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