------------------------------------------------------------
2729
2730
2731 //------------------------------------------------------------------------------
2732 void vvMainWindow::UpdateTSlice(int slicer, int slice)
2733 {
2734   switch (slicer) {
2735   case 0:
2736     NOHorizontalSlider->setValue(slice);
2737     break;
2738   case 1:
2739     NEHorizontalSlider->setValue(slice);
2740     break;
2741   case 2:
2742     SOHorizontalSlider->setValue(slice);
2743     break;
2744   case 3:
2745     SEHorizontalSlider->setValue(slice);
2746     break;
2747   }
2748 }
2749 //------------------------------------------------------------------------------
2750
2751
2752 //------------------------------------------------------------------------------
2753 void vvMainWindow::UpdateSliceRange(int slicer, int min, int max, int tmin, int tmax)
2754 {
2755   //int position = int((min+max)/2);
2756   int position = mSlicerManagers[mCurrentPickedImageIndex]->GetSlicer(slicer)->GetSlice();
2757   if (slicer == 0) {
2758     NOVerticalSlider->setRange(min,max);
2759     NOHorizontalSlider->setRange(tmin,tmax);
2760     NOVerticalSlider->setValue(position);
2761   } else if (slicer == 1) {
2762     NEVerticalSlider->setRange(min,max);
2763     NEHorizontalSlider->setRange(tmin,tmax);
2764     NEVerticalSlider->setValue(position);
2765   } else if (slicer == 2) {
2766     SOVerticalSlider->setRange(min,max);
2767     SOHorizontalSlider->setRange(tmin,tmax);
2768     SOVerticalSlider->setValue(position);
2769   } else if (slicer == 3) {
2770     SEVerticalSlider->setRange(min,max);
2771     SEHorizontalSlider->setRange(tmin,tmax);
2772     SEVerticalSlider->setValue(position);
2773   }
2774 }
2775 //------------------------------------------------------------------------------
2776
2777
2778 //------------------------------------------------------------------------------
2779 void vvMainWindow::SaveNOScreenshot()
2780 {
2781   SaveScreenshot(NOViewWidget);
2782 }
2783 //------------------------------------------------------------------------------
2784
2785
2786 //------------------------------------------------------------------------------
2787 void vvMainWindow::SaveNEScreenshot()
2788 {
2789   SaveScreenshot(NEViewWidget);
2790 }
2791 //------------------------------------------------------------------------------
2792
2793
2794 //------------------------------------------------------------------------------
2795 void vvMainWindow::SaveSOScreenshot()
2796 {
2797   SaveScreenshot(SOViewWidget);
2798 }
2799 //------------------------------------------------------------------------------
2800
2801
2802 //------------------------------------------------------------------------------
2803 void vvMainWindow::SaveSEScreenshot()
2804 {
2805   SaveScreenshot(SEViewWidget);
2806 }
2807 //------------------------------------------------------------------------------
2808
2809
2810 //------------------------------------------------------------------------------
2811 void vvMainWindow::SaveScreenshotAllSlices()
2812 {
2813   QVTKWidget *widget = NOViewWidget;
2814
2815   int index = 0;// GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2816   vvSlicerManager * SM = mSlicerManagers[index];
2817   vvImage * image = SM->GetImage();
2818   vvSlicer * slicer = SM->GetSlicer(0);
2819   int orientation = slicer->GetOrientation();
2820   int nbSlices = image->GetSize()[orientation];
2821   vtkSmartPointer<vtkRenderWindow>  renderWindow = widget->GetRenderWindow();
2822
2823   // Select filename base
