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   for (int i = 0; i < files.size(); i++)
 708     vector.push_back(files[i].toStdString());
 709   sort(vector.begin(),vector.end());
 710   if (vector.size() > 1)
 711     LoadImages(vector, vvImageReader::MERGEDWITHTIME);
 712   else
 713     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.");
 714 }
 715 //------------------------------------------------------------------------------
 716
 717
 718 //------------------------------------------------------------------------------
 719 void vvMainWindow::OpenDicom()
 720 {
 721   std::vector<std::string> files;
 722
 723   std::cout << "dicomSeriesSelector " << std::endl;
 724   if (dicomSeriesSelector->exec() == QDialog::Accepted) {
 725     files = *(dicomSeriesSelector->GetFilenames());
 726     LoadImages(files, vvImageReader::DICOM);
 727   }
 728 }
 729 //------------------------------------------------------------------------------
 730
 731 //------------------------------------------------------------------------------
 732 void vvMainWindow::OpenImages()
 733 {
 734   QString Extensions = EXTENSIONS;
 735   Extensions += ";;All Files (*)";
 736
 737   QStringList files = QFileDialog::getOpenFileNames(this,tr("Load Images"),mInputPathName,Extensions);
 738   if (files.isEmpty())
 739     return;
 740   mInputPathName = itksys::SystemTools::GetFilenamePath(files[0].toStdString()).c_str();
 741   std::vector<std::string> vector;
 742   for (int i = 0; i < files.size(); i++)
 743     vector.push_back(files[i].toStdString());
 744   LoadImages(vector, vvImageReader::IMAGE);
 745 }
 746 //------------------------------------------------------------------------------
 747 void vvMainWindow::OpenRecentImage()
 748 {
 749   QAction * caller = qobject_cast<QAction*>(sender());
 750   std::vector<std::string> images;
 751   images.push_back(caller->text().toStdString());
 752   mInputPathName = itksys::SystemTools::GetFilenamePath(images[0]).c_str();
 753   LoadImages(images, vvImageReader::IMAGE);
 754 }
 755 //------------------------------------------------------------------------------
 756
 757
 758 //------------------------------------------------------------------------------
 759 void vvMainWindow::OpenImageWithTime()
 760 {
 761   QString Extensions = EXTENSIONS;
 762   Extensions += ";;All Files (*)";
 763
 764   QStringList files = QFileDialog::getOpenFileNames(this,tr("Load Images With Time"),mInputPathName,Extensions);
 765   if (files.isEmpty())
 766     return;
 767   mInputPathName = itksys::SystemTools::GetFilenamePath(files[0].toStdString()).c_str();
 768   std::vector<std::string> vector;
 769   for (int i = 0; i < files.size(); i++) {
 770     vector.push_back(files[i].toStdString());
 771   }
 772   LoadImages(vector, vvImageReader::IMAGEWITHTIME);
 773 }
 774 //------------------------------------------------------------------------------
 775
 776
 777 //------------------------------------------------------------------------------
 778 void vvMainWindow::LoadImages(std::vector<std::string> files, vvImageReader::LoadedImageType filetype)
 779 {
 780   //Separate the way to open images and dicoms
 781   int fileSize;
 782   if (filetype == vvImageReader::IMAGE || filetype == vvImageReader::IMAGEWITHTIME)
 783     fileSize = files.size();
 784   else
 785     fileSize = 1;
 786
 787   // For SLICED, we need the number of slices (ndim and #slices)
 788   std::vector<unsigned int> nSlices;
 789   nSlices.resize(files.size());
 790   std::fill(nSlices.begin(), nSlices.end(), 1);
 791   if (filetype == vvImageReader::SLICED) {
 792     for (int i = 0; i < fileSize; i++) {
 793       itk::ImageIOBase::Pointer header = clitk::readImageHeader(files[i]);
 794       QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
 795       if (!header) {
 796         nSlices[i] = 0;
 797         QString error = "Cannot open file \n";
 798         error += files[i].c_str();
 799         QMessageBox::information(this,tr("Reading problem"),error);
 800         return;
 801       }
 802       if (header->GetNumberOfDimensions() < 3) {
 803         nSlices[i] = 0;
 804         QString error = "Dimension problem. Cannot slice \n";
 805         error += files[i].c_str();
 806         QMessageBox::information(this,tr("Reading problem"),error);
 807         return;
 808       }
 809       nSlices[i] = header->GetDimensions( header->GetNumberOfDimensions()-1 );
 810     }
 811   }
 812
 813   //Only add to the list of recently opened files when a single file is opened,
 814   //to avoid polluting the list of recently opened files
 815   if (files.size() == 1) {
 816     QFileInfo finfo=tr(files[0].c_str());
 817     AddToRecentlyOpenedImages(finfo.absoluteFilePath().toStdString());
 818     updateRecentlyOpenedFilesMenu(GetRecentlyOpenedImages());
 819   }
 820   //init the progress events
 821   QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
 822   vvProgressDialog progress("Opening " + files[0],fileSize>1);
 823   qApp->processEvents();
 824
 825   int numberofsuccesulreads=0;
 826   //open images as 1 or multiples
 827   for (int i = 0; i < fileSize; i++) {
 828
 829     progress.SetText("Opening " + files[i]);
 830     progress.SetProgress(i,fileSize);
 831     qApp->processEvents();
 832
 833     for (unsigned int j = 0; j < nSlices[i]; j++) {
 834       //read the image and put it in mSlicerManagers
 835       vvSlicerManager* imageManager = new vvSlicerManager(4);
 836       qApp->processEvents();
 837
 838       bool SetImageSucceed=false;
 839
 840       // Change filename if an image with the same already exist
 841       int number = GetImageDuplicateFilenameNumber(files[i] + std::string("_slice"));
 842
 843       if (filetype == vvImageReader::IMAGE || filetype == vvImageReader::IMAGEWITHTIME || filetype == vvImageReader::SLICED)
 844         SetImageSucceed = imageManager->SetImage(files[i],filetype, number, j);
 845       else {
 846         SetImageSucceed = imageManager->SetImages(files,filetype, number);
 847       }
 848       if (!SetImageSucceed) {
 849         QApplication::restoreOverrideCursor();
 850         QString error = "Cannot open file \n";
 851         error += imageManager->GetLastError().c_str();
 852         QMessageBox::information(this,tr("Reading problem"),error);
 853         delete imageManager;
 854       } else {
 855         mSlicerManagers.push_back(imageManager);
 856
 857         //create an item in the tree with good settings
 858         QTreeWidgetItem *item = new QTreeWidgetItem();
 859         item->setData(0,Qt::UserRole,files[i].c_str());
 860         QFileInfo fileinfo(imageManager->GetFileName().c_str()); //Do not show the path
 861         item->setData(COLUMN_IMAGE_NAME,Qt::DisplayRole,fileinfo.fileName());
 862         item->setData(1,Qt::UserRole,tr("image"));
 863         item->setToolTip(COLUMN_IMAGE_NAME, imageManager->GetListOfAbsoluteFilePathInOneString("image").c_str());
 864         qApp->processEvents();
 865
 866         //Create the buttons for reload and close
 867         qApp->processEvents();
 868         QTreePushButton* cButton = new QTreePushButton;
 869         cButton->setItem(item);
 870         cButton->setColumn(COLUMN_CLOSE_IMAGE);
 871         cButton->setToolTip(tr("close image"));
 872         cButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/exit.png")));
 873         connect(cButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
 874                 this,SLOT(CloseImage(QTreeWidgetItem*, int)));
 875
 876         QTreePushButton* rButton = new QTreePushButton;
 877         rButton->setItem(item);
 878         rButton->setColumn(COLUMN_RELOAD_IMAGE);
 879         rButton->setToolTip(tr("reload image"));
 880         rButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/rotateright.png")));
 881         connect(rButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
 882                 this,SLOT(ReloadImage(QTreeWidgetItem*, int)));
 883
 884         DataTree->addTopLevelItem(item);
 885         DataTree->setItemWidget(item, COLUMN_CLOSE_IMAGE, cButton);
 886         DataTree->setItemWidget(item, COLUMN_RELOAD_IMAGE, rButton);
 887
 888         //set the id of the image
 889         QString id = QDir::current().absoluteFilePath(files[i].c_str()) + QString::number(mSlicerManagers.size()-1);
 890         item->setData(COLUMN_IMAGE_NAME,Qt::UserRole,id.toStdString().c_str());
 891         mSlicerManagers.back()->SetId(id.toStdString());
 892
 893         linkPanel->addImage(imageManager->GetFileName(), id.toStdString());
 894
 895         connect(mSlicerManagers.back(), SIGNAL(currentImageChanged(std::string)),
 896                 this,SLOT(CurrentImageChanged(std::string)));
 897         connect(mSlicerManagers.back(), SIGNAL(currentPickedImageChanged(std::string)),
 898                 this, SLOT(CurrentPickedImageChanged(std::string)));
 899         connect(mSlicerManagers.back(), SIGNAL(UpdatePosition(int, double, double, double, double, double, double, double)),
 900                 this,SLOT(MousePositionChanged(int,double, double, double, double, double, double, double)));
 901         connect(mSlicerManagers.back(), SIGNAL(UpdateVector(int, double, double, double, double)),
 902                 this, SLOT(VectorChanged(int,double,double,double, double)));
 903         connect(mSlicerManagers.back(), SIGNAL(UpdateOverlay(int, double, double)),
 904                 this, SLOT(OverlayChanged(int,double,double)));
 905         connect(mSlicerManagers.back(), SIGNAL(UpdateFusion(int, double)),
 906                 this, SLOT(FusionChanged(int,double)));
 907         connect(mSlicerManagers.back(), SIGNAL(WindowLevelChanged()),
 908                 this,SLOT(WindowLevelChanged()));
 909         connect(mSlicerManagers.back(), SIGNAL(UpdateSlice(int,int)),
 910                 this,SLOT(UpdateSlice(int,int)));
 911         connect(mSlicerManagers.back(), SIGNAL(UpdateTSlice(int, int)),
 912                 this,SLOT(UpdateTSlice(int, int)));
 913         connect(mSlicerManagers.back(), SIGNAL(UpdateTSlice(int, int)),
 914                 this,SLOT(ImageInfoChanged()));
 915         connect(mSlicerManagers.back(), SIGNAL(UpdateSliceRange(int,int,int,int,int)),
 916                 this,SLOT(UpdateSliceRange(int,int,int,int,int)));
 917         connect(mSlicerManagers.back(), SIGNAL(UpdateLinkManager(std::string,int,double,double,double,int)),
 918                 this,SLOT(UpdateLinkManager(std::string,int,double,double,double,int)));
 919         connect(mSlicerManagers.back(), SIGNAL(UpdateLinkedNavigation(std::string,vvSlicerManager*,vvSlicer*)),
 920                 this,SLOT(UpdateLinkedNavigation(std::string,vvSlicerManager*,vvSlicer*)));
 921         connect(mSlicerManagers.back(), SIGNAL(ChangeImageWithIndexOffset(vvSlicerManager*,int,int)),
 922                 this,SLOT(ChangeImageWithIndexOffset(vvSlicerManager*,int,int)));
 923         connect(mSlicerManagers.back(),SIGNAL(LandmarkAdded()),landmarksPanel,SLOT(AddPoint()));
 924         InitSlicers();
 925         numberofsuccesulreads++;
 926       }
 927     }
 928   }
 929   if (numberofsuccesulreads) {
 930     NOViewWidget->show();
 931     NEViewWidget->show();
 932     SOViewWidget->show();
 933     SEViewWidget->show();
 934     UpdateTree();
 935     InitDisplay();
 936     ShowLastImage();
 937
 938     // Try to guess default WindowLevel
 939     double range[2];
 940     mSlicerManagers.back()->GetImage()->GetFirstVTKImageData()->GetScalarRange(range);
 941     if ((range[0] == 0) && (range[1] == 1)) {
 942       presetComboBox->setCurrentIndex(5);// binary
 943     } else {
 944       // TODO
 945     }
 946   }
 947   QApplication::restoreOverrideCursor();
 948 }
 949 //------------------------------------------------------------------------------
 950
 951 //------------------------------------------------------------------------------
 952 void vvMainWindow::UpdateTree()
 953 {
 954   DataTree->resizeColumnToContents(COLUMN_TREE);
 955   DataTree->resizeColumnToContents(COLUMN_UL_VIEW);
 956   DataTree->resizeColumnToContents(COLUMN_UR_VIEW);
 957   DataTree->resizeColumnToContents(COLUMN_DL_VIEW);
 958   DataTree->resizeColumnToContents(COLUMN_DR_VIEW);
 959   DataTree->resizeColumnToContents(COLUMN_IMAGE_NAME);
 960   DataTree->resizeColumnToContents(COLUMN_CLOSE_IMAGE);
 961   DataTree->resizeColumnToContents(COLUMN_RELOAD_IMAGE);
 962 }
 963 //------------------------------------------------------------------------------
 964
 965 //------------------------------------------------------------------------------
 966 void vvMainWindow::CurrentImageChanged(std::string id)
 967 {
 968   if (id == mCurrentSelectedImageId) return; // Do nothing
 969   int selected = 0;
 970   for (int i = 0; i < DataTree->topLevelItemCount(); i++) {
 971     if (DataTree->topLevelItem(i)->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString().toStdString() == id) {
 972       selected = i;
 973     } else {
 974       DataTree->topLevelItem(i)->setSelected(0);
 975     }
 976     for (int child = 0; child < DataTree->topLevelItem(i)->childCount(); child++)
 977       DataTree->topLevelItem(i)->child(child)->setSelected(0);
