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 "vvQPacsConnection.h"
  51 #include "clitkConfiguration.h"
  52
  53 // ITK include
  54 #include <itkImage.h>
  55 #include <itkImageFileReader.h>
  56 #include <itkByteSwapper.h>
  57 #include <itkCommand.h>
  58 #include <itkNumericSeriesFileNames.h>
  59
  60 // VTK include
  61 #include <vtkImageData.h>
  62 #include <vtkImageActor.h>
  63 #include <vtkCornerAnnotation.h>
  64 #include <vtkRenderWindow.h>
  65 #include <vtkRenderWindowInteractor.h>
  66 #include <vtkRenderer.h>
  67 #include <vtkRendererCollection.h>
  68 #include <vtkWindowToImageFilter.h>
  69 #include <vtkBMPWriter.h>
  70 #include <vtkTIFFWriter.h>
  71 #include <vtkPNMWriter.h>
  72 #include <vtkPNGWriter.h>
  73 #include <vtkJPEGWriter.h>
  74 #include <vtkGenericMovieWriter.h>
  75 #ifdef CLITK_EXPERIMENTAL
  76 #  include <vvAnimatedGIFWriter.h>
  77 #endif
  78 #ifdef VTK_USE_VIDEO_FOR_WINDOWS
  79 #  include <vtkAVIWriter.h>
  80 #endif
  81 #ifdef VTK_USE_FFMPEG_ENCODER
  82 #  include <vtkFFMPEGWriter.h>
  83 #endif
  84 #ifdef VTK_USE_MPEG2_ENCODER
  85 #  include <vtkMPEG2Writer.h>
  86 #endif
  87 #include <vtkMatrix4x4.h>
  88 #include <vtkTransform.h>
  89
  90 // Standard includes
  91 #include <iostream>
  92 #include <fstream>
  93 #include <sstream>
  94 #include <iomanip>
  95
  96 #define COLUMN_TREE 0
  97 #define COLUMN_UL_VIEW 1
  98 #define COLUMN_UR_VIEW 2
  99 #define COLUMN_DL_VIEW 3
 100 #define COLUMN_DR_VIEW 4
 101 #define COLUMN_CLOSE_IMAGE 5
 102 #define COLUMN_RELOAD_IMAGE 6
 103 #define COLUMN_IMAGE_NAME 7
 104
 105 #ifdef CLITK_PRIVATE_FEATURES
 106 #define EXTENSIONS "Images ( *.bmp *.png *.jpeg *.jpg *.tif *.mhd *.mha *.hdr *.vox *.his *.xdr *.SCAN *.nii *.nrrd *.nhdr *.refscan *.nii.gz *.usf *.svl)"
 107 #else
 108 #define EXTENSIONS "Images ( *.bmp *.png *.jpeg *.jpg *.tif *.mhd *.mha *.hdr *.vox *.his *.xdr *.SCAN *.nii *.nrrd *.nhdr *.refscan *.nii.gz)"
 109 #endif
 110
 111
 112 /*Data Tree values
 113 0,Qt::UserRole full filename
 114 1,Qt::CheckStateRole checkbutton UL View
 115 1,Qt::UserRole overlay, fusion or vector
 116 2,Qt::CheckStateRole checkbutton UR View
 117 3,Qt::CheckStateRole checkbutton DL View
 118 4,Qt::CheckStateRole checkbutton DR View
 119 5,0  short filename
 120 5,Qt::UserRole mSlicerManager id*/
 121
 122 //------------------------------------------------------------------------------
 123 vvMainWindow::vvMainWindow():vvMainWindowBase()
 124 {
 125   setupUi(this); // this sets up the GUI
 126
 127   mInputPathName = "";
 128   mMenuTools = menuTools;
 129   //  mMenuSegmentation = menuSegmentation;
 130   mContextMenu = &contextMenu;
 131   mMenuExperimentalTools = menuExperimental;
 132   mMainWidget = this;
 133   mCurrentTime = -1;
 134   mCurrentSelectedImageId = "";
 135   mCurrentPickedImageId = "";
 136   mCurrentPickedImageIndex = 0;
 137
 138   //Init the contextMenu
 139   this->setContextMenuPolicy(Qt::CustomContextMenu);
 140   contextActions.resize(0);
 141   QAction* actionOpen_new_image = contextMenu.addAction(QIcon(QString::fromUtf8(":/common/icons/fileopen.png")),
 142     tr("O&pen new Image"));
 143   actionOpen_new_image->setShortcut(QKeySequence(tr("Ctrl+O")));
 144   connect(actionOpen_new_image,SIGNAL(triggered()),this,SLOT(OpenImages()));
 145   contextActions.push_back(actionOpen_new_image);
 146   contextMenu.addSeparator();
 147
 148   QAction* actionClose_Image = contextMenu.addAction(QIcon(QString::fromUtf8(":/common/icons/exit.png")),
 149     tr("Close Current Image"));
 150   connect(actionClose_Image,SIGNAL(triggered()),this,SLOT(CloseImage()));
 151   contextActions.push_back(actionClose_Image);
 152
 153   QAction* actionReload_image = contextMenu.addAction(QIcon(QString::fromUtf8(":/common/icons/rotateright.png")),
 154     tr("Reload Current Image"));
 155   connect(actionReload_image,SIGNAL(triggered()),this,SLOT(ReloadImage()));
 156   contextActions.push_back(actionReload_image);
 157
 158   QAction* actionSave_image = contextMenu.addAction(QIcon(QString::fromUtf8(":/common/icons/filesave.png")),
 159     tr("Save Current Image"));
 160   connect(actionSave_image,SIGNAL(triggered()),this,SLOT(SaveAs()));
 161   contextActions.push_back(actionSave_image);
 162
 163   QAction* actionSave_state = contextMenu.addAction(QIcon(QString::fromUtf8(":/common/icons/filesave.png")),
 164     tr("Save Current State"));
 165   connect(actionSave_state,SIGNAL(triggered()),this,SLOT(SaveCurrentState()));
 166   contextActions.push_back(actionSave_state);
 167
 168   QAction* actionRead_state = contextMenu.addAction(QIcon(QString::fromUtf8(":/common/icons/filesave.png")),
 169     tr("Read Saved State"));
 170   connect(actionRead_state,SIGNAL(triggered()),this,SLOT(ReadSavedState()));
 171   contextActions.push_back(actionRead_state);
 172
 173   contextMenu.addSeparator();
 174
 175   contextMenu.addAction(actionAdd_VF_to_current_Image);
 176   contextActions.push_back(actionAdd_VF_to_current_Image);
 177
 178   //QAction* actionAdd_Overlay_to_current_Image = menuOverlay->addAction(QIcon(QString::fromUtf8(":/common/icons/GPSup.png")),
 179   //    tr("Add overlay image to current image"));
 180   contextMenu.addAction(actionAdd_overlay_image_to_current_image);
 181   contextActions.push_back(actionAdd_overlay_image_to_current_image);
 182
 183   contextMenu.addAction(actionAdd_fusion_image);
 184   contextActions.push_back(actionAdd_fusion_image);
 185
 186 #ifdef CLITK_EXPERIMENTAL
 187   contextMenu.addAction(actionAdd_USSequence_toCT);
 188   contextActions.push_back(actionAdd_USSequence_toCT);
 189 #endif
 190
 191
 192   contextMenu.addSeparator();
 193   QAction* actionResetMatrix = contextMenu.addAction(QIcon(QString::fromUtf8(":/common/icons/identity.png")),
 194     tr("Reset transformation to identity"));
 195   connect(actionResetMatrix, SIGNAL(triggered()), this,SLOT(ResetTransformationToIdentity()));
 196
 197   // TRIAL DS
 198   /*
 199   QMenu * m = new QMenu(menubar);
 200   m->setTitle("TOTO");
 201   //  m->setObjectName(QString::fromUtf8("TOTOTO"));
 202   contextMenu.addMenu(m);
 203   QAction * a = m->addAction(QIcon(QString::fromUtf8(":/common/icons/GPSup.png")),
 204   tr("BIDON"));
 205   QAction * b = m->addAction(QIcon(QString::fromUtf8(":/common/icons/GPSup.png")),
 206   tr("BIDON2"));
 207   m->addAction(a);
 208   m->addAction(b);
 209   connect(a,SIGNAL(triggered()),this,SLOT(AddFusionImage()));
 210   */
 211
 212   //init the DataTree
 213   mSlicerManagers.resize(0);
 214
 215   QStringList header;
 216   header.append("");
 217   header.append("TL");
 218   header.append("TR");
 219   header.append("BL");
 220   header.append("BR");
 221   header.append("");
 222   header.append("");
 223   header.append("Name");
 224
 225   DataTree->setHeaderLabels(header);
 226   DataTree->resizeColumnToContents(COLUMN_TREE);
 227   DataTree->resizeColumnToContents(COLUMN_UL_VIEW);
 228   DataTree->resizeColumnToContents(COLUMN_UR_VIEW);
 229   DataTree->resizeColumnToContents(COLUMN_DL_VIEW);
 230   DataTree->resizeColumnToContents(COLUMN_DR_VIEW);
 231   DataTree->resizeColumnToContents(COLUMN_CLOSE_IMAGE);
 232   DataTree->resizeColumnToContents(COLUMN_RELOAD_IMAGE);
 233   DataTree->resizeColumnToContents(COLUMN_IMAGE_NAME);
 234
 235   viewMode = 1;
 236   documentation = new vvDocumentation();
 237   help_dialog = new vvHelpDialog();
 238   dicomSeriesSelector = new vvDicomSeriesSelector();
 239   pacsconnect = new vvQPacsConnection(this);
 240
 241   inverseButton->setEnabled(0);
 242   actionAdd_overlay_image_to_current_image->setEnabled(0);
 243   actionSave_As->setEnabled(0);
 244   actionAdd_VF_to_current_Image->setEnabled(0);
 245   actionAdd_fusion_image->setEnabled(0);
 246   actionAdd_USSequence_toCT->setEnabled(0);
 247
 248   //init the sliders
 249   verticalSliders.push_back(NOVerticalSlider);
 250   verticalSliders.push_back(NEVerticalSlider);
 251   verticalSliders.push_back(SOVerticalSlider);
 252   verticalSliders.push_back(SEVerticalSlider);
 253
 254   for (int i =0; i < 4; i++)
 255     verticalSliders[i]->hide();
 256
 257   horizontalSliders.push_back(NOHorizontalSlider);
 258   horizontalSliders.push_back(NEHorizontalSlider);
 259   horizontalSliders.push_back(SOHorizontalSlider);
 260   horizontalSliders.push_back(SEHorizontalSlider);
 261
 262   for (int i =0; i < 4; i++)
 263     horizontalSliders[i]->hide();
 264
 265
 266   connect(NOVerticalSlider,SIGNAL(valueChanged(int)),this,SLOT(NOVerticalSliderChanged()));
 267   connect(NEVerticalSlider,SIGNAL(valueChanged(int)),this,SLOT(NEVerticalSliderChanged()));
 268   connect(SOVerticalSlider,SIGNAL(valueChanged(int)),this,SLOT(SOVerticalSliderChanged()));
 269   connect(SEVerticalSlider,SIGNAL(valueChanged(int)),this,SLOT(SEVerticalSliderChanged()));
 270
 271   connect(NOHorizontalSlider,SIGNAL(valueChanged(int)),this,SLOT(NOHorizontalSliderMoved()));
 272   connect(NEHorizontalSlider,SIGNAL(valueChanged(int)),this,SLOT(NEHorizontalSliderMoved()));
 273   connect(SOHorizontalSlider,SIGNAL(valueChanged(int)),this,SLOT(SOHorizontalSliderMoved()));
 274   connect(SEHorizontalSlider,SIGNAL(valueChanged(int)),this,SLOT(SEHorizontalSliderMoved()));
 275
 276   //connect everything
 277   connect(actionCompute_mid_position_image,SIGNAL(triggered()),this,SLOT(ComputeMidPosition()));
 278   connect(actionDeformable_Registration,SIGNAL(triggered()),this,SLOT(ComputeDeformableRegistration()));
 279   connect(actionWarp_image_with_vector_field,SIGNAL(triggered()),this,SLOT(WarpImage()));
 280   connect(actionLoad_images,SIGNAL(triggered()),this,SLOT(OpenImages()));
 281   connect(actionOpen_Dicom,SIGNAL(triggered()),this,SLOT(OpenDicom()));
 282 connect(actionConnect_Pacs,SIGNAL(triggered()),this,SLOT(ConnectPacs()));
 283
 284   //  connect(actionOpen_Dicom_Struct,SIGNAL(triggered()),this,SLOT(OpenDCStructContour()));
 285   connect(actionOpen_VTK_contour,SIGNAL(triggered()),this,SLOT(OpenVTKContour()));
 286   connect(actionOpen_Multiple_Images_As_One,SIGNAL(triggered()),this,SLOT(MergeImages()));
 287   connect(actionSlice_Image_As_Multiple_Images,SIGNAL(triggered()),this,SLOT(SliceImages()));
 288   connect(actionOpen_Image_With_Time,SIGNAL(triggered()),this,SLOT(OpenImageWithTime()));
 289   connect(actionMerge_images_as_n_dim_t, SIGNAL(triggered()), this, SLOT(MergeImagesWithTime()));
 290   connect(actionSave_As,SIGNAL(triggered()),this,SLOT(SaveAs()));
 291   connect(actionSave_current_state,SIGNAL(triggered()),this,SLOT(SaveCurrentState()));
 292   connect(actionRead_saved_state,SIGNAL(triggered()),this,SLOT(ReadSavedState()));
 293   connect(actionExit,SIGNAL(triggered()),this,SLOT(close()));
 294   connect(actionAdd_VF_to_current_Image,SIGNAL(triggered()),this,SLOT(OpenField()));
 295   connect(actionAdd_fusion_image,SIGNAL(triggered()),this,SLOT(SelectFusionImage()));
 296   connect(actionAdd_overlay_image_to_current_image,SIGNAL(triggered()), this,SLOT(SelectOverlayImage()));
 297   connect(actionAdd_USSequence_toCT,SIGNAL(triggered()), this,SLOT(SelectFusionSequence()));
 298   connect(actionNavigation_Help,SIGNAL(triggered()),this,SLOT(ShowHelpDialog()));
 299   connect(actionDocumentation,SIGNAL(triggered()),this,SLOT(ShowDocumentation()));
 300   connect(actionRegister_vv,SIGNAL(triggered()),this,SLOT(PopupRegisterForm()));
 301
 302   connect(overlayPanel, SIGNAL(FusionSequenceCorrespondancesButtonPressed()), this, SLOT(SelectFusionSequenceCorrespondances()));
 303
 304
 305   ///////////////////////////////////////////////
 306   connect(actionSegmentation,SIGNAL(triggered()),this,SLOT(SegmentationOnCurrentImage()));
 307   connect(actionSurface_Viewer,SIGNAL(triggered()),this,SLOT(SurfaceViewerLaunch()));
 308   ///////////////////////////////////////////////
 309
 310   actionNorth_East_Window->setEnabled(0);
 311   actionNorth_West_Window->setEnabled(0);
 312   actionSouth_East_Window->setEnabled(0);
 313   actionSouth_West_Window->setEnabled(0);
 314
 315   connect(actionNorth_East_Window,SIGNAL(triggered()),this,SLOT(SaveNEScreenshot()));
 316   connect(actionNorth_West_Window,SIGNAL(triggered()),this,SLOT(SaveNOScreenshot()));
 317   connect(actionSouth_East_Window,SIGNAL(triggered()),this,SLOT(SaveSEScreenshot()));
 318   connect(actionSouth_West_Window,SIGNAL(triggered()),this,SLOT(SaveSOScreenshot()));
 319   connect(actionSave_all_slices,SIGNAL(triggered()),this,SLOT(SaveScreenshotAllSlices()));
 320
 321   connect(DataTree,SIGNAL(itemSelectionChanged()),this,SLOT(ImageInfoChanged()));
 322   connect(DataTree,SIGNAL(itemClicked(QTreeWidgetItem*, int)),this,
 323     SLOT(DisplayChanged(QTreeWidgetItem*, int)));
 324
 325   connect(viewButton,SIGNAL(clicked()),this, SLOT(ChangeViewMode()) );
 326   connect(windowSpinBox,SIGNAL(editingFinished()),this,SLOT(WindowLevelEdited()));
 327   connect(levelSpinBox,SIGNAL(editingFinished()),this,SLOT(WindowLevelEdited()));
 328   connect(colorMapComboBox,SIGNAL(currentIndexChanged(int)),this,SLOT(UpdateColorMap()));
 329   connect(presetComboBox,SIGNAL(currentIndexChanged(int)),this,SLOT(UpdateWindowLevel()));
 330   connect(slicingPresetComboBox, SIGNAL(currentIndexChanged(int)),this,SLOT(UpdateSlicingPreset()));
 331   connect(inverseButton,SIGNAL(clicked()),this,SLOT(SwitchWindowLevel()));
 332   connect(applyWindowLevelToAllButton,SIGNAL(clicked()),this,SLOT(ApplyWindowLevelToAllImages()));
 333
 334   connect(this,SIGNAL(customContextMenuRequested(QPoint)),this,SLOT(ShowContextMenu(QPoint)));
 335
 336   connect(linkPanel,SIGNAL(addLink(QString,QString,bool)),this,SLOT(AddLink(QString,QString,bool)));
 337   connect(linkPanel,SIGNAL(removeLink(QString,QString)),this,SLOT(RemoveLink(QString,QString)));