2824   QString filename = QFileDialog::getSaveFileName(this,
2825                                                   tr("Save As (filename will be completed by slice number)"),
2826                                                   itksys::SystemTools::GetFilenamePath(mSlicerManagers[index]->GetFileName()).c_str(),
2827                                                   "Images( *.png);;Images( *.jpg)");
2828
2829   // Loop on slices
2830   for(int i=0; i<nbSlices; i++) {
2831     // Change the slice
2832     slicer->SetSlice(i); // -> change the slice of the current slicer
2833     SM->UpdateSlice(0); // --> this one emit UpdateSlice
2834     QCoreApplication::flush(); // -> needed to force display of contours
2835
2836     // Screenshot
2837     vtkSmartPointer<vtkWindowToImageFilter> windowToImageFilter = vtkSmartPointer<vtkWindowToImageFilter>::New();
2838     windowToImageFilter->SetInput(renderWindow);
2839     windowToImageFilter->SetMagnification(1);
2840     windowToImageFilter->SetInputBufferTypeToRGBA(); //also record the alpha (transparency) channel
2841     windowToImageFilter->Update();
2842
2843     vtkSmartPointer<vtkPNGWriter> writer = vtkSmartPointer<vtkPNGWriter>::New();
2844     std::string fn = itksys::SystemTools::GetFilenameWithoutLastExtension(filename.toStdString());
2845     std::string num = clitk::toString(i);
2846     if (i<10) num = "0"+num;
2847     if (i<100) num = "0"+num;
2848     if (i<1000) num = "0"+num;
2849
2850     fn = itksys::SystemTools::GetFilenamePath(filename.toStdString()) + "/"+ fn
2851       + "_" + num + itksys::SystemTools::GetFilenameLastExtension(filename.toStdString());
2852     writer->SetFileName(fn.c_str());
2853     writer->SetInput(windowToImageFilter->GetOutput());
2854     writer->Write();
2855   }
2856 }
2857 //------------------------------------------------------------------------------
2858
2859
2860 //------------------------------------------------------------------------------
2861 void vvMainWindow::SaveScreenshot(QVTKWidget *widget)
2862 {
2863   QString Extensions = "Images( *.png);;";
2864   Extensions += "Images( *.jpg);;";
2865   Extensions += "Images( *.bmp);;";
2866   Extensions += "Images( *.tif);;";
2867   Extensions += "Images( *.ppm)";
2868 #if defined(VTK_USE_FFMPEG_ENCODER) || defined(VTK_USE_VIDEO_FOR_WINDOWS)
2869   Extensions += ";;Video( *.avi)";
2870 #endif
2871 #ifdef VTK_USE_MPEG2_ENCODER
2872   Extensions += ";;Video( *.mpg)";
2873 #endif
2874 #ifdef CLITK_EXPERIMENTAL
2875   Extensions += ";;Video( *.gif)";
2876 #endif
2877
2878   int smIndex=GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2879   QString fileName = QFileDialog::getSaveFileName(this,
2880                      tr("Save As"),
2881                      itksys::SystemTools::GetFilenamePath(mSlicerManagers[smIndex]->GetFileName()).c_str(),
2882                      Extensions);
2883
2884   if (!fileName.isEmpty()) {
2885     vtkSmartPointer<vtkWindowToImageFilter> w2i = vtkSmartPointer<vtkWindowToImageFilter>::New();
2886     w2i->SetInput(widget->GetRenderWindow());
2887     w2i->Update();
2888     vtkImageData *image = w2i->GetOutput();
2889
2890     std::string ext(itksys::SystemTools::GetFilenameLastExtension(fileName.toStdString()));
2891
2892     // Image
2893     vtkImageWriter *imgwriter = NULL;
2894     if (ext==".bmp")
2895       imgwriter = vtkBMPWriter::New();
2896     else if (ext==".tif")
2897       imgwriter = vtkTIFFWriter::New();
2898     else if (ext==".ppm")
2899       imgwriter = vtkPNMWriter::New();
2900     else if (ext==".png")