 978
 979   }
 980   DataTree->topLevelItem(selected)->setSelected(1);
 981   mCurrentSelectedImageId = id;
 982   emit SelectedImageHasChanged(mSlicerManagers[selected]);
 983 }
 984 //------------------------------------------------------------------------------
 985
 986 //------------------------------------------------------------------------------
 987 void vvMainWindow::CurrentPickedImageChanged(std::string id)
 988 {
 989   if (id == mCurrentPickedImageId) return; // Do nothing
 990   int selected = 0;
 991   for (int i = 0; i < DataTree->topLevelItemCount(); i++) {
 992     if (DataTree->topLevelItem(i)->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString().toStdString() == id) {
 993       selected = i;
 994     } else {
 995       DataTree->topLevelItem(i)->setSelected(0);
 996     }
 997     for (int child = 0; child < DataTree->topLevelItem(i)->childCount(); child++)
 998       DataTree->topLevelItem(i)->child(child)->setSelected(0);
 999
1000   }
1001   DataTree->topLevelItem(selected)->setSelected(1);
1002   mCurrentPickedImageId = id;
1003   mCurrentPickedImageIndex = selected;
1004 }
1005 //------------------------------------------------------------------------------
1006
1007 //------------------------------------------------------------------------------
1008 void vvMainWindow::ImageInfoChanged()
1009 {
1010   contextActions[6]->setEnabled(1);
1011   contextActions[5]->setEnabled(1);
1012   actionSave_As->setEnabled(1);
1013   actionAdd_VF_to_current_Image->setEnabled(1);
1014   actionAdd_fusion_image->setEnabled(1);
1015   actionAdd_overlay_image_to_current_image->setEnabled(1);
1016   actionNorth_East_Window->setEnabled(1);
1017   actionNorth_West_Window->setEnabled(1);
1018   actionSouth_East_Window->setEnabled(1);
1019   actionSouth_West_Window->setEnabled(1);
1020   vvToolManager::GetInstance()->EnableToolsInMenu(this, true);
1021   inverseButton->setEnabled(1);
1022
1023   goToCursorPushButton->setEnabled(1);
1024
1025   if (DataTree->selectedItems().size()) {
1026     int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1027
1028     colorMapComboBox->setEnabled(1);
1029     for (int i = 0; i < DataTree->topLevelItem(index)->childCount(); i++) {
1030       if (DataTree->topLevelItem(index)->child(i)->data(1,Qt::UserRole).toString() == "overlay" ||
1031           DataTree->topLevelItem(index)->child(i)->data(1,Qt::UserRole).toString() == "fusion") {
1032         colorMapComboBox->setEnabled(0);
1033         break;
1034       }
1035     }
1036
1037     std::vector<double> origin;
1038     std::vector<double> inputSpacing;
1039     std::vector<int> inputSize;
1040     std::vector<double> sizeMM;
1041     vtkSmartPointer<vtkMatrix4x4> transformation;
1042     int dimension=0;
1043     QString pixelType;
1044     QString inputSizeInBytes;
1045     QString image = DataTree->selectedItems()[0]->data(COLUMN_IMAGE_NAME,Qt::DisplayRole).toString();
1046
1047     int nframes = mSlicerManagers[index]->GetSlicer(0)->GetTMax();
1048     if (nframes > 1 || playMode == 1) {
1049       playButton->setEnabled(1);
1050       frameRateLabel->setEnabled(1);
1051       frameRateSpinBox->setEnabled(1);
1052     } else {
1053       playButton->setEnabled(0);
1054       frameRateLabel->setEnabled(0);
1055       frameRateSpinBox->setEnabled(0);
1056     }
1057
1058     //read image header
1059     int NPixel = 1;
1060
1061     int tSlice = 0;
1062     vvImage::Pointer imageSelected;
1063     if (DataTree->topLevelItem(index) == DataTree->selectedItems()[0]) {
1064       imageSelected = mSlicerManagers[index]->GetSlicer(0)->GetImage();
1065       tSlice = mSlicerManagers[index]->GetSlicer(0)->GetTSlice();
1066     } else if (DataTree->selectedItems()[0]->data(1,Qt::UserRole).toString() == "vector") {
1067       imageSelected = mSlicerManagers[index]->GetSlicer(0)->GetVF();
1068       tSlice = mSlicerManagers[index]->GetSlicer(0)->GetOverlayTSlice();
1069     } else if (DataTree->selectedItems()[0]->data(1,Qt::UserRole).toString() == "overlay") {
1070       imageSelected = mSlicerManagers[index]->GetSlicer(0)->GetOverlay();
1071       tSlice = mSlicerManagers[index]->GetSlicer(0)->GetOverlayTSlice();
1072     } else if (DataTree->selectedItems()[0]->data(1,Qt::UserRole).toString() == "fusion") {
1073       imageSelected = mSlicerManagers[index]->GetSlicer(0)->GetFusion();
1074       tSlice = mSlicerManagers[index]->GetSlicer(0)->GetFusionTSlice();
1075     }
1076     else if (DataTree->selectedItems()[0]->data(1,Qt::UserRole).toString() == "contour") {
1077       imageSelected = mSlicerManagers[index]->GetSlicer(0)->GetImage();
1078       tSlice = mSlicerManagers[index]->GetSlicer(0)->GetTSlice();
1079     }
1080     else {
1081       imageSelected = mSlicerManagers[index]->GetSlicer(0)->GetImage();
1082       tSlice = mSlicerManagers[index]->GetSlicer(0)->GetTSlice();
1083     }
1084
1085     dimension = imageSelected->GetNumberOfDimensions();
1086     origin.resize(dimension);
1087     inputSpacing.resize(dimension);
1088     inputSize.resize(dimension);
1089     sizeMM.resize(dimension);
1090     pixelType = mSlicerManagers[index]->GetImage()->GetScalarTypeAsITKString().c_str();
1091     for (int i = 0; i < dimension; i++) {
1092       origin[i] = imageSelected->GetOrigin()[i];
1093       inputSpacing[i] = imageSelected->GetSpacing()[i];
1094       inputSize[i] = imageSelected->GetSize()[i];
1095       sizeMM[i] = inputSize[i]*inputSpacing[i];
1096       NPixel *= inputSize[i];
1097     }
1098     inputSizeInBytes = GetSizeInBytes(imageSelected->GetActualMemorySize()*1000);
1099
1100     QString dim = QString::number(dimension) + " (";
1101     dim += pixelType + ")";
1102
1103     infoPanel->setFileName(image);
1104     infoPanel->setDimension(dim);
1105     infoPanel->setSizePixel(GetVectorIntAsString(inputSize));
1106     infoPanel->setSizeMM(GetVectorDoubleAsString(sizeMM));
1107     infoPanel->setOrigin(GetVectorDoubleAsString(origin));
1108     infoPanel->setSpacing(GetVectorDoubleAsString(inputSpacing));
1109     infoPanel->setNPixel(QString::number(NPixel)+" ("+inputSizeInBytes+")");
1110     transformation = imageSelected->GetTransform()[tSlice]->GetMatrix();
1111     infoPanel->setTransformation(Get4x4MatrixDoubleAsString(transformation));
1112
1113     landmarksPanel->SetCurrentLandmarks(mSlicerManagers[index]->GetLandmarks(),
1114                                         mSlicerManagers[index]->GetSlicer(0)->GetImage()->GetVTKImages().size());
1115     landmarksPanel->SetCurrentPath(mInputPathName.toStdString());
1116     landmarksPanel->SetCurrentImage(mSlicerManagers[index]->GetFileName().c_str());
1117
1118     overlayPanel->getCurrentImageName(mSlicerManagers[index]->GetFileName().c_str());
1119     for (int i = 0; i < 4; i++) {
1120       if (DataTree->selectedItems()[0]->data(i+1,Qt::CheckStateRole).toInt() > 0 || i == 3) {
1121         mSlicerManagers[index]->UpdateInfoOnCursorPosition(i);
1122         break;
1123       }
1124     }
1125
1126     infoPanel->setFileName(image);
1127     infoPanel->setDimension(dim);
1128     infoPanel->setSizePixel(GetVectorIntAsString(inputSize));
1129     infoPanel->setSizeMM(GetVectorDoubleAsString(sizeMM));
1130     infoPanel->setOrigin(GetVectorDoubleAsString(origin));
1131     infoPanel->setSpacing(GetVectorDoubleAsString(inputSpacing));
1132     infoPanel->setNPixel(QString::number(NPixel)+" ("+inputSizeInBytes+")");
1133
1134     landmarksPanel->SetCurrentLandmarks(mSlicerManagers[index]->GetLandmarks(),
1135                                         mSlicerManagers[index]->GetSlicer(0)->GetImage()->GetVTKImages().size());
1136     landmarksPanel->SetCurrentPath(mInputPathName.toStdString());
1137     landmarksPanel->SetCurrentImage(mSlicerManagers[index]->GetFileName().c_str());
1138
1139     overlayPanel->getCurrentImageName(mSlicerManagers[index]->GetFileName().c_str());
1140     for (int i = 0; i < 4; i++) {
1141       if (DataTree->selectedItems()[0]->data(i+1,Qt::CheckStateRole).toInt() > 0 || i == 3) {
1142         mSlicerManagers[index]->UpdateInfoOnCursorPosition(i);
1143         break;
1144       }
1145     }
1146     WindowLevelChanged();
1147     slicingPresetComboBox->setCurrentIndex(mSlicerManagers[index]->GetSlicingPreset());
1148
1149     if (mSlicerManagers[index]->GetSlicer(0)->GetVF()) {
1150       overlayPanel->getVFName(mSlicerManagers[index]->GetVFName().c_str());
1151       overlayPanel->getVFProperty(mSlicerManagers[index]->GetSlicer(0)->GetVFSubSampling(),
1152                                   mSlicerManagers[index]->GetSlicer(0)->GetVFScale(),
1153                                   mSlicerManagers[index]->GetSlicer(0)->GetVFLog());
1154     } else {
1155       overlayPanel->getVFName(mSlicerManagers[index]->GetVFName().c_str());
1156       overlayPanel->getVFProperty(-1,-1,-1);
1157     }
1158     if (mSlicerManagers[index]->GetSlicer(0)->GetOverlay()) {
1159       overlayPanel->getOverlayName(mSlicerManagers[index]->GetOverlayName().c_str());
1160     } else {
1161       overlayPanel->getOverlayName(mSlicerManagers[index]->GetOverlayName().c_str());
1162     }
1163
1164     if (mSlicerManagers[index]->GetSlicer(0)->GetFusion()) {
1165       overlayPanel->getFusionName(mSlicerManagers[index]->GetFusionName().c_str());
1166     } else {
1167       overlayPanel->getFusionName(mSlicerManagers[index]->GetFusionName().c_str());
1168     }
1169   }
1170 }
1171 //------------------------------------------------------------------------------
1172
1173 //------------------------------------------------------------------------------
1174 void vvMainWindow::ShowDocumentation()
1175 {
1176   documentation->show();
1177 }
1178 //------------------------------------------------------------------------------
1179
1180 //------------------------------------------------------------------------------
1181 void vvMainWindow::PopupRegisterForm(bool checkCanPush)
1182 {
1183   vvRegisterForm* registerForm = new vvRegisterForm(QUrl("http://www.creatis.insa-lyon.fr/~dsarrut/vvregister/write.php"), getVVSettingsPath(), getSettingsOptionFormat());
1184   if(!checkCanPush) {
1185     registerForm->show();
1186   } else {
1187     if(registerForm->canPush()) {
1188       registerForm->show();
1189       registerForm->acquitPushed();//too bad if there is not internet connection anymore.
1190     }
1191   }
1192 }
1193 //------------------------------------------------------------------------------
1194
1195 //------------------------------------------------------------------------------
1196 void vvMainWindow::ShowHelpDialog()
1197 {
1198   help_dialog->show();
1199 }
1200 //------------------------------------------------------------------------------
1201
1202 //------------------------------------------------------------------------------
1203 void vvMainWindow::ChangeViewMode()
1204 {
1205   typedef struct _SIZE{
1206     QSplitter* splitter;
1207     QList<int> size1, size2;
1208     int cols[3];
1209   }SplitterSize;
1210   SplitterSize sizes[4];
1211   sizes[0].splitter = OSplitter;
1212   sizes[0].size1.push_back(1);
1213   sizes[0].size1.push_back(0);
1214   sizes[0].size2.push_back(1);
1215   sizes[0].size2.push_back(0);
1216   sizes[0].cols[0] = 2;
1217   sizes[0].cols[1] = 3;
1218   sizes[0].cols[2] = 4;
1219
1220   sizes[1].splitter = ESplitter;
1221   sizes[1].size1.push_back(0);
1222   sizes[1].size1.push_back(1);
1223   sizes[1].size2.push_back(1);
1224   sizes[1].size2.push_back(0);
1225   sizes[1].cols[0] = 1;
1226   sizes[1].cols[1] = 3;
1227   sizes[1].cols[2] = 4;
1228
1229   sizes[2].splitter = OSplitter;
1230   sizes[2].size1.push_back(1);
1231   sizes[2].size1.push_back(0);
1232   sizes[2].size2.push_back(0);
1233   sizes[2].size2.push_back(1);
1234   sizes[2].cols[0] = 1;
1235   sizes[2].cols[1] = 2;
1236   sizes[2].cols[2] = 4;
1237
1238   sizes[3].splitter = ESplitter;
1239   sizes[3].size1.push_back(0);
1240   sizes[3].size1.push_back(1);
1241   sizes[3].size2.push_back(0);
1242   sizes[3].size2.push_back(1);
1243   sizes[3].cols[0] = 1;
1244   sizes[3].cols[1] = 2;
1245   sizes[3].cols[2] = 3;
1246
1247   int slicer = mSlicerManagers[mCurrentPickedImageIndex]->GetSelectedSlicer();
1248   if (viewMode == 1) {
1249     if (slicer >= 0) {
1250       viewMode = 0;
1251       splitter_3->setSizes(sizes[slicer].size1);
1252       sizes[slicer].splitter->setSizes(sizes[slicer].size2);
1253       DataTree->setColumnHidden(sizes[slicer].cols[0],1);
1254       DataTree->setColumnHidden(sizes[slicer].cols[1],1);
1255       DataTree->setColumnHidden(sizes[slicer].cols[2],1);
1256     }
1257   } else {
1258     QList<int> size;
1259     if (slicer >= 0) {
1260       viewMode = 1;
1261       size.push_back(1);
1262       size.push_back(1);
1263       splitter_3->setSizes(size);
1264       sizes[slicer].splitter->setSizes(size);
1265       DataTree->setColumnHidden(sizes[slicer].cols[0],0);
1266       DataTree->setColumnHidden(sizes[slicer].cols[1],0);
1267       DataTree->setColumnHidden(sizes[slicer].cols[2],0);
1268     }
1269   }
1270   UpdateRenderWindows();
1271   /*
1272   ** I don't know why but for both resized QVTKWidget we also need to render
1273   ** the associated Slicer to redraw crosses.
