vv/vvMainWindow.cxx

   1 /*=========================================================================
   2   Program:   vv                     http://www.creatis.insa-lyon.fr/rio/vv
   3
   4   Authors belong to:
   5   - University of LYON              http://www.universite-lyon.fr/
   6   - Léon Bérard cancer center       http://www.centreleonberard.fr
   7   - CREATIS CNRS laboratory         http://www.creatis.insa-lyon.fr
   8
   9   This software is distributed WITHOUT ANY WARRANTY; without even
  10   the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
  11   PURPOSE.  See the copyright notices for more information.
  12
  13   It is distributed under dual licence
  14
  15   - BSD        See included LICENSE.txt file
  16   - CeCILL-B   http://www.cecill.info/licences/Licence_CeCILL-B_V1-en.html
  17 ===========================================================================**/
  18
  19 #include <algorithm>
  20 #include <QMessageBox>
  21 #include <QInputDialog>
  22 #include <QTimer>
  23 #include "QTreePushButton.h"
  24 #include <QUrl>
  25 #include <QSettings>
  26
  27 // VV include
  28 #include "vvMainWindow.h"
  29 #include "vvHelpDialog.h"
  30 #include "vvRegisterForm.h"
  31 #include "vvDocumentation.h"
  32 #include "vvProgressDialog.h"
  33 #include "vvQDicomSeriesSelector.h"
  34 #include "vvSlicerManager.h"
  35 #include "clitkImageCommon.h"
  36 #include "vvSlicer.h"
  37 #include "vvInteractorStyleNavigator.h"
  38 #include "vvImageWriter.h"
  39 #include "vvSegmentationDialog.h"
  40 #include "vvSurfaceViewerDialog.h"
  41 #include "vvDeformationDialog.h"
  42 #include "vvImageWarp.h"
  43 #include "vvUtils.h"
  44 #include "vvMidPosition.h"
  45 #include "vvMesh.h"
  46 #include "vvStructSelector.h"
  47 #include "vvMeshReader.h"
  48 #include "vvSaveState.h"
  49 #include "vvReadState.h"
  50 #include "clitkConfiguration.h"
  51
  52 // ITK include
  53 #include <itkImage.h>
  54 #include <itkImageFileReader.h>
  55 #include <itkByteSwapper.h>
  56 #include <itkCommand.h>
  57 #include <itkNumericSeriesFileNames.h>
  58
  59 // VTK include
  60 #include <vtkImageData.h>
  61 #include <vtkImageActor.h>
  62 #include <vtkCornerAnnotation.h>
  63 #include <vtkRenderWindow.h>
  64 #include <vtkRenderWindowInteractor.h>
  65 #include <vtkRenderer.h>
  66 #include <vtkRendererCollection.h>
  67 #include <vtkWindowToImageFilter.h>
  68 #include <vtkBMPWriter.h>
  69 #include <vtkTIFFWriter.h>
  70 #include <vtkPNMWriter.h>
  71 #include <vtkPNGWriter.h>
  72 #include <vtkJPEGWriter.h>
  73 #include <vtkGenericMovieWriter.h>
  74 #ifdef CLITK_EXPERIMENTAL
  75 #  include <vvAnimatedGIFWriter.h>
  76 #endif
  77 #ifdef VTK_USE_VIDEO_FOR_WINDOWS
  78 #  include <vtkAVIWriter.h>
  79 #endif
  80 #ifdef VTK_USE_FFMPEG_ENCODER
  81 #  include <vtkFFMPEGWriter.h>
  82 #endif
  83 #ifdef VTK_USE_MPEG2_ENCODER
  84 #  include <vtkMPEG2Writer.h>
  85 #endif
  86 #include <vtkMatrix4x4.h>
  87 #include <vtkTransform.h>
  88
  89 // Standard includes
  90 #include <iostream>
  91 #include <sstream>
  92 #include <iomanip>
  93
  94 #define COLUMN_TREE 0
  95 #define COLUMN_UL_VIEW 1
  96 #define COLUMN_UR_VIEW 2
  97 #define COLUMN_DL_VIEW 3
  98 #define COLUMN_DR_VIEW 4
  99 #define COLUMN_CLOSE_IMAGE 5
 100 #define COLUMN_RELOAD_IMAGE 6
 101 #define COLUMN_IMAGE_NAME 7
 102
 103 #ifdef CLITK_PRIVATE_FEATURES
 104 #define EXTENSIONS "Images ( *.bmp *.png *.jpeg *.jpg *.tif *.mhd *.mha *.hdr *.vox *.his *.xdr *.SCAN *.nii *.nrrd *.nhdr *.refscan *.nii.gz *.usf)"
 105 #else
 106 #define EXTENSIONS "Images ( *.bmp *.png *.jpeg *.jpg *.tif *.mhd *.mha *.hdr *.vox *.his *.xdr *.SCAN *.nii *.nrrd *.nhdr *.refscan *.nii.gz)"
 107 #endif
 108
 109
 110 /*Data Tree values
 111   0,Qt::UserRole full filename
 112   1,Qt::CheckStateRole checkbutton UL View
 113   1,Qt::UserRole overlay, fusion or vector
 114   2,Qt::CheckStateRole checkbutton UR View
 115   3,Qt::CheckStateRole checkbutton DL View
 116   4,Qt::CheckStateRole checkbutton DR View
 117   5,0  short filename
 118   5,Qt::UserRole mSlicerManager id*/
 119
 120 //------------------------------------------------------------------------------
 121 vvMainWindow::vvMainWindow():vvMainWindowBase()
 122 {
 123   setupUi(this); // this sets up the GUI
 124
 125   mInputPathName = "";
 126   mMenuTools = menuTools;
 127   //  mMenuSegmentation = menuSegmentation;
 128   mContextMenu = &contextMenu;
 129   mMenuExperimentalTools = menuExperimental;
 130   mMainWidget = this;
 131   mCurrentTime = -1;
 132   mCurrentSelectedImageId = "";
 133   mCurrentPickedImageId = "";
 134   mCurrentPickedImageIndex = 0;
 135
 136   //Init the contextMenu
 137   this->setContextMenuPolicy(Qt::CustomContextMenu);
 138   contextActions.resize(0);
 139   QAction* actionOpen_new_image = contextMenu.addAction(QIcon(QString::fromUtf8(":/common/icons/fileopen.png")),
 140                                   tr("O&pen new Image"));
 141   actionOpen_new_image->setShortcut(QKeySequence(tr("Ctrl+O")));
 142   connect(actionOpen_new_image,SIGNAL(triggered()),this,SLOT(OpenImages()));
 143   contextActions.push_back(actionOpen_new_image);
 144   contextMenu.addSeparator();
 145
 146   QAction* actionClose_Image = contextMenu.addAction(QIcon(QString::fromUtf8(":/common/icons/exit.png")),
 147                                tr("Close Current Image"));
 148   connect(actionClose_Image,SIGNAL(triggered()),this,SLOT(CloseImage()));
 149   contextActions.push_back(actionClose_Image);
 150
 151   QAction* actionReload_image = contextMenu.addAction(QIcon(QString::fromUtf8(":/common/icons/rotateright.png")),
 152                                 tr("Reload Current Image"));
 153   connect(actionReload_image,SIGNAL(triggered()),this,SLOT(ReloadImage()));
 154   contextActions.push_back(actionReload_image);
 155
 156   QAction* actionSave_image = contextMenu.addAction(QIcon(QString::fromUtf8(":/common/icons/filesave.png")),
 157                               tr("Save Current Image"));
 158   connect(actionSave_image,SIGNAL(triggered()),this,SLOT(SaveAs()));
 159   contextActions.push_back(actionSave_image);
 160
 161   QAction* actionSave_state = contextMenu.addAction(QIcon(QString::fromUtf8(":/common/icons/filesave.png")),
 162                               tr("Save Current State"));
 163   connect(actionSave_state,SIGNAL(triggered()),this,SLOT(SaveCurrentState()));
 164   contextActions.push_back(actionSave_state);
 165
 166   QAction* actionRead_state = contextMenu.addAction(QIcon(QString::fromUtf8(":/common/icons/filesave.png")),
 167                               tr("Read Saved State"));
 168   connect(actionRead_state,SIGNAL(triggered()),this,SLOT(ReadSavedState()));
 169   contextActions.push_back(actionRead_state);
 170
 171   contextMenu.addSeparator();
 172
 173   contextMenu.addAction(actionAdd_VF_to_current_Image);
 174   contextActions.push_back(actionAdd_VF_to_current_Image);
 175
 176   //QAction* actionAdd_Overlay_to_current_Image = menuOverlay->addAction(QIcon(QString::fromUtf8(":/common/icons/GPSup.png")),
 177   //    tr("Add overlay image to current image"));
 178   contextMenu.addAction(actionAdd_overlay_image_to_current_image);
 179   contextActions.push_back(actionAdd_overlay_image_to_current_image);
 180
 181   contextMenu.addAction(actionAdd_fusion_image);
 182   contextActions.push_back(actionAdd_fusion_image);
 183
 184   contextMenu.addSeparator();
 185   QAction* actionResetMatrix = contextMenu.addAction(QIcon(QString::fromUtf8(":/common/icons/identity.png")),
 186                                                       tr("Reset transformation to identity"));
 187   connect(actionResetMatrix, SIGNAL(triggered()), this,SLOT(ResetTransformationToIdentity()));
 188
 189   // TRIAL DS
 190   /*
 191   QMenu * m = new QMenu(menubar);
 192   m->setTitle("TOTO");
 193   //  m->setObjectName(QString::fromUtf8("TOTOTO"));
 194   contextMenu.addMenu(m);
 195   QAction * a = m->addAction(QIcon(QString::fromUtf8(":/common/icons/GPSup.png")),
 196                      tr("BIDON"));
 197   QAction * b = m->addAction(QIcon(QString::fromUtf8(":/common/icons/GPSup.png")),
 198                      tr("BIDON2"));
 199   m->addAction(a);
 200   m->addAction(b);
 201   connect(a,SIGNAL(triggered()),this,SLOT(AddFusionImage()));
 202   */
 203
 204   //init the DataTree
 205   mSlicerManagers.resize(0);
 206
 207   QStringList header;
 208   header.append("");
 209   header.append("TL");
 210   header.append("TR");
 211   header.append("BL");
 212   header.append("BR");
 213   header.append("");
 214   header.append("");
 215   header.append("Name");
 216
 217   DataTree->setHeaderLabels(header);
 218   DataTree->resizeColumnToContents(COLUMN_TREE);
 219   DataTree->resizeColumnToContents(COLUMN_UL_VIEW);
 220   DataTree->resizeColumnToContents(COLUMN_UR_VIEW);
 221   DataTree->resizeColumnToContents(COLUMN_DL_VIEW);
 222   DataTree->resizeColumnToContents(COLUMN_DR_VIEW);
 223   DataTree->resizeColumnToContents(COLUMN_CLOSE_IMAGE);
 224   DataTree->resizeColumnToContents(COLUMN_RELOAD_IMAGE);
 225   DataTree->resizeColumnToContents(COLUMN_IMAGE_NAME);
 226
 227   viewMode = 1;
 228   documentation = new vvDocumentation();
 229   help_dialog = new vvHelpDialog();
 230   dicomSeriesSelector = new vvDicomSeriesSelector();
 231
 232   inverseButton->setEnabled(0);
 233   actionAdd_overlay_image_to_current_image->setEnabled(0);
 234   actionSave_As->setEnabled(0);
 235   actionAdd_VF_to_current_Image->setEnabled(0);
 236   actionAdd_fusion_image->setEnabled(0);
 237
 238   //init the sliders
 239   verticalSliders.push_back(NOVerticalSlider);
 240   verticalSliders.push_back(NEVerticalSlider);
 241   verticalSliders.push_back(SOVerticalSlider);
 242   verticalSliders.push_back(SEVerticalSlider);
 243
 244   for (int i =0; i < 4; i++)
 245     verticalSliders[i]->hide();
 246
 247   horizontalSliders.push_back(NOHorizontalSlider);
 248   horizontalSliders.push_back(NEHorizontalSlider);
 249   horizontalSliders.push_back(SOHorizontalSlider);
 250   horizontalSliders.push_back(SEHorizontalSlider);
 251
 252   for (int i =0; i < 4; i++)
 253     horizontalSliders[i]->hide();
 254
 255
 256   connect(NOVerticalSlider,SIGNAL(valueChanged(int)),this,SLOT(NOVerticalSliderChanged()));
 257   connect(NEVerticalSlider,SIGNAL(valueChanged(int)),this,SLOT(NEVerticalSliderChanged()));
 258   connect(SOVerticalSlider,SIGNAL(valueChanged(int)),this,SLOT(SOVerticalSliderChanged()));
 259   connect(SEVerticalSlider,SIGNAL(valueChanged(int)),this,SLOT(SEVerticalSliderChanged()));
 260
 261   connect(NOHorizontalSlider,SIGNAL(valueChanged(int)),this,SLOT(NOHorizontalSliderMoved()));
 262   connect(NEHorizontalSlider,SIGNAL(valueChanged(int)),this,SLOT(NEHorizontalSliderMoved()));
 263   connect(SOHorizontalSlider,SIGNAL(valueChanged(int)),this,SLOT(SOHorizontalSliderMoved()));
 264   connect(SEHorizontalSlider,SIGNAL(valueChanged(int)),this,SLOT(SEHorizontalSliderMoved()));
 265
 266   //connect everything
 267   connect(actionCompute_mid_position_image,SIGNAL(triggered()),this,SLOT(ComputeMidPosition()));
 268   connect(actionDeformable_Registration,SIGNAL(triggered()),this,SLOT(ComputeDeformableRegistration()));
 269   connect(actionWarp_image_with_vector_field,SIGNAL(triggered()),this,SLOT(WarpImage()));
 270   connect(actionLoad_images,SIGNAL(triggered()),this,SLOT(OpenImages()));
 271   connect(actionOpen_Dicom,SIGNAL(triggered()),this,SLOT(OpenDicom()));
 272   connect(actionOpen_Dicom_Struct,SIGNAL(triggered()),this,SLOT(OpenDCStructContour()));
 273   connect(actionOpen_VTK_contour,SIGNAL(triggered()),this,SLOT(OpenVTKContour()));
 274   connect(actionOpen_Multiple_Images_As_One,SIGNAL(triggered()),this,SLOT(MergeImages()));
 275   connect(actionSlice_Image_As_Multiple_Images,SIGNAL(triggered()),this,SLOT(SliceImages()));
 276   connect(actionOpen_Image_With_Time,SIGNAL(triggered()),this,SLOT(OpenImageWithTime()));
 277   connect(actionMerge_images_as_n_dim_t, SIGNAL(triggered()), this, SLOT(MergeImagesWithTime()));
 278   connect(actionSave_As,SIGNAL(triggered()),this,SLOT(SaveAs()));
 279   connect(actionSave_current_state,SIGNAL(triggered()),this,SLOT(SaveCurrentState()));
 280   connect(actionRead_saved_state,SIGNAL(triggered()),this,SLOT(ReadSavedState()));
 281   connect(actionExit,SIGNAL(triggered()),this,SLOT(close()));
 282   connect(actionAdd_VF_to_current_Image,SIGNAL(triggered()),this,SLOT(OpenField()));
 283   connect(actionAdd_fusion_image,SIGNAL(triggered()),this,SLOT(SelectFusionImage()));
 284   connect(actionAdd_overlay_image_to_current_image,SIGNAL(triggered()), this,SLOT(SelectOverlayImage()));  connect(actionNavigation_Help,SIGNAL(triggered()),this,SLOT(ShowHelpDialog()));
 285   connect(actionDocumentation,SIGNAL(triggered()),this,SLOT(ShowDocumentation()));
 286   connect(actionRegister_vv,SIGNAL(triggered()),this,SLOT(PopupRegisterForm()));
 287
 288   ///////////////////////////////////////////////
 289   connect(actionSegmentation,SIGNAL(triggered()),this,SLOT(SegmentationOnCurrentImage()));
 290   connect(actionSurface_Viewer,SIGNAL(triggered()),this,SLOT(SurfaceViewerLaunch()));
 291   ///////////////////////////////////////////////
 292
 293   actionNorth_East_Window->setEnabled(0);
 294   actionNorth_West_Window->setEnabled(0);
 295   actionSouth_East_Window->setEnabled(0);
 296   actionSouth_West_Window->setEnabled(0);
 297
 298   connect(actionNorth_East_Window,SIGNAL(triggered()),this,SLOT(SaveNEScreenshot()));
 299   connect(actionNorth_West_Window,SIGNAL(triggered()),this,SLOT(SaveNOScreenshot()));
 300   connect(actionSouth_East_Window,SIGNAL(triggered()),this,SLOT(SaveSEScreenshot()));
 301   connect(actionSouth_West_Window,SIGNAL(triggered()),this,SLOT(SaveSOScreenshot()));
 302   connect(actionSave_all_slices,SIGNAL(triggered()),this,SLOT(SaveScreenshotAllSlices()));
 303
 304   connect(DataTree,SIGNAL(itemSelectionChanged()),this,SLOT(ImageInfoChanged()));
 305   connect(DataTree,SIGNAL(itemClicked(QTreeWidgetItem*, int)),this,
 306           SLOT(DisplayChanged(QTreeWidgetItem*, int)));
 307
 308   connect(viewButton,SIGNAL(clicked()),this, SLOT(ChangeViewMode()) );
 309   connect(windowSpinBox,SIGNAL(editingFinished()),this,SLOT(WindowLevelEdited()));
 310   connect(levelSpinBox,SIGNAL(editingFinished()),this,SLOT(WindowLevelEdited()));
 311   connect(colorMapComboBox,SIGNAL(currentIndexChanged(int)),this,SLOT(UpdateColorMap()));
 312   connect(presetComboBox,SIGNAL(currentIndexChanged(int)),this,SLOT(UpdateWindowLevel()));
 313   connect(slicingPresetComboBox, SIGNAL(currentIndexChanged(int)),this,SLOT(UpdateSlicingPreset()));
 314   connect(inverseButton,SIGNAL(clicked()),this,SLOT(SwitchWindowLevel()));
 315   connect(applyWindowLevelToAllButton,SIGNAL(clicked()),this,SLOT(ApplyWindowLevelToAllImages()));
 316
 317   connect(this,SIGNAL(customContextMenuRequested(QPoint)),this,SLOT(ShowContextMenu(QPoint)));
 318
 319   connect(linkPanel,SIGNAL(addLink(QString,QString,bool)),this,SLOT(AddLink(QString,QString,bool)));
 320   connect(linkPanel,SIGNAL(removeLink(QString,QString)),this,SLOT(RemoveLink(QString,QString)));
 321   connect(overlayPanel,SIGNAL(VFPropertyUpdated(int,int,int,int,double,double,double)),this,SLOT(SetVFProperty(int,int,int,int,double,double,double)));
 322   connect(overlayPanel,SIGNAL(OverlayPropertyUpdated(int,int,double,double)),
 323           this,SLOT(SetOverlayProperty(int,int,double,double)));
 324   connect(overlayPanel,SIGNAL(FusionPropertyUpdated(int,int,int,double,double, bool)),
 325           this,SLOT(SetFusionProperty(int,int,int,double,double, bool)));
 326   connect(landmarksPanel,SIGNAL(UpdateRenderWindows()),this,SLOT(UpdateRenderWindows()));
 327
 328   playMode = 0;//pause
 329   mFrameRate = 10;
 330   playButton->setEnabled(0);
 331   frameRateLabel->setEnabled(0);
 332   frameRateSpinBox->setEnabled(0);
 333   connect(playButton, SIGNAL(clicked()),this,SLOT(PlayPause()));
 334   connect(frameRateSpinBox, SIGNAL(valueChanged(int)),this,SLOT(ChangeFrameRate(int)));
 335
 336   goToCursorPushButton->setEnabled(0);
 337   connect(goToCursorPushButton, SIGNAL(clicked()),this,SLOT(GoToCursor()));
 338
 339   NOViewWidget->hide();
 340   NEViewWidget->hide();
 341   SOViewWidget->hide();
 342   SEViewWidget->hide();
 343
 344   //Recently opened files
 345   std::list<std::string> recent_files = GetRecentlyOpenedImages();
 346   recentlyOpenedFilesMenu=NULL;
 347   if ( !recent_files.empty() ) {
 348     createRecentlyOpenedFilesMenu();
 349     updateRecentlyOpenedFilesMenu(recent_files);
 350   }
 351
 352   // Adding all new tools (insertion in the menu)
 353   vvToolManager::GetInstance()->InsertToolsInMenu(this);
 354   vvToolManager::GetInstance()->EnableToolsInMenu(this, false);
 355
 356   if (!CLITK_EXPERIMENTAL)
 357     menuExperimental->menuAction()->setVisible(false);
 358
 359
 360   QTimer * timerMemory = new QTimer(this);
 361   //timerMemory->setInterval(5);
 362   connect(timerMemory, SIGNAL(timeout()), this, SLOT(UpdateMemoryUsage()));
 363   timerMemory->start(2000);
 364 }
 365 //------------------------------------------------------------------------------
 366 void vvMainWindow::show()
 367 {
 368   vvMainWindowBase::show();
 369   PopupRegisterForm(true);
 370 }
 371 //------------------------------------------------------------------------------
 372 void vvMainWindow::UpdateMemoryUsage()
 373 {
 374   //  clitk::PrintMemory(true);
 375   if (clitk::GetMemoryUsageInMb() == 0) infoPanel->setMemoryInMb("NA");
 376   else infoPanel->setMemoryInMb(QString::number(clitk::GetMemoryUsageInMb())+" MiB");
 377 }
 378 //------------------------------------------------------------------------------
 379
 380
 381 //------------------------------------------------------------------------------
 382 void vvMainWindow::createRecentlyOpenedFilesMenu()
 383 {
 384   recentlyOpenedFilesMenu = new QMenu("Recently opened files...");
 385   recentlyOpenedFilesMenu->setIcon(QIcon(QString::fromUtf8(":/common/icons/open.png")));
 386   menuFile->insertMenu(actionOpen_Image_With_Time,recentlyOpenedFilesMenu);
 387   menuFile->insertSeparator(actionOpen_Image_With_Time);
 388 }
 389 //------------------------------------------------------------------------------
 390
 391
 392 //------------------------------------------------------------------------------
 393
 394 void vvMainWindow::updateRecentlyOpenedFilesMenu(const std::list<std::string> &recent_files)
 395 {
 396   if(recentlyOpenedFilesMenu==NULL) {
 397     createRecentlyOpenedFilesMenu();
 398   } else {
 399     recentlyOpenedFilesMenu->clear();
 400   }
 401   for (std::list<std::string>::const_iterator i = recent_files.begin(); i!=recent_files.end(); i++) {
 402     QAction* current=new QAction(QIcon(QString::fromUtf8(":/common/icons/open.png")), i->c_str(),this);
 403     recentlyOpenedFilesMenu->addAction(current);
 404     connect(current,SIGNAL(triggered()),this,SLOT(OpenRecentImage()));
 405   }
 406 }
 407 //------------------------------------------------------------------------------
 408
 409
 410 //------------------------------------------------------------------------------
 411 void vvMainWindow::ComputeMidPosition()
 412 {
 413   bool ok;
 414   int index=GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
 415   int ref = QInputDialog::getInteger(this,"Chose reference phase","Reference phase",0,0,\
 416                                      mSlicerManagers[index]->GetImage()->GetVTKImages().size()-1,1,&ok);