 338   connect(overlayPanel,SIGNAL(VFPropertyUpdated(int,int,int,int,double,double,double)),this,SLOT(SetVFProperty(int,int,int,int,double,double,double)));
 339   connect(overlayPanel,SIGNAL(OverlayPropertyUpdated(int,int,double,double)),
 340     this,SLOT(SetOverlayProperty(int,int,double,double)));
 341   connect(overlayPanel,SIGNAL(FusionPropertyUpdated(int,int,int,double,double, bool)),
 342     this,SLOT(SetFusionProperty(int,int,int,double,double, bool)));
 343   connect(landmarksPanel,SIGNAL(UpdateRenderWindows()),this,SLOT(UpdateRenderWindows()));
 344   connect(landmarksPanel,SIGNAL(SelectedPointChanged()),this,SLOT(GoToLandmark()));
 345
 346   connect(overlayPanel,SIGNAL(FusionSequencePropertyUpdated(int, bool, unsigned int, bool)),
 347     this,SLOT(SetFusionSequenceProperty(int, bool,unsigned int, bool)));
 348
 349
 350   playMode = 0;//pause
 351   mFrameRate = 10;
 352   playButton->setEnabled(0);
 353   frameRateLabel->setEnabled(0);
 354   frameRateSpinBox->setEnabled(0);
 355   connect(playButton, SIGNAL(clicked()),this,SLOT(PlayPause()));
 356   connect(frameRateSpinBox, SIGNAL(valueChanged(int)),this,SLOT(ChangeFrameRate(int)));
 357
 358   goToCursorPushButton->setEnabled(0);
 359   connect(goToCursorPushButton, SIGNAL(clicked()),this,SLOT(GoToCursor()));
 360
 361   NOViewWidget->hide();
 362   NEViewWidget->hide();
 363   SOViewWidget->hide();
 364   SEViewWidget->hide();
 365
 366   //Recently opened files
 367   std::list<std::string> recent_files = GetRecentlyOpenedImages();
 368   recentlyOpenedFilesMenu=NULL;
 369   if ( !recent_files.empty() ) {
 370     createRecentlyOpenedFilesMenu();
 371     updateRecentlyOpenedFilesMenu(recent_files);
 372   }
 373
 374   // Adding all new tools (insertion in the menu)
 375   vvToolManager::GetInstance()->InsertToolsInMenu(this);
 376   vvToolManager::GetInstance()->EnableToolsInMenu(this, false);
 377
 378   if (!CLITK_EXPERIMENTAL)
 379     menuExperimental->menuAction()->setVisible(false);
 380
 381
 382   QTimer * timerMemory = new QTimer(this);
 383   //timerMemory->setInterval(5);
 384   connect(timerMemory, SIGNAL(timeout()), this, SLOT(UpdateMemoryUsage()));
 385   timerMemory->start(2000);
 386
 387 }
 388 //------------------------------------------------------------------------------
 389 void vvMainWindow::show()
 390 {
 391   vvMainWindowBase::show();
 392   PopupRegisterForm(true);
 393 }
 394 //------------------------------------------------------------------------------
 395 void vvMainWindow::UpdateMemoryUsage()
 396 {
 397   //  clitk::PrintMemory(true);
 398   if (clitk::GetMemoryUsageInMb() == 0) infoPanel->setMemoryInMb("NA");
 399   else infoPanel->setMemoryInMb(QString::number(clitk::GetMemoryUsageInMb())+" MiB");
 400 }
 401 //------------------------------------------------------------------------------
 402
 403
 404 //------------------------------------------------------------------------------
 405 void vvMainWindow::createRecentlyOpenedFilesMenu()
 406 {
 407   recentlyOpenedFilesMenu = new QMenu("Recently opened files...");
 408   recentlyOpenedFilesMenu->setIcon(QIcon(QString::fromUtf8(":/common/icons/open.png")));
 409   menuFile->insertMenu(actionOpen_Image_With_Time,recentlyOpenedFilesMenu);
 410   menuFile->insertSeparator(actionOpen_Image_With_Time);
 411 }
 412 //------------------------------------------------------------------------------
 413
 414
 415 //------------------------------------------------------------------------------
 416
 417 void vvMainWindow::updateRecentlyOpenedFilesMenu(const std::list<std::string> &recent_files)
 418 {
 419   if(recentlyOpenedFilesMenu==NULL) {
 420     createRecentlyOpenedFilesMenu();
 421   } else {
 422     recentlyOpenedFilesMenu->clear();
 423   }
 424   for (std::list<std::string>::const_iterator i = recent_files.begin(); i!=recent_files.end(); i++) {
 425     QAction* current=new QAction(QIcon(QString::fromUtf8(":/common/icons/open.png")), i->c_str(),this);
 426     recentlyOpenedFilesMenu->addAction(current);
 427     connect(current,SIGNAL(triggered()),this,SLOT(OpenRecentImage()));
 428   }
 429 }
 430 //------------------------------------------------------------------------------
 431
 432
 433 //------------------------------------------------------------------------------
 434 void vvMainWindow::ComputeMidPosition()
 435 {
 436   bool ok;
 437   int index=GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
 438   int ref = QInputDialog::getInteger(this,"Chose reference phase","Reference phase",0,0,\
 439     mSlicerManagers[index]->GetImage()->GetVTKImages().size()-1,1,&ok);
 440   if (ok) {
 441     vvMidPosition midp;
 442     midp.slicer_manager = mSlicerManagers[index];
 443     midp.reference_image_index = ref;
 444     QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
 445     midp.Update();
 446     if (midp.error)
 447       QMessageBox::warning(this, "Error computing midposition image",midp.error_message.c_str());
 448     else {
 449       QFileInfo info(midp.slicer_manager->GetFileName().c_str());
 450       AddImage(midp.output,info.path().toStdString()+"/"+info.completeBaseName().toStdString()+"_midposition.mhd");
 451     }
 452     QApplication::restoreOverrideCursor();
 453   }
 454 }
 455 //------------------------------------------------------------------------------
 456
 457
 458 //------------------------------------------------------------------------------
 459 void vvMainWindow::AddContour(int image_index, vvMesh::Pointer contour, bool propagation)
 460 {
 461   QTreeWidgetItem *item = new QTreeWidgetItem();
 462   item->setData(0,Qt::UserRole,"filename.vtk");
 463   item->setData(1,Qt::UserRole,tr("contour"));
 464   QBrush brush;
 465   brush.setColor(QColor(contour->r*255,contour->g*255,contour->b*255));
 466   brush.setStyle(Qt::SolidPattern);
 467   item->setData(COLUMN_IMAGE_NAME,Qt::BackgroundRole,brush);
 468   //  item->setData(COLUMN_IMAGE_NAME,Qt::DisplayRole,contour->structure_name.c_str());
 469
 470   for (int j = 1; j <= 4; j++)
 471     item->setData(j,Qt::CheckStateRole,DataTree->topLevelItem(image_index)->data(j,Qt::CheckStateRole));
 472
 473   QTreePushButton* cButton = new QTreePushButton;
 474   cButton->setItem(item);
 475   cButton->setColumn(COLUMN_CLOSE_IMAGE);
 476   cButton->setToolTip(tr("close image"));
 477   cButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/exit.png")));
 478   connect(cButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
 479     this,SLOT(CloseImage(QTreeWidgetItem*, int)));
 480
 481   QTreePushButton* rButton = new QTreePushButton;
 482   rButton->setItem(item);
 483   rButton->setColumn(COLUMN_RELOAD_IMAGE);
 484   rButton->setToolTip(tr("reload image"));
 485   rButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/rotateright.png")));
 486   rButton->setEnabled(false);
 487   //Not implemented
 488   //connect(rButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
 489   //this,SLOT(ReloadImage(QTreeWidgetItem*, int)));
 490
 491   DataTree->topLevelItem(image_index)->setExpanded(1);
 492   DataTree->topLevelItem(image_index)->addChild(item);
 493   DataTree->setItemWidget(item, COLUMN_CLOSE_IMAGE, cButton);
 494   DataTree->setItemWidget(item, COLUMN_RELOAD_IMAGE, rButton);
 495   QString id = DataTree->topLevelItem(image_index)->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString();
 496   item->setData(COLUMN_IMAGE_NAME,Qt::UserRole,id.toStdString().c_str());
 497
 498   UpdateTree();
 499   mSlicerManagers[image_index]->AddContour(contour,propagation);
 500   mSlicerManagers[image_index]->Render();
 501 }
 502 //------------------------------------------------------------------------------
 503
 504
 505 //------------------------------------------------------------------------------
 506 void vvMainWindow::OpenVTKContour()
 507 {
 508   if (mSlicerManagers.size() > 0) {
 509     QString Extensions = "Images ( *.vtk *.obj)";
 510     Extensions += ";;All Files (*)";
 511     QString file = QFileDialog::getOpenFileName(this,tr("Open vtkPolyData"),mInputPathName,Extensions);
 512     if (file.isNull())
 513       return;
 514     QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
 515     int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
 516     vvMeshReader reader;
 517     reader.SetImage(mSlicerManagers[index]->GetImage());
 518     reader.SetModeToVTK();
 519     reader.SetFilename(file.toStdString());
 520     reader.Update();
 521     AddContour(index,reader.GetOutput()[0],false);
 522     QApplication::restoreOverrideCursor();
 523   }
 524 }
 525 //------------------------------------------------------------------------------
 526
 527
 528 //------------------------------------------------------------------------------
 529 void vvMainWindow::AddDCStructContour(int index, QString file)
 530 {
 531   vvMeshReader reader;
 532   reader.SetFilename(file.toStdString());
 533   vvStructSelector selector;
 534   selector.SetStructures(reader.GetROINames());
 535   if (!mSlicerManagers[index]->GetVF().IsNull())
 536     selector.EnablePropagationCheckBox();
 537   if (selector.exec()) {
 538     QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
 539     reader.SetSelectedItems(selector.getSelectedItems());
 540     reader.SetImage(mSlicerManagers[index]->GetImage());
 541     if (selector.PropagationEnabled())
 542       reader.SetPropagationVF(mSlicerManagers[index]->GetVF());
 543     reader.Update();
 544     std::vector<vvMesh::Pointer> contours=reader.GetOutput();
 545     for (std::vector<vvMesh::Pointer>::iterator i=contours.begin();
 546       i!=contours.end(); i++)
 547       AddContour(index,*i,selector.PropagationEnabled());
 548     QApplication::restoreOverrideCursor();
 549   }
 550 }
 551
 552 //------------------------------------------------------------------------------
 553 void vvMainWindow::OpenDCStructContour()
 554 {
 555   if (mSlicerManagers.size() > 0) {
 556     QString Extensions = "Dicom Files ( *.dcm RS*)";
 557     Extensions += ";;All Files (*)";
 558     QString file = QFileDialog::getOpenFileName(this,tr("Merge Images"),mInputPathName,Extensions);
 559     if (file.isNull())
 560       return;
 561     int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
 562     AddDCStructContour(index, file);
 563   }
 564 }
 565 //------------------------------------------------------------------------------
 566
 567
 568 //------------------------------------------------------------------------------
 569 void vvMainWindow::ComputeDeformableRegistration()
 570 {
 571   if (mSlicerManagers.size() > 0) {
 572     int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
 573     vvDeformationDialog dialog(index,mSlicerManagers);
 574     if (dialog.exec()) {
 575       std::string base_name=itksys::SystemTools::GetFilenameWithoutExtension(mSlicerManagers[dialog.GetInputFileIndex()]->GetFileName());
 576       AddField(dialog.GetOutput(),dialog.getFieldFile(),dialog.GetInputFileIndex());
 577       WarpImage(dialog.GetSelectedSlicer(),dialog.GetReferenceFrameIndex());
 578     } else
 579       std::cout << "Error or user cancellation while computing deformation field..." << std::endl;
 580   } else QMessageBox::information(this, "Need to open image","You must open an image first.");
 581 }
 582 //------------------------------------------------------------------------------
 583
 584
 585 //------------------------------------------------------------------------------
 586 void vvMainWindow::WarpImage()
 587 {
 588   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
 589   if (!mSlicerManagers[index]->GetVF().IsNull()) {
 590     bool ok;
 591     int ref = QInputDialog::getInteger(this,"Chose reference phase","Reference phase",0,0,\
 592       mSlicerManagers[index]->GetImage()->GetVTKImages().size()-1,1,&ok);
 593     if (ok) {
 594       WarpImage(mSlicerManagers[index],ref);
 595     }
 596   } else
 597     QMessageBox::warning(this,tr("No vector field"),tr("Sorry, can't warp without a vector field"));
 598 }
 599 //------------------------------------------------------------------------------
 600
 601
 602 //------------------------------------------------------------------------------
 603 void vvMainWindow::WarpImage(vvSlicerManager* selected_slicer,int reference_phase)
 604 {
 605   if (!selected_slicer->GetVF().IsNull()) {
 606     QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
 607     QFileInfo info(selected_slicer->GetFileName().c_str());
 608     vvImageWarp warp(selected_slicer->GetImage(),selected_slicer->GetVF(),
 609       reference_phase,this);
 610     if (warp.ComputeWarpedImage()) {
 611       AddImage(warp.GetWarpedImage(),info.path().toStdString()+"/"+info.completeBaseName().toStdString()+"_warped.mhd");
 612       AddImage(warp.GetDiffImage()  ,info.path().toStdString()+"/"+info.completeBaseName().toStdString()+"_diff.mhd");
 613       AddImage(warp.GetJacobianImage()  ,info.path().toStdString()+"/"+info.completeBaseName().toStdString()+"_jacobian.mhd");
 614       QApplication::restoreOverrideCursor();
 615     } else {
 616       QApplication::restoreOverrideCursor();
 617       QMessageBox::warning(this,tr("Different spacings"),tr("The vector field and image spacings must be the same in order to warp."));
 618     }
 619   } else
 620     QMessageBox::warning(this,tr("No vector field"),tr("Sorry, can't warp without a vector field."));
 621 }
 622 //------------------------------------------------------------------------------
 623
 624
 625 //------------------------------------------------------------------------------
 626 vvMainWindow::~vvMainWindow()
 627 {
 628   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
 629     if (mSlicerManagers[i] != NULL)