1274   */
1275   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
1276 //     if (DataTree->topLevelItem(i)->data(COLUMN_UL_VIEW,Qt::CheckStateRole).toInt() > 1)
1277       mSlicerManagers[i]->GetSlicer(0)->Render();
1278       mSlicerManagers[i]->GetSlicer(1)->Render();
1279 //     if (DataTree->topLevelItem(i)->data(COLUMN_DL_VIEW,Qt::CheckStateRole).toInt() > 1)
1280       mSlicerManagers[i]->GetSlicer(2)->Render();
1281       mSlicerManagers[i]->GetSlicer(3)->Render();
1282   }
1283 }
1284 //------------------------------------------------------------------------------
1285
1286 //------------------------------------------------------------------------------
1287 QString vvMainWindow::GetSizeInBytes(unsigned long size)
1288 {
1289   QString result = "";// QString::number(size);
1290   //result += " bytes (";
1291   if (size > 1000000000) {
1292     size /= 1000000000;
1293     result += QString::number(size);
1294     result += "Gb";//)";
1295   } else if (size > 1000000) {
1296     size /= 1000000;
1297     result += QString::number(size);
1298     result += "Mb";//)";
1299   } else if (size > 1000) {
1300     size /= 1000;
1301     result += QString::number(size);
1302     result += "kb";//)";
1303   }
1304   return result;
1305 }
1306 //------------------------------------------------------------------------------
1307
1308 //------------------------------------------------------------------------------
1309 QString vvMainWindow::Get4x4MatrixDoubleAsString(vtkSmartPointer<vtkMatrix4x4> matrix, const int precision)
1310 {
1311   std::ostringstream strmatrix;
1312
1313   // Figure out the number of digits of the integer part of the largest absolute value
1314   // for each column
1315   unsigned width[4];
1316   for (unsigned int j = 0; j < 4; j++){
1317     double absmax = 0.;
1318     for (unsigned int i = 0; i < 4; i++)
1319       absmax = std::max(absmax, vnl_math_abs(matrix->GetElement(i, j)));
1320     unsigned ndigits = (unsigned)std::max(0.,std::log10(absmax))+1;
1321     width[j] = precision+ndigits+3;
1322   }
1323
1324   // Output with correct width, aligned to the right
1325   for (unsigned int i = 0; i < 4; i++) {
1326     for (unsigned int j = 0; j < 4; j++) {
1327       strmatrix.setf(ios::fixed,ios::floatfield);
1328       strmatrix.precision(precision);
1329       strmatrix.fill(' ');
1330       strmatrix.width(width[j]);
1331       strmatrix << std::right << matrix->GetElement(i, j);
1332     }
1333     strmatrix << std::endl;
1334   }
1335   QString result = strmatrix.str().c_str();
1336   return result;
1337 }
1338 //------------------------------------------------------------------------------
1339
1340 //------------------------------------------------------------------------------
1341 QString vvMainWindow::GetVectorDoubleAsString(std::vector<double> vectorDouble)
1342 {
1343   QString result;
1344   for (unsigned int i= 0; i < vectorDouble.size(); i++) {
1345     if (i != 0)
1346       result += " ";
1347     result += QString::number(vectorDouble[i]);
1348   }
1349   return result;
1350 }
1351 //------------------------------------------------------------------------------
1352
1353 //------------------------------------------------------------------------------
1354 QString vvMainWindow::GetVectorIntAsString(std::vector<int> vectorInt)
1355 {
1356   QString result;
1357   for (unsigned int i= 0; i < vectorInt.size(); i++) {
1358     if (i != 0)
1359       result += " ";
1360     result += QString::number(vectorInt[i]);
1361   }
1362   return result;
1363 }
1364 //------------------------------------------------------------------------------
1365
1366 //------------------------------------------------------------------------------
1367 int vvMainWindow::GetSlicerIndexFromItem(QTreeWidgetItem* item)
1368 {
1369   QString id = item->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString();
1370   for (int i = 0; i < DataTree->topLevelItemCount(); i++) {
1371     if (DataTree->topLevelItem(i)->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString() == id)
1372       return i;
1373   }
1374   return -1;
1375 }
1376 //------------------------------------------------------------------------------
1377
1378 //------------------------------------------------------------------------------
1379 QTreeWidgetItem* vvMainWindow::GetItemFromSlicerManager(vvSlicerManager* sm)
1380 {
1381   QString id = sm->GetId().c_str();
1382   for (int i = 0; i < DataTree->topLevelItemCount(); i++) {
1383     if (DataTree->topLevelItem(i)->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString() == id)
1384       return DataTree->topLevelItem(i);
1385   }
1386   return NULL;
1387 }
1388 //------------------------------------------------------------------------------
1389
1390 //------------------------------------------------------------------------------
1391 void vvMainWindow::DisplayChanged(QTreeWidgetItem *clickedItem, int column)
1392 {
1393   if ( column >= COLUMN_CLOSE_IMAGE || column <= 0)
1394     return;
1395
1396   // Get parent information (might be the same item)
1397   int slicerManagerIndex = GetSlicerIndexFromItem(clickedItem);
1398   QTreeWidgetItem* clickedParentItem = DataTree->topLevelItem(slicerManagerIndex);
1399   vvSlicer* clickedSlicer = mSlicerManagers[slicerManagerIndex]->GetSlicer(column-1);
1400
1401   // Go over the complete item tree (only 2 levels, parents and children)
1402   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
1403     // Trick to avoid redoing twice the job for a key (sr)
1404     mSlicerManagers[i]->GetSlicer(column-1)->GetRenderWindow()->GetInteractor()->SetKeySym("Crap");
1405
1406     QTreeWidgetItem* currentParentItem = DataTree->topLevelItem(i);
1407     if(currentParentItem != clickedParentItem) {
1408       // Not the branch of the clicked item, uncheck all
1409
1410       // Parent
1411       currentParentItem->setData(column,Qt::CheckStateRole, 0);
1412       mSlicerManagers[i]->UpdateSlicer(column-1, false);
1413
1414       // Children
1415       for (int iChild = 0; iChild < currentParentItem->childCount(); iChild++) {
1416         currentParentItem->child(iChild)->setData(column,Qt::CheckStateRole, 0);
1417       }
1418     }
1419     else {
1420       // Branch of the clicked one: get check status from actor visibility in slicer
1421       // and toggle the clicked one
1422
1423       // Parent
1424       bool vis = clickedSlicer->GetActorVisibility("image", 0);
1425       bool draw = clickedSlicer->GetRenderer()->GetDraw();
1426
1427       // Update slicer (after getting visibility)
1428       mSlicerManagers[slicerManagerIndex]->UpdateSlicer(column-1, true);
1429       mSlicerManagers[slicerManagerIndex]->UpdateInfoOnCursorPosition(column-1);
1430       DisplaySliders(slicerManagerIndex, column-1);
1431       if(clickedParentItem == clickedItem) {
1432         // Toggle
1433         vis = !draw || !vis;
1434       }
1435       clickedSlicer->SetActorVisibility("image", 0, vis);
1436       clickedParentItem->setData(column, Qt::CheckStateRole, vis?2:0);
1437
1438       // Children
1439       std::map<std::string, int> actorTypeCounts;
1440       for (int iChild = 0; iChild < clickedParentItem->childCount(); iChild++) {
1441         QTreeWidgetItem* currentChildItem = clickedParentItem->child(iChild);
1442         std::string actorType = currentChildItem->data(1,Qt::UserRole).toString().toStdString();
1443         vis = clickedSlicer->GetActorVisibility(actorType, actorTypeCounts[actorType]);
1444         if(currentChildItem == clickedItem) {
1445           // Toggle or force visibility if it was not on this branch so far
1446           vis = !draw || !vis;
1447           clickedSlicer->SetActorVisibility(actorType, actorTypeCounts[actorType], vis);
1448         }
1449         currentChildItem->setData(column, Qt::CheckStateRole, vis?2:0);
1450         actorTypeCounts[actorType]++;
1451       }
1452     }
1453   }
1454
1455   clickedSlicer->Render();
1456 }
1457 //------------------------------------------------------------------------------
1458
1459 void vvMainWindow::InitSlicers()
1460 {
1461   if (mSlicerManagers.size()) {
1462     mSlicerManagers.back()->GenerateDefaultLookupTable();
1463
1464     mSlicerManagers.back()->SetSlicerWindow(0,NOViewWidget->GetRenderWindow());
1465     mSlicerManagers.back()->SetSlicerWindow(1,NEViewWidget->GetRenderWindow());
1466     mSlicerManagers.back()->SetSlicerWindow(2,SOViewWidget->GetRenderWindow());
1467     mSlicerManagers.back()->SetSlicerWindow(3,SEViewWidget->GetRenderWindow());
1468   }
1469 }
1470
1471 //------------------------------------------------------------------------------
1472 void vvMainWindow::InitDisplay()
1473 {
1474   if (mSlicerManagers.size()) {
1475     //BE CAREFUL : this is absolutely necessary to set the interactor style
1476     //in order to have the same style instanciation for all SlicerManagers in
1477     // a same window
1478     for (int j = 0; j < 4; j++) {
1479       vvInteractorStyleNavigator* style = vvInteractorStyleNavigator::New();
1480       style->SetAutoAdjustCameraClippingRange(1);
1481       bool AlreadySelected = false;
1482       for (int i = 0; i < DataTree->topLevelItemCount(); i++) {
1483         mSlicerManagers[i]->SetInteractorStyleNavigator(j,style);
1484
1485         //select the image only if previous are not selected
1486         if (DataTree->topLevelItem(i)->data(j+1,Qt::CheckStateRole).toInt() > 1) {
1487           mSlicerManagers[i]->UpdateSlicer(j,1);
1488           AlreadySelected = true;
1489         } else if (i == DataTree->topLevelItemCount()-1 && !AlreadySelected) {
1490           if (DataTree->selectedItems().size() == 0)
1491             DataTree->topLevelItem(i)->setSelected(1);
1492           DataTree->topLevelItem(i)->setData(j+1,Qt::CheckStateRole,2);
1493           mSlicerManagers[i]->UpdateSlicer(j,1);
1494           DisplaySliders(i,j);
1495         } else {
1496           DataTree->topLevelItem(i)->setData(j+1,Qt::CheckStateRole,0);
1497           mSlicerManagers[i]->UpdateSlicer(j,0);
1498         }
1499       }
1500       style->Delete();
1501     }
1502   }
1503 }
1504 //------------------------------------------------------------------------------
1505
1506 //------------------------------------------------------------------------------
1507 void vvMainWindow::DisplaySliders(int slicer, int window)
1508 {
1509   if(!mSlicerManagers[slicer]->GetSlicer(window)->GetRenderer()->GetDraw())
1510     return;
1511
1512   int range[2];
1513   mSlicerManagers[slicer]->GetSlicer(window)->GetSliceRange(range);
1514   int position = mSlicerManagers[slicer]->GetSlicer(window)->GetSlice();
1515   if (range[1]>0)
1516     verticalSliders[window]->show();
1517   else
1518     verticalSliders[window]->hide();
1519   verticalSliders[window]->setRange(range[0],range[1]);
1520   verticalSliders[window]->setValue(position);
1521
1522   int tRange[2];
1523   tRange[0] = 0;
1524   tRange[1] = mSlicerManagers[slicer]->GetSlicer(window)->GetTMax();
1525   if (tRange[1]>0)
1526     horizontalSliders[window]->show();
1527   else
1528     horizontalSliders[window]->hide();
1529   horizontalSliders[window]->setRange(tRange[0],tRange[1]);
1530   int tPosition = mSlicerManagers[slicer]->GetSlicer(window)->GetMaxCurrentTSlice();
1531   horizontalSliders[window]->setValue(tPosition);
1532 }
1533 //------------------------------------------------------------------------------
1534
1535 //------------------------------------------------------------------------------
1536 void vvMainWindow::CloseImage(QTreeWidgetItem* item, int column)
1537 {
1538   int index = GetSlicerIndexFromItem(item);
1539
1540   if (DataTree->topLevelItem(index) != item) {
1541     QString warning = "Do you really want to close the overlay : ";
1542     warning += item->data(COLUMN_IMAGE_NAME,Qt::DisplayRole).toString();
1543     QMessageBox msgBox(QMessageBox::Warning, tr("Close Overlay"),
1544                        warning, 0, this);
1545     msgBox.addButton(tr("Close"), QMessageBox::AcceptRole);
1546     msgBox.addButton(tr("Cancel"), QMessageBox::RejectRole);
1547     if (msgBox.exec() == QMessageBox::AcceptRole) {
1548       std::string overlay_type=item->data(1,Qt::UserRole).toString().toStdString();
1549       int overlay_index=0;
1550       for (int child = 0; child < DataTree->topLevelItem(index)->childCount(); child++) {
1551         if (DataTree->topLevelItem(index)->\
1552             child(child)->data(1,Qt::UserRole).toString().toStdString() == overlay_type)
1553           overlay_index++;
1554         if (DataTree->topLevelItem(index)->child(child) == item) break;
1555       }
1556       mSlicerManagers[index]->RemoveActor(overlay_type, overlay_index-1);
1557       mSlicerManagers[index]->SetColorMap(0);
1558       DataTree->topLevelItem(index)->takeChild(DataTree->topLevelItem(index)->indexOfChild(item));
1559       mSlicerManagers[index]->Render();
1560     }
1561   } else if (DataTree->topLevelItemCount() <= 1) {
1562     QString warning = "Do you really want to close the image : ";
1563     warning += item->data(COLUMN_IMAGE_NAME,Qt::DisplayRole).toString();
1564     warning += "\nThis is the last image, you're about to close vv !!!";
1565     QMessageBox msgBox(QMessageBox::Warning, tr("Close Image"),
1566                        warning, 0, this);
1567     msgBox.addButton(tr("Close vv"), QMessageBox::AcceptRole);
1568     msgBox.addButton(tr("Cancel"), QMessageBox::RejectRole);
1569     if (msgBox.exec() == QMessageBox::AcceptRole) {
1570       this->close();
1571     }
1572   } else {
1573     QString warning = "Do you really want to close the image : ";
1574     warning += item->data(COLUMN_IMAGE_NAME,Qt::DisplayRole).toString();
1575     QMessageBox msgBox(QMessageBox::Warning, tr("Close Image"),
1576                        warning, 0, this);
1577     msgBox.addButton(tr("Close"), QMessageBox::AcceptRole);
1578     msgBox.addButton(tr("Cancel"), QMessageBox::RejectRole);
1579     if (msgBox.exec() == QMessageBox::AcceptRole) {
1580
1581       // Tell tools that we close an image
1582       emit AnImageIsBeingClosed(mSlicerManagers[index]);
1583
1584       std::vector<vvSlicerManager*>::iterator Manageriter = mSlicerManagers.begin();
1585       DataTree->takeTopLevelItem(index);
1586       for (int i = 0; i < index; i++) {
1587         Manageriter++;
1588       }
1589       linkPanel->removeImage(index);
1590       mSlicerManagers[index]->RemoveActors();
1591       delete mSlicerManagers[index];
1592       mSlicerManagers.erase(Manageriter);
1593
1594       //
1595       InitDisplay();
1596     }
1597   }
1598   ImageInfoChanged();
1599 }
1600 //------------------------------------------------------------------------------
1601
1602 //------------------------------------------------------------------------------
1603 void vvMainWindow::ReloadImage(QTreeWidgetItem* item, int column)
1604 {
1605   // int index = GetSlicerIndexFromItem(item);
1606   //   QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
1607   //   if (item->data(1,Qt::UserRole).toString() == "vector")