 417   if (ok) {
 418     vvMidPosition midp;
 419     midp.slicer_manager = mSlicerManagers[index];
 420     midp.reference_image_index = ref;
 421     QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
 422     midp.Update();
 423     if (midp.error)
 424       QMessageBox::warning(this, "Error computing midposition image",midp.error_message.c_str());
 425     else {
 426       QFileInfo info(midp.slicer_manager->GetFileName().c_str());
 427       AddImage(midp.output,info.path().toStdString()+"/"+info.completeBaseName().toStdString()+"_midposition.mhd");
 428     }
 429     QApplication::restoreOverrideCursor();
 430   }
 431 }
 432 //------------------------------------------------------------------------------
 433
 434
 435 //------------------------------------------------------------------------------
 436 void vvMainWindow::AddContour(int image_index, vvMesh::Pointer contour, bool propagation)
 437 {
 438   QTreeWidgetItem *item = new QTreeWidgetItem();
 439   item->setData(0,Qt::UserRole,"filename.vtk");
 440   item->setData(1,Qt::UserRole,tr("contour"));
 441   QBrush brush;
 442   brush.setColor(QColor(contour->r*255,contour->g*255,contour->b*255));
 443   brush.setStyle(Qt::SolidPattern);
 444   item->setData(COLUMN_IMAGE_NAME,Qt::BackgroundRole,brush);
 445   item->setData(COLUMN_IMAGE_NAME,Qt::DisplayRole,contour->structure_name.c_str());
 446
 447   for (int j = 1; j <= 4; j++)
 448     item->setData(j,Qt::CheckStateRole,DataTree->topLevelItem(image_index)->data(j,Qt::CheckStateRole));
 449
 450   QTreePushButton* cButton = new QTreePushButton;
 451   cButton->setItem(item);
 452   cButton->setColumn(COLUMN_CLOSE_IMAGE);
 453   cButton->setToolTip(tr("close image"));
 454   cButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/exit.png")));
 455   connect(cButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
 456           this,SLOT(CloseImage(QTreeWidgetItem*, int)));
 457
 458   QTreePushButton* rButton = new QTreePushButton;
 459   rButton->setItem(item);
 460   rButton->setColumn(COLUMN_RELOAD_IMAGE);
 461   rButton->setToolTip(tr("reload image"));
 462   rButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/rotateright.png")));
 463   rButton->setEnabled(false);
 464   //Not implemented
 465   //connect(rButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
 466   //this,SLOT(ReloadImage(QTreeWidgetItem*, int)));
 467
 468   DataTree->topLevelItem(image_index)->setExpanded(1);
 469   DataTree->topLevelItem(image_index)->addChild(item);
 470   DataTree->setItemWidget(item, COLUMN_CLOSE_IMAGE, cButton);
 471   DataTree->setItemWidget(item, COLUMN_RELOAD_IMAGE, rButton);
 472   QString id = DataTree->topLevelItem(image_index)->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString();
 473   item->setData(COLUMN_IMAGE_NAME,Qt::UserRole,id.toStdString().c_str());
 474
 475   UpdateTree();
 476   mSlicerManagers[image_index]->AddContour(contour,propagation);
 477   mSlicerManagers[image_index]->Render();
 478 }
 479 //------------------------------------------------------------------------------
 480
 481
 482 //------------------------------------------------------------------------------
 483 void vvMainWindow::OpenVTKContour()
 484 {
 485   if (mSlicerManagers.size() > 0) {
 486     QString Extensions = "Images ( *.vtk *.obj)";
 487     Extensions += ";;All Files (*)";
 488     QString file = QFileDialog::getOpenFileName(this,tr("Open vtkPolyData"),mInputPathName,Extensions);
 489     if (file.isNull())
 490       return;
 491     QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
 492     int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
 493     vvMeshReader reader;
 494     reader.SetImage(mSlicerManagers[index]->GetImage());
 495     reader.SetModeToVTK();
 496     reader.SetFilename(file.toStdString());
 497     reader.Update();
 498     AddContour(index,reader.GetOutput()[0],false);
 499     QApplication::restoreOverrideCursor();
 500   }
 501 }
 502 //------------------------------------------------------------------------------
 503
 504
 505 //------------------------------------------------------------------------------
 506 void vvMainWindow::AddDCStructContour(int index, QString file)
 507 {
 508     vvMeshReader reader;
 509     reader.SetFilename(file.toStdString());
 510     vvStructSelector selector;
 511     selector.SetStructures(reader.GetROINames());
 512     if (!mSlicerManagers[index]->GetVF().IsNull())
 513       selector.EnablePropagationCheckBox();
 514     if (selector.exec()) {
 515       QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
 516       reader.SetSelectedItems(selector.getSelectedItems());
 517       reader.SetImage(mSlicerManagers[index]->GetImage());
 518       if (selector.PropagationEnabled())
 519         reader.SetPropagationVF(mSlicerManagers[index]->GetVF());
 520       reader.Update();
 521       std::vector<vvMesh::Pointer> contours=reader.GetOutput();
 522       for (std::vector<vvMesh::Pointer>::iterator i=contours.begin();
 523            i!=contours.end(); i++)
 524         AddContour(index,*i,selector.PropagationEnabled());
 525       QApplication::restoreOverrideCursor();
 526     }
 527 }
 528
 529 //------------------------------------------------------------------------------
 530 void vvMainWindow::OpenDCStructContour()
 531 {
 532   if (mSlicerManagers.size() > 0) {
 533     QString Extensions = "Dicom Files ( *.dcm RS*)";
 534     Extensions += ";;All Files (*)";
 535     QString file = QFileDialog::getOpenFileName(this,tr("Merge Images"),mInputPathName,Extensions);
 536     if (file.isNull())
 537       return;
 538     int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
 539     AddDCStructContour(index, file);
 540   }
 541 }
 542 //------------------------------------------------------------------------------
 543
 544
 545 //------------------------------------------------------------------------------
 546 void vvMainWindow::ComputeDeformableRegistration()
 547 {
 548   if (mSlicerManagers.size() > 0) {
 549     int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
 550     vvDeformationDialog dialog(index,mSlicerManagers);
 551     if (dialog.exec()) {
 552       std::string base_name=itksys::SystemTools::GetFilenameWithoutExtension(mSlicerManagers[dialog.GetInputFileIndex()]->GetFileName());
 553       AddField(dialog.GetOutput(),dialog.getFieldFile(),dialog.GetInputFileIndex());
 554       WarpImage(dialog.GetSelectedSlicer(),dialog.GetReferenceFrameIndex());
 555     } else
 556       std::cout << "Error or user cancellation while computing deformation field..." << std::endl;
 557   } else QMessageBox::information(this, "Need to open image","You must open an image first.");
 558 }
 559 //------------------------------------------------------------------------------
 560
 561
 562 //------------------------------------------------------------------------------
 563 void vvMainWindow::WarpImage()
 564 {
 565   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
 566   if (!mSlicerManagers[index]->GetVF().IsNull()) {
 567     bool ok;
 568     int ref = QInputDialog::getInteger(this,"Chose reference phase","Reference phase",0,0,\
 569                                        mSlicerManagers[index]->GetImage()->GetVTKImages().size()-1,1,&ok);
 570     if (ok) {
 571       WarpImage(mSlicerManagers[index],ref);
 572     }
 573   } else
 574     QMessageBox::warning(this,tr("No vector field"),tr("Sorry, can't warp without a vector field"));
 575 }
 576 //------------------------------------------------------------------------------
 577
 578
 579 //------------------------------------------------------------------------------
 580 void vvMainWindow::WarpImage(vvSlicerManager* selected_slicer,int reference_phase)
 581 {
 582   if (!selected_slicer->GetVF().IsNull()) {
 583     QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
 584     QFileInfo info(selected_slicer->GetFileName().c_str());
 585     vvImageWarp warp(selected_slicer->GetImage(),selected_slicer->GetVF(),
 586                      reference_phase,this);
 587     if (warp.ComputeWarpedImage()) {
 588       AddImage(warp.GetWarpedImage(),info.path().toStdString()+"/"+info.completeBaseName().toStdString()+"_warped.mhd");
 589       AddImage(warp.GetDiffImage()  ,info.path().toStdString()+"/"+info.completeBaseName().toStdString()+"_diff.mhd");
 590       AddImage(warp.GetJacobianImage()  ,info.path().toStdString()+"/"+info.completeBaseName().toStdString()+"_jacobian.mhd");
 591       QApplication::restoreOverrideCursor();
 592     } else {
 593       QApplication::restoreOverrideCursor();
 594       QMessageBox::warning(this,tr("Different spacings"),tr("The vector field and image spacings must be the same in order to warp."));
 595     }
 596   } else
 597     QMessageBox::warning(this,tr("No vector field"),tr("Sorry, can't warp without a vector field."));
 598 }
 599 //------------------------------------------------------------------------------
 600
 601
 602 //------------------------------------------------------------------------------
 603 vvMainWindow::~vvMainWindow()
 604 {
 605   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
 606     if (mSlicerManagers[i] != NULL)
 607       delete mSlicerManagers[i];
 608   }
 609 }
 610 //------------------------------------------------------------------------------
 611
 612 //------------------------------------------------------------------------------
 613 QTabWidget * vvMainWindow::GetTab()
 614 {
 615   return tabWidget;
 616 }
 617 //------------------------------------------------------------------------------
 618
 619
 620 //------------------------------------------------------------------------------
 621 void vvMainWindow::MergeImages()
 622 {
 623   QString Extensions = EXTENSIONS;
 624   Extensions += ";;All Files (*)";
 625   QStringList files = QFileDialog::getOpenFileNames(this,tr("Merge Images"),mInputPathName,Extensions);
 626   if (files.isEmpty())
 627     return;
 628   mInputPathName = itksys::SystemTools::GetFilenamePath(files[0].toStdString()).c_str();
 629   std::vector<std::string> vector;
 630
 631   unsigned int currentDim = 0;
 632   std::vector<double> currentSpacing;
 633   std::vector<int> currentSize;
 634   std::vector<double> currentOrigin;
 635
 636   for (int i = 0; i < files.size(); i++) {
 637     itk::ImageIOBase::Pointer reader = itk::ImageIOFactory::CreateImageIO(
 638                                          files[i].toStdString().c_str(), itk::ImageIOFactory::ReadMode);
 639     reader->SetFileName(files[i].toStdString().c_str());
 640     reader->ReadImageInformation();
 641     if (reader)        {
 642       //NOViewWidget->hide();
 643       //NEViewWidget->hide();
 644       //SOViewWidget->hide();
 645       //SEViewWidget->hide();
 646       if (i == 0)
 647         currentDim = reader->GetNumberOfDimensions();
 648       bool IsOk = true;
 649       for (unsigned int j = 0; j < currentDim; j++) {
 650         if (i == 0) {
 651           if (j == 0) {
 652             currentSpacing.resize(currentDim);
 653             currentSize.resize(currentDim);
 654             currentOrigin.resize(currentDim);
 655           }
 656           currentOrigin[j] = reader->GetOrigin(j);
 657           currentSpacing[j] = reader->GetSpacing(j);
 658           currentSize[j] = reader->GetDimensions(j);
 659         } else if (currentDim != reader->GetNumberOfDimensions()
 660                    || currentSpacing[j] != reader->GetSpacing(j)
 661                    || currentSize[j] != (int)reader->GetDimensions(j)
 662                    || currentOrigin[j] != reader->GetOrigin(j)) {
 663           QString error = "Cannot read file (too different from others ";
 664           error += files[i].toStdString().c_str();
 665           QMessageBox::information(this,tr("Reading problem"),error);
 666           IsOk = false;
 667           break;
 668         }
 669       }
 670       if (IsOk)
 671         vector.push_back(files[i].toStdString());
 672     }
 673   }
 674   if (vector.size() > 0)
 675     LoadImages(vector, vvImageReader::MERGED);
 676 }
 677 //------------------------------------------------------------------------------
 678
 679 //------------------------------------------------------------------------------
 680 void vvMainWindow::SliceImages()
 681 {
 682   QString Extensions = EXTENSIONS;
 683   Extensions += ";;All Files (*)";
 684
 685   QStringList files = QFileDialog::getOpenFileNames(this,tr("Slice Images"),mInputPathName,Extensions);
 686   if (files.isEmpty())
 687     return;
 688   mInputPathName = itksys::SystemTools::GetFilenamePath(files[0].toStdString()).c_str();
 689   std::vector<std::string> vector;
 690   for (int i = 0; i < files.size(); i++)
 691     vector.push_back(files[i].toStdString());
 692   LoadImages(vector, vvImageReader::SLICED);
 693 }
 694 //------------------------------------------------------------------------------
 695
 696 //------------------------------------------------------------------------------
 697 void vvMainWindow::MergeImagesWithTime()
 698 {
 699   QString Extensions = EXTENSIONS;
 700   Extensions += ";;All Files (*)";
 701   QStringList files = QFileDialog::getOpenFileNames(this,tr("Merge Images With Time"),mInputPathName,Extensions);
 702   if (files.isEmpty())
 703     return;
 704   mInputPathName = itksys::SystemTools::GetFilenamePath(files[0].toStdString()).c_str();
 705   std::vector<std::string> vector;
 706
 707   unsigned int currentDim = 0;
 708   std::vector<double> currentSpacing;
 709   std::vector<int> currentSize;
 710   std::vector<double> currentOrigin;
 711
 712   for (int i = 0; i < files.size(); i++) {
 713     itk::ImageIOBase::Pointer reader = itk::ImageIOFactory::CreateImageIO(
 714                                          files[i].toStdString().c_str(), itk::ImageIOFactory::ReadMode);
 715     if (reader) {
 716       reader->SetFileName(files[i].toStdString().c_str());
 717       reader->ReadImageInformation();
 718       if (i == 0)
 719         currentDim = reader->GetNumberOfDimensions();
 720       bool IsOk = true;
 721       for (unsigned int j = 0; j < currentDim; j++) {
 722         if (i == 0) {
 723           if (j == 0) {
 724             currentSpacing.resize(currentDim);
 725             currentSize.resize(currentDim);
 726             currentOrigin.resize(currentDim);
 727           }
 728           currentOrigin[j] = reader->GetOrigin(j);
 729           currentSpacing[j] = reader->GetSpacing(j);
 730           currentSize[j] = reader->GetDimensions(j);
 731         } else if (currentDim != reader->GetNumberOfDimensions()
 732                    || currentSpacing[j] != reader->GetSpacing(j)
 733                    || currentSize[j] != (int)reader->GetDimensions(j)
 734                    || currentOrigin[j] != reader->GetOrigin(j)) {
 735           QString error = "Cannot read file (too different from others ";
 736           error += files[i].toStdString().c_str();
 737           QMessageBox::information(this,tr("Reading problem"),error);
 738           IsOk = false;
 739           break;
 740         }
 741       }
 742       if (IsOk)
 743         vector.push_back(files[i].toStdString());
 744     } else {
 745       QString error = "Cannot read file info for ";
 746       error += files[i].toStdString().c_str();
 747       error += "\n";
 748       error += "Maybe you're trying to open an image in an unsupported format?\n";
 749       QMessageBox::information(this,tr("Reading problem"),error);
 750     }
 751   }
 752   sort(vector.begin(),vector.end());
 753   if (vector.size() > 1)
 754     LoadImages(vector, vvImageReader::MERGEDWITHTIME);
 755   else
 756     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.");
 757 }
 758 //------------------------------------------------------------------------------
 759
 760
 761 //------------------------------------------------------------------------------
 762 void vvMainWindow::OpenDicom()
 763 {
 764   std::vector<std::string> files;
 765
 766   std::cout << "dicomSeriesSelector " << std::endl;
 767   if (dicomSeriesSelector->exec() == QDialog::Accepted) {
 768     files = *(dicomSeriesSelector->GetFilenames());
 769     LoadImages(files, vvImageReader::DICOM);
 770   }
 771 }
 772 //------------------------------------------------------------------------------
 773
 774 //------------------------------------------------------------------------------
 775 void vvMainWindow::OpenImages()
 776 {
 777   QString Extensions = EXTENSIONS;
 778   Extensions += ";;All Files (*)";
 779
 780   QStringList files = QFileDialog::getOpenFileNames(this,tr("Load Images"),mInputPathName,Extensions);
 781   if (files.isEmpty())
 782     return;
 783   mInputPathName = itksys::SystemTools::GetFilenamePath(files[0].toStdString()).c_str();
 784   std::vector<std::string> vector;
 785   for (int i = 0; i < files.size(); i++)
 786     vector.push_back(files[i].toStdString());
 787   LoadImages(vector, vvImageReader::IMAGE);
 788 }
 789 //------------------------------------------------------------------------------
 790 void vvMainWindow::OpenRecentImage()
 791 {
 792   QAction * caller = qobject_cast<QAction*>(sender());
 793   std::vector<std::string> images;
 794   images.push_back(caller->text().toStdString());
 795   mInputPathName = itksys::SystemTools::GetFilenamePath(images[0]).c_str();
 796   LoadImages(images, vvImageReader::IMAGE);
 797 }
 798 //------------------------------------------------------------------------------
 799
 800
 801 //------------------------------------------------------------------------------
 802 void vvMainWindow::OpenImageWithTime()
 803 {
 804   QString Extensions = EXTENSIONS;
 805   Extensions += ";;All Files (*)";
 806
 807   QStringList files = QFileDialog::getOpenFileNames(this,tr("Load Images With Time"),mInputPathName,Extensions);
 808   if (files.isEmpty())
 809     return;
 810   mInputPathName = itksys::SystemTools::GetFilenamePath(files[0].toStdString()).c_str();
 811   std::vector<std::string> vector;
 812   for (int i = 0; i < files.size(); i++) {
 813     vector.push_back(files[i].toStdString());
 814   }
 815   LoadImages(vector, vvImageReader::IMAGEWITHTIME);
 816 }
 817 //------------------------------------------------------------------------------
 818
 819
 820 //------------------------------------------------------------------------------
 821 void vvMainWindow::LoadImages(std::vector<std::string> files, vvImageReader::LoadedImageType filetype)
 822 {
 823   //Separate the way to open images and dicoms
 824   int fileSize;
 825   if (filetype == vvImageReader::IMAGE || filetype == vvImageReader::IMAGEWITHTIME)
 826     fileSize = files.size();
 827   else
 828     fileSize = 1;
 829
 830   // For SLICED, we need the number of slices (ndim and #slices)
 831   std::vector<unsigned int> nSlices;
 832   nSlices.resize(files.size());
 833   std::fill(nSlices.begin(), nSlices.end(), 1);
 834   if (filetype == vvImageReader::SLICED) {
 835     for (int i = 0; i < fileSize; i++) {
 836       itk::ImageIOBase::Pointer header = clitk::readImageHeader(files[i]);
 837       QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
 838       if (!header) {
 839         nSlices[i] = 0;
 840         QString error = "Cannot open file \n";
 841         error += files[i].c_str();
 842         QMessageBox::information(this,tr("Reading problem"),error);
 843         return;
 844       }
