vv/vvMainWindow.cxx

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