1608   //     mSlicerManagers[index]->ReloadVF();
1609   //   else
1610   //     mSlicerManagers[index]->Reload();
1611
1612   //   QApplication::restoreOverrideCursor();
1613   int index = GetSlicerIndexFromItem(item);
1614   QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
1615   QString role=item->data(1,Qt::UserRole).toString();
1616   if ( role == "vector"){
1617     mSlicerManagers[index]->ReloadVF();
1618   }
1619   else if (role == "overlay"){
1620     mSlicerManagers[index]->ReloadOverlay();
1621   }
1622   else if (role == "fusion"){
1623     mSlicerManagers[index]->ReloadFusion();
1624   }
1625   else{
1626     mSlicerManagers[index]->Reload();
1627   }
1628   // Update view and info
1629   ImageInfoChanged();
1630   mSlicerManagers[index]->Render();
1631   QApplication::restoreOverrideCursor();
1632 }
1633 //------------------------------------------------------------------------------
1634
1635 //------------------------------------------------------------------------------
1636 void vvMainWindow::MousePositionChanged(int visibility,double x, double y, double z, double X, double Y, double Z , double value)
1637 {
1638   infoPanel->setCurrentInfo(visibility,x,y,z,X,Y,Z,value);
1639 }
1640 //------------------------------------------------------------------------------
1641
1642 //------------------------------------------------------------------------------
1643 void vvMainWindow::VectorChanged(int visibility,double x, double y, double z, double value)
1644 {
1645   overlayPanel->getCurrentVectorInfo(visibility,x,y,z,value);
1646 }
1647 //------------------------------------------------------------------------------
1648
1649 //------------------------------------------------------------------------------
1650 void vvMainWindow::OverlayChanged(int visibility, double valueOver, double valueRef)
1651 {
1652   overlayPanel->getCurrentOverlayInfo(visibility,valueOver, valueRef);
1653 }
1654 //------------------------------------------------------------------------------
1655
1656 //------------------------------------------------------------------------------
1657 void vvMainWindow::FusionChanged(int visibility, double value)
1658 {
1659   overlayPanel->getCurrentFusionInfo(visibility,value);
1660 }
1661 //------------------------------------------------------------------------------
1662
1663 //------------------------------------------------------------------------------
1664 void vvMainWindow::WindowLevelChanged()
1665 {
1666   // Base image
1667   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1668   if(index==-1) return;
1669   windowSpinBox->setValue(mSlicerManagers[index]->GetColorWindow());
1670   levelSpinBox->setValue(mSlicerManagers[index]->GetColorLevel());
1671   colorMapComboBox->setCurrentIndex(mSlicerManagers[index]->GetColorMap());
1672   presetComboBox->setCurrentIndex(mSlicerManagers[index]->GetPreset());
1673
1674   // Overlay image
1675   if (mSlicerManagers[index]->GetSlicer(0)->GetOverlay())
1676     overlayPanel->getOverlayProperty(mSlicerManagers[index]->GetOverlayColor(),
1677                                      mSlicerManagers[index]->GetLinkOverlayWindowLevel(),
1678                                      mSlicerManagers[index]->GetOverlayColorWindow(),
1679                                      mSlicerManagers[index]->GetOverlayColorLevel());
1680   else
1681     overlayPanel->getOverlayProperty(-1,0,0.,0.);
1682
1683   // Fusion image
1684   if (mSlicerManagers[index]->GetSlicer(0)->GetFusion())
1685     overlayPanel->getFusionProperty(mSlicerManagers[index]->GetFusionOpacity(),
1686                                     mSlicerManagers[index]->GetFusionThresholdOpacity(),
1687                                     mSlicerManagers[index]->GetFusionColorMap(),
1688                                     mSlicerManagers[index]->GetFusionWindow(),
1689                                     mSlicerManagers[index]->GetFusionLevel());
1690   else
1691     overlayPanel->getFusionProperty(-1, -1, -1, -1, -1);
1692 }
1693 //------------------------------------------------------------------------------
1694
1695 //------------------------------------------------------------------------------
1696 void vvMainWindow::WindowLevelEdited()
1697 {
1698   presetComboBox->setCurrentIndex(6);
1699   UpdateWindowLevel();
1700 }
1701 //------------------------------------------------------------------------------
1702
1703 //------------------------------------------------------------------------------
1704 void vvMainWindow::SetWindowLevel(double w, double l)
1705 {
1706   windowSpinBox->setValue(w);
1707   levelSpinBox->setValue(l);
1708   presetComboBox->setCurrentIndex(6);
1709   colorMapComboBox->setCurrentIndex(0);
1710   UpdateWindowLevel();
1711 }
1712 //------------------------------------------------------------------------------
1713
1714 //------------------------------------------------------------------------------
1715 void vvMainWindow::UpdateWindowLevel()
1716 {
1717   if (DataTree->selectedItems().size()) {
1718     if (presetComboBox->currentIndex() == 7) //For ventilation
1719       colorMapComboBox->setCurrentIndex(5);
1720     int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1721     mSlicerManagers[index]->SetColorWindow(windowSpinBox->value());
1722     mSlicerManagers[index]->SetColorLevel(levelSpinBox->value());
1723     mSlicerManagers[index]->SetPreset(presetComboBox->currentIndex());
1724     mSlicerManagers[index]->Render();
1725     WindowLevelChanged();
1726   }
1727 }
1728 //------------------------------------------------------------------------------
1729
1730 //------------------------------------------------------------------------------
1731 void vvMainWindow::UpdateSlicingPreset()
1732 {
1733   if (DataTree->selectedItems().size()) {
1734     int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1735     mSlicerManagers[index]->SetSlicingPreset(vvSlicerManager::SlicingPresetType(slicingPresetComboBox->currentIndex()));
1736   }
1737 }
1738 //------------------------------------------------------------------------------
1739
1740 //------------------------------------------------------------------------------
1741 void vvMainWindow::UpdateColorMap()
1742 {
1743   if (DataTree->selectedItems().size()) {
1744     int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1745     mSlicerManagers[index]->SetColorMap(colorMapComboBox->currentIndex());
1746     mSlicerManagers[index]->Render();
1747   }
1748 }
1749 //------------------------------------------------------------------------------
1750 void vvMainWindow::SwitchWindowLevel()
1751 {
1752   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1753   int window = mSlicerManagers[index]->GetColorWindow();
1754   presetComboBox->setCurrentIndex(6);
1755   windowSpinBox->setValue(-window);
1756   UpdateWindowLevel();
1757 }
1758 //------------------------------------------------------------------------------
1759
1760 //------------------------------------------------------------------------------
1761 void vvMainWindow::ApplyWindowLevelToAllImages()
1762 {
1763   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1764   if(index==-1) return;
1765   double window = mSlicerManagers[index]->GetColorWindow();
1766   double level = mSlicerManagers[index]->GetColorLevel();
1767
1768   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
1769     if (mSlicerManagers[i] == NULL)
1770       continue;
1771     mSlicerManagers[i]->SetColorWindow(window);
1772     mSlicerManagers[i]->SetColorLevel(level);
1773     mSlicerManagers[i]->SetPreset(6);
1774     mSlicerManagers[i]->Render();
1775   }
1776 }
1777 //------------------------------------------------------------------------------
1778
1779 //------------------------------------------------------------------------------
1780 void vvMainWindow::ApplyWindowToSetOfImages(double window, unsigned int indexMin, unsigned int indexMax)
1781 {
1782   for (unsigned int i = indexMin; i <= indexMax && i < mSlicerManagers.size(); i++) {
1783     if (mSlicerManagers[i] == NULL)
1784       continue;
1785     mSlicerManagers[i]->SetColorWindow(window);
1786     mSlicerManagers[i]->SetPreset(6);
1787     mSlicerManagers[i]->Render();
1788   }
1789 }
1790 //------------------------------------------------------------------------------
1791
1792 //------------------------------------------------------------------------------
1793 void vvMainWindow::ApplyLevelToSetOfImages(double level, unsigned int indexMin, unsigned int indexMax)
1794 {
1795   for (unsigned int i = indexMin; i <= indexMax && i < mSlicerManagers.size(); i++) {
1796     if (mSlicerManagers[i] == NULL)
1797       continue;
1798     mSlicerManagers[i]->SetColorLevel(level);
1799     mSlicerManagers[i]->SetPreset(6);
1800     mSlicerManagers[i]->Render();
1801   }
1802 }
1803 //------------------------------------------------------------------------------
1804
1805 //------------------------------------------------------------------------------
1806 void vvMainWindow::UpdateLinkManager(std::string id, int slicer, double x, double y, double z, int temps)
1807 {
1808   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
1809     if (mSlicerManagers[i]->GetId() == id) {
1810       //mSlicerManagers[i]->SetTSlice(temps);
1811       mSlicerManagers[i]->GetSlicer(slicer)->SetCurrentPosition(x,y,z,temps);
1812       mSlicerManagers[i]->UpdateViews(0,slicer);
1813       break;
1814     }
1815   }
1816 }
1817 //------------------------------------------------------------------------------
1818
1819 //------------------------------------------------------------------------------
1820 void vvMainWindow::UpdateLinkedNavigation(std::string id, vvSlicerManager * sm, vvSlicer* refSlicer)
1821 {
1822   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
1823     if (id == mSlicerManagers[i]->GetId()) {
1824       mSlicerManagers[i]->UpdateLinkedNavigation(refSlicer);
1825     }
1826   }
1827 }
1828 //------------------------------------------------------------------------------
1829
1830 //------------------------------------------------------------------------------
1831 void vvMainWindow::ShowContextMenu(QPoint point)
1832 {
1833   if (!DataTree->selectedItems().size()) {
1834     contextActions[1]->setEnabled(0);
1835     contextActions[2]->setEnabled(0);
1836     contextActions[3]->setEnabled(0);
1837     contextActions[4]->setEnabled(0);
1838     contextActions[5]->setEnabled(0);
1839     contextActions[6]->setEnabled(0);
1840   } else {
1841     int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1842     contextActions[1]->setEnabled(1);
1843     contextActions[2]->setEnabled(
1844       DataTree->itemWidget(DataTree->selectedItems()[0],
1845                            COLUMN_RELOAD_IMAGE)->isEnabled());
1846     contextActions[3]->setEnabled(1);
1847     contextActions[5]->setEnabled(1);
1848     contextActions[6]->setEnabled(1);
1849
1850     if (mSlicerManagers[index]->GetDimension() < 3)
1851       contextActions[4]->setEnabled(0);
1852     else
1853       contextActions[4]->setEnabled(1);
1854   }
1855   contextMenu.exec(QCursor::pos());
1856 }
1857 //------------------------------------------------------------------------------
1858
1859 //------------------------------------------------------------------------------
1860 void vvMainWindow::CloseImage()
1861 {
1862   CloseImage(DataTree->selectedItems()[0],0);
1863 }
1864 //------------------------------------------------------------------------------
1865
1866 //------------------------------------------------------------------------------
1867 void vvMainWindow::ReloadImage()
1868 {
1869   ReloadImage(DataTree->selectedItems()[0],0);
1870 }
1871 //------------------------------------------------------------------------------
1872
1873 //------------------------------------------------------------------------------
1874 void vvMainWindow::SelectOverlayImage()
1875 {
1876   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1877
1878   //check if one overlay image is added
1879   for (int child = 0; child < DataTree->topLevelItem(index)->childCount(); child++)
1880     if (DataTree->topLevelItem(index)->child(child)->data(1,Qt::UserRole).toString() == "overlay") {
1881       QString error = "Cannot add more than one compared image\n";
1882       error += "Please remove first ";
1883       error += DataTree->topLevelItem(index)->child(child)->data(COLUMN_IMAGE_NAME,Qt::DisplayRole).toString();
1884       QMessageBox::information(this,tr("Problem adding compared image !"),error);
1885       return;
1886     }
1887
1888   QString Extensions = EXTENSIONS;
1889   Extensions += ";;All Files (*)";
1890   QStringList files = QFileDialog::getOpenFileNames(this,tr("Load Overlay image"),mInputPathName,Extensions);
1891   if (files.isEmpty())
1892     return;
1893
1894   std::vector<std::string> vecFileNames;
1895   for (int i = 0; i < files.size(); i++) {
1896     vecFileNames.push_back(files[i].toStdString());
1897   }
1898   AddOverlayImage(index,vecFileNames,vvImageReader::IMAGE);
1899 }
1900 //------------------------------------------------------------------------------
1901
1902 //------------------------------------------------------------------------------
1903 void vvMainWindow::AddOverlayImage(int index, std::vector<std::string> fileNames, vvImageReader::LoadedImageType type)
1904 {
1905   QString file(fileNames[0].c_str());
1906   if (QFile::exists(file))
1907   {
1908     mInputPathName = itksys::SystemTools::GetFilenamePath(file.toStdString()).c_str();
1909     itk::ImageIOBase::Pointer reader = itk::ImageIOFactory::CreateImageIO(
1910         file.toStdString().c_str(), itk::ImageIOFactory::ReadMode);
1911     reader->SetFileName(fileNames[0].c_str());
1912     reader->ReadImageInformation();
1913     std::string component = reader->GetComponentTypeAsString(reader->GetComponentType());
1914     int dimension = reader->GetNumberOfDimensions();
1915     QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
1916     vvProgressDialog progress("Opening " + file.toStdString());
1917     qApp->processEvents();
1918
1919     std::string filename = itksys::SystemTools::GetFilenameWithoutExtension(file.toStdString()).c_str();
1920     if (mSlicerManagers[index]->SetOverlay(fileNames,dimension, component,type)) {
1921       //create an item in the tree with good settings
1922       QTreeWidgetItem *item = new QTreeWidgetItem();
1923       item->setData(0,Qt::UserRole,file.toStdString().c_str());
1924       item->setData(1,Qt::UserRole,tr("overlay"));
1925       QFileInfo fileinfo(file); //Do not show the path
1926       item->setData(COLUMN_IMAGE_NAME,Qt::DisplayRole,fileinfo.fileName());
1927       item->setToolTip(COLUMN_IMAGE_NAME, mSlicerManagers[index]->GetListOfAbsoluteFilePathInOneString("overlay").c_str());
1928       qApp->processEvents();
1929
1930       for (int j = 1; j <= 4; j++) {
1931         item->setData(j,Qt::CheckStateRole,DataTree->topLevelItem(index)->data(j,Qt::CheckStateRole));
1932       }
1933
1934       //Create the buttons for reload and close