 630       delete mSlicerManagers[i];
 631   }
 632 }
 633 //------------------------------------------------------------------------------
 634
 635 //------------------------------------------------------------------------------
 636 QTabWidget * vvMainWindow::GetTab()
 637 {
 638   return tabWidget;
 639 }
 640 //------------------------------------------------------------------------------
 641
 642
 643 //------------------------------------------------------------------------------
 644 void vvMainWindow::MergeImages()
 645 {
 646   QString Extensions = EXTENSIONS;
 647   Extensions += ";;All Files (*)";
 648   QStringList files = QFileDialog::getOpenFileNames(this,tr("Merge Images"),mInputPathName,Extensions);
 649   if (files.isEmpty())
 650     return;
 651   mInputPathName = itksys::SystemTools::GetFilenamePath(files[0].toStdString()).c_str();
 652   std::vector<std::string> vector;
 653
 654   unsigned int currentDim = 0;
 655   std::vector<double> currentSpacing;
 656   std::vector<int> currentSize;
 657   std::vector<double> currentOrigin;
 658
 659   for (int i = 0; i < files.size(); i++) {
 660     itk::ImageIOBase::Pointer reader = itk::ImageIOFactory::CreateImageIO(
 661       files[i].toStdString().c_str(), itk::ImageIOFactory::ReadMode);
 662     reader->SetFileName(files[i].toStdString().c_str());
 663     reader->ReadImageInformation();
 664     if (reader)        {
 665       //NOViewWidget->hide();
 666       //NEViewWidget->hide();
 667       //SOViewWidget->hide();
 668       //SEViewWidget->hide();
 669       if (i == 0)
 670         currentDim = reader->GetNumberOfDimensions();
 671       bool IsOk = true;
 672       for (unsigned int j = 0; j < currentDim; j++) {
 673         if (i == 0) {
 674           if (j == 0) {
 675             currentSpacing.resize(currentDim);
 676             currentSize.resize(currentDim);
 677             currentOrigin.resize(currentDim);
 678           }
 679           currentOrigin[j] = reader->GetOrigin(j);
 680           currentSpacing[j] = reader->GetSpacing(j);
 681           currentSize[j] = reader->GetDimensions(j);
 682         } else if (currentDim != reader->GetNumberOfDimensions()
 683           || currentSpacing[j] != reader->GetSpacing(j)
 684           || currentSize[j] != (int)reader->GetDimensions(j)
 685           || currentOrigin[j] != reader->GetOrigin(j)) {
 686             QString error = "Cannot read file (too different from others ";
 687             error += files[i].toStdString().c_str();
 688             QMessageBox::information(this,tr("Reading problem"),error);
 689             IsOk = false;
 690             break;
 691         }
 692       }
 693       if (IsOk)
 694         vector.push_back(files[i].toStdString());
 695     }
 696   }
 697   if (vector.size() > 0)
 698     LoadImages(vector, vvImageReader::MERGED);
 699 }
 700 //------------------------------------------------------------------------------
 701
 702 //------------------------------------------------------------------------------
 703 void vvMainWindow::SliceImages()
 704 {
 705   QString Extensions = EXTENSIONS;
 706   Extensions += ";;All Files (*)";
 707
 708   QStringList files = QFileDialog::getOpenFileNames(this,tr("Slice Images"),mInputPathName,Extensions);
 709   if (files.isEmpty())
 710     return;
 711   mInputPathName = itksys::SystemTools::GetFilenamePath(files[0].toStdString()).c_str();
 712   std::vector<std::string> vector;
 713   for (int i = 0; i < files.size(); i++)
 714     vector.push_back(files[i].toStdString());
 715   LoadImages(vector, vvImageReader::SLICED);
 716 }
 717 //------------------------------------------------------------------------------
 718
 719 //------------------------------------------------------------------------------
 720 void vvMainWindow::MergeImagesWithTime()
 721 {
 722   QString Extensions = EXTENSIONS;
 723   Extensions += ";;All Files (*)";
 724   QStringList files = QFileDialog::getOpenFileNames(this,tr("Merge Images With Time"),mInputPathName,Extensions);
 725   if (files.isEmpty())
 726     return;
 727   mInputPathName = itksys::SystemTools::GetFilenamePath(files[0].toStdString()).c_str();
 728   std::vector<std::string> vector;
 729
 730   for (int i = 0; i < files.size(); i++)
 731     vector.push_back(files[i].toStdString());
 732   sort(vector.begin(),vector.end());
 733   if (vector.size() > 1)
 734     LoadImages(vector, vvImageReader::MERGEDWITHTIME);
 735   else
 736     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.");
 737 }
 738 //------------------------------------------------------------------------------
 739
 740
 741 //------------------------------------------------------------------------------
 742 void vvMainWindow::OpenDicom()
 743 {
 744   std::vector<std::string> files;
 745
 746   //std::cout << "dicomSeriesSelector " << std::endl;
 747   if (dicomSeriesSelector->exec() == QDialog::Accepted) {
 748     files = *(dicomSeriesSelector->GetFilenames());
 749     LoadImages(files, vvImageReader::DICOM);
 750   }
 751 }
 752   void vvMainWindow::ConnectPacs()
 753 {
 754   std::vector<std::string> files;
 755
 756   //std::cout << "dicomSeriesSelector " << std::endl;
 757 if (pacsconnect->exec() == QDialog::Accepted) {
 758 //    files = *(pacsconnect->GetFilenames());
 759    // LoadImages(files, vvImageReader::DICOM);
 760   }
 761   }
 762
 763
 764 //------------------------------------------------------------------------------
 765
 766 //------------------------------------------------------------------------------
 767 void vvMainWindow::OpenImages()
 768 {
 769   QString Extensions = EXTENSIONS;
 770   Extensions += ";;All Files (*)";
 771
 772   QStringList files = QFileDialog::getOpenFileNames(this,tr("Load Images"),mInputPathName,Extensions);
 773   if (files.isEmpty())
 774     return;
 775   mInputPathName = itksys::SystemTools::GetFilenamePath(files[0].toStdString()).c_str();
 776   std::vector<std::string> vector;
 777   for (int i = 0; i < files.size(); i++)
 778     vector.push_back(files[i].toStdString());
 779   LoadImages(vector, vvImageReader::IMAGE);
 780 }
 781 //------------------------------------------------------------------------------
 782 void vvMainWindow::OpenRecentImage()
 783 {
 784   QAction * caller = qobject_cast<QAction*>(sender());
 785   std::vector<std::string> images;
 786   images.push_back(caller->text().toStdString());
 787   mInputPathName = itksys::SystemTools::GetFilenamePath(images[0]).c_str();
 788   LoadImages(images, vvImageReader::IMAGE);
 789 }
 790 //------------------------------------------------------------------------------
 791
 792
 793 //------------------------------------------------------------------------------
 794 void vvMainWindow::OpenImageWithTime()
 795 {
 796   QString Extensions = EXTENSIONS;
 797   Extensions += ";;All Files (*)";
 798
 799   QStringList files = QFileDialog::getOpenFileNames(this,tr("Load Images With Time"),mInputPathName,Extensions);
 800   if (files.isEmpty())
 801     return;
 802   mInputPathName = itksys::SystemTools::GetFilenamePath(files[0].toStdString()).c_str();
 803   std::vector<std::string> vector;
 804   for (int i = 0; i < files.size(); i++) {
 805     vector.push_back(files[i].toStdString());
 806   }
 807   LoadImages(vector, vvImageReader::IMAGEWITHTIME);
 808 }
 809 //------------------------------------------------------------------------------
 810
 811
 812 //------------------------------------------------------------------------------
 813 void vvMainWindow::LoadImages(std::vector<std::string> files, vvImageReader::LoadedImageType filetype)
 814 {
 815   //Separate the way to open images and dicoms
 816   int fileSize;
 817   if (filetype == vvImageReader::IMAGE || filetype == vvImageReader::IMAGEWITHTIME)
 818     fileSize = files.size();
 819   else
 820     fileSize = 1;
 821
 822   // For SLICED, we need the number of slices (ndim and #slices)
 823   std::vector<unsigned int> nSlices;
 824   nSlices.resize(files.size());
 825   std::fill(nSlices.begin(), nSlices.end(), 1);
 826   if (filetype == vvImageReader::SLICED) {
 827     for (int i = 0; i < fileSize; i++) {
 828       itk::ImageIOBase::Pointer header = clitk::readImageHeader(files[i]);
 829       QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
 830       if (!header) {
 831         nSlices[i] = 0;
 832         QString error = "Cannot open file \n";
 833         error += files[i].c_str();
 834         QMessageBox::information(this,tr("Reading problem"),error);
 835         return;
 836       }
 837       if (header->GetNumberOfDimensions() < 3) {
 838         nSlices[i] = 0;
 839         QString error = "Dimension problem. Cannot slice \n";
 840         error += files[i].c_str();
 841         QMessageBox::information(this,tr("Reading problem"),error);
 842         return;
 843       }
 844       nSlices[i] = header->GetDimensions( header->GetNumberOfDimensions()-1 );
 845     }
 846   }
 847
 848   //Only add to the list of recently opened files when a single file is opened,
 849   //to avoid polluting the list of recently opened files
 850   if (files.size() == 1) {
 851     QFileInfo finfo=tr(files[0].c_str());
 852     AddToRecentlyOpenedImages(finfo.absoluteFilePath().toStdString());
 853     updateRecentlyOpenedFilesMenu(GetRecentlyOpenedImages());
 854   }
 855   //init the progress events
 856   QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
 857   vvProgressDialog progress("Opening " + files[0],fileSize>1);
 858   qApp->processEvents();
 859
 860   int numberofsuccesulreads=0;
 861   //open images as 1 or multiples
 862   for (int i = 0; i < fileSize; i++) {
 863     progress.SetText("Opening " + files[i]);
 864     progress.SetProgress(i,fileSize);
 865     qApp->processEvents();
 866
 867     for (unsigned int j = 0; j < nSlices[i]; j++) {
 868       //read the image and put it in mSlicerManagers
 869       vvSlicerManager* imageManager = new vvSlicerManager(4);
 870       qApp->processEvents();
 871
 872       bool SetImageSucceed=false;
 873
 874       // Change filename if an image with the same already exist
 875       int number = GetImageDuplicateFilenameNumber(files[i] + std::string("_slice"));
 876
 877       if (filetype == vvImageReader::IMAGE || filetype == vvImageReader::IMAGEWITHTIME || filetype == vvImageReader::SLICED)
 878         SetImageSucceed = imageManager->SetImage(files[i],filetype, number, j);
 879       else {
 880         SetImageSucceed = imageManager->SetImages(files,filetype, number);
 881       }
 882
 883       if (!SetImageSucceed) {
 884         QApplication::restoreOverrideCursor();
 885         QString error = "Cannot open file \n";
 886         error += imageManager->GetLastError().c_str();
 887         QMessageBox::information(this,tr("Reading problem"),error);
 888         delete imageManager;
 889       } else {
 890         mSlicerManagers.push_back(imageManager);
 891
 892         //create an item in the tree with good settings
 893         QTreeWidgetItem *item = new QTreeWidgetItem();
 894         item->setData(0,Qt::UserRole,files[i].c_str());
 895         QFileInfo fileinfo(imageManager->GetFileName().c_str()); //Do not show the path
 896         item->setData(COLUMN_IMAGE_NAME,Qt::DisplayRole,fileinfo.fileName());
 897         item->setData(1,Qt::UserRole,tr("image"));
 898         item->setToolTip(COLUMN_IMAGE_NAME, imageManager->GetListOfAbsoluteFilePathInOneString("image").c_str());
 899         qApp->processEvents();
 900
 901         //Create the buttons for reload and close
 902         qApp->processEvents();
 903         QTreePushButton* cButton = new QTreePushButton;
 904         cButton->setItem(item);
 905         cButton->setColumn(COLUMN_CLOSE_IMAGE);
 906         cButton->setToolTip(tr("close image"));
 907         cButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/exit.png")));
 908         connect(cButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
 909           this,SLOT(CloseImage(QTreeWidgetItem*, int)));
 910
 911         QTreePushButton* rButton = new QTreePushButton;
 912         rButton->setItem(item);
 913         rButton->setColumn(COLUMN_RELOAD_IMAGE);
 914         rButton->setToolTip(tr("reload image"));
 915         rButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/rotateright.png")));
 916         connect(rButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
 917           this,SLOT(ReloadImage(QTreeWidgetItem*, int)));
 918
 919         DataTree->addTopLevelItem(item);
 920         DataTree->setItemWidget(item, COLUMN_CLOSE_IMAGE, cButton);
 921         DataTree->setItemWidget(item, COLUMN_RELOAD_IMAGE, rButton);
 922
 923         //set the id of the image
 924         QString id = QDir::current().absoluteFilePath(files[i].c_str()) + QString::number(mSlicerManagers.size()-1);
 925         item->setData(COLUMN_IMAGE_NAME,Qt::UserRole,id.toStdString().c_str());
 926         mSlicerManagers.back()->SetId(id.toStdString());
 927
 928         linkPanel->addImage(imageManager->GetFileName(), id.toStdString());
 929
 930         connect(mSlicerManagers.back(), SIGNAL(currentImageChanged(std::string)),
 931           this,SLOT(CurrentImageChanged(std::string)));
 932         connect(mSlicerManagers.back(), SIGNAL(currentPickedImageChanged(std::string)),
 933           this, SLOT(CurrentPickedImageChanged(std::string)));
 934         connect(mSlicerManagers.back(), SIGNAL(UpdatePosition(int, double, double, double, double, double, double, double)),
 935           this,SLOT(MousePositionChanged(int,double, double, double, double, double, double, double)));
 936         connect(mSlicerManagers.back(), SIGNAL(UpdateVector(int, double, double, double, double)),
 937           this, SLOT(VectorChanged(int,double,double,double, double)));