 845       if (header->GetNumberOfDimensions() < 3) {
 846         nSlices[i] = 0;
 847         QString error = "Dimension problem. Cannot slice \n";
 848         error += files[i].c_str();
 849         QMessageBox::information(this,tr("Reading problem"),error);
 850         return;
 851       }
 852       nSlices[i] = header->GetDimensions( header->GetNumberOfDimensions()-1 );
 853     }
 854   }
 855
 856   //Only add to the list of recently opened files when a single file is opened,
 857   //to avoid polluting the list of recently opened files
 858   if (files.size() == 1) {
 859     QFileInfo finfo=tr(files[0].c_str());
 860     AddToRecentlyOpenedImages(finfo.absoluteFilePath().toStdString());
 861     updateRecentlyOpenedFilesMenu(GetRecentlyOpenedImages());
 862   }
 863   //init the progress events
 864   QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
 865   vvProgressDialog progress("Opening " + files[0],fileSize>1);
 866   qApp->processEvents();
 867
 868   int numberofsuccesulreads=0;
 869   //open images as 1 or multiples
 870   for (int i = 0; i < fileSize; i++) {
 871
 872     progress.SetText("Opening " + files[i]);
 873     progress.SetProgress(i,fileSize);
 874     qApp->processEvents();
 875
 876     for (unsigned int j = 0; j < nSlices[i]; j++) {
 877       //read the image and put it in mSlicerManagers
 878       vvSlicerManager* imageManager = new vvSlicerManager(4);
 879       qApp->processEvents();
 880
 881       bool SetImageSucceed=false;
 882
 883       // Change filename if an image with the same already exist
 884       int number = GetImageDuplicateFilenameNumber(files[i] + std::string("_slice"));
 885
 886       if (filetype == vvImageReader::IMAGE || filetype == vvImageReader::IMAGEWITHTIME || filetype == vvImageReader::SLICED)
 887         SetImageSucceed = imageManager->SetImage(files[i],filetype, number, j);
 888       else {
 889         SetImageSucceed = imageManager->SetImages(files,filetype, number);
 890       }
 891       if (!SetImageSucceed) {
 892         QApplication::restoreOverrideCursor();
 893         QString error = "Cannot open file \n";
 894         error += imageManager->GetLastError().c_str();
 895         QMessageBox::information(this,tr("Reading problem"),error);
 896         delete imageManager;
 897       } else {
 898         mSlicerManagers.push_back(imageManager);
 899
 900         //create an item in the tree with good settings
 901         QTreeWidgetItem *item = new QTreeWidgetItem();
 902         item->setData(0,Qt::UserRole,files[i].c_str());
 903         QFileInfo fileinfo(imageManager->GetFileName().c_str()); //Do not show the path
 904         item->setData(COLUMN_IMAGE_NAME,Qt::DisplayRole,fileinfo.fileName());
 905         item->setData(1,Qt::UserRole,tr("image"));
 906         item->setToolTip(COLUMN_IMAGE_NAME, imageManager->GetListOfAbsoluteFilePathInOneString("image").c_str());
 907         qApp->processEvents();
 908
 909         //Create the buttons for reload and close
 910         qApp->processEvents();
 911         QTreePushButton* cButton = new QTreePushButton;
 912         cButton->setItem(item);
 913         cButton->setColumn(COLUMN_CLOSE_IMAGE);
 914         cButton->setToolTip(tr("close image"));
 915         cButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/exit.png")));
 916         connect(cButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
 917                 this,SLOT(CloseImage(QTreeWidgetItem*, int)));
 918
 919         QTreePushButton* rButton = new QTreePushButton;
 920         rButton->setItem(item);
 921         rButton->setColumn(COLUMN_RELOAD_IMAGE);
 922         rButton->setToolTip(tr("reload image"));
 923         rButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/rotateright.png")));
 924         connect(rButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
 925                 this,SLOT(ReloadImage(QTreeWidgetItem*, int)));
 926
 927         DataTree->addTopLevelItem(item);
 928         DataTree->setItemWidget(item, COLUMN_CLOSE_IMAGE, cButton);
 929         DataTree->setItemWidget(item, COLUMN_RELOAD_IMAGE, rButton);
 930
 931         //set the id of the image
 932         QString id = QDir::current().absoluteFilePath(files[i].c_str()) + QString::number(mSlicerManagers.size()-1);
 933         item->setData(COLUMN_IMAGE_NAME,Qt::UserRole,id.toStdString().c_str());
 934         mSlicerManagers.back()->SetId(id.toStdString());
 935
 936         linkPanel->addImage(imageManager->GetFileName(), id.toStdString());
 937
 938         connect(mSlicerManagers.back(), SIGNAL(currentImageChanged(std::string)),
 939                 this,SLOT(CurrentImageChanged(std::string)));
 940         connect(mSlicerManagers.back(), SIGNAL(currentPickedImageChanged(std::string)),
 941                 this, SLOT(CurrentPickedImageChanged(std::string)));
 942         connect(mSlicerManagers.back(), SIGNAL(UpdatePosition(int, double, double, double, double, double, double, double)),
 943                 this,SLOT(MousePositionChanged(int,double, double, double, double, double, double, double)));
 944         connect(mSlicerManagers.back(), SIGNAL(UpdateVector(int, double, double, double, double)),
 945                 this, SLOT(VectorChanged(int,double,double,double, double)));
 946         connect(mSlicerManagers.back(), SIGNAL(UpdateOverlay(int, double, double)),
 947                 this, SLOT(OverlayChanged(int,double,double)));
 948         connect(mSlicerManagers.back(), SIGNAL(UpdateFusion(int, double)),
 949                 this, SLOT(FusionChanged(int,double)));
 950         connect(mSlicerManagers.back(), SIGNAL(WindowLevelChanged()),
 951                 this,SLOT(WindowLevelChanged()));
 952         connect(mSlicerManagers.back(), SIGNAL(UpdateSlice(int,int)),
 953                 this,SLOT(UpdateSlice(int,int)));
 954         connect(mSlicerManagers.back(), SIGNAL(UpdateTSlice(int, int)),
 955                 this,SLOT(UpdateTSlice(int, int)));
 956         connect(mSlicerManagers.back(), SIGNAL(UpdateTSlice(int, int)),
 957                 this,SLOT(ImageInfoChanged()));
 958         connect(mSlicerManagers.back(), SIGNAL(UpdateSliceRange(int,int,int,int,int)),
 959                 this,SLOT(UpdateSliceRange(int,int,int,int,int)));
 960         connect(mSlicerManagers.back(), SIGNAL(UpdateLinkManager(std::string,int,double,double,double,int)),
 961                 this,SLOT(UpdateLinkManager(std::string,int,double,double,double,int)));
 962         connect(mSlicerManagers.back(), SIGNAL(UpdateLinkedNavigation(std::string,vvSlicerManager*,vvSlicer*)),
 963                 this,SLOT(UpdateLinkedNavigation(std::string,vvSlicerManager*,vvSlicer*)));
 964         connect(mSlicerManagers.back(), SIGNAL(ChangeImageWithIndexOffset(vvSlicerManager*,int,int)),
 965                 this,SLOT(ChangeImageWithIndexOffset(vvSlicerManager*,int,int)));
 966         connect(mSlicerManagers.back(),SIGNAL(LandmarkAdded()),landmarksPanel,SLOT(AddPoint()));
 967         InitSlicers();
 968         numberofsuccesulreads++;
 969       }
 970     }
 971   }
 972   if (numberofsuccesulreads) {
 973     NOViewWidget->show();
 974     NEViewWidget->show();
 975     SOViewWidget->show();
 976     SEViewWidget->show();
 977     UpdateTree();
 978     InitDisplay();
 979     ShowLastImage();
 980
 981     // Try to guess default WindowLevel
 982     double range[2];
 983     mSlicerManagers.back()->GetImage()->GetFirstVTKImageData()->GetScalarRange(range);
 984     if ((range[0] == 0) && (range[1] == 1)) {
 985       presetComboBox->setCurrentIndex(5);// binary
 986     } else {
 987       // TODO
 988     }
 989   }
 990   QApplication::restoreOverrideCursor();
 991 }
 992 //------------------------------------------------------------------------------
 993
 994 //------------------------------------------------------------------------------
 995 void vvMainWindow::UpdateTree()
 996 {
 997   DataTree->resizeColumnToContents(COLUMN_TREE);
 998   DataTree->resizeColumnToContents(COLUMN_UL_VIEW);
 999   DataTree->resizeColumnToContents(COLUMN_UR_VIEW);
1000   DataTree->resizeColumnToContents(COLUMN_DL_VIEW);
1001   DataTree->resizeColumnToContents(COLUMN_DR_VIEW);
1002   DataTree->resizeColumnToContents(COLUMN_IMAGE_NAME);
1003   DataTree->resizeColumnToContents(COLUMN_CLOSE_IMAGE);
1004   DataTree->resizeColumnToContents(COLUMN_RELOAD_IMAGE);
1005 }
1006 //------------------------------------------------------------------------------
1007
1008 //------------------------------------------------------------------------------
1009 void vvMainWindow::CurrentImageChanged(std::string id)
1010 {
1011   if (id == mCurrentSelectedImageId) return; // Do nothing
1012   int selected = 0;
1013   for (int i = 0; i < DataTree->topLevelItemCount(); i++) {
1014     if (DataTree->topLevelItem(i)->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString().toStdString() == id) {
1015       selected = i;
1016     } else {
1017       DataTree->topLevelItem(i)->setSelected(0);
1018     }
1019     for (int child = 0; child < DataTree->topLevelItem(i)->childCount(); child++)
1020       DataTree->topLevelItem(i)->child(child)->setSelected(0);
1021
1022   }
1023   DataTree->topLevelItem(selected)->setSelected(1);
1024   mCurrentSelectedImageId = id;
1025   emit SelectedImageHasChanged(mSlicerManagers[selected]);
1026 }
1027 //------------------------------------------------------------------------------
1028
1029 //------------------------------------------------------------------------------
1030 void vvMainWindow::CurrentPickedImageChanged(std::string id)
1031 {
1032   if (id == mCurrentPickedImageId) return; // Do nothing
1033   int selected = 0;
1034   for (int i = 0; i < DataTree->topLevelItemCount(); i++) {
1035     if (DataTree->topLevelItem(i)->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString().toStdString() == id) {
1036       selected = i;
1037     } else {
1038       DataTree->topLevelItem(i)->setSelected(0);
1039     }
1040     for (int child = 0; child < DataTree->topLevelItem(i)->childCount(); child++)
1041       DataTree->topLevelItem(i)->child(child)->setSelected(0);
1042
1043   }
1044   DataTree->topLevelItem(selected)->setSelected(1);
1045   mCurrentPickedImageId = id;
1046   mCurrentPickedImageIndex = selected;
1047 }
1048 //------------------------------------------------------------------------------
1049
1050 //------------------------------------------------------------------------------
1051 void vvMainWindow::ImageInfoChanged()
1052 {
1053   contextActions[6]->setEnabled(1);
1054   contextActions[5]->setEnabled(1);
1055   actionSave_As->setEnabled(1);
1056   actionAdd_VF_to_current_Image->setEnabled(1);
1057   actionAdd_fusion_image->setEnabled(1);
1058   actionAdd_overlay_image_to_current_image->setEnabled(1);
1059   actionNorth_East_Window->setEnabled(1);
1060   actionNorth_West_Window->setEnabled(1);
1061   actionSouth_East_Window->setEnabled(1);
1062   actionSouth_West_Window->setEnabled(1);
1063   vvToolManager::GetInstance()->EnableToolsInMenu(this, true);
1064   inverseButton->setEnabled(1);
1065
1066   goToCursorPushButton->setEnabled(1);
1067
1068   if (DataTree->selectedItems().size()) {
1069     int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1070
1071     colorMapComboBox->setEnabled(1);
1072     for (int i = 0; i < DataTree->topLevelItem(index)->childCount(); i++) {
1073       if (DataTree->topLevelItem(index)->child(i)->data(1,Qt::UserRole).toString() == "overlay" ||
1074           DataTree->topLevelItem(index)->child(i)->data(1,Qt::UserRole).toString() == "fusion") {
1075         colorMapComboBox->setEnabled(0);
1076         break;
1077       }
1078     }
1079
1080     std::vector<double> origin;
1081     std::vector<double> inputSpacing;
1082     std::vector<int> inputSize;
1083     std::vector<double> sizeMM;
1084     vtkSmartPointer<vtkMatrix4x4> transformation;
1085     int dimension=0;
1086     QString pixelType;
1087     QString inputSizeInBytes;
1088     QString image = DataTree->selectedItems()[0]->data(COLUMN_IMAGE_NAME,Qt::DisplayRole).toString();
1089
1090     int nframes = mSlicerManagers[index]->GetSlicer(0)->GetTMax();
1091     if (nframes > 1 || playMode == 1) {
1092       playButton->setEnabled(1);
1093       frameRateLabel->setEnabled(1);
1094       frameRateSpinBox->setEnabled(1);
1095     } else {
1096       playButton->setEnabled(0);
1097       frameRateLabel->setEnabled(0);
1098       frameRateSpinBox->setEnabled(0);
1099     }
1100
1101     //read image header
1102     int NPixel = 1;
1103
1104     int tSlice = 0;
1105     vvImage::Pointer imageSelected;
1106     if (DataTree->topLevelItem(index) == DataTree->selectedItems()[0]) {
1107       imageSelected = mSlicerManagers[index]->GetSlicer(0)->GetImage();
1108       tSlice = mSlicerManagers[index]->GetSlicer(0)->GetTSlice();
1109     } else if (DataTree->selectedItems()[0]->data(1,Qt::UserRole).toString() == "vector") {
1110       imageSelected = mSlicerManagers[index]->GetSlicer(0)->GetVF();
1111       tSlice = mSlicerManagers[index]->GetSlicer(0)->GetOverlayTSlice();
1112     } else if (DataTree->selectedItems()[0]->data(1,Qt::UserRole).toString() == "overlay") {
1113       imageSelected = mSlicerManagers[index]->GetSlicer(0)->GetOverlay();
1114       tSlice = mSlicerManagers[index]->GetSlicer(0)->GetOverlayTSlice();
1115     } else if (DataTree->selectedItems()[0]->data(1,Qt::UserRole).toString() == "fusion") {
1116       imageSelected = mSlicerManagers[index]->GetSlicer(0)->GetFusion();
1117       tSlice = mSlicerManagers[index]->GetSlicer(0)->GetFusionTSlice();
1118     }
1119     else if (DataTree->selectedItems()[0]->data(1,Qt::UserRole).toString() == "contour") {
1120       imageSelected = mSlicerManagers[index]->GetSlicer(0)->GetImage();
1121       tSlice = mSlicerManagers[index]->GetSlicer(0)->GetTSlice();
1122     }
1123     else {
1124       imageSelected = mSlicerManagers[index]->GetSlicer(0)->GetImage();
1125       tSlice = mSlicerManagers[index]->GetSlicer(0)->GetTSlice();
1126     }
1127
1128     dimension = imageSelected->GetNumberOfDimensions();
1129     origin.resize(dimension);
1130     inputSpacing.resize(dimension);
1131     inputSize.resize(dimension);
1132     sizeMM.resize(dimension);
1133     pixelType = mSlicerManagers[index]->GetImage()->GetScalarTypeAsITKString().c_str();
1134     for (int i = 0; i < dimension; i++) {
1135       origin[i] = imageSelected->GetOrigin()[i];
1136       inputSpacing[i] = imageSelected->GetSpacing()[i];
1137       inputSize[i] = imageSelected->GetSize()[i];
1138       sizeMM[i] = inputSize[i]*inputSpacing[i];
1139       NPixel *= inputSize[i];
1140     }
1141     inputSizeInBytes = GetSizeInBytes(imageSelected->GetActualMemorySize()*1000);
1142
1143     QString dim = QString::number(dimension) + " (";
1144     dim += pixelType + ")";
1145
1146     infoPanel->setFileName(image);
1147     infoPanel->setDimension(dim);
1148     infoPanel->setSizePixel(GetVectorIntAsString(inputSize));
1149     infoPanel->setSizeMM(GetVectorDoubleAsString(sizeMM));
1150     infoPanel->setOrigin(GetVectorDoubleAsString(origin));
1151     infoPanel->setSpacing(GetVectorDoubleAsString(inputSpacing));
1152     infoPanel->setNPixel(QString::number(NPixel)+" ("+inputSizeInBytes+")");
1153     transformation = imageSelected->GetTransform()[tSlice]->GetMatrix();
1154     infoPanel->setTransformation(Get4x4MatrixDoubleAsString(transformation));
1155
1156     landmarksPanel->SetCurrentLandmarks(mSlicerManagers[index]->GetLandmarks(),
1157                                         mSlicerManagers[index]->GetSlicer(0)->GetImage()->GetVTKImages().size());
1158     landmarksPanel->SetCurrentPath(mInputPathName.toStdString());
1159     landmarksPanel->SetCurrentImage(mSlicerManagers[index]->GetFileName().c_str());
1160
1161     overlayPanel->getCurrentImageName(mSlicerManagers[index]->GetFileName().c_str());
1162     for (int i = 0; i < 4; i++) {
1163       if (DataTree->selectedItems()[0]->data(i+1,Qt::CheckStateRole).toInt() > 0 || i == 3) {
1164         mSlicerManagers[index]->UpdateInfoOnCursorPosition(i);
1165         break;
1166       }
1167     }
1168
1169     infoPanel->setFileName(image);
1170     infoPanel->setDimension(dim);
1171     infoPanel->setSizePixel(GetVectorIntAsString(inputSize));
1172     infoPanel->setSizeMM(GetVectorDoubleAsString(sizeMM));
1173     infoPanel->setOrigin(GetVectorDoubleAsString(origin));
1174     infoPanel->setSpacing(GetVectorDoubleAsString(inputSpacing));
1175     infoPanel->setNPixel(QString::number(NPixel)+" ("+inputSizeInBytes+")");
1176
1177     landmarksPanel->SetCurrentLandmarks(mSlicerManagers[index]->GetLandmarks(),
1178                                         mSlicerManagers[index]->GetSlicer(0)->GetImage()->GetVTKImages().size());
1179     landmarksPanel->SetCurrentPath(mInputPathName.toStdString());
1180     landmarksPanel->SetCurrentImage(mSlicerManagers[index]->GetFileName().c_str());
1181
1182     overlayPanel->getCurrentImageName(mSlicerManagers[index]->GetFileName().c_str());
1183     for (int i = 0; i < 4; i++) {
1184       if (DataTree->selectedItems()[0]->data(i+1,Qt::CheckStateRole).toInt() > 0 || i == 3) {
1185         mSlicerManagers[index]->UpdateInfoOnCursorPosition(i);
1186         break;
1187       }
1188     }
1189     WindowLevelChanged();
1190     slicingPresetComboBox->setCurrentIndex(mSlicerManagers[index]->GetSlicingPreset());
1191
1192     if (mSlicerManagers[index]->GetSlicer(0)->GetVF()) {
1193       overlayPanel->getVFName(mSlicerManagers[index]->GetVFName().c_str());
1194       overlayPanel->getVFProperty(mSlicerManagers[index]->GetSlicer(0)->GetVFSubSampling(),
1195                                   mSlicerManagers[index]->GetSlicer(0)->GetVFScale(),
1196                                   mSlicerManagers[index]->GetSlicer(0)->GetVFLog());
1197     } else {
1198       overlayPanel->getVFName(mSlicerManagers[index]->GetVFName().c_str());
1199       overlayPanel->getVFProperty(-1,-1,-1);
1200     }
1201     if (mSlicerManagers[index]->GetSlicer(0)->GetOverlay()) {
1202       overlayPanel->getOverlayName(mSlicerManagers[index]->GetOverlayName().c_str());
1203     } else {
1204       overlayPanel->getOverlayName(mSlicerManagers[index]->GetOverlayName().c_str());
1205     }
1206
1207     if (mSlicerManagers[index]->GetSlicer(0)->GetFusion()) {
1208       overlayPanel->getFusionName(mSlicerManagers[index]->GetFusionName().c_str());
1209     } else {
1210       overlayPanel->getFusionName(mSlicerManagers[index]->GetFusionName().c_str());
1211     }
1212   }
1213 }
1214 //------------------------------------------------------------------------------
1215
1216 //------------------------------------------------------------------------------
1217 void vvMainWindow::ShowDocumentation()
1218 {
1219   documentation->show();
1220 }
1221 //------------------------------------------------------------------------------
1222
1223 //------------------------------------------------------------------------------
1224 void vvMainWindow::PopupRegisterForm(bool checkCanPush)
1225 {
1226   vvRegisterForm* registerForm = new vvRegisterForm(QUrl("http://www.creatis.insa-lyon.fr/~dsarrut/vvregister/write.php"), getVVSettingsPath(), getSettingsOptionFormat());
1227   if(!checkCanPush) {
1228     registerForm->show();
1229   } else {
1230     if(registerForm->canPush()) {
1231       registerForm->show();
1232       registerForm->acquitPushed();//too bad if there is not internet connection anymore.