1935       qApp->processEvents();
1936       QTreePushButton* cButton = new QTreePushButton;
1937       cButton->setItem(item);
1938       cButton->setColumn(COLUMN_CLOSE_IMAGE);
1939       cButton->setToolTip(tr("close image"));
1940       cButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/exit.png")));
1941       connect(cButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
1942           this,SLOT(CloseImage(QTreeWidgetItem*, int)));
1943
1944       QTreePushButton* rButton = new QTreePushButton;
1945       rButton->setItem(item);
1946       rButton->setColumn(COLUMN_RELOAD_IMAGE);
1947       rButton->setToolTip(tr("reload image"));
1948       rButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/rotateright.png")));
1949       connect(rButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
1950           this,SLOT(ReloadImage(QTreeWidgetItem*, int)));
1951
1952       DataTree->topLevelItem(index)->setExpanded(1);
1953       DataTree->topLevelItem(index)->addChild(item);
1954       DataTree->setItemWidget(item, COLUMN_CLOSE_IMAGE, cButton);
1955       DataTree->setItemWidget(item, COLUMN_RELOAD_IMAGE, rButton);
1956
1957       //set the id of the image
1958       QString id = DataTree->topLevelItem(index)->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString();
1959       item->setData(COLUMN_IMAGE_NAME,Qt::UserRole,id.toStdString().c_str());
1960       UpdateTree();
1961       qApp->processEvents();
1962       ImageInfoChanged();
1963       QApplication::restoreOverrideCursor();
1964
1965       // Update the display to update, e.g., the sliders
1966       for(int i=0; i<4; i++)
1967         DisplaySliders(index, i);
1968     } else {
1969       QApplication::restoreOverrideCursor();
1970       QString error = "Cannot import the new image.\n";
1971       error += mSlicerManagers[index]->GetLastError().c_str();
1972       QMessageBox::information(this,tr("Problem reading image !"),error);
1973     }
1974     WindowLevelChanged();
1975   }
1976   else
1977     QMessageBox::information(this,tr("Problem reading Overlay !"),"File doesn't exist!");
1978 }
1979 //------------------------------------------------------------------------------
1980
1981
1982 //------------------------------------------------------------------------------
1983 void vvMainWindow::AddROI(int index, QString file)
1984 {
1985   /*
1986   // Get slice manager
1987
1988   // Load image
1989
1990   vvImageReader * mReader = new vvImageReader;
1991   mReader->SetInputFilename(filename.toStdString());
1992   mReader->Update(IMAGE);
1993   if (mReader->GetLastError().size() != 0) {
1994     std::cerr << "Error while reading " << filename.toStdString() << std::endl;
1995     QString error = "Cannot open file \n";
1996     error += mReader->GetLastError().c_str();
1997     QMessageBox::information(this,tr("Reading problem"),error);
1998     delete mReader;
1999     return;
2000   }
2001   vvImage::Pointer roi = mReader->GetOutput();
2002
2003   // Create roi in new tool
2004   vvToolStructureSetManager::AddImage(mCurrentSlicerManager, roi);
2005   */
2006 }
2007 //------------------------------------------------------------------------------
2008
2009 //------------------------------------------------------------------------------
2010 void vvMainWindow::SelectFusionImage()
2011 {
2012   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2013
2014   //check if one fusion image is added
2015   for (int child = 0; child < DataTree->topLevelItem(index)->childCount(); child++)
2016     if (DataTree->topLevelItem(index)->child(child)->data(1,Qt::UserRole).toString() == "fusion") {
2017       QString error = "Cannot add more than one fusion image\n";
2018       error += "Please remove first ";
2019       error += DataTree->topLevelItem(index)->child(child)->data(COLUMN_IMAGE_NAME,Qt::DisplayRole).toString();
2020       QMessageBox::information(this,tr("Problem adding fusion image !"),error);
2021       return;
2022     }
2023
2024   QString Extensions = EXTENSIONS;
2025   Extensions += ";;All Files (*)";
2026   QString file = QFileDialog::getOpenFileName(this,tr("Load Fusion image"),mInputPathName,Extensions);
2027   if (!file.isEmpty())
2028     AddFusionImage(index,file);
2029 }
2030 //------------------------------------------------------------------------------
2031
2032 //------------------------------------------------------------------------------
2033 void vvMainWindow::ResetTransformationToIdentity()
2034 {
2035   std::string actorType = DataTree->selectedItems()[0]->data(1,Qt::UserRole).toString().toStdString();
2036   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2037   mSlicerManagers[index]->ResetTransformationToIdentity(actorType);
2038   ImageInfoChanged();
2039 }
2040 //------------------------------------------------------------------------------
2041
2042 //------------------------------------------------------------------------------
2043 void vvMainWindow::AddFusionImage(int index, QString file)
2044 {
2045   if (QFile::exists(file))
2046   {
2047     mInputPathName = itksys::SystemTools::GetFilenamePath(file.toStdString()).c_str();
2048     itk::ImageIOBase::Pointer reader = itk::ImageIOFactory::CreateImageIO(
2049         file.toStdString().c_str(), itk::ImageIOFactory::ReadMode);
2050     reader->SetFileName(file.toStdString().c_str());
2051     reader->ReadImageInformation();
2052     std::string component = reader->GetComponentTypeAsString(reader->GetComponentType());
2053     if (reader) {
2054       QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
2055       vvProgressDialog progress("Opening fusion");
2056       qApp->processEvents();
2057
2058       std::string filename = itksys::SystemTools::GetFilenameWithoutExtension(file.toStdString()).c_str();
2059       if (mSlicerManagers[index]->SetFusion(file.toStdString(),
2060             reader->GetNumberOfDimensions(), component)) {
2061         //create an item in the tree with good settings
2062         QTreeWidgetItem *item = new QTreeWidgetItem();
2063         item->setData(0,Qt::UserRole,file.toStdString().c_str());
2064         item->setData(1,Qt::UserRole,tr("fusion"));
2065         QFileInfo fileinfo(filename.c_str()); //Do not show the path
2066         item->setData(COLUMN_IMAGE_NAME,Qt::DisplayRole,fileinfo.fileName());
2067         item->setToolTip(COLUMN_IMAGE_NAME, mSlicerManagers[index]->GetListOfAbsoluteFilePathInOneString("fusion").c_str());
2068         qApp->processEvents();
2069
2070         for (int j = 1; j <= 4; j++) {
2071           item->setData(j,Qt::CheckStateRole,DataTree->topLevelItem(index)->data(j,Qt::CheckStateRole));
2072         }
2073
2074         //Create the buttons for reload and close
2075         qApp->processEvents();
2076         QTreePushButton* cButton = new QTreePushButton;
2077         cButton->setItem(item);
2078         cButton->setColumn(COLUMN_CLOSE_IMAGE);
2079         cButton->setToolTip(tr("close image"));
2080         cButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/exit.png")));
2081         connect(cButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
2082             this,SLOT(CloseImage(QTreeWidgetItem*, int)));
2083
2084         QTreePushButton* rButton = new QTreePushButton;
2085         rButton->setItem(item);
2086         rButton->setColumn(COLUMN_RELOAD_IMAGE);
2087         rButton->setToolTip(tr("reload image"));
2088         rButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/rotateright.png")));
2089         connect(rButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
2090             this,SLOT(ReloadImage(QTreeWidgetItem*, int)));
2091
2092         DataTree->topLevelItem(index)->setExpanded(1);
2093         DataTree->topLevelItem(index)->addChild(item);
2094         DataTree->setItemWidget(item, COLUMN_CLOSE_IMAGE, cButton);
2095         DataTree->setItemWidget(item, COLUMN_RELOAD_IMAGE, rButton);
2096
2097         //set the id of the image
2098         QString id = DataTree->topLevelItem(index)->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString();
2099         item->setData(COLUMN_IMAGE_NAME,Qt::UserRole,id.toStdString().c_str());
2100         UpdateTree();
2101         qApp->processEvents();
2102         ImageInfoChanged();
2103         QApplication::restoreOverrideCursor();
2104       } else {
2105         QApplication::restoreOverrideCursor();
2106         QString error = "Cannot import the new image.\n";
2107         error += mSlicerManagers[index]->GetLastError().c_str();
2108         QMessageBox::information(this,tr("Problem reading image !"),error);
2109       }
2110     } else {
2111       QString error = "Cannot import the new image.\n";
2112       QMessageBox::information(this,tr("Problem reading image !"),error);
2113     }
2114   }
2115   else
2116     QMessageBox::information(this,tr("Problem reading Fusion !"),"File doesn't exist!");
2117 }
2118 //------------------------------------------------------------------------------
2119
2120
2121 //------------------------------------------------------------------------------
2122 void vvMainWindow::OpenField()
2123 {
2124   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2125   //check if a vector field has already been added
2126   for (int child = 0; child < DataTree->topLevelItem(index)->childCount(); child++)
2127     if (DataTree->topLevelItem(index)->child(child)->data(1,Qt::UserRole).toString() == "vector") {
2128       QString error = "Cannot add more than one vector field\n";
2129       error += "Please remove first ";
2130       error += DataTree->topLevelItem(index)->child(child)->data(COLUMN_IMAGE_NAME,Qt::DisplayRole).toString();
2131       QMessageBox::information(this,tr("Problem adding vector field!"),error);
2132       return;
2133     }
2134
2135   QString Extensions = "Images ( *.mhd)";
2136   Extensions += ";;Images ( *.mha)";
2137   Extensions += ";;VF Images ( *.vf)";
2138   Extensions += ";;nii Images ( *.nii)";
2139   Extensions += ";;nrrd Images ( *.nrrd)";
2140   Extensions += ";;nhdr Images ( *.nhdr)";
2141   Extensions += ";;All Files (*)";
2142   QString file = QFileDialog::getOpenFileName(this,tr("Load deformation field"),mInputPathName,Extensions);
2143   if (!file.isEmpty())
2144     AddField(file,index);
2145 }
2146 //------------------------------------------------------------------------------
2147
2148
2149 //------------------------------------------------------------------------------
2150 void vvMainWindow::AddFieldEntry(QString filename,int index,bool from_disk)
2151 {
2152   //create an item in the tree with good settings
2153   QTreeWidgetItem *item = new QTreeWidgetItem();
2154   item->setData(0,Qt::UserRole,filename.toStdString().c_str());
2155   item->setData(1,Qt::UserRole,tr("vector"));
2156   QFileInfo fileinfo(filename); //Do not show the path
2157   item->setData(COLUMN_IMAGE_NAME,Qt::DisplayRole,fileinfo.fileName());
2158   item->setToolTip(COLUMN_IMAGE_NAME, mSlicerManagers[index]->GetListOfAbsoluteFilePathInOneString("vector").c_str());
2159   qApp->processEvents();
2160
2161   for (int j = 1; j <= 4; j++) {
2162     item->setData(j,Qt::CheckStateRole,DataTree->topLevelItem(index)->data(j,Qt::CheckStateRole));
2163   }
2164
2165   //Create the buttons for reload and close
2166   qApp->processEvents();
2167   QTreePushButton* cButton = new QTreePushButton;
2168   cButton->setItem(item);
2169   cButton->setColumn(COLUMN_CLOSE_IMAGE);
2170   cButton->setToolTip(tr("close vector field"));
2171   cButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/exit.png")));
2172   connect(cButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
2173           this,SLOT(CloseImage(QTreeWidgetItem*, int)));
2174
2175   QTreePushButton* rButton = new QTreePushButton;
2176   rButton->setItem(item);
2177   rButton->setColumn(COLUMN_RELOAD_IMAGE);
2178   rButton->setToolTip(tr("reload vector field"));
2179   rButton->setEnabled(from_disk);
2180   rButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/rotateright.png")));
2181   connect(rButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
2182           this,SLOT(ReloadImage(QTreeWidgetItem*, int)));
2183
2184   DataTree->topLevelItem(index)->setExpanded(1);
2185   DataTree->topLevelItem(index)->addChild(item);
2186   DataTree->setItemWidget(item, COLUMN_RELOAD_IMAGE, rButton);
2187   DataTree->setItemWidget(item, COLUMN_CLOSE_IMAGE, cButton);
2188
2189   //set the id of the image
2190   QString id = DataTree->topLevelItem(index)->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString();
2191   item->setData(COLUMN_IMAGE_NAME,Qt::UserRole,id.toStdString().c_str());
2192   UpdateTree();
2193   qApp->processEvents();
2194   ImageInfoChanged();
2195   QApplication::restoreOverrideCursor();
2196 }
2197 //------------------------------------------------------------------------------
2198
2199
2200 //------------------------------------------------------------------------------
2201 void vvMainWindow::AddField(vvImage::Pointer vf,QString file,int index)
2202 {
2203   QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
2204   vvSlicerManager* imageManager = mSlicerManagers[index];
2205   if (imageManager->SetVF(vf,file.toStdString())) {
2206     AddFieldEntry(file,index,false);
2207   } else {
2208     QString error = "Cannot import the vector field for this image.\n";
2209     error += imageManager->GetLastError().c_str();
2210     QMessageBox::information(this,tr("Problem reading VF !"),error);
2211   }
2212   QApplication::restoreOverrideCursor();
2213 }
2214 //------------------------------------------------------------------------------
2215
2216
2217 //------------------------------------------------------------------------------
2218 void vvMainWindow::AddField(QString file,int index)
2219 {
2220   if (QFile::exists(file)) {
2221     mInputPathName = itksys::SystemTools::GetFilenamePath(file.toStdString()).c_str();
2222
2223     //init the progress events
2224     QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
2225     vvProgressDialog progress("Opening " + file.toStdString());
2226     qApp->processEvents();
2227
2228     //read the vector and put it in the current mSlicerManager
2229     vvSlicerManager* imageManager = mSlicerManagers[index];
2230     qApp->processEvents();
2231
2232     std::string filename = itksys::SystemTools::GetFilenameWithoutExtension(file.toStdString()).c_str();
2233     if (imageManager->SetVF(file.toStdString())) {
2234       imageManager->Render();
2235       AddFieldEntry(file,index,true);
2236     } else {
2237       QApplication::restoreOverrideCursor();
2238       QString error = "Cannot import the vector field for this image.\n";
2239       error += imageManager->GetLastError().c_str();
2240       QMessageBox::information(this,tr("Problem reading VF !"),error);
2241     }
2242   } else
2243     QMessageBox::information(this,tr("Problem reading VF !"),"File doesn't exist!");
2244
2245 }
2246 //------------------------------------------------------------------------------
2247
2248
2249 //------------------------------------------------------------------------------