2901       imgwriter = vtkPNGWriter::New();
2902     else if (ext==".jpg")
2903       imgwriter = vtkJPEGWriter::New();
2904
2905     // Snapshot image if not null
2906     if(imgwriter!=NULL) {
2907       imgwriter->SetInput(image);
2908       imgwriter->SetFileName(fileName.toStdString().c_str());
2909       imgwriter->Write();
2910       return;
2911     }
2912
2913     // Video
2914     vtkGenericMovieWriter *vidwriter = NULL;
2915 #if CLITK_EXPERIMENTAL == 1
2916     if (ext==".gif") {
2917       vvAnimatedGIFWriter *gif = vvAnimatedGIFWriter::New();
2918       vidwriter = gif;
2919
2920       // FPS
2921       bool ok;
2922       int fps = QInputDialog::getInteger(this, tr("Number of frames per second"),
2923                                      tr("FPS:"), 5, 0, 1000, 1, &ok);
2924       if(ok)
2925         gif->SetRate(fps);
2926
2927       // Loops
2928       int loops = QInputDialog::getInteger(this, tr("Loops"),
2929                                      tr("Number of loops (0 means infinite):"), 0, 0, 1000000000, 1, &ok);
2930       if(ok)
2931         gif->SetLoops(loops);
2932
2933       // Dithering
2934       QString msg = "Would you like to activate dithering?";
2935       QMessageBox msgBox(QMessageBox::Question, tr("Dithering"),msg, 0, this);
2936       msgBox.addButton(tr("Yes"), QMessageBox::AcceptRole);
2937       msgBox.addButton(tr("No"), QMessageBox::RejectRole);
2938       gif->SetDither(msgBox.exec() == QMessageBox::AcceptRole);
2939     }
2940 #endif
2941 #ifdef VTK_USE_VIDEO_FOR_WINDOWS
2942     if (ext==".avi") {
2943       vtkAVIWriter *mpg = vtkAVIWriter::New();
2944       vidwriter = mpg;
2945       mpg->SetQuality(2);
2946       bool ok;
2947       int fps = QInputDialog::getInteger(this, tr("Number of frames per second"),
2948                                      tr("FPS:"), 5, 0, 1024, 1, &ok);
2949       if(!ok)
2950         fps = 5;
2951       mpg->SetRate(fps);
2952     }
2953 #endif
2954 #ifdef VTK_USE_FFMPEG_ENCODER
2955     if (ext==".avi") {
2956       vtkFFMPEGWriter *mpg = vtkFFMPEGWriter::New();
2957       vidwriter = mpg;
2958       mpg->SetQuality(2);
2959       bool ok;
2960       int fps = QInputDialog::getInteger(this, tr("Number of frames per second"),
2961                                      tr("FPS:"), 5, 0, 1024, 1, &ok);
2962       if(!ok)
2963         fps = 5;
2964       mpg->SetRate(fps);
2965       mpg->SetBitRateTolerance(int(ceil(12.0*1024*1024/fps)));
2966     }
2967 #endif
2968 #ifdef VTK_USE_MPEG2_ENCODER
2969     if (ext==".mpg") {
2970       vtkMPEG2Writer *mpg = vtkMPEG2Writer::New();
2971       vidwriter = mpg;
2972     }
2973 #endif
2974
2975     // Take video if not null
2976     if(vidwriter!=NULL){
2977       vidwriter->SetInput(image);
2978       vidwriter->SetFileName(fileName.toStdString().c_str());
2979       vidwriter->Start();
2980       int nSlice = mSlicerManagers[smIndex]->GetSlicer(0)->GetTMax();
2981       for(int i=0; i<=nSlice; i++) {
2982         mSlicerManagers[smIndex]->SetNextTSlice(0);
2983         vtkSmartPointer<vtkWindowToImageFilter> w2i = vtkSmartPointer<vtkWindowToImageFilter>::New();
2984         w2i->SetInput(widget->GetRenderWindow());
2985         w2i->Update();
2986         vidwriter->SetInput(w2i->GetOutput());
2987         vidwriter->Write();
2988       }
2989       vidwriter->End();
2990       vidwriter->Delete();
2991       return;
2992     }
2993
2994     QMessageBox::information(this,tr("Problem saving screenshot !"),tr("Cannot save image.\nPlease set a file extension !!!"));