1233     }
1234   }
1235 }
1236 //------------------------------------------------------------------------------
1237
1238 //------------------------------------------------------------------------------
1239 void vvMainWindow::ShowHelpDialog()
1240 {
1241   help_dialog->show();
1242 }
1243 //------------------------------------------------------------------------------
1244
1245 //------------------------------------------------------------------------------
1246 void vvMainWindow::ChangeViewMode()
1247 {
1248   typedef struct _SIZE{
1249     QSplitter* splitter;
1250     QList<int> size1, size2;
1251     int cols[3];
1252   }SplitterSize;
1253   SplitterSize sizes[4];
1254   sizes[0].splitter = OSplitter;
1255   sizes[0].size1.push_back(1);
1256   sizes[0].size1.push_back(0);
1257   sizes[0].size2.push_back(1);
1258   sizes[0].size2.push_back(0);
1259   sizes[0].cols[0] = 2;
1260   sizes[0].cols[1] = 3;
1261   sizes[0].cols[2] = 4;
1262
1263   sizes[1].splitter = ESplitter;
1264   sizes[1].size1.push_back(0);
1265   sizes[1].size1.push_back(1);
1266   sizes[1].size2.push_back(1);
1267   sizes[1].size2.push_back(0);
1268   sizes[1].cols[0] = 1;
1269   sizes[1].cols[1] = 3;
1270   sizes[1].cols[2] = 4;
1271
1272   sizes[2].splitter = OSplitter;
1273   sizes[2].size1.push_back(1);
1274   sizes[2].size1.push_back(0);
1275   sizes[2].size2.push_back(0);
1276   sizes[2].size2.push_back(1);
1277   sizes[2].cols[0] = 1;
1278   sizes[2].cols[1] = 2;
1279   sizes[2].cols[2] = 4;
1280
1281   sizes[3].splitter = ESplitter;
1282   sizes[3].size1.push_back(0);
1283   sizes[3].size1.push_back(1);
1284   sizes[3].size2.push_back(0);
1285   sizes[3].size2.push_back(1);
1286   sizes[3].cols[0] = 1;
1287   sizes[3].cols[1] = 2;
1288   sizes[3].cols[2] = 3;
1289
1290   int slicer = mSlicerManagers[mCurrentPickedImageIndex]->GetSelectedSlicer();
1291   if (viewMode == 1) {
1292     if (slicer >= 0) {
1293       viewMode = 0;
1294       splitter_3->setSizes(sizes[slicer].size1);
1295       sizes[slicer].splitter->setSizes(sizes[slicer].size2);
1296       DataTree->setColumnHidden(sizes[slicer].cols[0],1);
1297       DataTree->setColumnHidden(sizes[slicer].cols[1],1);
1298       DataTree->setColumnHidden(sizes[slicer].cols[2],1);
1299     }
1300   } else {
1301     QList<int> size;
1302     if (slicer >= 0) {
1303       viewMode = 1;
1304       size.push_back(1);
1305       size.push_back(1);
1306       splitter_3->setSizes(size);
1307       sizes[slicer].splitter->setSizes(size);
1308       DataTree->setColumnHidden(sizes[slicer].cols[0],0);
1309       DataTree->setColumnHidden(sizes[slicer].cols[1],0);
1310       DataTree->setColumnHidden(sizes[slicer].cols[2],0);
1311     }
1312   }
1313   UpdateRenderWindows();
1314   /*
1315   ** I don't know why but for both resized QVTKWidget we also need to render
1316   ** the associated Slicer to redraw crosses.
1317   */
1318   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
1319 //     if (DataTree->topLevelItem(i)->data(COLUMN_UL_VIEW,Qt::CheckStateRole).toInt() > 1)
1320       mSlicerManagers[i]->GetSlicer(0)->Render();
1321       mSlicerManagers[i]->GetSlicer(1)->Render();
1322 //     if (DataTree->topLevelItem(i)->data(COLUMN_DL_VIEW,Qt::CheckStateRole).toInt() > 1)
1323       mSlicerManagers[i]->GetSlicer(2)->Render();
1324       mSlicerManagers[i]->GetSlicer(3)->Render();
1325   }
1326 }
1327 //------------------------------------------------------------------------------
1328
1329 //------------------------------------------------------------------------------
1330 QString vvMainWindow::GetSizeInBytes(unsigned long size)
1331 {
1332   QString result = "";// QString::number(size);
1333   //result += " bytes (";
1334   if (size > 1000000000) {
1335     size /= 1000000000;
1336     result += QString::number(size);
1337     result += "Gb";//)";
1338   } else if (size > 1000000) {
1339     size /= 1000000;
1340     result += QString::number(size);
1341     result += "Mb";//)";
1342   } else if (size > 1000) {
1343     size /= 1000;
1344     result += QString::number(size);
1345     result += "kb";//)";
1346   }
1347   return result;
1348 }
1349 //------------------------------------------------------------------------------
1350
1351 //------------------------------------------------------------------------------
1352 QString vvMainWindow::Get4x4MatrixDoubleAsString(vtkSmartPointer<vtkMatrix4x4> matrix, const int precision)
1353 {
1354   std::ostringstream strmatrix;
1355
1356   // Figure out the number of digits of the integer part of the largest absolute value
1357   // for each column
1358   unsigned width[4];
1359   for (unsigned int j = 0; j < 4; j++){
1360     double absmax = 0.;
1361     for (unsigned int i = 0; i < 4; i++)
1362       absmax = std::max(absmax, vnl_math_abs(matrix->GetElement(i, j)));
1363     unsigned ndigits = (unsigned)std::max(0.,std::log10(absmax))+1;
1364     width[j] = precision+ndigits+3;
1365   }
1366
1367   // Output with correct width, aligned to the right
1368   for (unsigned int i = 0; i < 4; i++) {
1369     for (unsigned int j = 0; j < 4; j++) {
1370       strmatrix.setf(ios::fixed,ios::floatfield);
1371       strmatrix.precision(precision);
1372       strmatrix.fill(' ');
1373       strmatrix.width(width[j]);
1374       strmatrix << std::right << matrix->GetElement(i, j);
1375     }
1376     strmatrix << std::endl;
1377   }
1378   QString result = strmatrix.str().c_str();
1379   return result;
1380 }
1381 //------------------------------------------------------------------------------
1382
1383 //------------------------------------------------------------------------------
1384 QString vvMainWindow::GetVectorDoubleAsString(std::vector<double> vectorDouble)
1385 {
1386   QString result;
1387   for (unsigned int i= 0; i < vectorDouble.size(); i++) {
1388     if (i != 0)
1389       result += " ";
1390     result += QString::number(vectorDouble[i]);
1391   }
1392   return result;
1393 }
1394 //------------------------------------------------------------------------------
1395
1396 //------------------------------------------------------------------------------
1397 QString vvMainWindow::GetVectorIntAsString(std::vector<int> vectorInt)
1398 {
1399   QString result;
1400   for (unsigned int i= 0; i < vectorInt.size(); i++) {
1401     if (i != 0)
1402       result += " ";
1403     result += QString::number(vectorInt[i]);
1404   }
1405   return result;
1406 }
1407 //------------------------------------------------------------------------------
1408
1409 //------------------------------------------------------------------------------
1410 int vvMainWindow::GetSlicerIndexFromItem(QTreeWidgetItem* item)
1411 {
1412   QString id = item->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString();
1413   for (int i = 0; i < DataTree->topLevelItemCount(); i++) {
1414     if (DataTree->topLevelItem(i)->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString() == id)
1415       return i;
1416   }
1417   return -1;
1418 }
1419 //------------------------------------------------------------------------------
1420
1421 //------------------------------------------------------------------------------
1422 QTreeWidgetItem* vvMainWindow::GetItemFromSlicerManager(vvSlicerManager* sm)
1423 {
1424   QString id = sm->GetId().c_str();
1425   for (int i = 0; i < DataTree->topLevelItemCount(); i++) {
1426     if (DataTree->topLevelItem(i)->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString() == id)
1427       return DataTree->topLevelItem(i);
1428   }
1429   return NULL;
1430 }
1431 //------------------------------------------------------------------------------
1432
1433 //------------------------------------------------------------------------------
1434 void vvMainWindow::DisplayChanged(QTreeWidgetItem *clickedItem, int column)
1435 {
1436   if ( column >= COLUMN_CLOSE_IMAGE || column <= 0)
1437     return;
1438
1439   // Get parent information (might be the same item)
1440   int slicerManagerIndex = GetSlicerIndexFromItem(clickedItem);
1441   QTreeWidgetItem* clickedParentItem = DataTree->topLevelItem(slicerManagerIndex);
1442   vvSlicer* clickedSlicer = mSlicerManagers[slicerManagerIndex]->GetSlicer(column-1);
1443
1444   // Go over the complete item tree (only 2 levels, parents and children)
1445   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
1446     // Trick to avoid redoing twice the job for a key (sr)
1447     mSlicerManagers[i]->GetSlicer(column-1)->GetRenderWindow()->GetInteractor()->SetKeySym("Crap");
1448
1449     QTreeWidgetItem* currentParentItem = DataTree->topLevelItem(i);
1450     if(currentParentItem != clickedParentItem) {
1451       // Not the branch of the clicked item, uncheck all
1452
1453       // Parent
1454       currentParentItem->setData(column,Qt::CheckStateRole, 0);
1455       mSlicerManagers[i]->UpdateSlicer(column-1, false);
1456
1457       // Children
1458       for (int iChild = 0; iChild < currentParentItem->childCount(); iChild++) {
1459         currentParentItem->child(iChild)->setData(column,Qt::CheckStateRole, 0);
1460       }
1461     }
1462     else {
1463       // Branch of the clicked one: get check status from actor visibility in slicer
1464       // and toggle the clicked one
1465
1466       // Parent
1467       bool vis = clickedSlicer->GetActorVisibility("image", 0);
1468       bool draw = clickedSlicer->GetRenderer()->GetDraw();
1469
1470       // Update slicer (after getting visibility)
1471       mSlicerManagers[slicerManagerIndex]->UpdateSlicer(column-1, true);
1472       mSlicerManagers[slicerManagerIndex]->UpdateInfoOnCursorPosition(column-1);
1473       DisplaySliders(slicerManagerIndex, column-1);
1474       if(clickedParentItem == clickedItem) {
1475         // Toggle
1476         vis = !draw || !vis;
1477       }
1478       clickedSlicer->SetActorVisibility("image", 0, vis);
1479       clickedParentItem->setData(column, Qt::CheckStateRole, vis?2:0);
1480
1481       // Children
1482       std::map<std::string, int> actorTypeCounts;
1483       for (int iChild = 0; iChild < clickedParentItem->childCount(); iChild++) {
1484         QTreeWidgetItem* currentChildItem = clickedParentItem->child(iChild);
1485         std::string actorType = currentChildItem->data(1,Qt::UserRole).toString().toStdString();
1486         vis = clickedSlicer->GetActorVisibility(actorType, actorTypeCounts[actorType]);
1487         if(currentChildItem == clickedItem) {
1488           // Toggle or force visibility if it was not on this branch so far
1489           vis = !draw || !vis;
1490           clickedSlicer->SetActorVisibility(actorType, actorTypeCounts[actorType], vis);
1491         }
1492         currentChildItem->setData(column, Qt::CheckStateRole, vis?2:0);
1493         actorTypeCounts[actorType]++;
1494       }
1495     }
1496   }
1497
1498   clickedSlicer->Render();
1499 }
1500 //------------------------------------------------------------------------------
1501
1502 void vvMainWindow::InitSlicers()
1503 {
1504   if (mSlicerManagers.size()) {
1505     mSlicerManagers.back()->GenerateDefaultLookupTable();
1506
1507     mSlicerManagers.back()->SetSlicerWindow(0,NOViewWidget->GetRenderWindow());
1508     mSlicerManagers.back()->SetSlicerWindow(1,NEViewWidget->GetRenderWindow());
1509     mSlicerManagers.back()->SetSlicerWindow(2,SOViewWidget->GetRenderWindow());
1510     mSlicerManagers.back()->SetSlicerWindow(3,SEViewWidget->GetRenderWindow());
1511   }
1512 }
1513
1514 //------------------------------------------------------------------------------
1515 void vvMainWindow::InitDisplay()
1516 {
1517   if (mSlicerManagers.size()) {
1518     //BE CAREFUL : this is absolutely necessary to set the interactor style
1519     //in order to have the same style instanciation for all SlicerManagers in
1520     // a same window
1521     for (int j = 0; j < 4; j++) {
1522       vvInteractorStyleNavigator* style = vvInteractorStyleNavigator::New();
1523       style->SetAutoAdjustCameraClippingRange(1);
1524       bool AlreadySelected = false;
1525       for (int i = 0; i < DataTree->topLevelItemCount(); i++) {
1526         mSlicerManagers[i]->SetInteractorStyleNavigator(j,style);
1527
1528         //select the image only if previous are not selected
1529         if (DataTree->topLevelItem(i)->data(j+1,Qt::CheckStateRole).toInt() > 1) {
1530           mSlicerManagers[i]->UpdateSlicer(j,1);
1531           AlreadySelected = true;
1532         } else if (i == DataTree->topLevelItemCount()-1 && !AlreadySelected) {
1533           if (DataTree->selectedItems().size() == 0)
1534             DataTree->topLevelItem(i)->setSelected(1);
1535           DataTree->topLevelItem(i)->setData(j+1,Qt::CheckStateRole,2);
1536           mSlicerManagers[i]->UpdateSlicer(j,1);
1537           DisplaySliders(i,j);
1538         } else {
1539           DataTree->topLevelItem(i)->setData(j+1,Qt::CheckStateRole,0);
1540           mSlicerManagers[i]->UpdateSlicer(j,0);
1541         }
1542       }
1543       style->Delete();
1544     }
1545   }
1546 }
1547 //------------------------------------------------------------------------------
1548
1549 //------------------------------------------------------------------------------
1550 void vvMainWindow::DisplaySliders(int slicer, int window)
1551 {
1552   if(!mSlicerManagers[slicer]->GetSlicer(window)->GetRenderer()->GetDraw())
1553     return;
1554
1555   int range[2];
1556   mSlicerManagers[slicer]->GetSlicer(window)->GetSliceRange(range);
1557   int position = mSlicerManagers[slicer]->GetSlicer(window)->GetSlice();
1558   if (range[1]>0)
1559     verticalSliders[window]->show();
1560   else
1561     verticalSliders[window]->hide();
1562   verticalSliders[window]->setRange(range[0],range[1]);
1563   verticalSliders[window]->setValue(position);
1564
1565   int tRange[2];
1566   tRange[0] = 0;
1567   tRange[1] = mSlicerManagers[slicer]->GetSlicer(window)->GetTMax();
1568   if (tRange[1]>0)
1569     horizontalSliders[window]->show();
1570   else
1571     horizontalSliders[window]->hide();
1572   horizontalSliders[window]->setRange(tRange[0],tRange[1]);
1573   int tPosition = mSlicerManagers[slicer]->GetSlicer(window)->GetMaxCurrentTSlice();
1574   horizontalSliders[window]->setValue(tPosition);
1575 }
1576 //------------------------------------------------------------------------------
1577
1578 //------------------------------------------------------------------------------
1579 void vvMainWindow::CloseImage(QTreeWidgetItem* item, int column)
1580 {
1581   int index = GetSlicerIndexFromItem(item);
1582
1583   if (DataTree->topLevelItem(index) != item) {
1584     QString warning = "Do you really want to close the overlay : ";
1585     warning += item->data(COLUMN_IMAGE_NAME,Qt::DisplayRole).toString();
1586     QMessageBox msgBox(QMessageBox::Warning, tr("Close Overlay"),
1587                        warning, 0, this);
1588     msgBox.addButton(tr("Close"), QMessageBox::AcceptRole);
1589     msgBox.addButton(tr("Cancel"), QMessageBox::RejectRole);
1590     if (msgBox.exec() == QMessageBox::AcceptRole) {
1591       std::string overlay_type=item->data(1,Qt::UserRole).toString().toStdString();
1592       int overlay_index=0;
1593       for (int child = 0; child < DataTree->topLevelItem(index)->childCount(); child++) {
1594         if (DataTree->topLevelItem(index)->\
1595             child(child)->data(1,Qt::UserRole).toString().toStdString() == overlay_type)
1596           overlay_index++;
1597         if (DataTree->topLevelItem(index)->child(child) == item) break;
1598       }
1599       mSlicerManagers[index]->RemoveActor(overlay_type, overlay_index-1);
1600       mSlicerManagers[index]->SetColorMap(0);
1601       DataTree->topLevelItem(index)->takeChild(DataTree->topLevelItem(index)->indexOfChild(item));
1602       mSlicerManagers[index]->Render();
1603     }
1604   } else if (DataTree->topLevelItemCount() <= 1) {
1605     QString warning = "Do you really want to close the image : ";
1606     warning += item->data(COLUMN_IMAGE_NAME,Qt::DisplayRole).toString();
1607     warning += "\nThis is the last image, you're about to close vv !!!";
1608     QMessageBox msgBox(QMessageBox::Warning, tr("Close Image"),
1609                        warning, 0, this);
1610     msgBox.addButton(tr("Close vv"), QMessageBox::AcceptRole);
1611     msgBox.addButton(tr("Cancel"), QMessageBox::RejectRole);
1612     if (msgBox.exec() == QMessageBox::AcceptRole) {
1613       this->close();
1614     }
1615   } else {
1616     QString warning = "Do you really want to close the image : ";
1617     warning += item->data(COLUMN_IMAGE_NAME,Qt::DisplayRole).toString();
1618     QMessageBox msgBox(QMessageBox::Warning, tr("Close Image"),
1619                        warning, 0, this);
1620     msgBox.addButton(tr("Close"), QMessageBox::AcceptRole);
1621     msgBox.addButton(tr("Cancel"), QMessageBox::RejectRole);
1622     if (msgBox.exec() == QMessageBox::AcceptRole) {
1623
1624       // Tell tools that we close an image
1625       emit AnImageIsBeingClosed(mSlicerManagers[index]);
1626
1627       std::vector<vvSlicerManager*>::iterator Manageriter = mSlicerManagers.begin();
1628       DataTree->takeTopLevelItem(index);
1629       for (int i = 0; i < index; i++) {
1630         Manageriter++;
1631       }
1632       linkPanel->removeImage(index);
1633       mSlicerManagers[index]->RemoveActors();
1634       delete mSlicerManagers[index];
1635       mSlicerManagers.erase(Manageriter);
1636
1637       //
1638       InitDisplay();
1639     }
1640   }
1641   ImageInfoChanged();
1642 }
1643 //------------------------------------------------------------------------------
1644
1645 //------------------------------------------------------------------------------
1646 void vvMainWindow::ReloadImage(QTreeWidgetItem* item, int column)
1647 {
1648   // int index = GetSlicerIndexFromItem(item);
1649   //   QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
1650   //   if (item->data(1,Qt::UserRole).toString() == "vector")
1651   //     mSlicerManagers[index]->ReloadVF();
1652   //   else
1653   //     mSlicerManagers[index]->Reload();
1654
1655   //   QApplication::restoreOverrideCursor();