2250 void vvMainWindow::SetVFProperty(int subsampling, int scale, int log, int width, double r, double g, double b)
2251 {
2252   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2253   if (mSlicerManagers[index]->GetSlicer(0)->GetVF()) {
2254     for (int i = 0; i < 4; i++) {
2255       mSlicerManagers[index]->GetSlicer(i)->SetVFSubSampling(subsampling);
2256       mSlicerManagers[index]->GetSlicer(i)->SetVFScale(scale);
2257       mSlicerManagers[index]->GetSlicer(i)->SetVFWidth(width);
2258       mSlicerManagers[index]->GetSlicer(i)->SetVFColor(r,g,b);
2259       if (log > 0)
2260         mSlicerManagers[index]->GetSlicer(i)->SetVFLog(1);
2261       else
2262         mSlicerManagers[index]->GetSlicer(i)->SetVFLog(0);
2263     }
2264   }
2265 }
2266 //------------------------------------------------------------------------------
2267
2268
2269 //------------------------------------------------------------------------------
2270 void vvMainWindow::SetOverlayProperty(int color, int linked, double window, double level)
2271 {
2272   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2273   if (mSlicerManagers[index]->GetSlicer(0)->GetOverlay()) {
2274     mSlicerManagers[index]->SetOverlayColor(color);
2275     mSlicerManagers[index]->SetColorMap(0);
2276     mSlicerManagers[index]->SetLinkOverlayWindowLevel(linked);
2277     mSlicerManagers[index]->SetOverlayColorWindow(window);
2278     mSlicerManagers[index]->SetOverlayColorLevel(level);
2279     mSlicerManagers[index]->Render();
2280   }
2281 }
2282 //------------------------------------------------------------------------------
2283
2284 //------------------------------------------------------------------------------
2285 void vvMainWindow::SetFusionProperty(int opacity, int thresOpacity, int colormap,double window, double level, bool showLegend)
2286 {
2287   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2288   if (mSlicerManagers[index]->GetSlicer(0)->GetFusion()) {
2289     mSlicerManagers[index]->SetFusionColorMap(colormap);
2290     mSlicerManagers[index]->SetFusionOpacity(opacity);
2291     mSlicerManagers[index]->SetFusionThresholdOpacity(thresOpacity);
2292     mSlicerManagers[index]->SetFusionWindow(window);
2293     mSlicerManagers[index]->SetFusionLevel(level);
2294     mSlicerManagers[index]->SetFusionShowLegend(showLegend);
2295     mSlicerManagers[index]->SetColorMap(0);
2296     mSlicerManagers[index]->Render();
2297   }
2298 }
2299 //------------------------------------------------------------------------------
2300
2301 //------------------------------------------------------------------------------
2302 void vvMainWindow::SaveAs()
2303 {
2304   if (DataTree->selectedItems()[0]->data(1,Qt::UserRole).toString() == "vector") {
2305     QMessageBox::warning(this,tr("Unsupported type"),tr("Sorry, saving a vector field is unsupported for the moment"));
2306     return;
2307   }
2308
2309   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2310   int dimension = mSlicerManagers[index]->GetDimension();
2311   QStringList OutputListeFormat;
2312   OutputListeFormat.clear();
2313   if (dimension == 1) {
2314     OutputListeFormat.push_back(".mhd");
2315     OutputListeFormat.push_back(".mha");
2316   }
2317   if (dimension == 2) {
2318     OutputListeFormat.push_back(".bmp");
2319     OutputListeFormat.push_back(".png");
2320     OutputListeFormat.push_back(".jpeg");
2321     OutputListeFormat.push_back(".tif");
2322     OutputListeFormat.push_back(".mhd");
2323     OutputListeFormat.push_back(".mha");
2324     OutputListeFormat.push_back(".hdr");
2325     OutputListeFormat.push_back(".vox");
2326   } else if (dimension == 3) {
2327     OutputListeFormat.push_back(".mhd");
2328     OutputListeFormat.push_back(".mha");
2329     OutputListeFormat.push_back(".nii");
2330     OutputListeFormat.push_back(".nrrd");
2331     OutputListeFormat.push_back(".nhdr");
2332     OutputListeFormat.push_back(".hdr");
2333     OutputListeFormat.push_back(".vox");
2334   } else if (dimension == 4) {
2335     OutputListeFormat.push_back(".mhd");
2336     OutputListeFormat.push_back(".mha");
2337     OutputListeFormat.push_back(".nii");
2338     OutputListeFormat.push_back(".nrrd");
2339     OutputListeFormat.push_back(".nhdr");
2340   }
2341   QString Extensions = "AllFiles(*.*)";
2342   for (int i = 0; i < OutputListeFormat.count(); i++) {
2343     Extensions += ";;Images ( *";
2344     Extensions += OutputListeFormat[i];
2345     Extensions += ")";
2346   }
2347   QString fileName = QFileDialog::getSaveFileName(this,
2348                      tr("Save As"),
2349                      mSlicerManagers[index]->GetFileName().c_str(),
2350                      Extensions);
2351   if (!fileName.isEmpty()) {
2352     std::string fileformat = itksys::SystemTools::GetFilenameLastExtension(fileName.toStdString());
2353     if (OutputListeFormat.contains(
2354           fileformat.c_str())) {
2355       QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
2356       std::string action = "Saving";
2357       vvProgressDialog progress("Saving "+fileName.toStdString());
2358       qApp->processEvents();
2359       vvImageWriter::Pointer writer = vvImageWriter::New();
2360       writer->SetOutputFileName(fileName.toStdString());
2361       writer->SetInput(mSlicerManagers[index]->GetImage());
2362
2363       // Check on transform and prompt user
2364       writer->SetSaveTransform(false);
2365       bool bId = true;
2366       for(int i=0; i<4; i++)
2367         for(int j=0; j<4; j++) {
2368           // TODO SR and BP: check on the list of transforms and not the first only
2369           double elt = mSlicerManagers[index]->GetImage()->GetTransform()[0]->GetMatrix()->GetElement(i,j);
2370           if(i==j && elt!=1.)
2371             bId = false;
2372           if(i!=j && elt!=0.)
2373             bId = false;
2374         }
2375       if( !bId ) {
2376         QString warning = "The image has an associated linear transform. Do you want to save it along?";
2377         QMessageBox msgBox(QMessageBox::Warning, tr("Save transform"), warning, 0, this);
2378         msgBox.addButton(tr("Yes"), QMessageBox::AcceptRole);
2379         msgBox.addButton(tr("No"), QMessageBox::RejectRole);
2380         if (msgBox.exec() == QMessageBox::AcceptRole)
2381           writer->SetSaveTransform(true);
2382       }
2383
2384       writer->Update();
2385       QApplication::restoreOverrideCursor();
2386       if (writer->GetLastError().size()) {
2387         QString error = "Saving did not succeed\n";
2388         error += writer->GetLastError().c_str();
2389         QMessageBox::information(this,tr("Saving Problem"),error);
2390         SaveAs();
2391       }
2392     } else {
2393       QString error = fileformat.c_str();
2394       if (error.isEmpty())
2395         error += "no file format specified !";
2396       else
2397         error += " format unknown !!!\n";
2398       QMessageBox::information(this,tr("Saving Problem"),error);
2399       SaveAs();
2400     }
2401   }
2402 }
2403 //------------------------------------------------------------------------------
2404
2405 //------------------------------------------------------------------------------
2406 void vvMainWindow::SaveCurrentState()
2407 {
2408   QString Extensions = "XML Files(*.xml)";
2409   QString fileName = QFileDialog::getSaveFileName(this,
2410                      tr("Save Current Window State"),
2411                      "",
2412                      Extensions);
2413
2414   SaveCurrentStateAs(fileName.toStdString());
2415 }
2416 //------------------------------------------------------------------------------
2417
2418 //------------------------------------------------------------------------------
2419 void vvMainWindow::SaveCurrentStateAs(const std::string& stateFile)
2420 {
2421   vvSaveState save_state;
2422   save_state.Run(this, stateFile);
2423 }
2424
2425 //------------------------------------------------------------------------------
2426 void vvMainWindow::ReadSavedState()
2427 {
2428   QString Extensions = "XML Files(*.xml)";
2429   QString fileName = QFileDialog::getOpenFileName(this,
2430                      tr("Load Window State"),
2431                      "",
2432                      Extensions);
2433
2434   ReadSavedStateFile(fileName.toStdString());
2435 }
2436 //------------------------------------------------------------------------------
2437
2438 //------------------------------------------------------------------------------
2439 void vvMainWindow::ReadSavedStateFile(const std::string& stateFile)
2440 {
2441   vvReadState read_state;
2442   read_state.Run(this, stateFile);
2443 }
2444 //------------------------------------------------------------------------------
2445
2446 //------------------------------------------------------------------------------
2447 void vvMainWindow::LinkAllImages()
2448 {
2449         linkPanel->linkAll();
2450 }
2451
2452 //------------------------------------------------------------------------------
2453 void vvMainWindow::AddLink(QString image1,QString image2,bool fromPanel)
2454 {
2455   if (!fromPanel) {
2456     // delegate to linkPanel if call came from elsewhere...
2457     linkPanel->addLinkFromIds(image1, image2);
2458     return;
2459   }
2460
2461   unsigned int sm1 = 0;
2462   unsigned int sm2 = 0;
2463
2464   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
2465     if (image1.toStdString() == mSlicerManagers[i]->GetId()) {
2466       mSlicerManagers[i]->AddLink(image2.toStdString());
2467       sm1 = i;
2468     }
2469     if (image2.toStdString() == mSlicerManagers[i]->GetId()) {
2470       mSlicerManagers[i]->AddLink(image1.toStdString());
2471       sm2 = i;
2472     }
2473   }
2474
2475   if (linkPanel->isLinkAll())   {
2476     emit UpdateLinkedNavigation(mSlicerManagers[sm1]->GetId(), mSlicerManagers[mCurrentPickedImageIndex], mSlicerManagers[mCurrentPickedImageIndex]->GetSlicer(0));
2477     emit UpdateLinkedNavigation(mSlicerManagers[sm2]->GetId(), mSlicerManagers[mCurrentPickedImageIndex], mSlicerManagers[mCurrentPickedImageIndex]->GetSlicer(0));
2478   } else {
2479     emit UpdateLinkedNavigation(mSlicerManagers[sm2]->GetId(), mSlicerManagers[sm1], mSlicerManagers[sm1]->GetSlicer(0));
2480   }
2481 }
2482
2483 //------------------------------------------------------------------------------
2484
2485
2486 //------------------------------------------------------------------------------
2487 void vvMainWindow::RemoveLink(QString image1,QString image2)
2488 {
2489   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
2490     if (image1.toStdString() == mSlicerManagers[i]->GetId()) {
2491       mSlicerManagers[i]->RemoveLink(image2.toStdString());
2492     }
2493     if (image2.toStdString() == mSlicerManagers[i]->GetId()) {
2494       mSlicerManagers[i]->RemoveLink(image1.toStdString());
2495     }
2496   }
2497 }
2498 //------------------------------------------------------------------------------
2499
2500 //------------------------------------------------------------------------------
2501 void vvMainWindow::ChangeImageWithIndexOffset(vvSlicerManager *sm, int slicer, int offset)
2502 {
2503   if(mSlicerManagers.size()==1)
2504     return;
2505
2506   int index = 0;
2507   while(sm != mSlicerManagers[index])
2508     index++;
2509   index = (index+offset+mSlicerManagers.size()) % mSlicerManagers.size();
2510
2511   QTreeWidgetItem* item = GetItemFromSlicerManager(mSlicerManagers[index]);
2512   item->setData(slicer+1,Qt::CheckStateRole,2);         //change checkbox
2513   CurrentImageChanged(mSlicerManagers[index]->GetId()); //select new image
2514   DisplayChanged(item,slicer+1);
2515 }
2516 //------------------------------------------------------------------------------
2517
2518 void vvMainWindow::HorizontalSliderMoved(int value,int column, int slicer_index)
2519 {
2520   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
2521     if (DataTree->topLevelItem(i)->data(column,Qt::CheckStateRole).toInt() > 1) {
2522       for (int j = 0; j < 4; j++) {
2523         mSlicerManagers[i]->SetTSliceInSlicer(value,j);
2524         //if (mSlicerManagers[i]->GetSlicer(j)->GetImageActor()->GetVisibility())
2525         //UpdateTSlice(j,value);
2526       }
2527       mSlicerManagers[i]->GetSlicer(slicer_index)->Render();
2528       break;
2529     }
2530   }
2531 }
2532 //------------------------------------------------------------------------------
2533
2534
2535 //------------------------------------------------------------------------------
2536 void vvMainWindow::NOHorizontalSliderMoved()
2537 {
2538   // if (mCurrentTime == NOHorizontalSlider->value()) return;
2539   HorizontalSliderMoved(NOHorizontalSlider->value(),COLUMN_UL_VIEW,0);
2540 //  mCurrentTime = NOHorizontalSlider->value();
2541 }
2542 //------------------------------------------------------------------------------
2543
2544
2545 //------------------------------------------------------------------------------
2546 void vvMainWindow::NEHorizontalSliderMoved()
2547 {
2548   // if (mCurrentTime == NEHorizontalSlider->value()) return;
2549   HorizontalSliderMoved(NEHorizontalSlider->value(),COLUMN_UR_VIEW,1);
2550 //  mCurrentTime = NEHorizontalSlider->value();
2551 }
2552 //------------------------------------------------------------------------------
2553
2554
2555 //------------------------------------------------------------------------------
2556 void vvMainWindow::SOHorizontalSliderMoved()
2557 {
2558   // if (mCurrentTime == SOHorizontalSlider->value()) return;
2559   HorizontalSliderMoved(SOHorizontalSlider->value(),COLUMN_DL_VIEW,2);
2560   // mCurrentTime = SOHorizontalSlider->value();
2561 }
2562 //------------------------------------------------------------------------------
2563
2564
2565 //------------------------------------------------------------------------------
2566 void vvMainWindow::SEHorizontalSliderMoved()
2567 {
2568   // if (mCurrentTime == SEHorizontalSlider->value()) return;
2569   HorizontalSliderMoved(SEHorizontalSlider->value(),COLUMN_DR_VIEW,3);
2570   // mCurrentTime = SEHorizontalSlider->value();
2571 }
2572 //------------------------------------------------------------------------------
2573
2574 //------------------------------------------------------------------------------
2575 void vvMainWindow::NOVerticalSliderChanged()
2576 {
2577   static int value=-1;
2578   if (value == NOVerticalSlider->value()) return;
2579   else value = NOVerticalSlider->value();
2580   //  int value = NOVerticalSlider->value();
2581   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
2582     if (DataTree->topLevelItem(i)->data(COLUMN_UL_VIEW,Qt::CheckStateRole).toInt() > 1) {
2583       if (mSlicerManagers[i]->GetSlicer(0)->GetSlice() != value) {
2584         mSlicerManagers[i]->GetSlicer(0)->SetSlice(value);
2585         mSlicerManagers[i]->VerticalSliderHasChanged(0, value);
2586
2587         // If nor Update/Render -> slider not work
2588         // only render = ok navigation, but for contour Update needed but slower ?