 938         connect(mSlicerManagers.back(), SIGNAL(UpdateOverlay(int, double, double)),
 939           this, SLOT(OverlayChanged(int,double,double)));
 940         connect(mSlicerManagers.back(), SIGNAL(UpdateFusion(int, double)),
 941           this, SLOT(FusionChanged(int,double)));
 942         connect(mSlicerManagers.back(), SIGNAL(WindowLevelChanged()),
 943           this,SLOT(WindowLevelChanged()));
 944         connect(mSlicerManagers.back(), SIGNAL(UpdateSlice(int,int)),
 945           this,SLOT(UpdateSlice(int,int)));
 946         connect(mSlicerManagers.back(), SIGNAL(UpdateTSlice(int, int, int)),
 947           this,SLOT(UpdateTSlice(int, int, int)));
 948         connect(mSlicerManagers.back(), SIGNAL(UpdateTSlice(int, int, int)),
 949           this,SLOT(ImageInfoChanged()));
 950         connect(mSlicerManagers.back(), SIGNAL(UpdateSliceRange(int,int,int,int,int)),
 951           this,SLOT(UpdateSliceRange(int,int,int,int,int)));
 952         connect(mSlicerManagers.back(), SIGNAL(UpdateLinkManager(std::string,int,double,double,double,int)),
 953           this,SLOT(UpdateLinkManager(std::string,int,double,double,double,int)));
 954         connect(mSlicerManagers.back(), SIGNAL(UpdateLinkedNavigation(std::string,vvSlicerManager*,vvSlicer*)),
 955           this,SLOT(UpdateLinkedNavigation(std::string,vvSlicerManager*,vvSlicer*)));
 956         connect(mSlicerManagers.back(), SIGNAL(ChangeImageWithIndexOffset(vvSlicerManager*,int,int)),
 957           this,SLOT(ChangeImageWithIndexOffset(vvSlicerManager*,int,int)));
 958         connect(mSlicerManagers.back(),SIGNAL(LandmarkAdded()),landmarksPanel,SLOT(AddPoint()));
 959
 960         InitSlicers();
 961         numberofsuccesulreads++;
 962       }
 963     }
 964   }
 965   if (numberofsuccesulreads) {
 966     NOViewWidget->show();
 967     NEViewWidget->show();
 968     SOViewWidget->show();
 969     SEViewWidget->show();
 970     UpdateTree();
 971     InitDisplay();
 972     ShowLastImage();
 973
 974     // Try to guess default WindowLevel
 975     double range[2];
 976     mSlicerManagers.back()->GetImage()->GetFirstVTKImageData()->GetScalarRange(range);
 977     if ((range[0] == 0) && (range[1] == 1)) {
 978       presetComboBox->setCurrentIndex(WL_BINARY);// binary
 979     } else {
 980       // TODO
 981     }
 982   }
 983   QApplication::restoreOverrideCursor();
 984 }
 985 //------------------------------------------------------------------------------
 986
 987 //------------------------------------------------------------------------------
 988 void vvMainWindow::UpdateTree()
 989 {
 990   DataTree->resizeColumnToContents(COLUMN_TREE);
 991   DataTree->resizeColumnToContents(COLUMN_UL_VIEW);
 992   DataTree->resizeColumnToContents(COLUMN_UR_VIEW);
 993   DataTree->resizeColumnToContents(COLUMN_DL_VIEW);
 994   DataTree->resizeColumnToContents(COLUMN_DR_VIEW);
 995   DataTree->resizeColumnToContents(COLUMN_IMAGE_NAME);
 996   DataTree->resizeColumnToContents(COLUMN_CLOSE_IMAGE);
 997   DataTree->resizeColumnToContents(COLUMN_RELOAD_IMAGE);
 998 }
 999 //------------------------------------------------------------------------------
1000
1001 //------------------------------------------------------------------------------
1002 void vvMainWindow::CurrentImageChanged(std::string id)
1003 {
1004   if (id == mCurrentSelectedImageId) return; // Do nothing
1005   int selected = 0;
1006   for (int i = 0; i < DataTree->topLevelItemCount(); i++) {
1007     if (DataTree->topLevelItem(i)->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString().toStdString() == id) {
1008       selected = i;
1009     } else {
1010       DataTree->topLevelItem(i)->setSelected(0);
1011     }
1012     for (int child = 0; child < DataTree->topLevelItem(i)->childCount(); child++)
1013       DataTree->topLevelItem(i)->child(child)->setSelected(0);
1014
1015   }
1016   DataTree->topLevelItem(selected)->setSelected(1);
1017   mCurrentSelectedImageId = id;
1018
1019   landmarksPanel->SetCurrentLandmarks(mSlicerManagers[selected]->GetLandmarks(),
1020                                       mSlicerManagers[selected]->GetTSlice());
1021   landmarksPanel->SetCurrentPath(mInputPathName.toStdString());
1022   landmarksPanel->SetCurrentImage(mSlicerManagers[selected]->GetFileName().c_str());
1023
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   actionAdd_USSequence_toCT->setEnabled(1);
1059   actionNorth_East_Window->setEnabled(1);
1060   actionNorth_West_Window->setEnabled(1);
1061   actionSouth_East_Window->setEnabled(1);
1062   actionSouth_West_Window->setEnabled(1);
1063   vvToolManager::GetInstance()->EnableToolsInMenu(this, true);
1064   inverseButton->setEnabled(1);
1065
1066   goToCursorPushButton->setEnabled(1);
1067
1068   if (DataTree->selectedItems().size()) {
1069     int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1070
1071     colorMapComboBox->setEnabled(1);
1072     for (int i = 0; i < DataTree->topLevelItem(index)->childCount(); i++) {
1073       if (DataTree->topLevelItem(index)->child(i)->data(1,Qt::UserRole).toString() == "overlay" ||
1074         DataTree->topLevelItem(index)->child(i)->data(1,Qt::UserRole).toString() == "fusion" ||
1075         DataTree->topLevelItem(index)->child(i)->data(1,Qt::UserRole).toString() == "fusionSequence") {
1076           colorMapComboBox->setEnabled(0);
1077           break;
1078       }
1079     }
1080
1081     std::vector<double> origin;
1082     std::vector<double> inputSpacing;
1083     std::vector<int> inputSize;
1084     std::vector<double> sizeMM;
1085     vtkSmartPointer<vtkMatrix4x4> transformation;
1086     int dimension=0;
1087     QString pixelType;
1088     QString inputSizeInBytes;
1089     QString image = DataTree->selectedItems()[0]->data(COLUMN_IMAGE_NAME,Qt::DisplayRole).toString();
1090
1091     int nframes = mSlicerManagers[index]->GetSlicer(0)->GetTMax();
1092
1093     if (nframes > 1 || playMode == 1) {
1094       playButton->setEnabled(1);
1095       frameRateLabel->setEnabled(1);
1096       frameRateSpinBox->setEnabled(1);
1097     } else {
1098       playButton->setEnabled(0);
1099       frameRateLabel->setEnabled(0);
1100       frameRateSpinBox->setEnabled(0);
1101     }
1102
1103     //read image header
1104     int NPixel = 1;
1105
1106     int tSlice = 0;
1107     vvImage::Pointer imageSelected;
1108     if (DataTree->topLevelItem(index) == DataTree->selectedItems()[0]) {
1109       imageSelected = mSlicerManagers[index]->GetSlicer(0)->GetImage();
1110       tSlice = mSlicerManagers[index]->GetSlicer(0)->GetTSlice();
1111     } else if (DataTree->selectedItems()[0]->data(1,Qt::UserRole).toString() == "vector") {
1112       imageSelected = mSlicerManagers[index]->GetSlicer(0)->GetVF();
1113       tSlice = mSlicerManagers[index]->GetSlicer(0)->GetOverlayTSlice();
1114     } else if (DataTree->selectedItems()[0]->data(1,Qt::UserRole).toString() == "overlay") {
1115       imageSelected = mSlicerManagers[index]->GetSlicer(0)->GetOverlay();
1116       tSlice = mSlicerManagers[index]->GetSlicer(0)->GetOverlayTSlice();
1117     } else if (DataTree->selectedItems()[0]->data(1,Qt::UserRole).toString() == "fusion") {
1118       imageSelected = mSlicerManagers[index]->GetSlicer(0)->GetFusion();
1119       tSlice = mSlicerManagers[index]->GetSlicer(0)->GetFusionTSlice();
1120     }
1121     else if (DataTree->selectedItems()[0]->data(1,Qt::UserRole).toString() == "fusionSequence") {
1122       imageSelected = mSlicerManagers[index]->GetSlicer(0)->GetFusion();
1123       tSlice = mSlicerManagers[index]->GetSlicer(0)->GetFusionTSlice();
1124     }
1125     else if (DataTree->selectedItems()[0]->data(1,Qt::UserRole).toString() == "contour") {
1126       imageSelected = mSlicerManagers[index]->GetSlicer(0)->GetImage();
1127       tSlice = mSlicerManagers[index]->GetSlicer(0)->GetTSlice();
1128     }
1129     else {
1130       imageSelected = mSlicerManagers[index]->GetSlicer(0)->GetImage();
1131       tSlice = mSlicerManagers[index]->GetSlicer(0)->GetTSlice();
1132     }
1133
1134     dimension = imageSelected->GetNumberOfDimensions();
1135     origin.resize(dimension);
1136     inputSpacing.resize(dimension);
1137     inputSize.resize(dimension);
1138     sizeMM.resize(dimension);
1139     pixelType = mSlicerManagers[index]->GetImage()->GetScalarTypeAsITKString().c_str();
1140     for (int i = 0; i < dimension; i++) {
1141       origin[i] = imageSelected->GetOrigin()[i];
1142       inputSpacing[i] = imageSelected->GetSpacing()[i];
1143       inputSize[i] = imageSelected->GetSize()[i];
1144       sizeMM[i] = inputSize[i]*inputSpacing[i];
1145       NPixel *= inputSize[i];
1146     }
1147     inputSizeInBytes = GetSizeInBytes(imageSelected->GetActualMemorySize()*1000);
1148
1149     QString dim = QString::number(dimension) + " (";
1150     dim += pixelType + ")";
1151
1152     infoPanel->setFileName(image);
1153     std::string creationImageTimeValue("No creation time");
1154     itk::ExposeMetaData< std::string > (*imageSelected->GetFirstMetaDataDictionary(), "creationImageTime", creationImageTimeValue);
1155     infoPanel->setImageCreationTime(QString(creationImageTimeValue.c_str()));
1156     infoPanel->setDimension(dim);
1157     infoPanel->setSizePixel(GetVectorIntAsString(inputSize));
1158     infoPanel->setSizeMM(GetVectorDoubleAsString(sizeMM));
1159     infoPanel->setOrigin(GetVectorDoubleAsString(origin));
1160     infoPanel->setSpacing(GetVectorDoubleAsString(inputSpacing));
1161     infoPanel->setNPixel(QString::number(NPixel)+" ("+inputSizeInBytes+")");
1162
1163     transformation = imageSelected->GetTransform()[tSlice]->GetMatrix();
1164     infoPanel->setTransformation(Get4x4MatrixDoubleAsString(transformation));
1165
1166     landmarksPanel->SetCurrentLandmarks(mSlicerManagers[index]->GetLandmarks(),
1167                                         mSlicerManagers[index]->GetTSlice());
1168     landmarksPanel->SetCurrentPath(mInputPathName.toStdString());
1169     landmarksPanel->SetCurrentImage(mSlicerManagers[index]->GetFileName().c_str());
1170
1171     overlayPanel->getCurrentImageName(mSlicerManagers[index]->GetFileName().c_str());
1172     for (int i = 0; i < 4; i++) {
1173       if (DataTree->selectedItems()[0]->data(i+1,Qt::CheckStateRole).toInt() > 0 || i == 3) {
1174         mSlicerManagers[index]->UpdateInfoOnCursorPosition(i);
1175         break;
1176       }
1177     }
1178
1179 //     infoPanel->setFileName(image);
1180 //     infoPanel->setDimension(dim);
1181 //     infoPanel->setSizePixel(GetVectorIntAsString(inputSize));
1182 //     infoPanel->setSizeMM(GetVectorDoubleAsString(sizeMM));
1183 //     infoPanel->setOrigin(GetVectorDoubleAsString(origin));
1184 //     infoPanel->setSpacing(GetVectorDoubleAsString(inputSpacing));
1185 //     infoPanel->setNPixel(QString::number(NPixel)+" ("+inputSizeInBytes+")");
1186 //
1187 //     landmarksPanel->SetCurrentLandmarks(mSlicerManagers[index]->GetLandmarks(),
1188 //                                         mSlicerManagers[index]->GetTSlice());
1189 //     landmarksPanel->SetCurrentPath(mInputPathName.toStdString());
1190 //     landmarksPanel->SetCurrentImage(mSlicerManagers[index]->GetFileName().c_str());
1191 //
1192 //     overlayPanel->getCurrentImageName(mSlicerManagers[index]->GetFileName().c_str());
1193 //     for (int i = 0; i < 4; i++) {
1194 //       if (DataTree->selectedItems()[0]->data(i+1,Qt::CheckStateRole).toInt() > 0 || i == 3) {
1195 //         mSlicerManagers[index]->UpdateInfoOnCursorPosition(i);
1196 //         break;
1197 //       }
1198 //     }
1199     WindowLevelChanged();
1200
1201     slicingPresetComboBox->setCurrentIndex(mSlicerManagers[index]->GetSlicingPreset());
1202
1203     if (mSlicerManagers[index]->GetSlicer(0)->GetVF()) {
1204       overlayPanel->getVFName(mSlicerManagers[index]->GetVFName().c_str());
1205       overlayPanel->getVFProperty(mSlicerManagers[index]->GetSlicer(0)->GetVFSubSampling(),
1206         mSlicerManagers[index]->GetSlicer(0)->GetVFScale(),
1207         mSlicerManagers[index]->GetSlicer(0)->GetVFLog());
1208     } else {
1209       overlayPanel->getVFName(mSlicerManagers[index]->GetVFName().c_str());
1210       overlayPanel->getVFProperty(-1,-1,-1);
1211     }
1212     if (mSlicerManagers[index]->GetSlicer(0)->GetOverlay()) {
1213       overlayPanel->getOverlayName(mSlicerManagers[index]->GetOverlayName().c_str());
1214     } else {
1215       overlayPanel->getOverlayName(mSlicerManagers[index]->GetOverlayName().c_str());
1216     }
1217
1218     if (mSlicerManagers[index]->GetSlicer(0)->GetFusion()) {
1219       overlayPanel->getFusionName(mSlicerManagers[index]->GetFusionName().c_str());
1220     } else {
1221       overlayPanel->getFusionName(mSlicerManagers[index]->GetFusionName().c_str());
1222     }
1223   }
1224 }
1225 //------------------------------------------------------------------------------
1226
1227 //------------------------------------------------------------------------------
1228 void vvMainWindow::ShowDocumentation()
1229 {
1230   documentation->show();
1231 }
1232 //------------------------------------------------------------------------------
1233
1234 //------------------------------------------------------------------------------
1235 void vvMainWindow::PopupRegisterForm(bool checkCanPush)
1236 {
1237   vvRegisterForm* registerForm = new vvRegisterForm(QUrl("http://www.creatis.insa-lyon.fr/~dsarrut/vvregister/write.php"), getVVSettingsPath(), getSettingsOptionFormat());
1238   if(!checkCanPush) {
1239     registerForm->show();
1240   } else {
1241     if(registerForm->canPush()) {
1242       registerForm->show();
1243       registerForm->acquitPushed();//too bad if there is not internet connection anymore.