1656   int index = GetSlicerIndexFromItem(item);
1657   QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
1658   QString role=item->data(1,Qt::UserRole).toString();
1659   if ( role == "vector"){
1660     mSlicerManagers[index]->ReloadVF();
1661   }
1662   else if (role == "overlay"){
1663     mSlicerManagers[index]->ReloadOverlay();
1664   }
1665   else if (role == "fusion"){
1666     mSlicerManagers[index]->ReloadFusion();
1667   }
1668   else{
1669     mSlicerManagers[index]->Reload();
1670   }
1671   // Update view and info
1672   ImageInfoChanged();
1673   mSlicerManagers[index]->Render();
1674   QApplication::restoreOverrideCursor();
1675 }
1676 //------------------------------------------------------------------------------
1677
1678 //------------------------------------------------------------------------------
1679 void vvMainWindow::MousePositionChanged(int visibility,double x, double y, double z, double X, double Y, double Z , double value)
1680 {
1681   infoPanel->setCurrentInfo(visibility,x,y,z,X,Y,Z,value);
1682 }
1683 //------------------------------------------------------------------------------
1684
1685 //------------------------------------------------------------------------------
1686 void vvMainWindow::VectorChanged(int visibility,double x, double y, double z, double value)
1687 {
1688   overlayPanel->getCurrentVectorInfo(visibility,x,y,z,value);
1689 }
1690 //------------------------------------------------------------------------------
1691
1692 //------------------------------------------------------------------------------
1693 void vvMainWindow::OverlayChanged(int visibility, double valueOver, double valueRef)
1694 {
1695   overlayPanel->getCurrentOverlayInfo(visibility,valueOver, valueRef);
1696 }
1697 //------------------------------------------------------------------------------
1698
1699 //------------------------------------------------------------------------------
1700 void vvMainWindow::FusionChanged(int visibility, double value)
1701 {
1702   overlayPanel->getCurrentFusionInfo(visibility,value);
1703 }
1704 //------------------------------------------------------------------------------
1705
1706 //------------------------------------------------------------------------------
1707 void vvMainWindow::WindowLevelChanged()
1708 {
1709   // Base image
1710   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1711   if(index==-1) return;
1712   windowSpinBox->setValue(mSlicerManagers[index]->GetColorWindow());
1713   levelSpinBox->setValue(mSlicerManagers[index]->GetColorLevel());
1714   colorMapComboBox->setCurrentIndex(mSlicerManagers[index]->GetColorMap());
1715   presetComboBox->setCurrentIndex(mSlicerManagers[index]->GetPreset());
1716
1717   // Overlay image
1718   if (mSlicerManagers[index]->GetSlicer(0)->GetOverlay())
1719     overlayPanel->getOverlayProperty(mSlicerManagers[index]->GetOverlayColor(),
1720                                      mSlicerManagers[index]->GetLinkOverlayWindowLevel(),
1721                                      mSlicerManagers[index]->GetOverlayColorWindow(),
1722                                      mSlicerManagers[index]->GetOverlayColorLevel());
1723   else
1724     overlayPanel->getOverlayProperty(-1,0,0.,0.);
1725
1726   // Fusion image
1727   if (mSlicerManagers[index]->GetSlicer(0)->GetFusion())
1728     overlayPanel->getFusionProperty(mSlicerManagers[index]->GetFusionOpacity(),
1729                                     mSlicerManagers[index]->GetFusionThresholdOpacity(),
1730                                     mSlicerManagers[index]->GetFusionColorMap(),
1731                                     mSlicerManagers[index]->GetFusionWindow(),
1732                                     mSlicerManagers[index]->GetFusionLevel());
1733   else
1734     overlayPanel->getFusionProperty(-1, -1, -1, -1, -1);
1735 }
1736 //------------------------------------------------------------------------------
1737
1738 //------------------------------------------------------------------------------
1739 void vvMainWindow::WindowLevelEdited()
1740 {
1741   presetComboBox->setCurrentIndex(6);
1742   UpdateWindowLevel();
1743 }
1744 //------------------------------------------------------------------------------
1745
1746 //------------------------------------------------------------------------------
1747 void vvMainWindow::SetWindowLevel(double w, double l)
1748 {
1749   windowSpinBox->setValue(w);
1750   levelSpinBox->setValue(l);
1751   presetComboBox->setCurrentIndex(6);
1752   colorMapComboBox->setCurrentIndex(0);
1753   UpdateWindowLevel();
1754 }
1755 //------------------------------------------------------------------------------
1756
1757 //------------------------------------------------------------------------------
1758 void vvMainWindow::UpdateWindowLevel()
1759 {
1760   if (DataTree->selectedItems().size()) {
1761     if (presetComboBox->currentIndex() == 7) //For ventilation
1762       colorMapComboBox->setCurrentIndex(5);
1763     int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1764     mSlicerManagers[index]->SetColorWindow(windowSpinBox->value());
1765     mSlicerManagers[index]->SetColorLevel(levelSpinBox->value());
1766     mSlicerManagers[index]->SetPreset(presetComboBox->currentIndex());
1767     mSlicerManagers[index]->Render();
1768     WindowLevelChanged();
1769   }
1770 }
1771 //------------------------------------------------------------------------------
1772
1773 //------------------------------------------------------------------------------
1774 void vvMainWindow::UpdateSlicingPreset()
1775 {
1776   if (DataTree->selectedItems().size()) {
1777     int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1778     mSlicerManagers[index]->SetSlicingPreset(vvSlicerManager::SlicingPresetType(slicingPresetComboBox->currentIndex()));
1779   }
1780 }
1781 //------------------------------------------------------------------------------
1782
1783 //------------------------------------------------------------------------------
1784 void vvMainWindow::UpdateColorMap()
1785 {
1786   if (DataTree->selectedItems().size()) {
1787     int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1788     mSlicerManagers[index]->SetColorMap(colorMapComboBox->currentIndex());
1789     mSlicerManagers[index]->Render();
1790   }
1791 }
1792 //------------------------------------------------------------------------------
1793 void vvMainWindow::SwitchWindowLevel()
1794 {
1795   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1796   int window = mSlicerManagers[index]->GetColorWindow();
1797   presetComboBox->setCurrentIndex(6);
1798   windowSpinBox->setValue(-window);
1799   UpdateWindowLevel();
1800 }
1801 //------------------------------------------------------------------------------
1802
1803 //------------------------------------------------------------------------------
1804 void vvMainWindow::ApplyWindowLevelToAllImages()
1805 {
1806   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1807   if(index==-1) return;
1808   double window = mSlicerManagers[index]->GetColorWindow();
1809   double level = mSlicerManagers[index]->GetColorLevel();
1810
1811   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
1812     if (mSlicerManagers[i] == NULL)
1813       continue;
1814     mSlicerManagers[i]->SetColorWindow(window);
1815     mSlicerManagers[i]->SetColorLevel(level);
1816     mSlicerManagers[i]->SetPreset(6);
1817     mSlicerManagers[i]->Render();
1818   }
1819 }
1820 //------------------------------------------------------------------------------
1821
1822 //------------------------------------------------------------------------------
1823 void vvMainWindow::ApplyWindowToSetOfImages(double window, unsigned int indexMin, unsigned int indexMax)
1824 {
1825   for (unsigned int i = indexMin; i <= indexMax && i < mSlicerManagers.size(); i++) {
1826     if (mSlicerManagers[i] == NULL)
1827       continue;
1828     mSlicerManagers[i]->SetColorWindow(window);
1829     mSlicerManagers[i]->SetPreset(6);
1830     mSlicerManagers[i]->Render();
1831   }
1832 }
1833 //------------------------------------------------------------------------------
1834
1835 //------------------------------------------------------------------------------
1836 void vvMainWindow::ApplyLevelToSetOfImages(double level, unsigned int indexMin, unsigned int indexMax)
1837 {
1838   for (unsigned int i = indexMin; i <= indexMax && i < mSlicerManagers.size(); i++) {
1839     if (mSlicerManagers[i] == NULL)
1840       continue;
1841     mSlicerManagers[i]->SetColorLevel(level);
1842     mSlicerManagers[i]->SetPreset(6);
1843     mSlicerManagers[i]->Render();
1844   }
1845 }
1846 //------------------------------------------------------------------------------
1847
1848 //------------------------------------------------------------------------------
1849 void vvMainWindow::UpdateLinkManager(std::string id, int slicer, double x, double y, double z, int temps)
1850 {
1851   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
1852     if (mSlicerManagers[i]->GetId() == id) {
1853       //mSlicerManagers[i]->SetTSlice(temps);
1854       mSlicerManagers[i]->GetSlicer(slicer)->SetCurrentPosition(x,y,z,temps);
1855       mSlicerManagers[i]->UpdateViews(0,slicer);
1856       break;
1857     }
1858   }
1859 }
1860 //------------------------------------------------------------------------------
1861
1862 //------------------------------------------------------------------------------
1863 void vvMainWindow::UpdateLinkedNavigation(std::string id, vvSlicerManager * sm, vvSlicer* refSlicer)
1864 {
1865   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
1866     if (id == mSlicerManagers[i]->GetId()) {
1867       mSlicerManagers[i]->UpdateLinkedNavigation(refSlicer);
1868     }
1869   }
1870 }
1871 //------------------------------------------------------------------------------
1872
1873 //------------------------------------------------------------------------------
1874 void vvMainWindow::ShowContextMenu(QPoint point)
1875 {
1876   if (!DataTree->selectedItems().size()) {
1877     contextActions[1]->setEnabled(0);
1878     contextActions[2]->setEnabled(0);
1879     contextActions[3]->setEnabled(0);
1880     contextActions[4]->setEnabled(0);
1881     contextActions[5]->setEnabled(0);
1882     contextActions[6]->setEnabled(0);
1883   } else {
1884     int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1885     contextActions[1]->setEnabled(1);
1886     contextActions[2]->setEnabled(
1887       DataTree->itemWidget(DataTree->selectedItems()[0],
1888                            COLUMN_RELOAD_IMAGE)->isEnabled());
1889     contextActions[3]->setEnabled(1);
1890     contextActions[5]->setEnabled(1);
1891     contextActions[6]->setEnabled(1);
1892
1893     if (mSlicerManagers[index]->GetDimension() < 3)
1894       contextActions[4]->setEnabled(0);
1895     else
1896       contextActions[4]->setEnabled(1);
1897   }
1898   contextMenu.exec(QCursor::pos());
1899 }
1900 //------------------------------------------------------------------------------
1901
1902 //------------------------------------------------------------------------------
1903 void vvMainWindow::CloseImage()
1904 {
1905   CloseImage(DataTree->selectedItems()[0],0);
1906 }
1907 //------------------------------------------------------------------------------
1908
1909 //------------------------------------------------------------------------------
1910 void vvMainWindow::ReloadImage()
1911 {
1912   ReloadImage(DataTree->selectedItems()[0],0);
1913 }
1914 //------------------------------------------------------------------------------
1915
1916 //------------------------------------------------------------------------------
1917 void vvMainWindow::SelectOverlayImage()
1918 {
1919   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1920
1921   //check if one overlay image is added
1922   for (int child = 0; child < DataTree->topLevelItem(index)->childCount(); child++)
1923     if (DataTree->topLevelItem(index)->child(child)->data(1,Qt::UserRole).toString() == "overlay") {
1924       QString error = "Cannot add more than one compared image\n";
1925       error += "Please remove first ";
1926       error += DataTree->topLevelItem(index)->child(child)->data(COLUMN_IMAGE_NAME,Qt::DisplayRole).toString();
1927       QMessageBox::information(this,tr("Problem adding compared image !"),error);
1928       return;
1929     }
1930
1931   QString Extensions = EXTENSIONS;
1932   Extensions += ";;All Files (*)";
1933   QStringList files = QFileDialog::getOpenFileNames(this,tr("Load Overlay image"),mInputPathName,Extensions);
1934   if (files.isEmpty())
1935     return;
1936
1937   std::vector<std::string> vecFileNames;
1938   for (int i = 0; i < files.size(); i++) {
1939     vecFileNames.push_back(files[i].toStdString());
1940   }
1941   AddOverlayImage(index,vecFileNames,vvImageReader::IMAGE);
1942 }
1943 //------------------------------------------------------------------------------
1944
1945 //------------------------------------------------------------------------------
1946 void vvMainWindow::AddOverlayImage(int index, std::vector<std::string> fileNames, vvImageReader::LoadedImageType type)
1947 {
1948   QString file(fileNames[0].c_str());
1949   if (QFile::exists(file))
1950   {
1951     mInputPathName = itksys::SystemTools::GetFilenamePath(file.toStdString()).c_str();
1952     itk::ImageIOBase::Pointer reader = itk::ImageIOFactory::CreateImageIO(
1953         file.toStdString().c_str(), itk::ImageIOFactory::ReadMode);
1954     reader->SetFileName(fileNames[0].c_str());
1955     reader->ReadImageInformation();
1956     std::string component = reader->GetComponentTypeAsString(reader->GetComponentType());
1957     int dimension = reader->GetNumberOfDimensions();
1958     QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
1959     vvProgressDialog progress("Opening " + file.toStdString());
1960     qApp->processEvents();
1961
1962     std::string filename = itksys::SystemTools::GetFilenameWithoutExtension(file.toStdString()).c_str();
1963     if (mSlicerManagers[index]->SetOverlay(fileNames,dimension, component,type)) {
1964       //create an item in the tree with good settings
1965       QTreeWidgetItem *item = new QTreeWidgetItem();
1966       item->setData(0,Qt::UserRole,file.toStdString().c_str());
1967       item->setData(1,Qt::UserRole,tr("overlay"));
1968       QFileInfo fileinfo(file); //Do not show the path
1969       item->setData(COLUMN_IMAGE_NAME,Qt::DisplayRole,fileinfo.fileName());
1970       item->setToolTip(COLUMN_IMAGE_NAME, mSlicerManagers[index]->GetListOfAbsoluteFilePathInOneString("overlay").c_str());
1971       qApp->processEvents();
1972
1973       for (int j = 1; j <= 4; j++) {
1974         item->setData(j,Qt::CheckStateRole,DataTree->topLevelItem(index)->data(j,Qt::CheckStateRole));
1975       }
1976
1977       //Create the buttons for reload and close
1978       qApp->processEvents();
1979       QTreePushButton* cButton = new QTreePushButton;
1980       cButton->setItem(item);
1981       cButton->setColumn(COLUMN_CLOSE_IMAGE);
1982       cButton->setToolTip(tr("close image"));
1983       cButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/exit.png")));
1984       connect(cButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
1985           this,SLOT(CloseImage(QTreeWidgetItem*, int)));
1986
1987       QTreePushButton* rButton = new QTreePushButton;
1988       rButton->setItem(item);
1989       rButton->setColumn(COLUMN_RELOAD_IMAGE);
1990       rButton->setToolTip(tr("reload image"));
1991       rButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/rotateright.png")));
1992       connect(rButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
1993           this,SLOT(ReloadImage(QTreeWidgetItem*, int)));
1994
1995       DataTree->topLevelItem(index)->setExpanded(1);
1996       DataTree->topLevelItem(index)->addChild(item);
1997       DataTree->setItemWidget(item, COLUMN_CLOSE_IMAGE, cButton);
1998       DataTree->setItemWidget(item, COLUMN_RELOAD_IMAGE, rButton);
1999
2000       //set the id of the image
2001       QString id = DataTree->topLevelItem(index)->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString();
2002       item->setData(COLUMN_IMAGE_NAME,Qt::UserRole,id.toStdString().c_str());
2003       UpdateTree();
2004       qApp->processEvents();
2005       ImageInfoChanged();
2006       QApplication::restoreOverrideCursor();
2007
2008       // Update the display to update, e.g., the sliders
2009       for(int i=0; i<4; i++)
2010         DisplaySliders(index, i);
2011     } else {
2012       QApplication::restoreOverrideCursor();
2013       QString error = "Cannot import the new image.\n";
2014       error += mSlicerManagers[index]->GetLastError().c_str();
2015       QMessageBox::information(this,tr("Problem reading image !"),error);
2016     }
2017     WindowLevelChanged();
2018   }
2019   else
2020     QMessageBox::information(this,tr("Problem reading Overlay !"),"File doesn't exist!");
2021 }
2022 //------------------------------------------------------------------------------
2023
2024
2025 //------------------------------------------------------------------------------
2026 void vvMainWindow::AddROI(int index, QString file)
2027 {
2028   /*
2029   // Get slice manager
2030
2031   // Load image
2032
2033   vvImageReader * mReader = new vvImageReader;
2034   mReader->SetInputFilename(filename.toStdString());
2035   mReader->Update(IMAGE);
2036   if (mReader->GetLastError().size() != 0) {
2037     std::cerr << "Error while reading " << filename.toStdString() << std::endl;
2038     QString error = "Cannot open file \n";
2039     error += mReader->GetLastError().c_str();
2040     QMessageBox::information(this,tr("Reading problem"),error);
2041     delete mReader;
2042     return;
2043   }
2044   vvImage::Pointer roi = mReader->GetOutput();
2045
2046   // Create roi in new tool
2047   vvToolStructureSetManager::AddImage(mCurrentSlicerManager, roi);
2048   */
2049 }
2050 //------------------------------------------------------------------------------
2051
2052 //------------------------------------------------------------------------------