2589
2590         mSlicerManagers[i]->UpdateSlice(0);  // <-- DS add this. Not too much update ? YES. but needed for ImageContour ...
2591         //mSlicerManagers[i]->GetSlicer(0)->Render(); // <-- DS add this, needed for contour, seems ok ? not too slow ?
2592       }
2593       break;
2594     }
2595   }
2596 }
2597 //------------------------------------------------------------------------------
2598
2599
2600 //------------------------------------------------------------------------------
2601 void vvMainWindow::NEVerticalSliderChanged()
2602 {
2603   static int value=-1;
2604   if (value == NEVerticalSlider->value()) return;
2605   else value = NEVerticalSlider->value();
2606   //  int value = NEVerticalSlider->value();
2607   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
2608     if (DataTree->topLevelItem(i)->data(COLUMN_UR_VIEW,Qt::CheckStateRole).toInt() > 1) {
2609       if (mSlicerManagers[i]->GetSlicer(1)->GetSlice() != value) {
2610         mSlicerManagers[i]->GetSlicer(1)->SetSlice(value);
2611         mSlicerManagers[i]->VerticalSliderHasChanged(1, value);
2612         mSlicerManagers[i]->UpdateSlice(1);
2613         //mSlicerManagers[i]->GetSlicer(1)->Render(); // <-- DS add this, needed for contour, seems ok ? not too slow ?
2614       }
2615       break;
2616     }
2617   }
2618 }
2619 //------------------------------------------------------------------------------
2620
2621
2622 //------------------------------------------------------------------------------
2623 void vvMainWindow::SOVerticalSliderChanged()
2624 {
2625   static int value=-1;
2626   if (value == SOVerticalSlider->value()) return;
2627   else value = SOVerticalSlider->value();
2628   //int value = SOVerticalSlider->value();
2629   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
2630     if (DataTree->topLevelItem(i)->data(COLUMN_DL_VIEW,Qt::CheckStateRole).toInt() > 1) {
2631       if (mSlicerManagers[i]->GetSlicer(2)->GetSlice() != value) {
2632         mSlicerManagers[i]->GetSlicer(2)->SetSlice(value);
2633         mSlicerManagers[i]->VerticalSliderHasChanged(2, value);
2634         mSlicerManagers[i]->UpdateSlice(2);
2635         //mSlicerManagers[i]->GetSlicer(2)->Render(); // <-- DS add this, needed for contour, seems ok ? not too slow ?
2636       }
2637       // else { DD("avoid SOVerticalSlider slicer update"); }
2638       break;
2639     }
2640   }
2641 }
2642 //------------------------------------------------------------------------------
2643
2644
2645 //------------------------------------------------------------------------------
2646 void vvMainWindow::SEVerticalSliderChanged()
2647 {
2648   static int value=-1;
2649   if (value == SEVerticalSlider->value()) return;
2650   else value = SEVerticalSlider->value();
2651   // int value = SEVerticalSlider->value();
2652   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
2653     if (DataTree->topLevelItem(i)->data(COLUMN_DR_VIEW,Qt::CheckStateRole).toInt() > 1) {
2654       if (mSlicerManagers[i]->GetSlicer(3)->GetSlice() != value) {
2655         mSlicerManagers[i]->GetSlicer(3)->SetSlice(value);
2656         mSlicerManagers[i]->VerticalSliderHasChanged(3, value);
2657         mSlicerManagers[i]->UpdateSlice(3);
2658         //mSlicerManagers[i]->GetSlicer(3)->Render(); // <-- DS add this, needed for contour, seems ok ? not too slow ?
2659       }
2660       break;
2661     }
2662   }
2663 }
2664 //------------------------------------------------------------------------------
2665
2666
2667 //------------------------------------------------------------------------------
2668 void vvMainWindow::UpdateSlice(int slicer, int slice)
2669 {
2670   // DD("vvMainWindow::UpdateSlice");
2671 //   DD(slicer);
2672 //   DD(slice);
2673   if (slicer == 0) {
2674     //    if (slice != NOVerticalSlider->value())
2675     NOVerticalSlider->setValue(slice);
2676   } else {
2677     if (slicer == 1)
2678       NEVerticalSlider->setValue(slice);
2679     else {
2680       if (slicer == 2)
2681         SOVerticalSlider->setValue(slice);
2682       else {
2683         if (slicer == 3)
2684           SEVerticalSlider->setValue(slice);
2685       }
2686     }
2687   }
2688   // DD("vvMainWindow:UpdateSlice END");
2689 }
2690 //------------------------------------------------------------------------------
2691
2692
2693 //------------------------------------------------------------------------------
2694 void vvMainWindow::UpdateTSlice(int slicer, int slice)
2695 {
2696   switch (slicer) {
2697   case 0:
2698     NOHorizontalSlider->setValue(slice);
2699     break;
2700   case 1:
2701     NEHorizontalSlider->setValue(slice);
2702     break;
2703   case 2:
2704     SOHorizontalSlider->setValue(slice);
2705     break;
2706   case 3:
2707     SEHorizontalSlider->setValue(slice);
2708     break;
2709   }
2710 }
2711 //------------------------------------------------------------------------------
2712
2713
2714 //------------------------------------------------------------------------------
2715 void vvMainWindow::UpdateSliceRange(int slicer, int min, int max, int tmin, int tmax)
2716 {
2717   //int position = int((min+max)/2);
2718   int position = mSlicerManagers[mCurrentPickedImageIndex]->GetSlicer(slicer)->GetSlice();
2719   if (slicer == 0) {
2720     NOVerticalSlider->setRange(min,max);
2721     NOHorizontalSlider->setRange(tmin,tmax);
2722     NOVerticalSlider->setValue(position);
2723   } else if (slicer == 1) {
2724     NEVerticalSlider->setRange(min,max);
2725     NEHorizontalSlider->setRange(tmin,tmax);
2726     NEVerticalSlider->setValue(position);
2727   } else if (slicer == 2) {
2728     SOVerticalSlider->setRange(min,max);
2729     SOHorizontalSlider->setRange(tmin,tmax);
2730     SOVerticalSlider->setValue(position);
2731   } else if (slicer == 3) {
2732     SEVerticalSlider->setRange(min,max);
2733     SEHorizontalSlider->setRange(tmin,tmax);
2734     SEVerticalSlider->setValue(position);
2735   }
2736 }
2737 //------------------------------------------------------------------------------
2738
2739
2740 //------------------------------------------------------------------------------
2741 void vvMainWindow::SaveNOScreenshot()
2742 {
2743   SaveScreenshot(NOViewWidget);
2744 }
2745 //------------------------------------------------------------------------------
2746
2747
2748 //------------------------------------------------------------------------------
2749 void vvMainWindow::SaveNEScreenshot()
2750 {
2751   SaveScreenshot(NEViewWidget);
2752 }
2753 //------------------------------------------------------------------------------
2754
2755
2756 //------------------------------------------------------------------------------
2757 void vvMainWindow::SaveSOScreenshot()
2758 {
2759   SaveScreenshot(SOViewWidget);
2760 }
2761 //------------------------------------------------------------------------------
2762
2763
2764 //------------------------------------------------------------------------------
2765 void vvMainWindow::SaveSEScreenshot()
2766 {
2767   SaveScreenshot(SEViewWidget);
2768 }
2769 //------------------------------------------------------------------------------
2770
2771
2772 //------------------------------------------------------------------------------
2773 void vvMainWindow::SaveScreenshotAllSlices()
2774 {
2775   QVTKWidget *widget = NOViewWidget;
2776
2777   int index = 0;// GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2778   vvSlicerManager * SM = mSlicerManagers[index];
2779   vvImage * image = SM->GetImage();
2780   vvSlicer * slicer = SM->GetSlicer(0);
2781   int orientation = slicer->GetOrientation();
2782   int nbSlices = image->GetSize()[orientation];
2783   vtkSmartPointer<vtkRenderWindow>  renderWindow = widget->GetRenderWindow();
2784
2785   // Select filename base
2786   QString filename = QFileDialog::getSaveFileName(this,
2787                                                   tr("Save As (filename will be completed by slice number)"),
2788                                                   itksys::SystemTools::GetFilenamePath(mSlicerManagers[index]->GetFileName()).c_str(),
2789                                                   "Images( *.png);;Images( *.jpg)");
2790
2791   // Loop on slices
2792   for(int i=0; i<nbSlices; i++) {
2793     // Change the slice
2794     slicer->SetSlice(i); // -> change the slice of the current slicer
2795     SM->UpdateSlice(0); // --> this one emit UpdateSlice
2796     QCoreApplication::flush(); // -> needed to force display of contours
2797
2798     // Screenshot
2799     vtkSmartPointer<vtkWindowToImageFilter> windowToImageFilter = vtkSmartPointer<vtkWindowToImageFilter>::New();
2800     windowToImageFilter->SetInput(renderWindow);
2801     windowToImageFilter->SetMagnification(1);
2802     windowToImageFilter->SetInputBufferTypeToRGBA(); //also record the alpha (transparency) channel
2803     windowToImageFilter->Update();
2804
2805     vtkSmartPointer<vtkPNGWriter> writer = vtkSmartPointer<vtkPNGWriter>::New();
2806     std::string fn = itksys::SystemTools::GetFilenameWithoutLastExtension(filename.toStdString());
2807     std::string num = clitk::toString(i);
2808     if (i<10) num = "0"+num;
2809     if (i<100) num = "0"+num;
2810     if (i<1000) num = "0"+num;
2811
2812     fn = itksys::SystemTools::GetFilenamePath(filename.toStdString()) + "/"+ fn
2813       + "_" + num + itksys::SystemTools::GetFilenameLastExtension(filename.toStdString());
2814     writer->SetFileName(fn.c_str());
2815     writer->SetInput(windowToImageFilter->GetOutput());
2816     writer->Write();
2817   }
2818 }
2819 //------------------------------------------------------------------------------
2820
2821
2822 //------------------------------------------------------------------------------
2823 void vvMainWindow::SaveScreenshot(QVTKWidget *widget)
2824 {
2825   QString Extensions = "Images( *.png);;";
2826   Extensions += "Images( *.jpg);;";
2827   Extensions += "Images( *.bmp);;";
2828   Extensions += "Images( *.tif);;";
2829   Extensions += "Images( *.ppm)";
2830 #if defined(VTK_USE_FFMPEG_ENCODER) || defined(VTK_USE_VIDEO_FOR_WINDOWS)
2831   Extensions += ";;Video( *.avi)";
2832 #endif
2833 #ifdef VTK_USE_MPEG2_ENCODER
2834   Extensions += ";;Video( *.mpg)";
2835 #endif
2836 #ifdef CLITK_EXPERIMENTAL
2837   Extensions += ";;Video( *.gif)";
2838 #endif
2839
2840   int smIndex=GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2841   QString fileName = QFileDialog::getSaveFileName(this,
2842                      tr("Save As"),
2843                      itksys::SystemTools::GetFilenamePath(mSlicerManagers[smIndex]->GetFileName()).c_str(),
2844                      Extensions);
2845
2846   if (!fileName.isEmpty()) {
2847     vtkSmartPointer<vtkWindowToImageFilter> w2i = vtkSmartPointer<vtkWindowToImageFilter>::New();
2848     w2i->SetInput(widget->GetRenderWindow());
2849     w2i->Update();
2850     vtkImageData *image = w2i->GetOutput();
2851
2852     std::string ext(itksys::SystemTools::GetFilenameLastExtension(fileName.toStdString()));
2853
2854     // Image
2855     vtkImageWriter *imgwriter = NULL;
2856     if (ext==".bmp")
2857       imgwriter = vtkBMPWriter::New();
2858     else if (ext==".tif")
2859       imgwriter = vtkTIFFWriter::New();
2860     else if (ext==".ppm")
2861       imgwriter = vtkPNMWriter::New();
2862     else if (ext==".png")
2863       imgwriter = vtkPNGWriter::New();
2864     else if (ext==".jpg")
2865       imgwriter = vtkJPEGWriter::New();
2866
2867     // Snapshot image if not null
2868     if(imgwriter!=NULL) {
2869       imgwriter->SetInput(image);
2870       imgwriter->SetFileName(fileName.toStdString().c_str());
2871       imgwriter->Write();
2872       return;
2873     }
2874
2875     // Video
2876     vtkGenericMovieWriter *vidwriter = NULL;
2877 #if CLITK_EXPERIMENTAL == 1
2878     if (ext==".gif") {
2879       vvAnimatedGIFWriter *gif = vvAnimatedGIFWriter::New();
2880       vidwriter = gif;
2881
2882       // FPS
2883       bool ok;
2884       int fps = QInputDialog::getInteger(this, tr("Number of frames per second"),
2885                                      tr("FPS:"), 5, 0, 1000, 1, &ok);
2886       if(ok)
2887         gif->SetRate(fps);
2888
2889       // Loops
2890       int loops = QInputDialog::getInteger(this, tr("Loops"),
2891                                      tr("Number of loops (0 means infinite):"), 0, 0, 1000000000, 1, &ok);
2892       if(ok)
2893         gif->SetLoops(loops);
2894
2895       // Dithering
2896       QString msg = "Would you like to activate dithering?";
2897       QMessageBox msgBox(QMessageBox::Question, tr("Dithering"),msg, 0, this);
2898       msgBox.addButton(tr("Yes"), QMessageBox::AcceptRole);
2899       msgBox.addButton(tr("No"), QMessageBox::RejectRole);
2900       gif->SetDither(msgBox.exec() == QMessageBox::AcceptRole);
2901     }
2902 #endif
2903 #ifdef VTK_USE_VIDEO_FOR_WINDOWS
2904     if (ext==".avi") {