2995   }
2996 }
2997 //------------------------------------------------------------------------------
2998
2999
3000 //------------------------------------------------------------------------------
3001 void vvMainWindow::GoToCursor()
3002 {
3003   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
3004   for (int column = 1; column < 5; column++) {
3005     if (DataTree->selectedItems()[0]->data(column,Qt::CheckStateRole).toInt() > 1) {
3006       double* cursorPos = mSlicerManagers[index]->GetSlicer(column-1)->GetCursorPosition();
3007       mSlicerManagers[index]->GetSlicer(column-1)->SetCurrentPosition(
3008         cursorPos[0],cursorPos[1],cursorPos[2],cursorPos[3]);
3009       mSlicerManagers[index]->UpdateViews(1,column-1);
3010       mSlicerManagers[index]->UpdateLinked(column-1);
3011       break;
3012     }
3013   }
3014 }
3015 //------------------------------------------------------------------------------
3016
3017 //------------------------------------------------------------------------------
3018 void vvMainWindow::PlayPause()
3019 {
3020   if (playMode) {
3021     playMode = 0;
3022     playButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/player_play.png")));
3023     ImageInfoChanged();
3024     return;
3025   } else {
3026     int image_number=DataTree->topLevelItemCount();
3027     bool has_temporal;
3028     for (int i=0; i<image_number; i++)
3029       if (mSlicerManagers[i]->GetSlicer(0)->GetTMax() > 0) {
3030         has_temporal=true;
3031         break;
3032       }
3033     if (has_temporal) {
3034       playMode = 1;
3035       playButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/player_pause.png")));
3036       QTimer::singleShot(1000/mFrameRate, this, SLOT(PlayNext()));
3037     }
3038   }
3039 }
3040 //------------------------------------------------------------------------------
3041
3042 //------------------------------------------------------------------------------
3043 void vvMainWindow::PlayNext()
3044 {
3045   if (playMode && !this->isHidden()) {
3046     int image_number=DataTree->topLevelItemCount();
3047     ///Only play one slicer per SM, and only if the SM is being displayed
3048     for (int i=0; i<image_number; i++)
3049       for (int j=0; j<4; j++)
3050         if (mSlicerManagers[i]->GetSlicer(0)->GetTMax() > 0 &&
3051             DataTree->topLevelItem(i)->data(j+1,Qt::CheckStateRole).toInt() > 0) {
3052           mSlicerManagers[i]->SetNextTSlice(j);
3053           break;
3054         }
3055     QTimer::singleShot(1000/mFrameRate, this, SLOT(PlayNext()));
3056   }
3057 }
3058 //------------------------------------------------------------------------------
3059
3060 void vvMainWindow::ShowLastImage()
3061 {
3062   if (mSlicerManagers.size() > 1) {
3063     QTreeWidgetItem * item=DataTree->topLevelItem(DataTree->topLevelItemCount()-1);
3064     CurrentImageChanged(mSlicerManagers.back()->GetId()); //select new image
3065     item->setData(1,Qt::CheckStateRole,2); //show the new image in the first panel
3066     DisplayChanged(item,1);
3067   }
3068 }
3069
3070 //------------------------------------------------------------------------------
3071 void vvMainWindow::UpdateRenderWindows()
3072 {
3073   if (NOViewWidget->GetRenderWindow()) NOViewWidget->GetRenderWindow()->Render();
3074   if (NEViewWidget->GetRenderWindow()) NEViewWidget->GetRenderWindow()->Render();
3075   if (SOViewWidget->GetRenderWindow()) SOViewWidget->GetRenderWindow()->Render();
3076   if (SEViewWidget->GetRenderWindow()) SEViewWidget->GetRenderWindow()->Render();