1244     }
1245   }
1246 }
1247 //------------------------------------------------------------------------------
1248
1249 //------------------------------------------------------------------------------
1250 void vvMainWindow::ShowHelpDialog()
1251 {
1252   help_dialog->show();
1253 }
1254 //------------------------------------------------------------------------------
1255
1256 //------------------------------------------------------------------------------
1257 void vvMainWindow::ChangeViewMode()
1258 {
1259   typedef struct _SIZE{
1260     QSplitter* splitter;
1261     QList<int> size1, size2;
1262     int cols[3];
1263   }SplitterSize;
1264   SplitterSize sizes[4];
1265   sizes[0].splitter = OSplitter;
1266   sizes[0].size1.push_back(1);
1267   sizes[0].size1.push_back(0);
1268   sizes[0].size2.push_back(1);
1269   sizes[0].size2.push_back(0);
1270   sizes[0].cols[0] = 2;
1271   sizes[0].cols[1] = 3;
1272   sizes[0].cols[2] = 4;
1273
1274   sizes[1].splitter = ESplitter;
1275   sizes[1].size1.push_back(0);
1276   sizes[1].size1.push_back(1);
1277   sizes[1].size2.push_back(1);
1278   sizes[1].size2.push_back(0);
1279   sizes[1].cols[0] = 1;
1280   sizes[1].cols[1] = 3;
1281   sizes[1].cols[2] = 4;
1282
1283   sizes[2].splitter = OSplitter;
1284   sizes[2].size1.push_back(1);
1285   sizes[2].size1.push_back(0);
1286   sizes[2].size2.push_back(0);
1287   sizes[2].size2.push_back(1);
1288   sizes[2].cols[0] = 1;
1289   sizes[2].cols[1] = 2;
1290   sizes[2].cols[2] = 4;
1291
1292   sizes[3].splitter = ESplitter;
1293   sizes[3].size1.push_back(0);
1294   sizes[3].size1.push_back(1);
1295   sizes[3].size2.push_back(0);
1296   sizes[3].size2.push_back(1);
1297   sizes[3].cols[0] = 1;
1298   sizes[3].cols[1] = 2;
1299   sizes[3].cols[2] = 3;
1300
1301   int slicer = mSlicerManagers[mCurrentPickedImageIndex]->GetSelectedSlicer();
1302   if (viewMode == 1) {
1303     if (slicer >= 0) {
1304       viewMode = 0;
1305       splitter_3->setSizes(sizes[slicer].size1);
1306       sizes[slicer].splitter->setSizes(sizes[slicer].size2);
1307       DataTree->setColumnHidden(sizes[slicer].cols[0],1);
1308       DataTree->setColumnHidden(sizes[slicer].cols[1],1);
1309       DataTree->setColumnHidden(sizes[slicer].cols[2],1);
1310     }
1311   } else {
1312     QList<int> size;
1313     if (slicer >= 0) {
1314       viewMode = 1;
1315       size.push_back(1);
1316       size.push_back(1);
1317       splitter_3->setSizes(size);
1318       sizes[slicer].splitter->setSizes(size);
1319       DataTree->setColumnHidden(sizes[slicer].cols[0],0);
1320       DataTree->setColumnHidden(sizes[slicer].cols[1],0);
1321       DataTree->setColumnHidden(sizes[slicer].cols[2],0);
1322     }
1323   }
1324   UpdateRenderWindows();
1325   /*
1326   ** I don't know why but for both resized QVTKWidget we also need to render
1327   ** the associated Slicer to redraw crosses.
1328   */
1329   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
1330     //     if (DataTree->topLevelItem(i)->data(COLUMN_UL_VIEW,Qt::CheckStateRole).toInt() > 1)
1331     mSlicerManagers[i]->GetSlicer(0)->Render();
1332     mSlicerManagers[i]->GetSlicer(1)->Render();
1333     //     if (DataTree->topLevelItem(i)->data(COLUMN_DL_VIEW,Qt::CheckStateRole).toInt() > 1)
1334     mSlicerManagers[i]->GetSlicer(2)->Render();
1335     mSlicerManagers[i]->GetSlicer(3)->Render();
1336   }
1337 }
1338 //------------------------------------------------------------------------------
1339
1340 //------------------------------------------------------------------------------
1341 QString vvMainWindow::GetSizeInBytes(unsigned long size)
1342 {
1343   QString result = "";// QString::number(size);
1344   //result += " bytes (";
1345   if (size > 1000000000) {
1346     size /= 1000000000;
1347     result += QString::number(size);
1348     result += "Gb";//)";
1349   } else if (size > 1000000) {
1350     size /= 1000000;
1351     result += QString::number(size);
1352     result += "Mb";//)";
1353   } else if (size > 1000) {
1354     size /= 1000;
1355     result += QString::number(size);
1356     result += "kb";//)";
1357   }
1358   return result;
1359 }
1360 //------------------------------------------------------------------------------
1361
1362 //------------------------------------------------------------------------------
1363 QString vvMainWindow::Get4x4MatrixDoubleAsString(vtkSmartPointer<vtkMatrix4x4> matrix, const int precision)
1364 {
1365   std::ostringstream strmatrix;
1366
1367   // Figure out the number of digits of the integer part of the largest absolute value
1368   // for each column
1369   unsigned width[4];
1370   for (unsigned int j = 0; j < 4; j++){
1371     double absmax = 0.;
1372     for (unsigned int i = 0; i < 4; i++)
1373       absmax = std::max(absmax, vnl_math_abs(matrix->GetElement(i, j)));
1374     unsigned ndigits = (unsigned)std::max(0.,std::log10(absmax))+1;
1375     width[j] = precision+ndigits+3;
1376   }
1377
1378   // Output with correct width, aligned to the right
1379   for (unsigned int i = 0; i < 4; i++) {
1380     for (unsigned int j = 0; j < 4; j++) {
1381       strmatrix.setf(ios::fixed,ios::floatfield);
1382       strmatrix.precision(precision);
1383       strmatrix.fill(' ');
1384       strmatrix.width(width[j]);
1385       strmatrix << std::right << matrix->GetElement(i, j);
1386     }
1387     strmatrix << std::endl;
1388   }
1389   QString result = strmatrix.str().c_str();
1390   return result;
1391 }
1392 //------------------------------------------------------------------------------
1393
1394 //------------------------------------------------------------------------------
1395 QString vvMainWindow::GetVectorDoubleAsString(std::vector<double> vectorDouble)
1396 {
1397   QString result;
1398   for (unsigned int i= 0; i < vectorDouble.size(); i++) {
1399     if (i != 0)
1400       result += " ";
1401     result += QString::number(vectorDouble[i]);
1402   }
1403   return result;
1404 }
1405 //------------------------------------------------------------------------------
1406
1407 //------------------------------------------------------------------------------
1408 QString vvMainWindow::GetVectorIntAsString(std::vector<int> vectorInt)
1409 {
1410   QString result;
1411   for (unsigned int i= 0; i < vectorInt.size(); i++) {
1412     if (i != 0)
1413       result += " ";
1414     result += QString::number(vectorInt[i]);
1415   }
1416   return result;
1417 }
1418 //------------------------------------------------------------------------------
1419
1420 //------------------------------------------------------------------------------
1421 //this actually returns the SlicerManager index!