2905       vtkAVIWriter *mpg = vtkAVIWriter::New();
2906       vidwriter = mpg;
2907       mpg->SetQuality(2);
2908       bool ok;
2909       int fps = QInputDialog::getInteger(this, tr("Number of frames per second"),
2910                                      tr("FPS:"), 5, 0, 1024, 1, &ok);
2911       if(!ok)
2912         fps = 5;
2913       mpg->SetRate(fps);
2914     }
2915 #endif
2916 #ifdef VTK_USE_FFMPEG_ENCODER
2917     if (ext==".avi") {
2918       vtkFFMPEGWriter *mpg = vtkFFMPEGWriter::New();
2919       vidwriter = mpg;
2920       mpg->SetQuality(2);
2921       bool ok;
2922       int fps = QInputDialog::getInteger(this, tr("Number of frames per second"),
2923                                      tr("FPS:"), 5, 0, 1024, 1, &ok);
2924       if(!ok)
2925         fps = 5;
2926       mpg->SetRate(fps);
2927       mpg->SetBitRateTolerance(int(ceil(12.0*1024*1024/fps)));
2928     }
2929 #endif
2930 #ifdef VTK_USE_MPEG2_ENCODER
2931     if (ext==".mpg") {
2932       vtkMPEG2Writer *mpg = vtkMPEG2Writer::New();
2933       vidwriter = mpg;
2934     }
2935 #endif
2936
2937     // Take video if not null
2938     if(vidwriter!=NULL){
2939       vidwriter->SetInput(image);
2940       vidwriter->SetFileName(fileName.toStdString().c_str());
2941       vidwriter->Start();
2942       int nSlice = mSlicerManagers[smIndex]->GetSlicer(0)->GetTMax();
2943       for(int i=0; i<=nSlice; i++) {
2944         mSlicerManagers[smIndex]->SetNextTSlice(0);
2945         vtkSmartPointer<vtkWindowToImageFilter> w2i = vtkSmartPointer<vtkWindowToImageFilter>::New();
2946         w2i->SetInput(widget->GetRenderWindow());
2947         w2i->Update();
2948         vidwriter->SetInput(w2i->GetOutput());
2949         vidwriter->Write();
2950       }
2951       vidwriter->End();
2952       vidwriter->Delete();
2953       return;
2954     }
2955
2956     QMessageBox::information(this,tr("Problem saving screenshot !"),tr("Cannot save image.\nPlease set a file extension !!!"));
2957   }
2958 }
2959 //------------------------------------------------------------------------------
2960
2961
2962 //------------------------------------------------------------------------------
2963 void vvMainWindow::GoToCursor()
2964 {
2965   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2966   for (int column = 1; column < 5; column++) {
2967     if (DataTree->selectedItems()[0]->data(column,Qt::CheckStateRole).toInt() > 1) {
2968       double* cursorPos = mSlicerManagers[index]->GetSlicer(column-1)->GetCursorPosition();
2969       mSlicerManagers[index]->GetSlicer(column-1)->SetCurrentPosition(
2970         cursorPos[0],cursorPos[1],cursorPos[2],cursorPos[3]);
2971       mSlicerManagers[index]->UpdateViews(1,column-1);
2972       mSlicerManagers[index]->UpdateLinked(column-1);
2973       break;
2974     }
2975   }
2976 }
2977 //------------------------------------------------------------------------------
2978
2979 //------------------------------------------------------------------------------
2980 void vvMainWindow::PlayPause()
2981 {
2982   if (playMode) {
2983     playMode = 0;
2984     playButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/player_play.png")));
2985     ImageInfoChanged();
2986     return;
2987   } else {
2988     int image_number=DataTree->topLevelItemCount();
2989     bool has_temporal;
2990     for (int i=0; i<image_number; i++)
2991       if (mSlicerManagers[i]->GetSlicer(0)->GetTMax() > 0) {
2992         has_temporal=true;
2993         break;
2994       }
2995     if (has_temporal) {
2996       playMode = 1;
2997       playButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/player_pause.png")));
2998       QTimer::singleShot(1000/mFrameRate, this, SLOT(PlayNext()));
2999     }
3000   }
3001 }
3002 //------------------------------------------------------------------------------
3003
3004 //------------------------------------------------------------------------------
3005 void vvMainWindow::PlayNext()
3006 {
3007   if (playMode && !this->isHidden()) {
3008     int image_number=DataTree->topLevelItemCount();
3009     ///Only play one slicer per SM, and only if the SM is being displayed
3010     for (int i=0; i<image_number; i++)
3011       for (int j=0; j<4; j++)
3012         if (mSlicerManagers[i]->GetSlicer(0)->GetTMax() > 0 &&
3013             DataTree->topLevelItem(i)->data(j+1,Qt::CheckStateRole).toInt() > 0) {
3014           mSlicerManagers[i]->SetNextTSlice(j);
3015           break;
3016         }
3017     QTimer::singleShot(1000/mFrameRate, this, SLOT(PlayNext()));
3018   }
3019 }
3020 //------------------------------------------------------------------------------
3021
3022 void vvMainWindow::ShowLastImage()
3023 {
3024   if (mSlicerManagers.size() > 1) {
3025     QTreeWidgetItem * item=DataTree->topLevelItem(DataTree->topLevelItemCount()-1);
3026     CurrentImageChanged(mSlicerManagers.back()->GetId()); //select new image
3027     item->setData(1,Qt::CheckStateRole,2); //show the new image in the first panel
3028     DisplayChanged(item,1);
3029   }
3030 }
3031
3032 //------------------------------------------------------------------------------
3033 void vvMainWindow::UpdateRenderWindows()
3034 {
3035   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
3036     mSlicerManagers[i]->GetSlicer(0)->UpdateLandmarks();
3037     mSlicerManagers[i]->GetSlicer(1)->UpdateLandmarks();
3038     mSlicerManagers[i]->GetSlicer(2)->UpdateLandmarks();
3039     mSlicerManagers[i]->GetSlicer(3)->UpdateLandmarks();
3040   }
3041   if (NOViewWidget->GetRenderWindow()) NOViewWidget->GetRenderWindow()->Render();
3042   if (NEViewWidget->GetRenderWindow()) NEViewWidget->GetRenderWindow()->Render();
3043   if (SOViewWidget->GetRenderWindow()) SOViewWidget->GetRenderWindow()->Render();
3044   if (SEViewWidget->GetRenderWindow()) SEViewWidget->GetRenderWindow()->Render();
3045 }
3046 //------------------------------------------------------------------------------
3047
3048 //------------------------------------------------------------------------------
3049 void vvMainWindow::SegmentationOnCurrentImage()
3050 {
3051   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
3052
3053   vvSegmentationDialog segmentation;
3054   segmentation.SetImage(mSlicerManagers[index]->GetSlicer(0)->GetImage());
3055   segmentation.exec();
3056 }
3057 //------------------------------------------------------------------------------
3058
3059 void vvMainWindow::SurfaceViewerLaunch()
3060 {
3061   vvSurfaceViewerDialog surfaceViewer;
3062   surfaceViewer.exec();
3063 }
3064 //------------------------------------------------------------------------------
3065
3066
3067 //------------------------------------------------------------------------------
3068 int vvMainWindow::GetImageDuplicateFilenameNumber(std::string filename)
3069 {
3070   int number=0;
3071   for(unsigned int l=0; l<mSlicerManagers.size(); l++) {
3072     vvSlicerManager * v = mSlicerManagers[l];
3073     if (v->GetBaseFileName() ==
3074         vtksys::SystemTools::GetFilenameName(vtksys::SystemTools::GetFilenameWithoutLastExtension(filename))) {
3075       number = std::max(number, v->GetBaseFileNameNumber()+1);
3076     }
3077   }
3078   return number;
3079 }
3080 //------------------------------------------------------------------------------
3081
3082
3083 //------------------------------------------------------------------------------
3084 vvSlicerManager* vvMainWindow::AddImage(vvImage::Pointer image,std::string filename)
3085 {
3086   // Change filename if another image exist with the same name
3087   int number = GetImageDuplicateFilenameNumber(filename);
3088
3089   // Create new SliceManager
3090   vvSlicerManager* slicer_manager = new vvSlicerManager(4);
3091   slicer_manager->SetImage(image);//, IMAGE, number);
3092   //  filename = filename+"_"+clitk::toString(number);
3093   slicer_manager->SetFilename(filename, number);
3094   mSlicerManagers.push_back(slicer_manager);
3095
3096   //create an item in the tree with good settings
3097   QTreeWidgetItem *item = new QTreeWidgetItem();
3098   item->setData(0,Qt::UserRole,slicer_manager->GetFileName().c_str());//files[i].c_str());
3099   item->setData(1,Qt::UserRole,tr("image"));
3100   item->setData(COLUMN_IMAGE_NAME,Qt::DisplayRole,slicer_manager->GetFileName().c_str());//filename.c_str());
3101   qApp->processEvents();
3102
3103   for (int j = 1; j <= 4; j++) item->setData(j,Qt::CheckStateRole,1);
3104
3105   //Create the buttons for reload and close
3106   qApp->processEvents();
3107   QTreePushButton* cButton = new QTreePushButton;
3108   cButton->setItem(item);
3109   cButton->setColumn(COLUMN_CLOSE_IMAGE);
3110   cButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/exit.png")));
3111   connect(cButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
3112           this,SLOT(CloseImage(QTreeWidgetItem*, int)));
3113
3114   QTreePushButton* rButton = new QTreePushButton;
3115   rButton->setItem(item);
3116   rButton->setColumn(COLUMN_RELOAD_IMAGE);
3117   rButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/rotateright.png")));
3118   rButton->setEnabled(0);
3119   connect(rButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
3120           this,SLOT(ReloadImage(QTreeWidgetItem*, int)));
3121
3122   DataTree->addTopLevelItem(item);
3123   DataTree->setItemWidget(item, COLUMN_CLOSE_IMAGE, cButton);
3124   DataTree->setItemWidget(item, COLUMN_RELOAD_IMAGE, rButton);
3125
3126   //set the id of the image
3127   QString id = QDir::current().absoluteFilePath(slicer_manager->GetFileName().c_str()) + QString::number(mSlicerManagers.size()-1);
3128   item->setData(COLUMN_IMAGE_NAME,Qt::UserRole,id.toStdString().c_str());
3129   mSlicerManagers.back()->SetId(id.toStdString());
3130
3131   linkPanel->addImage(slicer_manager->GetFileName().c_str()// filename
3132                       , id.toStdString());
3133
3134   connect(mSlicerManagers.back(), SIGNAL(currentImageChanged(std::string)),
3135           this, SLOT(CurrentImageChanged(std::string)));
3136   connect(mSlicerManagers.back(), SIGNAL(currentPickedImageChanged(std::string)),
3137           this, SLOT(CurrentPickedImageChanged(std::string)));
3138   connect(mSlicerManagers.back(), SIGNAL(UpdatePosition(int, double, double, double, double, double, double, double)),
3139           this, SLOT(MousePositionChanged(int,double, double, double, double, double, double, double)));
3140   connect(mSlicerManagers.back(), SIGNAL(UpdateVector(int, double, double, double, double)),
3141           this, SLOT(VectorChanged(int,double,double,double, double)));
3142   connect(mSlicerManagers.back(), SIGNAL(UpdateOverlay(int, double, double)),
3143           this, SLOT(OverlayChanged(int,double,double)));
3144   connect(mSlicerManagers.back(), SIGNAL(UpdateFusion(int, double)),
3145           this, SLOT(FusionChanged(int,double)));
3146   connect(mSlicerManagers.back(), SIGNAL(WindowLevelChanged()),
3147           this,SLOT(WindowLevelChanged()));
3148   connect(mSlicerManagers.back(), SIGNAL(UpdateSlice(int,int)),
3149           this,SLOT(UpdateSlice(int,int)));
3150   connect(mSlicerManagers.back(), SIGNAL(UpdateTSlice(int, int)),
3151           this,SLOT(UpdateTSlice(int, int)));
3152   connect(mSlicerManagers.back(), SIGNAL(UpdateTSlice(int, int)),
3153           this,SLOT(ImageInfoChanged()));
3154   connect(mSlicerManagers.back(), SIGNAL(UpdateSliceRange(int,int,int,int,int)),
3155           this,SLOT(UpdateSliceRange(int,int,int,int,int)));
3156   connect(mSlicerManagers.back(), SIGNAL(UpdateLinkManager(std::string,int,double,double,double,int)),
3157           this,SLOT(UpdateLinkManager(std::string,int,double,double,double,int)));
3158   connect(mSlicerManagers.back(), SIGNAL(UpdateLinkedNavigation(std::string,vvSlicerManager*,vvSlicer*)),
3159           this,SLOT(UpdateLinkedNavigation(std::string,vvSlicerManager*,vvSlicer*)));
3160   connect(mSlicerManagers.back(), SIGNAL(ChangeImageWithIndexOffset(vvSlicerManager*,int,int)),
3161           this,SLOT(ChangeImageWithIndexOffset(vvSlicerManager*,int,int)));
3162   connect(mSlicerManagers.back(), SIGNAL(LandmarkAdded()),landmarksPanel,SLOT(AddPoint()));
3163   UpdateTree();
3164   qApp->processEvents();
3165   InitSlicers();
3166   ShowLastImage();
3167   InitDisplay();
3168   qApp->processEvents();
3169
3170   // End
3171   ImageInfoChanged();
3172   return slicer_manager;
3173 }
3174 //------------------------------------------------------------------------------
3175
3176
3177 //------------------------------------------------------------------------------
3178 void vvMainWindow::UpdateCurrentSlicer()
3179 {
3180   int index = -1;
3181   if (DataTree->selectedItems().size() > 0) {
3182     index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
3183   }
3184   mSlicerManagerCurrentIndex = index;
3185 }
3186 //------------------------------------------------------------------------------
3187