3077 }
3078 //------------------------------------------------------------------------------
3079
3080 //------------------------------------------------------------------------------
3081 void vvMainWindow::SegmentationOnCurrentImage()
3082 {
3083   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
3084
3085   vvSegmentationDialog segmentation;
3086   segmentation.SetImage(mSlicerManagers[index]->GetSlicer(0)->GetImage());
3087   segmentation.exec();
3088 }
3089 //------------------------------------------------------------------------------
3090
3091 void vvMainWindow::SurfaceViewerLaunch()
3092 {
3093   vvSurfaceViewerDialog surfaceViewer;
3094   surfaceViewer.exec();
3095 }
3096 //------------------------------------------------------------------------------
3097
3098
3099 //------------------------------------------------------------------------------
3100 int vvMainWindow::GetImageDuplicateFilenameNumber(std::string filename)
3101 {
3102   int number=0;
3103   for(unsigned int l=0; l<mSlicerManagers.size(); l++) {
3104     vvSlicerManager * v = mSlicerManagers[l];
3105     if (v->GetBaseFileName() ==
3106         vtksys::SystemTools::GetFilenameName(vtksys::SystemTools::GetFilenameWithoutLastExtension(filename))) {
3107       number = std::max(number, v->GetBaseFileNameNumber()+1);
3108     }
3109   }
3110   return number;
3111 }
3112 //------------------------------------------------------------------------------
3113
3114
3115 //------------------------------------------------------------------------------
3116 vvSlicerManager* vvMainWindow::AddImage(vvImage::Pointer image,std::string filename)
3117 {
3118   // Change filename if another image exist with the same name
3119   int number = GetImageDuplicateFilenameNumber(filename);
3120
3121   // Create new SliceManager
3122   vvSlicerManager* slicer_manager = new vvSlicerManager(4);
3123   slicer_manager->SetImage(image);//, IMAGE, number);
3124   //  filename = filename+"_"+clitk::toString(number);
3125   slicer_manager->SetFilename(filename, number);
3126   mSlicerManagers.push_back(slicer_manager);
3127
3128   //create an item in the tree with good settings
3129   QTreeWidgetItem *item = new QTreeWidgetItem();
3130   item->setData(0,Qt::UserRole,slicer_manager->GetFileName().c_str());//files[i].c_str());
3131   item->setData(1,Qt::UserRole,tr("image"));
3132   item->setData(COLUMN_IMAGE_NAME,Qt::DisplayRole,slicer_manager->GetFileName().c_str());//filename.c_str());
3133   qApp->processEvents();
3134
3135   for (int j = 1; j <= 4; j++) item->setData(j,Qt::CheckStateRole,1);
3136
3137   //Create the buttons for reload and close
3138   qApp->processEvents();
3139   QTreePushButton* cButton = new QTreePushButton;
3140   cButton->setItem(item);
3141   cButton->setColumn(COLUMN_CLOSE_IMAGE);
3142   cButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/exit.png")));
3143   connect(cButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
3144           this,SLOT(CloseImage(QTreeWidgetItem*, int)));
3145
3146   QTreePushButton* rButton = new QTreePushButton;
3147   rButton->setItem(item);
3148   rButton->setColumn(COLUMN_RELOAD_IMAGE);
3149   rButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/rotateright.png")));
3150   rButton->setEnabled(0);
3151   connect(rButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
3152           this,SLOT(ReloadImage(QTreeWidgetItem*, int)));
3153
3154   DataTree->addTopLevelItem(item);
3155   DataTree->setItemWidget(item, COLUMN_CLOSE_IMAGE, cButton);