1422 int vvMainWindow::GetSlicerIndexFromItem(QTreeWidgetItem* item)
1423 {
1424   QString id = item->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString();
1425   for (int i = 0; i < DataTree->topLevelItemCount(); i++) {
1426     if (DataTree->topLevelItem(i)->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString() == id)
1427       return i;
1428   }
1429   return -1;
1430 }
1431 //------------------------------------------------------------------------------
1432
1433 //------------------------------------------------------------------------------
1434 QTreeWidgetItem* vvMainWindow::GetItemFromSlicerManager(vvSlicerManager* sm)
1435 {
1436   QString id = sm->GetId().c_str();
1437   for (int i = 0; i < DataTree->topLevelItemCount(); i++) {
1438     if (DataTree->topLevelItem(i)->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString() == id)
1439       return DataTree->topLevelItem(i);
1440   }
1441   return NULL;
1442 }
1443 //------------------------------------------------------------------------------
1444
1445 //------------------------------------------------------------------------------
1446 void vvMainWindow::DisplayChanged(QTreeWidgetItem *clickedItem, int column)
1447 {
1448   if ( column >= COLUMN_CLOSE_IMAGE || column <= 0)
1449     return;
1450
1451   // Get parent information (might be the same item)
1452   int slicerManagerIndex = GetSlicerIndexFromItem(clickedItem);
1453   QTreeWidgetItem* clickedParentItem = DataTree->topLevelItem(slicerManagerIndex);
1454   vvSlicer* clickedSlicer = mSlicerManagers[slicerManagerIndex]->GetSlicer(column-1);
1455
1456   // Go over the complete item tree (only 2 levels, parents and children)
1457   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
1458     // Trick to avoid redoing twice the job for a key (sr)
1459     mSlicerManagers[i]->GetSlicer(column-1)->GetRenderWindow()->GetInteractor()->SetKeySym("Crap");
1460
1461     QTreeWidgetItem* currentParentItem = DataTree->topLevelItem(i);
1462     if(currentParentItem != clickedParentItem) {
1463       // Not the branch of the clicked item, uncheck all
1464
1465       // Parent
1466       currentParentItem->setData(column,Qt::CheckStateRole, 0);
1467       mSlicerManagers[i]->UpdateSlicer(column-1, false);
1468
1469       // Children
1470       for (int iChild = 0; iChild < currentParentItem->childCount(); iChild++) {
1471         currentParentItem->child(iChild)->setData(column,Qt::CheckStateRole, 0);
1472       }
1473     }
1474     else {
1475       // Branch of the clicked one: get check status from actor visibility in slicer
1476       // and toggle the clicked one
1477
1478       // Parent
1479       bool vis = clickedSlicer->GetActorVisibility("image", 0);
1480       bool draw = clickedSlicer->GetRenderer()->GetDraw();
1481
1482       // Update slicer (after getting visibility)
1483       mSlicerManagers[slicerManagerIndex]->UpdateSlicer(column-1, true);
1484       mSlicerManagers[slicerManagerIndex]->UpdateInfoOnCursorPosition(column-1);
1485       DisplaySliders(slicerManagerIndex, column-1);
1486       if(clickedParentItem == clickedItem) {
1487         // Toggle
1488         vis = !draw || !vis;
1489       }
1490       clickedSlicer->SetActorVisibility("image", 0, vis);
1491       clickedParentItem->setData(column, Qt::CheckStateRole, vis?2:0);
1492
1493       // Children
1494       std::map<std::string, int> actorTypeCounts;
1495       for (int iChild = 0; iChild < clickedParentItem->childCount(); iChild++) {
1496         QTreeWidgetItem* currentChildItem = clickedParentItem->child(iChild);
1497         std::string actorType = currentChildItem->data(1,Qt::UserRole).toString().toStdString();
1498         vis = clickedSlicer->GetActorVisibility(actorType, actorTypeCounts[actorType]);
1499         if(currentChildItem == clickedItem) {
1500           // Toggle or force visibility if it was not on this branch so far
1501           vis = !draw || !vis;
1502           clickedSlicer->SetActorVisibility(actorType, actorTypeCounts[actorType], vis);
1503         }
1504         currentChildItem->setData(column, Qt::CheckStateRole, vis?2:0);
1505         actorTypeCounts[actorType]++;
1506       }
1507     }
1508   }
1509
1510   clickedSlicer->Render();
1511 }
1512 //------------------------------------------------------------------------------
1513
1514 void vvMainWindow::InitSlicers()
1515 {
1516   if (mSlicerManagers.size()) {
1517     mSlicerManagers.back()->GenerateDefaultLookupTable();
1518
1519     mSlicerManagers.back()->SetSlicerWindow(0,NOViewWidget->GetRenderWindow());
1520     mSlicerManagers.back()->SetSlicerWindow(1,NEViewWidget->GetRenderWindow());
1521     mSlicerManagers.back()->SetSlicerWindow(2,SOViewWidget->GetRenderWindow());
1522     mSlicerManagers.back()->SetSlicerWindow(3,SEViewWidget->GetRenderWindow());
1523   }
1524 }
1525
1526 //------------------------------------------------------------------------------
1527 void vvMainWindow::InitDisplay()
1528 {
1529   if (mSlicerManagers.size()) {
1530     //BE CAREFUL : this is absolutely necessary to set the interactor style
1531     //in order to have the same style instanciation for all SlicerManagers in
1532     // a same window
1533     for (int j = 0; j < 4; j++) {
1534       vvInteractorStyleNavigator* style = vvInteractorStyleNavigator::New();
1535       style->SetAutoAdjustCameraClippingRange(1);
1536       bool AlreadySelected = false;
1537       for (int i = 0; i < DataTree->topLevelItemCount(); i++) {
1538         mSlicerManagers[i]->SetInteractorStyleNavigator(j,style);
1539
1540         //select the image only if previous are not selected
1541         if (DataTree->topLevelItem(i)->data(j+1,Qt::CheckStateRole).toInt() > 1) {
1542           mSlicerManagers[i]->UpdateSlicer(j,1);
1543           AlreadySelected = true;
1544         } else if (i == DataTree->topLevelItemCount()-1 && !AlreadySelected) {
1545           if (DataTree->selectedItems().size() == 0)
1546             DataTree->topLevelItem(i)->setSelected(1);
1547           DataTree->topLevelItem(i)->setData(j+1,Qt::CheckStateRole,2);
1548           mSlicerManagers[i]->UpdateSlicer(j,1);
1549           DisplaySliders(i,j);
1550         } else {
1551           DataTree->topLevelItem(i)->setData(j+1,Qt::CheckStateRole,0);
1552           mSlicerManagers[i]->UpdateSlicer(j,0);
1553         }
1554       }
1555       style->Delete();
1556     }
1557   }
1558 }
1559 //------------------------------------------------------------------------------
1560
1561 //------------------------------------------------------------------------------
1562 void vvMainWindow::DisplaySliders(int slicer, int window)
1563 {
1564   if(!mSlicerManagers[slicer]->GetSlicer(window)->GetRenderer()->GetDraw())
1565     return;
1566
1567   int range[2];
1568   mSlicerManagers[slicer]->GetSlicer(window)->GetSliceRange(range);
1569   int position = mSlicerManagers[slicer]->GetSlicer(window)->GetSlice();
1570   if (range[1]>0)
1571     verticalSliders[window]->show();
1572   else
1573     verticalSliders[window]->hide();
1574   verticalSliders[window]->setRange(range[0],range[1]);
1575   verticalSliders[window]->setValue(position);
1576
1577   int tRange[2];
1578   tRange[0] = 0;
1579   tRange[1] = mSlicerManagers[slicer]->GetSlicer(window)->GetTMax();
1580   if (tRange[1]>0)
1581     horizontalSliders[window]->show();
1582   else
1583     horizontalSliders[window]->hide();
1584   horizontalSliders[window]->setRange(tRange[0],tRange[1]);
1585   int tPosition = mSlicerManagers[slicer]->GetSlicer(window)->GetMaxCurrentTSlice();
1586   horizontalSliders[window]->setValue(tPosition);
1587 }
1588 //------------------------------------------------------------------------------
1589
1590 //------------------------------------------------------------------------------
1591 void vvMainWindow::CloseImage(QTreeWidgetItem* item, int column)
1592 {
1593   int index = GetSlicerIndexFromItem(item);
1594
1595   if (DataTree->topLevelItem(index) != item) {
1596     QString warning = "Do you really want to close the overlay : ";
1597     warning += item->data(COLUMN_IMAGE_NAME,Qt::DisplayRole).toString();
1598     QMessageBox msgBox(QMessageBox::Warning, tr("Close Overlay"),
1599       warning, 0, this);
1600     msgBox.addButton(tr("Close"), QMessageBox::AcceptRole);
1601     msgBox.addButton(tr("Cancel"), QMessageBox::RejectRole);
1602     if (msgBox.exec() == QMessageBox::AcceptRole) {
1603       std::string overlay_type=item->data(1,Qt::UserRole).toString().toStdString();
1604       int overlay_index=0;
1605       for (int child = 0; child < DataTree->topLevelItem(index)->childCount(); child++) {
1606         if (DataTree->topLevelItem(index)->\
1607           child(child)->data(1,Qt::UserRole).toString().toStdString() == overlay_type)
1608           overlay_index++;
1609         if (DataTree->topLevelItem(index)->child(child) == item) break;
1610       }
1611       if (overlay_type=="fusionSequence") {
1612         //removing the overlay sequence in a fusion sequence visualization mode
1613         //reset the transforms
1614         overlayPanel->getFusionSequenceProperty(-1, false, 0, false);
1615
1616         //unlink and untie the slicer managers
1617         RemoveLink(mSlicerManagers[index]->GetId().c_str(), mSlicerManagers[mSlicerManagers[index]->GetFusionSequenceIndexOfLinkedManager()]->GetId().c_str());
1618         mSlicerManagers[index]->SetFusionSequenceInvolvmentCode(-1);
1619         mSlicerManagers[mSlicerManagers[index]->GetFusionSequenceIndexOfLinkedManager()]->SetFusionSequenceInvolvmentCode(-1);
1620         for (unsigned i=0 ; i<4 ; i++) {
1621             mSlicerManagers[index]->GetSlicer(i)->SetFusionSequenceCode(-1);
1622             mSlicerManagers[mSlicerManagers[index]->GetFusionSequenceIndexOfLinkedManager()]->GetSlicer(i)->SetFusionSequenceCode(-1);
1623         }
1624
1625       }
1626       mSlicerManagers[index]->RemoveActor(overlay_type, overlay_index-1);
1627       mSlicerManagers[index]->SetColorMap(0);
1628       DataTree->topLevelItem(index)->takeChild(DataTree->topLevelItem(index)->indexOfChild(item));
1629       mSlicerManagers[index]->Render();
1630     }
1631   } else if (DataTree->topLevelItemCount() <= 1) {
1632     QString warning = "Do you really want to close the image : ";
1633     warning += item->data(COLUMN_IMAGE_NAME,Qt::DisplayRole).toString();
1634     warning += "\nThis is the last image, you're about to close vv !!!";
1635     QMessageBox msgBox(QMessageBox::Warning, tr("Close Image"),
1636       warning, 0, this);
1637     msgBox.addButton(tr("Close vv"), QMessageBox::AcceptRole);
1638     msgBox.addButton(tr("Cancel"), QMessageBox::RejectRole);
1639     if (msgBox.exec() == QMessageBox::AcceptRole) {
1640       this->close();
1641     }
1642   } else {
1643     QString warning = "Do you really want to close the image : ";
1644     warning += item->data(COLUMN_IMAGE_NAME,Qt::DisplayRole).toString();
1645     QMessageBox msgBox(QMessageBox::Warning, tr("Close Image"),
1646       warning, 0, this);
1647     msgBox.addButton(tr("Close"), QMessageBox::AcceptRole);
1648     msgBox.addButton(tr("Cancel"), QMessageBox::RejectRole);
1649     if (msgBox.exec() == QMessageBox::AcceptRole) {
1650
1651       // Tell tools that we close an image
1652       emit AnImageIsBeingClosed(mSlicerManagers[index]);
1653
1654       std::vector<vvSlicerManager*>::iterator Manageriter = mSlicerManagers.begin();
1655       DataTree->takeTopLevelItem(index);
1656       for (int i = 0; i < index; i++) {
1657         Manageriter++;
1658       }
1659       //if the slicer manager was involved in a fusion sequence visualization...
1660       if ( mSlicerManagers[index]->IsInvolvedInFusionSequence() ) {
1661         //in both cases, close the overlay: find it... and close it
1662         //ideally, I should duplicate the code, and avoid calling CloseImage, since this pops up another interactive box
1663         QTreeWidgetItem* overlayItem;
1664         if (mSlicerManagers[index]->IsMainSequenceOfFusionSequence()) {
1665           for (unsigned i=0 ; i<item->childCount() ; i++) {
1666             overlayItem = item->child(i);
1667             this->CloseImage( overlayItem, 0 );
1668           }
1669         }
1670         else {
1671           QTreeWidgetItem* linkedItem = this->GetItemFromSlicerManager( mSlicerManagers[mSlicerManagers[index]->GetFusionSequenceIndexOfLinkedManager()] );
1672           for (unsigned i=0 ; i<linkedItem->childCount() ; i++) {
1673             overlayItem = linkedItem->child(i);
1674             this->CloseImage( overlayItem, 0 );
1675           }
1676         }
1677
1678         /* -- this is normally already done when closing the overlay.
1679         //reset the transforms
1680         overlayPanel->getFusionSequenceProperty(-1, false, 0, false);
1681
1682         //unlink and untie the slicer managers
1683         RemoveLink(mSlicerManagers[index]->GetId().c_str(), mSlicerManagers[mSlicerManagers[index]->GetFusionSequenceIndexOfLinkedManager()]->GetId().c_str());
1684         mSlicerManagers[index]->SetFusionSequenceInvolvmentCode(-1);
1685         mSlicerManagers[mSlicerManagers[index]->GetFusionSequenceIndexOfLinkedManager()]->SetFusionSequenceInvolvmentCode(-1);
1686         for (unsigned i=0 ; i<4 ; i++) {
1687             mSlicerManagers[index]->GetSlicer(i)->SetFusionSequenceCode(-1);
1688             mSlicerManagers[mSlicerManagers[index]->GetFusionSequenceIndexOfLinkedManager()]->GetSlicer(i)->SetFusionSequenceCode(-1);
1689         }
1690         */
1691       }
1692
1693       linkPanel->removeImage(index);
1694       mSlicerManagers[index]->RemoveActors();
1695
1696       //remove the slicer manager
1697       delete mSlicerManagers[index];
1698       mSlicerManagers.erase(Manageriter);
1699
1700       //
1701       InitDisplay();
1702     }
1703   }
1704   ImageInfoChanged();
1705 }
1706 //------------------------------------------------------------------------------
1707
1708 //------------------------------------------------------------------------------
1709 void vvMainWindow::ReloadImage(QTreeWidgetItem* item, int column)
1710 {
1711   // int index = GetSlicerIndexFromItem(item);
1712   //   QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
1713   //   if (item->data(1,Qt::UserRole).toString() == "vector")
1714   //     mSlicerManagers[index]->ReloadVF();
1715   //   else
1716   //     mSlicerManagers[index]->Reload();
1717
1718   //   QApplication::restoreOverrideCursor();
1719   int index = GetSlicerIndexFromItem(item);
1720   QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
1721   QString role=item->data(1,Qt::UserRole).toString();
1722   if ( role == "vector") {
1723     mSlicerManagers[index]->ReloadVF();
1724   }
1725   else if (role == "overlay") {
1726     mSlicerManagers[index]->ReloadOverlay();
1727   }
1728   else if (role == "fusion") {
1729     mSlicerManagers[index]->ReloadFusion();
1730   }
1731   else if (role == "fusionSequence") {
1732     //both versions of the secondary sequence must be updated.
1733     mSlicerManagers[index]->ReloadFusionSequence();
1734     mSlicerManagers[mSlicerManagers[index]->GetFusionSequenceIndexOfLinkedManager()]->Reload();
1735   }
1736   else {
1737     mSlicerManagers[index]->Reload();
1738     //if we update the secondary sequence, then the overlay of the main sequence should also be updated
1739     if (mSlicerManagers[index]->IsSecondarySequenceOfFusionSequence()) mSlicerManagers[mSlicerManagers[index]->GetFusionSequenceIndexOfLinkedManager()]->ReloadFusionSequence();
1740   }
1741   // Update view and info
1742   ImageInfoChanged();
1743   mSlicerManagers[index]->Render();
1744   QApplication::restoreOverrideCursor();
1745 }
1746 //------------------------------------------------------------------------------
1747
1748 //------------------------------------------------------------------------------
1749 void vvMainWindow::MousePositionChanged(int visibility,double x, double y, double z, double X, double Y, double Z , double value)
1750 {
1751   infoPanel->setCurrentInfo(visibility,x,y,z,X,Y,Z,value);
1752 }
1753 //------------------------------------------------------------------------------
1754
1755 //------------------------------------------------------------------------------
1756 void vvMainWindow::VectorChanged(int visibility,double x, double y, double z, double value)
1757 {
1758   overlayPanel->getCurrentVectorInfo(visibility,x,y,z,value);
1759 }
1760 //------------------------------------------------------------------------------
1761
1762 //------------------------------------------------------------------------------
1763 void vvMainWindow::OverlayChanged(int visibility, double valueOver, double valueRef)
1764 {
1765   overlayPanel->getCurrentOverlayInfo(visibility,valueOver, valueRef);
1766 }
1767 //------------------------------------------------------------------------------
1768
1769 //------------------------------------------------------------------------------
1770 void vvMainWindow::FusionChanged(int visibility, double value)
1771 {
1772   overlayPanel->getCurrentFusionInfo(visibility,value);
1773 }
1774 //------------------------------------------------------------------------------
1775
1776 //------------------------------------------------------------------------------
1777 //called when AddOverlayImage, AddFusionSequence
1778 //or when UpdateWindowLevel() is called ; when slicerManager emits WindowLevelChanged
1779 //when ImageInfoChanged() is called
1780 void vvMainWindow::WindowLevelChanged()
1781 {
1782   // Base image
1783   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1784   if(index==-1) return;
1785   windowSpinBox->setValue(mSlicerManagers[index]->GetColorWindow());
1786   levelSpinBox->setValue(mSlicerManagers[index]->GetColorLevel());
1787   colorMapComboBox->setCurrentIndex(mSlicerManagers[index]->GetColorMap());
1788   presetComboBox->setCurrentIndex(mSlicerManagers[index]->GetPreset());
1789
1790   // Overlay image
1791   if (mSlicerManagers[index]->GetSlicer(0)->GetOverlay())
1792     overlayPanel->getOverlayProperty(mSlicerManagers[index]->GetOverlayColor(),
1793     mSlicerManagers[index]->GetLinkOverlayWindowLevel(),
1794     mSlicerManagers[index]->GetOverlayColorWindow(),
1795     mSlicerManagers[index]->GetOverlayColorLevel());
1796   else
1797     overlayPanel->getOverlayProperty(-1,0,0.,0.);
1798
1799   // Fusion & SequenceFusion image
1800   if (mSlicerManagers[index]->GetSlicer(0)->GetFusion()) {
1801     overlayPanel->getFusionProperty(mSlicerManagers[index]->GetFusionOpacity(),
1802       mSlicerManagers[index]->GetFusionThresholdOpacity(),
1803       mSlicerManagers[index]->GetFusionColorMap(),
1804       mSlicerManagers[index]->GetFusionWindow(),
1805       mSlicerManagers[index]->GetFusionLevel());
1806     if (mSlicerManagers[index]->IsMainSequenceOfFusionSequence()) {
1807       overlayPanel->getFusionSequenceProperty(mSlicerManagers[index]->GetFusionSequenceFrameIndex(),
1808         mSlicerManagers[index]->GetFusionSequenceSpatialSyncFlag(),
1809         mSlicerManagers[index]->GetFusionSequenceNbFrames(),
1810         mSlicerManagers[index]->GetFusionSequenceTemporalSyncFlag());
1811     }
1812   }
1813   else if ( mSlicerManagers[index]->IsSecondarySequenceOfFusionSequence() ) {
1814     //if the image is involved in a fusion sequence, preserve the overlay panel!