2053 void vvMainWindow::SelectFusionImage()
2054 {
2055   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2056
2057   //check if one fusion image is added
2058   for (int child = 0; child < DataTree->topLevelItem(index)->childCount(); child++)
2059     if (DataTree->topLevelItem(index)->child(child)->data(1,Qt::UserRole).toString() == "fusion") {
2060       QString error = "Cannot add more than one fusion image\n";
2061       error += "Please remove first ";
2062       error += DataTree->topLevelItem(index)->child(child)->data(COLUMN_IMAGE_NAME,Qt::DisplayRole).toString();
2063       QMessageBox::information(this,tr("Problem adding fusion image !"),error);
2064       return;
2065     }
2066
2067   QString Extensions = EXTENSIONS;
2068   Extensions += ";;All Files (*)";
2069   QString file = QFileDialog::getOpenFileName(this,tr("Load Fusion image"),mInputPathName,Extensions);
2070   if (!file.isEmpty())
2071     AddFusionImage(index,file);
2072 }
2073 //------------------------------------------------------------------------------
2074
2075 //------------------------------------------------------------------------------
2076 void vvMainWindow::ResetTransformationToIdentity()
2077 {
2078   std::string actorType = DataTree->selectedItems()[0]->data(1,Qt::UserRole).toString().toStdString();
2079   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2080   mSlicerManagers[index]->ResetTransformationToIdentity(actorType);
2081   ImageInfoChanged();
2082 }
2083 //------------------------------------------------------------------------------
2084
2085 //------------------------------------------------------------------------------
2086 void vvMainWindow::AddFusionImage(int index, QString file)
2087 {
2088   if (QFile::exists(file))
2089   {
2090     mInputPathName = itksys::SystemTools::GetFilenamePath(file.toStdString()).c_str();
2091     itk::ImageIOBase::Pointer reader = itk::ImageIOFactory::CreateImageIO(
2092         file.toStdString().c_str(), itk::ImageIOFactory::ReadMode);
2093     reader->SetFileName(file.toStdString().c_str());
2094     reader->ReadImageInformation();
2095     std::string component = reader->GetComponentTypeAsString(reader->GetComponentType());
2096     if (reader) {
2097       QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
2098       vvProgressDialog progress("Opening fusion");
2099       qApp->processEvents();
2100
2101       std::string filename = itksys::SystemTools::GetFilenameWithoutExtension(file.toStdString()).c_str();
2102       if (mSlicerManagers[index]->SetFusion(file.toStdString(),
2103             reader->GetNumberOfDimensions(), component)) {
2104         //create an item in the tree with good settings
2105         QTreeWidgetItem *item = new QTreeWidgetItem();
2106         item->setData(0,Qt::UserRole,file.toStdString().c_str());
2107         item->setData(1,Qt::UserRole,tr("fusion"));
2108         QFileInfo fileinfo(filename.c_str()); //Do not show the path
2109         item->setData(COLUMN_IMAGE_NAME,Qt::DisplayRole,fileinfo.fileName());
2110         item->setToolTip(COLUMN_IMAGE_NAME, mSlicerManagers[index]->GetListOfAbsoluteFilePathInOneString("fusion").c_str());
2111         qApp->processEvents();
2112
2113         for (int j = 1; j <= 4; j++) {
2114           item->setData(j,Qt::CheckStateRole,DataTree->topLevelItem(index)->data(j,Qt::CheckStateRole));
2115         }
2116
2117         //Create the buttons for reload and close
2118         qApp->processEvents();
2119         QTreePushButton* cButton = new QTreePushButton;
2120         cButton->setItem(item);
2121         cButton->setColumn(COLUMN_CLOSE_IMAGE);
2122         cButton->setToolTip(tr("close image"));
2123         cButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/exit.png")));
2124         connect(cButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
2125             this,SLOT(CloseImage(QTreeWidgetItem*, int)));
2126
2127         QTreePushButton* rButton = new QTreePushButton;
2128         rButton->setItem(item);
2129         rButton->setColumn(COLUMN_RELOAD_IMAGE);
2130         rButton->setToolTip(tr("reload image"));
2131         rButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/rotateright.png")));
2132         connect(rButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
2133             this,SLOT(ReloadImage(QTreeWidgetItem*, int)));
2134
2135         DataTree->topLevelItem(index)->setExpanded(1);
2136         DataTree->topLevelItem(index)->addChild(item);
2137         DataTree->setItemWidget(item, COLUMN_CLOSE_IMAGE, cButton);
2138         DataTree->setItemWidget(item, COLUMN_RELOAD_IMAGE, rButton);
2139
2140         //set the id of the image
2141         QString id = DataTree->topLevelItem(index)->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString();
2142         item->setData(COLUMN_IMAGE_NAME,Qt::UserRole,id.toStdString().c_str());
2143         UpdateTree();
2144         qApp->processEvents();
2145         ImageInfoChanged();
2146         QApplication::restoreOverrideCursor();
2147       } else {
2148         QApplication::restoreOverrideCursor();
2149         QString error = "Cannot import the new image.\n";
2150         error += mSlicerManagers[index]->GetLastError().c_str();
2151         QMessageBox::information(this,tr("Problem reading image !"),error);
2152       }
2153     } else {
2154       QString error = "Cannot import the new image.\n";
2155       QMessageBox::information(this,tr("Problem reading image !"),error);
2156     }
2157   }
2158   else
2159     QMessageBox::information(this,tr("Problem reading Fusion !"),"File doesn't exist!");
2160 }
2161 //------------------------------------------------------------------------------
2162 //------------------------------------------------------------------------------
2163 void vvMainWindow::AddLandmarks(int index, QString file)
2164 {
2165   if (QFile::exists(file))
2166   {
2167     landmarksPanel->LoadFromFile(file.toStdString());
2168     landmarksPanel->SetCurrentPath(mInputPathName.toStdString());
2169     landmarksPanel->SetCurrentImage(mSlicerManagers[index]->GetFileName().c_str());
2170   }
2171   else
2172     QMessageBox::information(this,tr("Problem reading Landmarks !"),"File doesn't exist!");
2173 }
2174
2175 //------------------------------------------------------------------------------
2176 void vvMainWindow::OpenField()
2177 {
2178   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2179   //check if a vector field has already been added
2180   for (int child = 0; child < DataTree->topLevelItem(index)->childCount(); child++)
2181     if (DataTree->topLevelItem(index)->child(child)->data(1,Qt::UserRole).toString() == "vector") {
2182       QString error = "Cannot add more than one vector field\n";
2183       error += "Please remove first ";
2184       error += DataTree->topLevelItem(index)->child(child)->data(COLUMN_IMAGE_NAME,Qt::DisplayRole).toString();
2185       QMessageBox::information(this,tr("Problem adding vector field!"),error);
2186       return;
2187     }
2188
2189   QString Extensions = "Images ( *.mhd)";
2190   Extensions += ";;Images ( *.mha)";
2191   Extensions += ";;VF Images ( *.vf)";
2192   Extensions += ";;nii Images ( *.nii)";
2193   Extensions += ";;nrrd Images ( *.nrrd)";
2194   Extensions += ";;nhdr Images ( *.nhdr)";
2195   Extensions += ";;All Files (*)";
2196   QString file = QFileDialog::getOpenFileName(this,tr("Load deformation field"),mInputPathName,Extensions);
2197   if (!file.isEmpty())
2198     AddField(file,index);
2199 }
2200 //------------------------------------------------------------------------------
2201
2202
2203 //------------------------------------------------------------------------------
2204 void vvMainWindow::AddFieldEntry(QString filename,int index,bool from_disk)
2205 {
2206   //create an item in the tree with good settings
2207   QTreeWidgetItem *item = new QTreeWidgetItem();
2208   item->setData(0,Qt::UserRole,filename.toStdString().c_str());
2209   item->setData(1,Qt::UserRole,tr("vector"));
2210   QFileInfo fileinfo(filename); //Do not show the path
2211   item->setData(COLUMN_IMAGE_NAME,Qt::DisplayRole,fileinfo.fileName());
2212   item->setToolTip(COLUMN_IMAGE_NAME, mSlicerManagers[index]->GetListOfAbsoluteFilePathInOneString("vector").c_str());
2213   qApp->processEvents();
2214
2215   for (int j = 1; j <= 4; j++) {
2216     item->setData(j,Qt::CheckStateRole,DataTree->topLevelItem(index)->data(j,Qt::CheckStateRole));
2217   }
2218
2219   //Create the buttons for reload and close
2220   qApp->processEvents();
2221   QTreePushButton* cButton = new QTreePushButton;
2222   cButton->setItem(item);
2223   cButton->setColumn(COLUMN_CLOSE_IMAGE);
2224   cButton->setToolTip(tr("close vector field"));
2225   cButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/exit.png")));
2226   connect(cButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
2227           this,SLOT(CloseImage(QTreeWidgetItem*, int)));
2228
2229   QTreePushButton* rButton = new QTreePushButton;
2230   rButton->setItem(item);
2231   rButton->setColumn(COLUMN_RELOAD_IMAGE);
2232   rButton->setToolTip(tr("reload vector field"));
2233   rButton->setEnabled(from_disk);
2234   rButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/rotateright.png")));
2235   connect(rButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
2236           this,SLOT(ReloadImage(QTreeWidgetItem*, int)));
2237
2238   DataTree->topLevelItem(index)->setExpanded(1);
2239   DataTree->topLevelItem(index)->addChild(item);
2240   DataTree->setItemWidget(item, COLUMN_RELOAD_IMAGE, rButton);
2241   DataTree->setItemWidget(item, COLUMN_CLOSE_IMAGE, cButton);
2242
2243   //set the id of the image
2244   QString id = DataTree->topLevelItem(index)->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString();
2245   item->setData(COLUMN_IMAGE_NAME,Qt::UserRole,id.toStdString().c_str());
2246   UpdateTree();
2247   qApp->processEvents();
2248   ImageInfoChanged();
2249   QApplication::restoreOverrideCursor();
2250 }
2251 //------------------------------------------------------------------------------
2252
2253
2254 //------------------------------------------------------------------------------
2255 void vvMainWindow::AddField(vvImage::Pointer vf,QString file,int index)
2256 {
2257   QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
2258   vvSlicerManager* imageManager = mSlicerManagers[index];
2259   if (imageManager->SetVF(vf,file.toStdString())) {
2260     AddFieldEntry(file,index,false);
2261   } else {
2262     QString error = "Cannot import the vector field for this image.\n";
2263     error += imageManager->GetLastError().c_str();
2264     QMessageBox::information(this,tr("Problem reading VF !"),error);
2265   }
2266   QApplication::restoreOverrideCursor();
2267 }
2268 //------------------------------------------------------------------------------
2269
2270
2271 //------------------------------------------------------------------------------
2272 void vvMainWindow::AddField(QString file,int index)
2273 {
2274   if (QFile::exists(file)) {
2275     mInputPathName = itksys::SystemTools::GetFilenamePath(file.toStdString()).c_str();
2276
2277     //init the progress events
2278     QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
2279     vvProgressDialog progress("Opening " + file.toStdString());
2280     qApp->processEvents();
2281
2282     //read the vector and put it in the current mSlicerManager
2283     vvSlicerManager* imageManager = mSlicerManagers[index];
2284     qApp->processEvents();
2285
2286     std::string filename = itksys::SystemTools::GetFilenameWithoutExtension(file.toStdString()).c_str();
2287     if (imageManager->SetVF(file.toStdString())) {
2288       imageManager->Render();
2289       AddFieldEntry(file,index,true);
2290     } else {
2291       QApplication::restoreOverrideCursor();
2292       QString error = "Cannot import the vector field for this image.\n";
2293       error += imageManager->GetLastError().c_str();
2294       QMessageBox::information(this,tr("Problem reading VF !"),error);
2295     }
2296   } else
2297     QMessageBox::information(this,tr("Problem reading VF !"),"File doesn't exist!");
2298
2299 }
2300 //------------------------------------------------------------------------------
2301
2302
2303 //------------------------------------------------------------------------------
2304 void vvMainWindow::SetVFProperty(int subsampling, int scale, int log, int width, double r, double g, double b)
2305 {
2306   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2307   if (mSlicerManagers[index]->GetSlicer(0)->GetVF()) {
2308     for (int i = 0; i < 4; i++) {
2309       mSlicerManagers[index]->GetSlicer(i)->SetVFSubSampling(subsampling);
2310       mSlicerManagers[index]->GetSlicer(i)->SetVFScale(scale);
2311       mSlicerManagers[index]->GetSlicer(i)->SetVFWidth(width);
2312       mSlicerManagers[index]->GetSlicer(i)->SetVFColor(r,g,b);
2313       if (log > 0)
2314         mSlicerManagers[index]->GetSlicer(i)->SetVFLog(1);
2315       else
2316         mSlicerManagers[index]->GetSlicer(i)->SetVFLog(0);
2317     }
2318   }
2319 }
2320 //------------------------------------------------------------------------------
2321
2322
2323 //------------------------------------------------------------------------------
2324 void vvMainWindow::SetOverlayProperty(int color, int linked, double window, double level)
2325 {
2326   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2327   if (mSlicerManagers[index]->GetSlicer(0)->GetOverlay()) {
2328     mSlicerManagers[index]->SetOverlayColor(color);
2329     mSlicerManagers[index]->SetColorMap(0);
2330     mSlicerManagers[index]->SetLinkOverlayWindowLevel(linked);
2331     mSlicerManagers[index]->SetOverlayColorWindow(window);
2332     mSlicerManagers[index]->SetOverlayColorLevel(level);
2333     mSlicerManagers[index]->Render();
2334   }
2335 }
2336 //------------------------------------------------------------------------------
2337
2338 //------------------------------------------------------------------------------
2339 void vvMainWindow::SetFusionProperty(int opacity, int thresOpacity, int colormap,double window, double level, bool showLegend)
2340 {
2341   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2342   if (mSlicerManagers[index]->GetSlicer(0)->GetFusion()) {
2343     mSlicerManagers[index]->SetFusionColorMap(colormap);
2344     mSlicerManagers[index]->SetFusionOpacity(opacity);
2345     mSlicerManagers[index]->SetFusionThresholdOpacity(thresOpacity);
2346     mSlicerManagers[index]->SetFusionWindow(window);
2347     mSlicerManagers[index]->SetFusionLevel(level);
2348     mSlicerManagers[index]->SetFusionShowLegend(showLegend);
2349     mSlicerManagers[index]->SetColorMap(0);
2350     mSlicerManagers[index]->Render();
2351   }
2352 }
2353 //------------------------------------------------------------------------------
2354
2355 //------------------------------------------------------------------------------
2356 void vvMainWindow::SaveAs()
2357 {
2358   if (DataTree->selectedItems()[0]->data(1,Qt::UserRole).toString() == "vector") {
2359     QMessageBox::warning(this,tr("Unsupported type"),tr("Sorry, saving a vector field is unsupported for the moment"));
2360     return;
2361   }
2362
2363   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2364   int dimension = mSlicerManagers[index]->GetDimension();
2365   QStringList OutputListeFormat;
2366   OutputListeFormat.clear();
2367   if (dimension == 1) {
2368     OutputListeFormat.push_back(".mhd");
2369     OutputListeFormat.push_back(".mha");
2370   }
2371   if (dimension == 2) {
2372     OutputListeFormat.push_back(".bmp");
2373     OutputListeFormat.push_back(".png");
2374     OutputListeFormat.push_back(".jpeg");
2375     OutputListeFormat.push_back(".tif");
2376     OutputListeFormat.push_back(".mhd");
2377     OutputListeFormat.push_back(".mha");
2378     OutputListeFormat.push_back(".hdr");
2379     OutputListeFormat.push_back(".vox");
2380   } else if (dimension == 3) {
2381     OutputListeFormat.push_back(".mhd");
2382     OutputListeFormat.push_back(".mha");
2383     OutputListeFormat.push_back(".nii");
2384     OutputListeFormat.push_back(".nrrd");
2385     OutputListeFormat.push_back(".nhdr");
2386     OutputListeFormat.push_back(".hdr");
2387     OutputListeFormat.push_back(".vox");
2388   } else if (dimension == 4) {
2389     OutputListeFormat.push_back(".mhd");
2390     OutputListeFormat.push_back(".mha");
2391     OutputListeFormat.push_back(".nii");
2392     OutputListeFormat.push_back(".nrrd");
2393     OutputListeFormat.push_back(".nhdr");
2394   }
2395   QString Extensions = "AllFiles(*.*)";
2396   for (int i = 0; i < OutputListeFormat.count(); i++) {
2397     Extensions += ";;Images ( *";
2398     Extensions += OutputListeFormat[i];
2399     Extensions += ")";
2400   }
2401   QString fileName = QFileDialog::getSaveFileName(this,
2402                      tr("Save As"),
2403                      mSlicerManagers[index]->GetFileName().c_str(),
2404                      Extensions);
2405   if (!fileName.isEmpty()) {
2406     std::string fileformat = itksys::SystemTools::GetFilenameLastExtension(fileName.toStdString());
2407     if (OutputListeFormat.contains(
2408           fileformat.c_str())) {
2409       QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
2410       std::string action = "Saving";
2411       vvProgressDialog progress("Saving "+fileName.toStdString());
2412       qApp->processEvents();
2413       vvImageWriter::Pointer writer = vvImageWriter::New();
2414       writer->SetOutputFileName(fileName.toStdString());
2415       writer->SetInput(mSlicerManagers[index]->GetImage());
2416
2417       // Check on transform and prompt user
2418       writer->SetSaveTransform(false);
2419       bool bId = true;
2420       for(int i=0; i<4; i++)
2421         for(int j=0; j<4; j++) {
2422           // TODO SR and BP: check on the list of transforms and not the first only
2423           double elt = mSlicerManagers[index]->GetImage()->GetTransform()[0]->GetMatrix()->GetElement(i,j);
2424           if(i==j && elt!=1.)
