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