1815     int ind = mSlicerManagers[index]->GetFusionSequenceIndexOfLinkedManager();
1816     overlayPanel->getFusionProperty(mSlicerManagers[ind]->GetFusionOpacity(),
1817       mSlicerManagers[ind]->GetFusionThresholdOpacity(),
1818       mSlicerManagers[ind]->GetFusionColorMap(),
1819       mSlicerManagers[ind]->GetFusionWindow(),
1820       mSlicerManagers[ind]->GetFusionLevel());
1821     overlayPanel->getFusionSequenceProperty(mSlicerManagers[ind]->GetFusionSequenceFrameIndex(),
1822       mSlicerManagers[ind]->GetFusionSequenceSpatialSyncFlag(),
1823       mSlicerManagers[ind]->GetFusionSequenceNbFrames(),
1824       mSlicerManagers[ind]->GetFusionSequenceTemporalSyncFlag());
1825   }
1826   else
1827   {
1828     overlayPanel->getFusionProperty(-1, -1, -1, -1, -1);
1829     overlayPanel->getFusionSequenceProperty(-1, false, 0, false);
1830   }
1831 }
1832 //------------------------------------------------------------------------------
1833
1834 //------------------------------------------------------------------------------
1835 void vvMainWindow::WindowLevelEdited()
1836 {
1837   presetComboBox->setCurrentIndex(WL_USER);
1838   UpdateWindowLevel();
1839 }
1840 //------------------------------------------------------------------------------
1841
1842 //------------------------------------------------------------------------------
1843 void vvMainWindow::SetWindowLevel(double w, double l)
1844 {
1845   windowSpinBox->setValue(w);
1846   levelSpinBox->setValue(l);
1847   presetComboBox->setCurrentIndex(WL_USER);
1848   colorMapComboBox->setCurrentIndex(0);
1849   UpdateWindowLevel();
1850 }
1851 //------------------------------------------------------------------------------
1852
1853 //------------------------------------------------------------------------------
1854 void vvMainWindow::UpdateWindowLevel()
1855 {
1856   if (DataTree->selectedItems().size()) {
1857     if (presetComboBox->currentIndex() == WL_VENTILATION) //For ventilation
1858       colorMapComboBox->setCurrentIndex(5);
1859     int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1860     mSlicerManagers[index]->SetColorWindow(windowSpinBox->value());
1861     mSlicerManagers[index]->SetColorLevel(levelSpinBox->value());
1862     mSlicerManagers[index]->SetPreset(presetComboBox->currentIndex());
1863     mSlicerManagers[index]->Render();
1864     WindowLevelChanged();
1865   }
1866 }
1867 //------------------------------------------------------------------------------
1868
1869 //------------------------------------------------------------------------------
1870 void vvMainWindow::UpdateSlicingPreset()
1871 {
1872   if (DataTree->selectedItems().size()) {
1873     int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1874     mSlicerManagers[index]->SetSlicingPreset(vvSlicerManager::SlicingPresetType(slicingPresetComboBox->currentIndex()));
1875   }
1876 }
1877 //------------------------------------------------------------------------------
1878
1879 //------------------------------------------------------------------------------
1880 void vvMainWindow::UpdateColorMap()
1881 {
1882   if (DataTree->selectedItems().size()) {
1883     int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1884     mSlicerManagers[index]->SetColorMap(colorMapComboBox->currentIndex());
1885     mSlicerManagers[index]->Render();
1886   }
1887 }
1888 //------------------------------------------------------------------------------
1889 void vvMainWindow::SwitchWindowLevel()
1890 {
1891   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1892   int window = mSlicerManagers[index]->GetColorWindow();
1893   presetComboBox->setCurrentIndex(WL_USER);
1894   windowSpinBox->setValue(-window);
1895   UpdateWindowLevel();
1896 }
1897 //------------------------------------------------------------------------------
1898
1899 //------------------------------------------------------------------------------
1900 void vvMainWindow::ApplyWindowLevelToAllImages()
1901 {
1902   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1903   if(index==-1) return;
1904   double window = mSlicerManagers[index]->GetColorWindow();
1905   double level = mSlicerManagers[index]->GetColorLevel();
1906
1907   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
1908     if (mSlicerManagers[i] == NULL)
1909       continue;
1910     mSlicerManagers[i]->SetColorWindow(window);
1911     mSlicerManagers[i]->SetColorLevel(level);
1912     mSlicerManagers[i]->SetPreset(WL_USER);
1913     mSlicerManagers[i]->Render();
1914   }
1915 }
1916 //------------------------------------------------------------------------------
1917
1918 //------------------------------------------------------------------------------
1919 void vvMainWindow::ApplyWindowToSetOfImages(double window, unsigned int indexMin, unsigned int indexMax)
1920 {
1921   for (unsigned int i = indexMin; i <= indexMax && i < mSlicerManagers.size(); i++) {
1922     if (mSlicerManagers[i] == NULL)
1923       continue;
1924     mSlicerManagers[i]->SetColorWindow(window);
1925     mSlicerManagers[i]->SetPreset(WL_USER);
1926     mSlicerManagers[i]->Render();
1927   }
1928 }
1929 //------------------------------------------------------------------------------
1930
1931 //------------------------------------------------------------------------------
1932 void vvMainWindow::ApplyLevelToSetOfImages(double level, unsigned int indexMin, unsigned int indexMax)
1933 {
1934   for (unsigned int i = indexMin; i <= indexMax && i < mSlicerManagers.size(); i++) {
1935     if (mSlicerManagers[i] == NULL)
1936       continue;
1937     mSlicerManagers[i]->SetColorLevel(level);
1938     mSlicerManagers[i]->SetPreset(WL_USER);
1939     mSlicerManagers[i]->Render();
1940   }
1941 }
1942 //------------------------------------------------------------------------------
1943
1944 //------------------------------------------------------------------------------
1945 void vvMainWindow::UpdateLinkManager(std::string id, int slicer, double x, double y, double z, int temps)
1946 {
1947   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
1948     if (mSlicerManagers[i]->GetId() == id) {
1949       mSlicerManagers[i]->GetSlicer(slicer)->SetCurrentPosition(x,y,z,temps);
1950       mSlicerManagers[i]->UpdateViews(0,slicer);
1951       break;
1952     }
1953   }
1954 }
1955 //------------------------------------------------------------------------------
1956
1957 //------------------------------------------------------------------------------
1958 void vvMainWindow::UpdateLinkedNavigation(std::string id, vvSlicerManager * sm, vvSlicer* refSlicer)
1959 {
1960   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
1961     if (id == mSlicerManagers[i]->GetId()) {
1962       mSlicerManagers[i]->UpdateLinkedNavigation(refSlicer);
1963     }
1964   }
1965 }
1966 //------------------------------------------------------------------------------
1967
1968 //------------------------------------------------------------------------------
1969 void vvMainWindow::ShowContextMenu(QPoint point)
1970 {
1971   if (!DataTree->selectedItems().size()) {
1972     contextActions[1]->setEnabled(0);
1973     contextActions[2]->setEnabled(0);
1974     contextActions[3]->setEnabled(0);
1975     contextActions[4]->setEnabled(0);
1976     contextActions[5]->setEnabled(0);
1977     contextActions[6]->setEnabled(0);
1978   } else {
1979     int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1980     contextActions[1]->setEnabled(1);
1981     contextActions[2]->setEnabled(
1982       DataTree->itemWidget(DataTree->selectedItems()[0],
1983       COLUMN_RELOAD_IMAGE)->isEnabled());
1984     contextActions[3]->setEnabled(1);
1985     contextActions[5]->setEnabled(1);
1986     contextActions[6]->setEnabled(1);
1987
1988     if (mSlicerManagers[index]->GetDimension() < 3)
1989       contextActions[4]->setEnabled(0);
1990     else
1991       contextActions[4]->setEnabled(1);
1992   }
1993   contextMenu.exec(QCursor::pos());
1994 }
1995 //------------------------------------------------------------------------------
1996
1997 //------------------------------------------------------------------------------
1998 void vvMainWindow::CloseImage()
1999 {
2000   CloseImage(DataTree->selectedItems()[0],0);
2001 }
2002 //------------------------------------------------------------------------------
2003
2004 //------------------------------------------------------------------------------
2005 void vvMainWindow::ReloadImage()
2006 {
2007   ReloadImage(DataTree->selectedItems()[0],0);
2008 }
2009 //------------------------------------------------------------------------------
2010
2011 //------------------------------------------------------------------------------
2012 void vvMainWindow::SelectOverlayImage()
2013 {
2014   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2015
2016   //check if one overlay image is added
2017   for (int child = 0; child < DataTree->topLevelItem(index)->childCount(); child++)
2018     if (DataTree->topLevelItem(index)->child(child)->data(1,Qt::UserRole).toString() == "overlay") {
2019       QString error = "Cannot add more than one compared image\n";
2020       error += "Please remove first ";
2021       error += DataTree->topLevelItem(index)->child(child)->data(COLUMN_IMAGE_NAME,Qt::DisplayRole).toString();
2022       QMessageBox::information(this,tr("Problem adding compared image !"),error);
2023       return;
2024     }
2025
2026     QString Extensions = EXTENSIONS;
2027     Extensions += ";;All Files (*)";
2028     QStringList files = QFileDialog::getOpenFileNames(this,tr("Load Overlay image"),mInputPathName,Extensions);
2029     if (files.isEmpty())
2030       return;
2031
2032     std::vector<std::string> vecFileNames;
2033     for (int i = 0; i < files.size(); i++) {
2034       vecFileNames.push_back(files[i].toStdString());
2035     }
2036     AddOverlayImage(index,vecFileNames,vvImageReader::IMAGE);
2037 }
2038 //------------------------------------------------------------------------------
2039
2040 //------------------------------------------------------------------------------
2041 void vvMainWindow::AddOverlayImage(int index, std::vector<std::string> fileNames, vvImageReader::LoadedImageType type)
2042 {
2043   QString file(fileNames[0].c_str());
2044   if (QFile::exists(file))
2045   {
2046     mInputPathName = itksys::SystemTools::GetFilenamePath(file.toStdString()).c_str();
2047     itk::ImageIOBase::Pointer reader = itk::ImageIOFactory::CreateImageIO(
2048       file.toStdString().c_str(), itk::ImageIOFactory::ReadMode);
2049     reader->SetFileName(fileNames[0].c_str());
2050     reader->ReadImageInformation();
2051     std::string component = reader->GetComponentTypeAsString(reader->GetComponentType());
2052     int dimension = reader->GetNumberOfDimensions();
2053     QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
2054     vvProgressDialog progress("Opening " + file.toStdString());
2055     qApp->processEvents();
2056
2057     std::string filename = itksys::SystemTools::GetFilenameWithoutExtension(file.toStdString()).c_str();
2058     if (mSlicerManagers[index]->SetOverlay(fileNames,dimension, component,type)) {
2059       //create an item in the tree with good settings
2060       QTreeWidgetItem *item = new QTreeWidgetItem();
2061       item->setData(0,Qt::UserRole,file.toStdString().c_str());
2062       item->setData(1,Qt::UserRole,tr("overlay"));
2063       QFileInfo fileinfo(file); //Do not show the path
2064       item->setData(COLUMN_IMAGE_NAME,Qt::DisplayRole,fileinfo.fileName());
2065       item->setToolTip(COLUMN_IMAGE_NAME, mSlicerManagers[index]->GetListOfAbsoluteFilePathInOneString("overlay").c_str());
2066       qApp->processEvents();
2067
2068       for (int j = 1; j <= 4; j++) {
2069         item->setData(j,Qt::CheckStateRole,DataTree->topLevelItem(index)->data(j,Qt::CheckStateRole));
2070       }
2071
2072       //Create the buttons for reload and close
2073       qApp->processEvents();
2074       QTreePushButton* cButton = new QTreePushButton;
2075       cButton->setItem(item);
2076       cButton->setColumn(COLUMN_CLOSE_IMAGE);
2077       cButton->setToolTip(tr("close image"));
2078       cButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/exit.png")));
2079       connect(cButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
2080         this,SLOT(CloseImage(QTreeWidgetItem*, int)));
2081
2082       QTreePushButton* rButton = new QTreePushButton;
2083       rButton->setItem(item);
2084       rButton->setColumn(COLUMN_RELOAD_IMAGE);
2085       rButton->setToolTip(tr("reload image"));
2086       rButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/rotateright.png")));
2087       connect(rButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
2088         this,SLOT(ReloadImage(QTreeWidgetItem*, int)));
2089
2090       DataTree->topLevelItem(index)->setExpanded(1);
2091       DataTree->topLevelItem(index)->addChild(item);
2092       DataTree->setItemWidget(item, COLUMN_CLOSE_IMAGE, cButton);
2093       DataTree->setItemWidget(item, COLUMN_RELOAD_IMAGE, rButton);
2094
2095       //set the id of the image
2096       QString id = DataTree->topLevelItem(index)->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString();
2097       item->setData(COLUMN_IMAGE_NAME,Qt::UserRole,id.toStdString().c_str());
2098       UpdateTree();
2099       qApp->processEvents();
2100       ImageInfoChanged();
2101       QApplication::restoreOverrideCursor();
2102
2103       // Update the display to update, e.g., the sliders
2104       for(int i=0; i<4; i++)
2105         DisplaySliders(index, i);
2106     } else {
2107       QApplication::restoreOverrideCursor();
2108       QString error = "Cannot import the new image.\n";
2109       error += mSlicerManagers[index]->GetLastError().c_str();
2110       QMessageBox::information(this,tr("Problem reading image !"),error);
2111     }
2112     WindowLevelChanged();
2113   }
2114   else
2115     QMessageBox::information(this,tr("Problem reading Overlay !"),"File doesn't exist!");
2116 }
2117 //------------------------------------------------------------------------------