2425             bId = false;
2426           if(i!=j && elt!=0.)
2427             bId = false;
2428         }
2429       if( !bId ) {
2430         QString warning = "The image has an associated linear transform. Do you want to save it along?";
2431         QMessageBox msgBox(QMessageBox::Warning, tr("Save transform"), warning, 0, this);
2432         msgBox.addButton(tr("Yes"), QMessageBox::AcceptRole);
2433         msgBox.addButton(tr("No"), QMessageBox::RejectRole);
2434         if (msgBox.exec() == QMessageBox::AcceptRole)
2435           writer->SetSaveTransform(true);
2436       }
2437
2438       writer->Update();
2439       QApplication::restoreOverrideCursor();
2440       if (writer->GetLastError().size()) {
2441         QString error = "Saving did not succeed\n";
2442         error += writer->GetLastError().c_str();
2443         QMessageBox::information(this,tr("Saving Problem"),error);
2444         SaveAs();
2445       }
2446     } else {
2447       QString error = fileformat.c_str();
2448       if (error.isEmpty())
2449         error += "no file format specified !";
2450       else
2451         error += " format unknown !!!\n";
2452       QMessageBox::information(this,tr("Saving Problem"),error);
2453       SaveAs();
2454     }
2455   }
2456 }
2457 //------------------------------------------------------------------------------
2458
2459 //------------------------------------------------------------------------------
2460 void vvMainWindow::SaveCurrentState()
2461 {
2462   QString Extensions = "XML Files(*.xml)";
2463   QString fileName = QFileDialog::getSaveFileName(this,
2464                      tr("Save Current Window State"),
2465                      "",
2466                      Extensions);
2467
2468   SaveCurrentStateAs(fileName.toStdString());
2469 }
2470 //------------------------------------------------------------------------------
2471
2472 //------------------------------------------------------------------------------
2473 void vvMainWindow::SaveCurrentStateAs(const std::string& stateFile)
2474 {
2475   vvSaveState save_state;
2476   save_state.Run(this, stateFile);
2477 }
2478
2479 //------------------------------------------------------------------------------
2480 void vvMainWindow::ReadSavedState()
2481 {
2482   QString Extensions = "XML Files(*.xml)";
2483   QString fileName = QFileDialog::getOpenFileName(this,
2484                      tr("Load Window State"),
2485                      "",
2486                      Extensions);
2487
2488   ReadSavedStateFile(fileName.toStdString());
2489 }
2490 //------------------------------------------------------------------------------
2491
2492 //------------------------------------------------------------------------------
2493 void vvMainWindow::ReadSavedStateFile(const std::string& stateFile)
2494 {
2495   vvReadState read_state;
2496   read_state.Run(this, stateFile);
2497 }
2498 //------------------------------------------------------------------------------
2499
2500 //------------------------------------------------------------------------------
2501 void vvMainWindow::LinkAllImages()
2502 {
2503         linkPanel->linkAll();
2504 }
2505
2506 //------------------------------------------------------------------------------
2507 void vvMainWindow::AddLink(QString image1,QString image2,bool fromPanel)
2508 {
2509   if (!fromPanel) {
2510     // delegate to linkPanel if call came from elsewhere...
2511     linkPanel->addLinkFromIds(image1, image2);
2512     return;
2513   }
2514
2515   unsigned int sm1 = 0;
2516   unsigned int sm2 = 0;
2517
2518   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
2519     if (image1.toStdString() == mSlicerManagers[i]->GetId()) {
2520       mSlicerManagers[i]->AddLink(image2.toStdString());
2521       sm1 = i;
2522     }
2523     if (image2.toStdString() == mSlicerManagers[i]->GetId()) {
2524       mSlicerManagers[i]->AddLink(image1.toStdString());
2525       sm2 = i;
2526     }
2527   }
2528
2529   if (linkPanel->isLinkAll())   {
2530     emit UpdateLinkedNavigation(mSlicerManagers[sm1]->GetId(), mSlicerManagers[mCurrentPickedImageIndex], mSlicerManagers[mCurrentPickedImageIndex]->GetSlicer(0));
2531     emit UpdateLinkedNavigation(mSlicerManagers[sm2]->GetId(), mSlicerManagers[mCurrentPickedImageIndex], mSlicerManagers[mCurrentPickedImageIndex]->GetSlicer(0));
2532   } else {
2533     emit UpdateLinkedNavigation(mSlicerManagers[sm2]->GetId(), mSlicerManagers[sm1], mSlicerManagers[sm1]->GetSlicer(0));
2534   }
2535 }
2536
2537 //------------------------------------------------------------------------------
2538
2539
2540 //------------------------------------------------------------------------------
2541 void vvMainWindow::RemoveLink(QString image1,QString image2)
2542 {
2543   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
2544     if (image1.toStdString() == mSlicerManagers[i]->GetId()) {
2545       mSlicerManagers[i]->RemoveLink(image2.toStdString());
2546     }
2547     if (image2.toStdString() == mSlicerManagers[i]->GetId()) {
2548       mSlicerManagers[i]->RemoveLink(image1.toStdString());
2549     }
2550   }
2551 }
2552 //------------------------------------------------------------------------------
2553
2554 //------------------------------------------------------------------------------
2555 void vvMainWindow::ChangeImageWithIndexOffset(vvSlicerManager *sm, int slicer, int offset)
2556 {
2557   if(mSlicerManagers.size()==1)
2558     return;
2559
2560   int index = 0;
2561   while(sm != mSlicerManagers[index])
2562     index++;
2563   index = (index+offset+mSlicerManagers.size()) % mSlicerManagers.size();
2564
2565   QTreeWidgetItem* item = GetItemFromSlicerManager(mSlicerManagers[index]);
2566   item->setData(slicer+1,Qt::CheckStateRole,2);         //change checkbox
2567   CurrentImageChanged(mSlicerManagers[index]->GetId()); //select new image
2568   DisplayChanged(item,slicer+1);
2569 }
2570 //------------------------------------------------------------------------------
2571
2572 void vvMainWindow::HorizontalSliderMoved(int value,int column, int slicer_index)
2573 {
2574   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
2575     if (DataTree->topLevelItem(i)->data(column,Qt::CheckStateRole).toInt() > 1) {
2576       for (int j = 0; j < 4; j++) {
2577         mSlicerManagers[i]->SetTSliceInSlicer(value,j);
2578         //if (mSlicerManagers[i]->GetSlicer(j)->GetImageActor()->GetVisibility())
2579         //UpdateTSlice(j,value);
2580       }
2581       mSlicerManagers[i]->GetSlicer(slicer_index)->Render();
2582       break;
2583     }
2584   }
2585 }
2586 //------------------------------------------------------------------------------
2587
2588
2589 //------------------------------------------------------------------------------
2590 void vvMainWindow::NOHorizontalSliderMoved()
2591 {
2592   // if (mCurrentTime == NOHorizontalSlider->value()) return;
2593   HorizontalSliderMoved(NOHorizontalSlider->value(),COLUMN_UL_VIEW,0);
2594 //  mCurrentTime = NOHorizontalSlider->value();
2595 }
2596 //------------------------------------------------------------------------------
2597
2598
2599 //------------------------------------------------------------------------------
2600 void vvMainWindow::NEHorizontalSliderMoved()
2601 {
2602   // if (mCurrentTime == NEHorizontalSlider->value()) return;
2603   HorizontalSliderMoved(NEHorizontalSlider->value(),COLUMN_UR_VIEW,1);
2604 //  mCurrentTime = NEHorizontalSlider->value();
2605 }
2606 //------------------------------------------------------------------------------
2607
2608
2609 //------------------------------------------------------------------------------
2610 void vvMainWindow::SOHorizontalSliderMoved()
2611 {
2612   // if (mCurrentTime == SOHorizontalSlider->value()) return;
2613   HorizontalSliderMoved(SOHorizontalSlider->value(),COLUMN_DL_VIEW,2);
2614   // mCurrentTime = SOHorizontalSlider->value();
2615 }
2616 //------------------------------------------------------------------------------
2617
2618
2619 //------------------------------------------------------------------------------
2620 void vvMainWindow::SEHorizontalSliderMoved()
2621 {
2622   // if (mCurrentTime == SEHorizontalSlider->value()) return;
2623   HorizontalSliderMoved(SEHorizontalSlider->value(),COLUMN_DR_VIEW,3);
2624   // mCurrentTime = SEHorizontalSlider->value();
2625 }
2626 //------------------------------------------------------------------------------
2627
2628 //------------------------------------------------------------------------------
2629 void vvMainWindow::NOVerticalSliderChanged()
2630 {
2631   static int value=-1;
2632   if (value == NOVerticalSlider->value()) return;
2633   else value = NOVerticalSlider->value();
2634   //  int value = NOVerticalSlider->value();
2635   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
2636     if (DataTree->topLevelItem(i)->data(COLUMN_UL_VIEW,Qt::CheckStateRole).toInt() > 1) {
2637       if (mSlicerManagers[i]->GetSlicer(0)->GetSlice() != value) {
2638         mSlicerManagers[i]->GetSlicer(0)->SetSlice(value);
2639         mSlicerManagers[i]->VerticalSliderHasChanged(0, value);
2640
2641         // If nor Update/Render -> slider not work
2642         // only render = ok navigation, but for contour Update needed but slower ?
2643
2644         mSlicerManagers[i]->UpdateSlice(0);  // <-- DS add this. Not too much update ? YES. but needed for ImageContour ...
2645         //mSlicerManagers[i]->GetSlicer(0)->Render(); // <-- DS add this, needed for contour, seems ok ? not too slow ?
2646       }
2647       break;
2648     }
2649   }
2650 }
2651 //------------------------------------------------------------------------------
2652
2653
2654 //------------------------------------------------------------------------------
2655 void vvMainWindow::NEVerticalSliderChanged()
2656 {
2657   static int value=-1;
2658   if (value == NEVerticalSlider->value()) return;
2659   else value = NEVerticalSlider->value();
2660   //  int value = NEVerticalSlider->value();
2661   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
2662     if (DataTree->topLevelItem(i)->data(COLUMN_UR_VIEW,Qt::CheckStateRole).toInt() > 1) {
2663       if (mSlicerManagers[i]->GetSlicer(1)->GetSlice() != value) {
2664         mSlicerManagers[i]->GetSlicer(1)->SetSlice(value);
2665         mSlicerManagers[i]->VerticalSliderHasChanged(1, value);
2666         mSlicerManagers[i]->UpdateSlice(1);
2667         //mSlicerManagers[i]->GetSlicer(1)->Render(); // <-- DS add this, needed for contour, seems ok ? not too slow ?
2668       }
2669       break;
2670     }
2671   }
2672 }
2673 //------------------------------------------------------------------------------
2674
2675
2676 //------------------------------------------------------------------------------
2677 void vvMainWindow::SOVerticalSliderChanged()
2678 {
2679   static int value=-1;
2680   if (value == SOVerticalSlider->value()) return;
2681   else value = SOVerticalSlider->value();
2682   //int value = SOVerticalSlider->value();
2683   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
2684     if (DataTree->topLevelItem(i)->data(COLUMN_DL_VIEW,Qt::CheckStateRole).toInt() > 1) {
2685       if (mSlicerManagers[i]->GetSlicer(2)->GetSlice() != value) {
2686         mSlicerManagers[i]->GetSlicer(2)->SetSlice(value);
2687         mSlicerManagers[i]->VerticalSliderHasChanged(2, value);
2688         mSlicerManagers[i]->UpdateSlice(2);
2689         //mSlicerManagers[i]->GetSlicer(2)->Render(); // <-- DS add this, needed for contour, seems ok ? not too slow ?
2690       }
2691       // else { DD("avoid SOVerticalSlider slicer update"); }
2692       break;
2693     }
2694   }
2695 }
2696 //------------------------------------------------------------------------------
2697
2698
2699 //------------------------------------------------------------------------------
2700 void vvMainWindow::SEVerticalSliderChanged()
2701 {
2702   static int value=-1;
2703   if (value == SEVerticalSlider->value()) return;
2704   else value = SEVerticalSlider->value();
2705   // int value = SEVerticalSlider->value();
2706   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
2707     if (DataTree->topLevelItem(i)->data(COLUMN_DR_VIEW,Qt::CheckStateRole).toInt() > 1) {
2708       if (mSlicerManagers[i]->GetSlicer(3)->GetSlice() != value) {
2709         mSlicerManagers[i]->GetSlicer(3)->SetSlice(value);
2710         mSlicerManagers[i]->VerticalSliderHasChanged(3, value);
2711         mSlicerManagers[i]->UpdateSlice(3);
2712         //mSlicerManagers[i]->GetSlicer(3)->Render(); // <-- DS add this, needed for contour, seems ok ? not too slow ?