3156   DataTree->setItemWidget(item, COLUMN_RELOAD_IMAGE, rButton);
3157
3158   //set the id of the image
3159   QString id = QDir::current().absoluteFilePath(slicer_manager->GetFileName().c_str()) + QString::number(mSlicerManagers.size()-1);
3160   item->setData(COLUMN_IMAGE_NAME,Qt::UserRole,id.toStdString().c_str());
3161   mSlicerManagers.back()->SetId(id.toStdString());
3162
3163   linkPanel->addImage(slicer_manager->GetFileName().c_str()// filename
3164                       , id.toStdString());
3165
3166   connect(mSlicerManagers.back(), SIGNAL(currentImageChanged(std::string)),
3167           this, SLOT(CurrentImageChanged(std::string)));
3168   connect(mSlicerManagers.back(), SIGNAL(currentPickedImageChanged(std::string)),
3169           this, SLOT(CurrentPickedImageChanged(std::string)));
3170   connect(mSlicerManagers.back(), SIGNAL(UpdatePosition(int, double, double, double, double, double, double, double)),
3171           this, SLOT(MousePositionChanged(int,double, double, double, double, double, double, double)));
3172   connect(mSlicerManagers.back(), SIGNAL(UpdateVector(int, double, double, double, double)),
3173           this, SLOT(VectorChanged(int,double,double,double, double)));
3174   connect(mSlicerManagers.back(), SIGNAL(UpdateOverlay(int, double, double)),
3175           this, SLOT(OverlayChanged(int,double,double)));
3176   connect(mSlicerManagers.back(), SIGNAL(UpdateFusion(int, double)),
3177           this, SLOT(FusionChanged(int,double)));
3178   connect(mSlicerManagers.back(), SIGNAL(WindowLevelChanged()),
3179           this,SLOT(WindowLevelChanged()));
3180   connect(mSlicerManagers.back(), SIGNAL(UpdateSlice(int,int)),
3181           this,SLOT(UpdateSlice(int,int)));
3182   connect(mSlicerManagers.back(), SIGNAL(UpdateTSlice(int, int)),
3183           this,SLOT(UpdateTSlice(int, int)));
3184   connect(mSlicerManagers.back(), SIGNAL(UpdateTSlice(int, int)),
3185           this,SLOT(ImageInfoChanged()));
3186   connect(mSlicerManagers.back(), SIGNAL(UpdateSliceRange(int,int,int,int,int)),
3187           this,SLOT(UpdateSliceRange(int,int,int,int,int)));
3188   connect(mSlicerManagers.back(), SIGNAL(UpdateLinkManager(std::string,int,double,double,double,int)),
3189           this,SLOT(UpdateLinkManager(std::string,int,double,double,double,int)));
3190   connect(mSlicerManagers.back(), SIGNAL(UpdateLinkedNavigation(std::string,vvSlicerManager*,vvSlicer*)),
3191           this,SLOT(UpdateLinkedNavigation(std::string,vvSlicerManager*,vvSlicer*)));
3192   connect(mSlicerManagers.back(), SIGNAL(ChangeImageWithIndexOffset(vvSlicerManager*,int,int)),
3193           this,SLOT(ChangeImageWithIndexOffset(vvSlicerManager*,int,int)));
3194   connect(mSlicerManagers.back(), SIGNAL(LandmarkAdded()),landmarksPanel,SLOT(AddPoint()));
3195   UpdateTree();
3196   qApp->processEvents();
3197   InitSlicers();
3198   ShowLastImage();
3199   InitDisplay();
3200   qApp->processEvents();
3201
3202   // End
3203   ImageInfoChanged();
3204   return slicer_manager;
3205 }
3206 //------------------------------------------------------------------------------
3207
3208
3209 //------------------------------------------------------------------------------
3210 void vvMainWindow::UpdateCurrentSlicer()
3211 {
3212   int index = -1;
3213   if (DataTree->selectedItems().size() > 0) {
3214     index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
3215   }
3216   mSlicerManagerCurrentIndex = index;
3217 }
3218 //------------------------------------------------------------------------------
3219