2713       }
2714       break;
2715     }
2716   }
2717 }
2718 //------------------------------------------------------------------------------
2719
2720
2721 //------------------------------------------------------------------------------
2722 void vvMainWindow::UpdateSlice(int slicer, int slice)
2723 {
2724   // DD("vvMainWindow::UpdateSlice");
2725 //   DD(slicer);
2726 //   DD(slice);
2727   if (slicer == 0) {
2728     //    if (slice != NOVerticalSlider->value())
2729     NOVerticalSlider->setValue(slice);
2730   } else {
2731     if (slicer == 1)
2732       NEVerticalSlider->setValue(slice);
2733     else {
2734       if (slicer == 2)
2735         SOVerticalSlider->setValue(slice);
2736       else {
2737         if (slicer == 3)
2738           SEVerticalSlider->setValue(slice);
2739       }
2740     }
2741   }
2742   // DD("vvMainWindow:UpdateSlice END");
2743 }
2744 //------------------------------------------------------------------------------
2745
2746
2747 //------------------------------------------------------------------------------
2748 void vvMainWindow::UpdateTSlice(int slicer, int slice)
2749 {
2750   switch (slicer) {
2751   case 0:
2752     NOHorizontalSlider->setValue(slice);
2753     break;
2754   case 1:
2755     NEHorizontalSlider->setValue(slice);
2756     break;
2757   case 2:
2758     SOHorizontalSlider->setValue(slice);
2759     break;
2760   case 3:
2761     SEHorizontalSlider->setValue(slice);
2762     break;
2763   }
2764 }
2765 //------------------------------------------------------------------------------
2766
2767
2768 //------------------------------------------------------------------------------
2769 void vvMainWindow::UpdateSliceRange(int slicer, int min, int max, int tmin, int tmax)
2770 {
2771   //int position = int((min+max)/2);
2772   int position = mSlicerManagers[mCurrentPickedImageIndex]->GetSlicer(slicer)->GetSlice();
2773   if (slicer == 0) {
2774     NOVerticalSlider->setRange(min,max);
2775     NOHorizontalSlider->setRange(tmin,tmax);
2776     NOVerticalSlider->setValue(position);
2777   } else if (slicer == 1) {
2778     NEVerticalSlider->setRange(min,max);
2779     NEHorizontalSlider->setRange(tmin,tmax);
2780     NEVerticalSlider->setValue(position);
2781   } else if (slicer == 2) {
2782     SOVerticalSlider->setRange(min,max);
2783     SOHorizontalSlider->setRange(tmin,tmax);
2784     SOVerticalSlider->setValue(position);
2785   } else if (slicer == 3) {
2786     SEVerticalSlider->setRange(min,max);
2787     SEHorizontalSlider->setRange(tmin,tmax);
2788     SEVerticalSlider->setValue(position);
2789   }
2790 }
2791 //------------------------------------------------------------------------------
2792
2793
2794 //------------------------------------------------------------------------------
2795 void vvMainWindow::SaveNOScreenshot()
2796 {
2797   SaveScreenshot(NOViewWidget);
2798 }
2799 //------------------------------------------------------------------------------
2800
2801
2802 //------------------------------------------------------------------------------
2803 void vvMainWindow::SaveNEScreenshot()
2804 {
2805   SaveScreenshot(NEViewWidget);
2806 }
2807 //------------------------------------------------------------------------------
2808
2809
2810 //------------------------------------------------------------------------------
2811 void vvMainWindow::SaveSOScreenshot()
2812 {
2813   SaveScreenshot(SOViewWidget);
2814 }
2815 //------------------------------------------------------------------------------
2816
2817
2818 //------------------------------------------------------------------------------
2819 void vvMainWindow::SaveSEScreenshot()
2820 {
2821   SaveScreenshot(SEViewWidget);
2822 }
2823 //------------------------------------------------------------------------------
2824
2825
2826 //------------------------------------------------------------------------------
2827 void vvMainWindow::SaveScreenshotAllSlices()
2828 {
2829   QVTKWidget *widget = NOViewWidget;
2830
2831   int index = 0;// GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2832   vvSlicerManager * SM = mSlicerManagers[index];
2833   vvImage * image = SM->GetImage();
2834   vvSlicer * slicer = SM->GetSlicer(0);
2835   int orientation = slicer->GetOrientation();
2836   int nbSlices = image->GetSize()[orientation];
2837   vtkSmartPointer<vtkRenderWindow>  renderWindow = widget->GetRenderWindow();
2838
2839   // Select filename base
2840   QString filename = QFileDialog::getSaveFileName(this,
2841                                                   tr("Save As (filename will be completed by slice number)"),
2842                                                   itksys::SystemTools::GetFilenamePath(mSlicerManagers[index]->GetFileName()).c_str(),
2843                                                   "Images( *.png);;Images( *.jpg)");
2844
2845   // Loop on slices
2846   for(int i=0; i<nbSlices; i++) {
2847     // Change the slice
2848     slicer->SetSlice(i); // -> change the slice of the current slicer
2849     SM->UpdateSlice(0); // --> this one emit UpdateSlice
2850     QCoreApplication::flush(); // -> needed to force display of contours
2851
2852     // Screenshot
2853     vtkSmartPointer<vtkWindowToImageFilter> windowToImageFilter = vtkSmartPointer<vtkWindowToImageFilter>::New();
2854     windowToImageFilter->SetInput(renderWindow);
2855     windowToImageFilter->SetMagnification(1);
2856     windowToImageFilter->SetInputBufferTypeToRGBA(); //also record the alpha (transparency) channel
2857     windowToImageFilter->Update();
2858
2859     vtkSmartPointer<vtkPNGWriter> writer = vtkSmartPointer<vtkPNGWriter>::New();
2860     std::string fn = itksys::SystemTools::GetFilenameWithoutLastExtension(filename.toStdString());
2861     std::string num = clitk::toString(i);
2862     if (i<10) num = "0"+num;
2863     if (i<100) num = "0"+num;
2864     if (i<1000) num = "0"+num;
2865
2866     fn = itksys::SystemTools::GetFilenamePath(filename.toStdString()) + "/"+ fn
2867       + "_" + num + itksys::SystemTools::GetFilenameLastExtension(filename.toStdString());
2868     writer->SetFileName(fn.c_str());
2869     writer->SetInput(windowToImageFilter->GetOutput());
2870     writer->Write();
2871   }
2872 }
2873 //------------------------------------------------------------------------------
2874
2875
2876 //------------------------------------------------------------------------------
2877 void vvMainWindow::SaveScreenshot(QVTKWidget *widget)
2878 {
2879   QString Extensions = "Images( *.png);;";
2880   Extensions += "Images( *.jpg);;";
2881   Extensions += "Images( *.bmp);;";
2882   Extensions += "Images( *.tif);;";
2883   Extensions += "Images( *.ppm)";
2884 #if defined(VTK_USE_FFMPEG_ENCODER) || defined(VTK_USE_VIDEO_FOR_WINDOWS)
2885   Extensions += ";;Video( *.avi)";
2886 #endif
2887 #ifdef VTK_USE_MPEG2_ENCODER
2888   Extensions += ";;Video( *.mpg)";
2889 #endif
2890 #ifdef CLITK_EXPERIMENTAL
2891   Extensions += ";;Video( *.gif)";
2892 #endif
2893
2894   int smIndex=GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2895   QString fileName = QFileDialog::getSaveFileName(this,
2896                      tr("Save As"),
2897                      itksys::SystemTools::GetFilenamePath(mSlicerManagers[smIndex]->GetFileName()).c_str(),
2898                      Extensions);
2899
2900   if (!fileName.isEmpty()) {
2901     vtkSmartPointer<vtkWindowToImageFilter> w2i = vtkSmartPointer<vtkWindowToImageFilter>::New();
2902     w2i->SetInput(widget->GetRenderWindow());
2903     w2i->Update();
2904     vtkImageData *image = w2i->GetOutput();
2905
2906     std::string ext(itksys::SystemTools::GetFilenameLastExtension(fileName.toStdString()));
2907
2908     // Image
2909     vtkImageWriter *imgwriter = NULL;
2910     if (ext==".bmp")
2911       imgwriter = vtkBMPWriter::New();
2912     else if (ext==".tif")
2913       imgwriter = vtkTIFFWriter::New();
2914     else if (ext==".ppm")
2915       imgwriter = vtkPNMWriter::New();
2916     else if (ext==".png")
2917       imgwriter = vtkPNGWriter::New();
2918     else if (ext==".jpg")
2919       imgwriter = vtkJPEGWriter::New();
2920
2921     // Snapshot image if not null
2922     if(imgwriter!=NULL) {
2923       imgwriter->SetInput(image);
2924       imgwriter->SetFileName(fileName.toStdString().c_str());
2925       imgwriter->Write();
2926       return;
2927     }
2928
2929     // Video
2930     vtkGenericMovieWriter *vidwriter = NULL;
2931 #if CLITK_EXPERIMENTAL == 1
2932     if (ext==".gif") {
2933       vvAnimatedGIFWriter *gif = vvAnimatedGIFWriter::New();
2934       vidwriter = gif;
2935
2936       // FPS
2937       bool ok;
2938       int fps = QInputDialog::getInteger(this, tr("Number of frames per second"),
2939                                      tr("FPS:"), 5, 0, 1000, 1, &ok);
2940       if(ok)
2941         gif->SetRate(fps);
2942
2943       // Loops
2944       int loops = QInputDialog::getInteger(this, tr("Loops"),
2945                                      tr("Number of loops (0 means infinite):"), 0, 0, 1000000000, 1, &ok);
2946       if(ok)
2947         gif->SetLoops(loops);
2948
2949       // Dithering
2950       QString msg = "Would you like to activate dithering?";
2951       QMessageBox msgBox(QMessageBox::Question, tr("Dithering"),msg, 0, this);
2952       msgBox.addButton(tr("Yes"), QMessageBox::AcceptRole);
2953       msgBox.addButton(tr("No"), QMessageBox::RejectRole);
2954       gif->SetDither(msgBox.exec() == QMessageBox::AcceptRole);
2955     }
2956 #endif
2957 #ifdef VTK_USE_VIDEO_FOR_WINDOWS
2958     if (ext==".avi") {
2959       vtkAVIWriter *mpg = vtkAVIWriter::New();
2960       vidwriter = mpg;
2961       mpg->SetQuality(2);
2962       bool ok;
2963       int fps = QInputDialog::getInteger(this, tr("Number of frames per second"),
2964                                      tr("FPS:"), 5, 0, 1024, 1, &ok);
2965       if(!ok)
2966         fps = 5;
2967       mpg->SetRate(fps);
2968     }
2969 #endif
2970 #ifdef VTK_USE_FFMPEG_ENCODER
2971     if (ext==".avi") {
2972       vtkFFMPEGWriter *mpg = vtkFFMPEGWriter::New();
2973       vidwriter = mpg;
2974       mpg->SetQuality(2);
2975       bool ok;
2976       int fps = QInputDialog::getInteger(this, tr("Number of frames per second"),
2977                                      tr("FPS:"), 5, 0, 1024, 1, &ok);
2978       if(!ok)
2979         fps = 5;
2980       mpg->SetRate(fps);
2981       mpg->SetBitRateTolerance(int(ceil(12.0*1024*1024/fps)));
2982     }
2983 #endif
2984 #ifdef VTK_USE_MPEG2_ENCODER
2985     if (ext==".mpg") {
2986       vtkMPEG2Writer *mpg = vtkMPEG2Writer::New();
2987       vidwriter = mpg;
2988     }
2989 #endif
2990
2991     // Take video if not null
2992     if(vidwriter!=NULL){
2993       vidwriter->SetInput(image);
2994       vidwriter->SetFileName(fileName.toStdString().c_str());
2995       vidwriter->Start();
2996       int nSlice = mSlicerManagers[smIndex]->GetSlicer(0)->GetTMax();
2997       for(int i=0; i<=nSlice; i++) {
2998         mSlicerManagers[smIndex]->SetNextTSlice(0);
2999         vtkSmartPointer<vtkWindowToImageFilter> w2i = vtkSmartPointer<vtkWindowToImageFilter>::New();
3000         w2i->SetInput(widget->GetRenderWindow());
3001         w2i->Update();
3002         vidwriter->SetInput(w2i->GetOutput());
3003         vidwriter->Write();
3004       }
3005       vidwriter->End();
3006       vidwriter->Delete();
3007       return;
3008     }
3009
3010     QMessageBox::information(this,tr("Problem saving screenshot !"),tr("Cannot save image.\nPlease set a file extension !!!"));
3011   }
3012 }
3013 //------------------------------------------------------------------------------
3014
3015
3016 //------------------------------------------------------------------------------
3017 void vvMainWindow::GoToCursor()
3018 {
3019   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
3020   for (int column = 1; column < 5; column++) {
3021     if (DataTree->selectedItems()[0]->data(column,Qt::CheckStateRole).toInt() > 1) {
3022       double* cursorPos = mSlicerManagers[index]->GetSlicer(column-1)->GetCursorPosition();
3023       mSlicerManagers[index]->GetSlicer(column-1)->SetCurrentPosition(
3024         cursorPos[0],cursorPos[1],cursorPos[2],cursorPos[3]);
3025       mSlicerManagers[index]->UpdateViews(1,column-1);
3026       mSlicerManagers[index]->UpdateLinked(column-1);
3027       break;
3028     }
3029   }
3030 }
3031 //------------------------------------------------------------------------------
3032
3033 //------------------------------------------------------------------------------
3034 void vvMainWindow::PlayPause()
3035 {
3036   if (playMode) {
3037     playMode = 0;
3038     playButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/player_play.png")));
3039     ImageInfoChanged();
3040     return;
3041   } else {
3042     int image_number=DataTree->topLevelItemCount();
3043     bool has_temporal;
3044     for (int i=0; i<image_number; i++)
3045       if (mSlicerManagers[i]->GetSlicer(0)->GetTMax() > 0) {
3046         has_temporal=true;
3047         break;
3048       }
3049     if (has_temporal) {
3050       playMode = 1;
3051       playButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/player_pause.png")));
3052       QTimer::singleShot(1000/mFrameRate, this, SLOT(PlayNext()));
3053     }
3054   }
3055 }
3056 //------------------------------------------------------------------------------
3057
3058 //------------------------------------------------------------------------------
3059 void vvMainWindow::PlayNext()
3060 {
3061   if (playMode && !this->isHidden()) {
3062     int image_number=DataTree->topLevelItemCount();
3063     ///Only play one slicer per SM, and only if the SM is being displayed
3064     for (int i=0; i<image_number; i++)
3065       for (int j=0; j<4; j++)
3066         if (mSlicerManagers[i]->GetSlicer(0)->GetTMax() > 0 &&
3067             DataTree->topLevelItem(i)->data(j+1,Qt::CheckStateRole).toInt() > 0) {
3068           mSlicerManagers[i]->SetNextTSlice(j);
3069           break;
3070         }
3071     QTimer::singleShot(1000/mFrameRate, this, SLOT(PlayNext()));
3072   }
3073 }
3074 //------------------------------------------------------------------------------
3075
3076 void vvMainWindow::ShowLastImage()
3077 {
3078   if (mSlicerManagers.size() > 1) {
3079     QTreeWidgetItem * item=DataTree->topLevelItem(DataTree->topLevelItemCount()-1);
3080     CurrentImageChanged(mSlicerManagers.back()->GetId()); //select new image
3081     item->setData(1,Qt::CheckStateRole,2); //show the new image in the first panel
3082     DisplayChanged(item,1);
3083   }
3084 }
3085
3086 //------------------------------------------------------------------------------
3087 void vvMainWindow::UpdateRenderWindows()
3088 {
3089   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
3090     mSlicerManagers[i]->GetSlicer(0)->UpdateLandmarks();
3091     mSlicerManagers[i]->GetSlicer(1)->UpdateLandmarks();
3092     mSlicerManagers[i]->GetSlicer(2)->UpdateLandmarks();
3093     mSlicerManagers[i]->GetSlicer(3)->UpdateLandmarks();
3094   }
3095   if (NOViewWidget->GetRenderWindow()) NOViewWidget->GetRenderWindow()->Render();
3096   if (NEViewWidget->GetRenderWindow()) NEViewWidget->GetRenderWindow()->Render();
3097   if (SOViewWidget->GetRenderWindow()) SOViewWidget->GetRenderWindow()->Render();
3098   if (SEViewWidget->GetRenderWindow()) SEViewWidget->GetRenderWindow()->Render();
3099 }
3100 //------------------------------------------------------------------------------
3101
3102 //------------------------------------------------------------------------------
3103 void vvMainWindow::SegmentationOnCurrentImage()
3104 {
3105   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
3106
3107   vvSegmentationDialog segmentation;
3108   segmentation.SetImage(mSlicerManagers[index]->GetSlicer(0)->GetImage());
3109   segmentation.exec();
3110 }
3111 //------------------------------------------------------------------------------
3112
3113 void vvMainWindow::SurfaceViewerLaunch()
3114 {
3115   vvSurfaceViewerDialog surfaceViewer;
3116   surfaceViewer.exec();
3117 }
3118 //------------------------------------------------------------------------------
3119
3120
3121 //------------------------------------------------------------------------------
3122 int vvMainWindow::GetImageDuplicateFilenameNumber(std::string filename)
3123 {
3124   int number=0;
3125   for(unsigned int l=0; l<mSlicerManagers.size(); l++) {
3126     vvSlicerManager * v = mSlicerManagers[l];
3127     if (v->GetBaseFileName() ==
3128         vtksys::SystemTools::GetFilenameName(vtksys::SystemTools::GetFilenameWithoutLastExtension(filename))) {
3129       number = std::max(number, v->GetBaseFileNameNumber()+1);
3130     }
3131   }
3132   return number;
3133 }
3134 //------------------------------------------------------------------------------
3135
3136
3137 //------------------------------------------------------------------------------
3138 vvSlicerManager* vvMainWindow::AddImage(vvImage::Pointer image,std::string filename)
3139 {
3140   // Change filename if another image exist with the same name
3141   int number = GetImageDuplicateFilenameNumber(filename);
3142
3143   // Create new SliceManager
3144   vvSlicerManager* slicer_manager = new vvSlicerManager(4);
3145   slicer_manager->SetImage(image);//, IMAGE, number);
3146   //  filename = filename+"_"+clitk::toString(number);
3147   slicer_manager->SetFilename(filename, number);
3148   mSlicerManagers.push_back(slicer_manager);
3149
3150   //create an item in the tree with good settings
3151   QTreeWidgetItem *item = new QTreeWidgetItem();
3152   item->setData(0,Qt::UserRole,slicer_manager->GetFileName().c_str());//files[i].c_str());
3153   item->setData(1,Qt::UserRole,tr("image"));
3154   item->setData(COLUMN_IMAGE_NAME,Qt::DisplayRole,slicer_manager->GetFileName().c_str());//filename.c_str());
3155   qApp->processEvents();
3156
3157   for (int j = 1; j <= 4; j++) item->setData(j,Qt::CheckStateRole,1);
3158
3159   //Create the buttons for reload and close
3160   qApp->processEvents();
3161   QTreePushButton* cButton = new QTreePushButton;
3162   cButton->setItem(item);
3163   cButton->setColumn(COLUMN_CLOSE_IMAGE);
3164   cButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/exit.png")));
3165   connect(cButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
3166           this,SLOT(CloseImage(QTreeWidgetItem*, int)));
3167
3168   QTreePushButton* rButton = new QTreePushButton;
3169   rButton->setItem(item);
3170   rButton->setColumn(COLUMN_RELOAD_IMAGE);
3171   rButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/rotateright.png")));
3172   rButton->setEnabled(0);
3173   connect(rButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
3174           this,SLOT(ReloadImage(QTreeWidgetItem*, int)));
3175
3176   DataTree->addTopLevelItem(item);
3177   DataTree->setItemWidget(item, COLUMN_CLOSE_IMAGE, cButton);
3178   DataTree->setItemWidget(item, COLUMN_RELOAD_IMAGE, rButton);
3179
3180   //set the id of the image
3181   QString id = QDir::current().absoluteFilePath(slicer_manager->GetFileName().c_str()) + QString::number(mSlicerManagers.size()-1);
3182   item->setData(COLUMN_IMAGE_NAME,Qt::UserRole,id.toStdString().c_str());
3183   mSlicerManagers.back()->SetId(id.toStdString());
3184
3185   linkPanel->addImage(slicer_manager->GetFileName().c_str()// filename
3186                       , id.toStdString());
3187
3188   connect(mSlicerManagers.back(), SIGNAL(currentImageChanged(std::string)),
3189           this, SLOT(CurrentImageChanged(std::string)));
3190   connect(mSlicerManagers.back(), SIGNAL(currentPickedImageChanged(std::string)),
3191           this, SLOT(CurrentPickedImageChanged(std::string)));
3192   connect(mSlicerManagers.back(), SIGNAL(UpdatePosition(int, double, double, double, double, double, double, double)),
3193           this, SLOT(MousePositionChanged(int,double, double, double, double, double, double, double)));
3194   connect(mSlicerManagers.back(), SIGNAL(UpdateVector(int, double, double, double, double)),
3195           this, SLOT(VectorChanged(int,double,double,double, double)));
3196   connect(mSlicerManagers.back(), SIGNAL(UpdateOverlay(int, double, double)),
3197           this, SLOT(OverlayChanged(int,double,double)));
3198   connect(mSlicerManagers.back(), SIGNAL(UpdateFusion(int, double)),
3199           this, SLOT(FusionChanged(int,double)));
3200   connect(mSlicerManagers.back(), SIGNAL(WindowLevelChanged()),
3201           this,SLOT(WindowLevelChanged()));
3202   connect(mSlicerManagers.back(), SIGNAL(UpdateSlice(int,int)),
3203           this,SLOT(UpdateSlice(int,int)));
3204   connect(mSlicerManagers.back(), SIGNAL(UpdateTSlice(int, int)),
3205           this,SLOT(UpdateTSlice(int, int)));
3206   connect(mSlicerManagers.back(), SIGNAL(UpdateTSlice(int, int)),
3207           this,SLOT(ImageInfoChanged()));
3208   connect(mSlicerManagers.back(), SIGNAL(UpdateSliceRange(int,int,int,int,int)),
3209           this,SLOT(UpdateSliceRange(int,int,int,int,int)));
3210   connect(mSlicerManagers.back(), SIGNAL(UpdateLinkManager(std::string,int,double,double,double,int)),
3211           this,SLOT(UpdateLinkManager(std::string,int,double,double,double,int)));
3212   connect(mSlicerManagers.back(), SIGNAL(UpdateLinkedNavigation(std::string,vvSlicerManager*,vvSlicer*)),
3213           this,SLOT(UpdateLinkedNavigation(std::string,vvSlicerManager*,vvSlicer*)));
3214   connect(mSlicerManagers.back(), SIGNAL(ChangeImageWithIndexOffset(vvSlicerManager*,int,int)),
3215           this,SLOT(ChangeImageWithIndexOffset(vvSlicerManager*,int,int)));
3216   connect(mSlicerManagers.back(), SIGNAL(LandmarkAdded()),landmarksPanel,SLOT(AddPoint()));
3217   UpdateTree();
3218   qApp->processEvents();
3219   InitSlicers();
3220   ShowLastImage();
3221   InitDisplay();
3222   qApp->processEvents();
3223
3224   // End
3225   ImageInfoChanged();
3226   return slicer_manager;
3227 }
3228 //------------------------------------------------------------------------------
3229
3230
3231 //------------------------------------------------------------------------------
3232 void vvMainWindow::UpdateCurrentSlicer()
3233 {
3234   int index = -1;
3235   if (DataTree->selectedItems().size() > 0) {
3236     index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
3237   }
3238   mSlicerManagerCurrentIndex = index;
3239 }
3240 //------------------------------------------------------------------------------
3241