2118
2119
2120 //------------------------------------------------------------------------------
2121 void vvMainWindow::AddROI(int index, QString file)
2122 {
2123   /*
2124   // Get slice manager
2125
2126   // Load image
2127
2128   vvImageReader * mReader = new vvImageReader;
2129   mReader->SetInputFilename(filename.toStdString());
2130   mReader->Update(IMAGE);
2131   if (mReader->GetLastError().size() != 0) {
2132   std::cerr << "Error while reading " << filename.toStdString() << std::endl;
2133   QString error = "Cannot open file \n";
2134   error += mReader->GetLastError().c_str();
2135   QMessageBox::information(this,tr("Reading problem"),error);
2136   delete mReader;
2137   return;
2138   }
2139   vvImage::Pointer roi = mReader->GetOutput();
2140
2141   // Create roi in new tool
2142   vvToolStructureSetManager::AddImage(mCurrentSlicerManager, roi);
2143   */
2144 }
2145 //------------------------------------------------------------------------------
2146
2147 //------------------------------------------------------------------------------
2148 void vvMainWindow::SelectFusionImage()
2149 {
2150   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2151
2152   //check if one fusion image is added
2153   for (int child = 0; child < DataTree->topLevelItem(index)->childCount(); child++)
2154     if ( (DataTree->topLevelItem(index)->child(child)->data(1,Qt::UserRole).toString() == "fusion") ||
2155       (DataTree->topLevelItem(index)->child(child)->data(1,Qt::UserRole).toString() == "fusionSequence") ) {
2156         QString error = "Cannot add more than one fusion image\n";
2157         error += "Please remove first ";
2158         error += DataTree->topLevelItem(index)->child(child)->data(COLUMN_IMAGE_NAME,Qt::DisplayRole).toString();
2159         QMessageBox::information(this,tr("Problem adding fusion image !"),error);
2160         return;
2161     }
2162
2163     QString Extensions = EXTENSIONS;
2164     Extensions += ";;All Files (*)";
2165     QStringList files = QFileDialog::getOpenFileNames(this,tr("Load Fusion image"),mInputPathName,Extensions);
2166     if (files.isEmpty())
2167       return;
2168
2169     std::vector<std::string> vecFileNames;
2170     for (int i = 0; i < files.size(); i++) {
2171       vecFileNames.push_back(files[i].toStdString());
2172     }
2173     AddFusionImage(index,vecFileNames,vvImageReader::IMAGE);
2174 }
2175 //------------------------------------------------------------------------------
2176
2177 //------------------------------------------------------------------------------
2178 void vvMainWindow::ResetTransformationToIdentity()
2179 {
2180   std::string actorType = DataTree->selectedItems()[0]->data(1,Qt::UserRole).toString().toStdString();
2181   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2182   mSlicerManagers[index]->ResetTransformationToIdentity(actorType);
2183   ImageInfoChanged();
2184 }
2185 //------------------------------------------------------------------------------
2186
2187 //------------------------------------------------------------------------------
2188 void vvMainWindow::AddFusionImage(int index, std::vector<std::string> fileNames, vvImageReader::LoadedImageType type)
2189 {
2190   QString file(fileNames[0].c_str());
2191   if (QFile::exists(file))
2192   {
2193     mInputPathName = itksys::SystemTools::GetFilenamePath(file.toStdString()).c_str();
2194     itk::ImageIOBase::Pointer reader = itk::ImageIOFactory::CreateImageIO(
2195       file.toStdString().c_str(), itk::ImageIOFactory::ReadMode);
2196     reader->SetFileName(fileNames[0].c_str());
2197     reader->ReadImageInformation();
2198     std::string component = reader->GetComponentTypeAsString(reader->GetComponentType());
2199     int dimension = reader->GetNumberOfDimensions();
2200     QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
2201     vvProgressDialog progress("Opening fusion");
2202     qApp->processEvents();
2203
2204     std::string filename = itksys::SystemTools::GetFilenameWithoutExtension(file.toStdString()).c_str();
2205     if (mSlicerManagers[index]->SetFusion(fileNames,dimension, component,type)) {
2206       //create an item in the tree with good settings
2207       QTreeWidgetItem *item = new QTreeWidgetItem();
2208       item->setData(0,Qt::UserRole,file.toStdString().c_str());
2209       item->setData(1,Qt::UserRole,tr("fusion"));
2210       QFileInfo fileinfo(file); //Do not show the path
2211           item->setData(COLUMN_IMAGE_NAME,Qt::DisplayRole,fileinfo.fileName());
2212           item->setToolTip(COLUMN_IMAGE_NAME, mSlicerManagers[index]->GetListOfAbsoluteFilePathInOneString("fusion").c_str());
2213           qApp->processEvents();
2214
2215       for (int j = 1; j <= 4; j++) {
2216         item->setData(j,Qt::CheckStateRole,DataTree->topLevelItem(index)->data(j,Qt::CheckStateRole));
2217       }
2218
2219       //Create the buttons for reload and close
2220       qApp->processEvents();
2221       QTreePushButton* cButton = new QTreePushButton;
2222       cButton->setItem(item);
2223       cButton->setColumn(COLUMN_CLOSE_IMAGE);
2224       cButton->setToolTip(tr("close image"));
2225       cButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/exit.png")));
2226       connect(cButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
2227         this,SLOT(CloseImage(QTreeWidgetItem*, int)));
2228
2229       QTreePushButton* rButton = new QTreePushButton;
2230       rButton->setItem(item);
2231       rButton->setColumn(COLUMN_RELOAD_IMAGE);
2232       rButton->setToolTip(tr("reload image"));
2233       rButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/rotateright.png")));
2234       connect(rButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
2235         this,SLOT(ReloadImage(QTreeWidgetItem*, int)));
2236
2237       DataTree->topLevelItem(index)->setExpanded(1);
2238       DataTree->topLevelItem(index)->addChild(item);
2239       DataTree->setItemWidget(item, COLUMN_CLOSE_IMAGE, cButton);
2240       DataTree->setItemWidget(item, COLUMN_RELOAD_IMAGE, rButton);
2241
2242       //set the id of the image
2243       QString id = DataTree->topLevelItem(index)->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString();
2244       item->setData(COLUMN_IMAGE_NAME,Qt::UserRole,id.toStdString().c_str());
2245       UpdateTree();
2246       qApp->processEvents();
2247       ImageInfoChanged();
2248       QApplication::restoreOverrideCursor();
2249
2250       // Update the display to update, e.g., the sliders
2251       for(int i=0; i<4; i++)
2252         DisplaySliders(index, i);
2253     } else {
2254       QApplication::restoreOverrideCursor();
2255       QString error = "Cannot import the new image.\n";
2256       error += mSlicerManagers[index]->GetLastError().c_str();
2257       QMessageBox::information(this,tr("Problem reading image !"),error);
2258     }
2259     WindowLevelChanged();
2260   }
2261   else
2262     QMessageBox::information(this,tr("Problem reading Fusion !"),"File doesn't exist!");
2263 }
2264 //------------------------------------------------------------------------------
2265 //------------------------------------------------------------------------------
2266 void vvMainWindow::AddLandmarks(int index, std::vector<std::string> files)
2267 {
2268     if (!landmarksPanel->LoadFromFile(files))
2269       QMessageBox::information(this,tr("Problem reading Landmarks !"),"File doesn't exist!");
2270
2271     landmarksPanel->SetCurrentPath(mInputPathName.toStdString());
2272     landmarksPanel->SetCurrentImage(mSlicerManagers[index]->GetFileName().c_str());
2273 }
2274
2275 //------------------------------------------------------------------------------
2276 void vvMainWindow::OpenField()
2277 {
2278   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2279   //check if a vector field has already been added
2280   for (int child = 0; child < DataTree->topLevelItem(index)->childCount(); child++)
2281     if (DataTree->topLevelItem(index)->child(child)->data(1,Qt::UserRole).toString() == "vector") {
2282       QString error = "Cannot add more than one vector field\n";
2283       error += "Please remove first ";
2284       error += DataTree->topLevelItem(index)->child(child)->data(COLUMN_IMAGE_NAME,Qt::DisplayRole).toString();
2285       QMessageBox::information(this,tr("Problem adding vector field!"),error);
2286       return;
2287     }
2288
2289     QString Extensions = "Images ( *.mhd)";
2290     Extensions += ";;Images ( *.mha)";
2291     Extensions += ";;VF Images ( *.vf)";
2292     Extensions += ";;nii Images ( *.nii)";
2293     Extensions += ";;nrrd Images ( *.nrrd)";
2294     Extensions += ";;nhdr Images ( *.nhdr)";
2295     Extensions += ";;All Files (*)";
2296     QString file = QFileDialog::getOpenFileName(this,tr("Load deformation field"),mInputPathName,Extensions);
2297     if (!file.isEmpty())
2298       AddField(file,index);
2299 }
2300 //------------------------------------------------------------------------------
2301
2302
2303 //------------------------------------------------------------------------------
2304 void vvMainWindow::AddFieldEntry(QString filename,int index,bool from_disk)
2305 {
2306   //create an item in the tree with good settings
2307   QTreeWidgetItem *item = new QTreeWidgetItem();
2308   item->setData(0,Qt::UserRole,filename.toStdString().c_str());
2309   item->setData(1,Qt::UserRole,tr("vector"));
2310   QFileInfo fileinfo(filename); //Do not show the path
2311   item->setData(COLUMN_IMAGE_NAME,Qt::DisplayRole,fileinfo.fileName());
2312   item->setToolTip(COLUMN_IMAGE_NAME, mSlicerManagers[index]->GetListOfAbsoluteFilePathInOneString("vector").c_str());
2313   qApp->processEvents();
2314
2315   for (int j = 1; j <= 4; j++) {
2316     item->setData(j,Qt::CheckStateRole,DataTree->topLevelItem(index)->data(j,Qt::CheckStateRole));
2317   }
2318
2319   //Create the buttons for reload and close
2320   qApp->processEvents();
2321   QTreePushButton* cButton = new QTreePushButton;
2322   cButton->setItem(item);
2323   cButton->setColumn(COLUMN_CLOSE_IMAGE);
2324   cButton->setToolTip(tr("close vector field"));
2325   cButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/exit.png")));
2326   connect(cButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
2327     this,SLOT(CloseImage(QTreeWidgetItem*, int)));
2328
2329   QTreePushButton* rButton = new QTreePushButton;
2330   rButton->setItem(item);
2331   rButton->setColumn(COLUMN_RELOAD_IMAGE);
2332   rButton->setToolTip(tr("reload vector field"));
2333   rButton->setEnabled(from_disk);
2334   rButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/rotateright.png")));
2335   connect(rButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
2336     this,SLOT(ReloadImage(QTreeWidgetItem*, int)));
2337
2338   DataTree->topLevelItem(index)->setExpanded(1);
2339   DataTree->topLevelItem(index)->addChild(item);
2340   DataTree->setItemWidget(item, COLUMN_RELOAD_IMAGE, rButton);
2341   DataTree->setItemWidget(item, COLUMN_CLOSE_IMAGE, cButton);
2342
2343   //set the id of the image
2344   QString id = DataTree->topLevelItem(index)->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString();
2345   item->setData(COLUMN_IMAGE_NAME,Qt::UserRole,id.toStdString().c_str());
2346   UpdateTree();
2347   qApp->processEvents();
2348   ImageInfoChanged();
2349   QApplication::restoreOverrideCursor();
2350 }
2351 //------------------------------------------------------------------------------
2352
2353
2354 //------------------------------------------------------------------------------
2355 void vvMainWindow::AddField(vvImage::Pointer vf,QString file,int index)
2356 {
2357   QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
2358   vvSlicerManager* imageManager = mSlicerManagers[index];
2359   if (imageManager->SetVF(vf,file.toStdString())) {
2360     AddFieldEntry(file,index,false);
2361   } else {
2362     QString error = "Cannot import the vector field for this image.\n";
2363     error += imageManager->GetLastError().c_str();
2364     QMessageBox::information(this,tr("Problem reading VF !"),error);
2365   }
2366   QApplication::restoreOverrideCursor();
2367 }
2368 //------------------------------------------------------------------------------
2369
2370
2371 //------------------------------------------------------------------------------
2372 void vvMainWindow::AddField(QString file,int index)
2373 {
2374   if (QFile::exists(file)) {
2375     mInputPathName = itksys::SystemTools::GetFilenamePath(file.toStdString()).c_str();
2376
2377     //init the progress events
2378     QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
2379     vvProgressDialog progress("Opening " + file.toStdString());
2380     qApp->processEvents();
2381
2382     //read the vector and put it in the current mSlicerManager
2383     vvSlicerManager* imageManager = mSlicerManagers[index];
2384     qApp->processEvents();
2385
2386     std::string filename = itksys::SystemTools::GetFilenameWithoutExtension(file.toStdString()).c_str();
2387     if (imageManager->SetVF(file.toStdString())) {
2388       imageManager->Render();
2389       AddFieldEntry(file,index,true);
2390     } else {
2391       QApplication::restoreOverrideCursor();
2392       QString error = "Cannot import the vector field for this image.\n";
2393       error += imageManager->GetLastError().c_str();
2394       QMessageBox::information(this,tr("Problem reading VF !"),error);
2395     }
2396   } else
2397     QMessageBox::information(this,tr("Problem reading VF !"),"File doesn't exist!");
2398
2399 }
2400 //------------------------------------------------------------------------------
2401
2402
2403 //------------------------------------------------------------------------------
2404 void vvMainWindow::SetVFProperty(int subsampling, int scale, int log, int width, double r, double g, double b)
2405 {
2406   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2407   if (mSlicerManagers[index]->GetSlicer(0)->GetVF()) {
2408     for (int i = 0; i < 4; i++) {
2409       mSlicerManagers[index]->GetSlicer(i)->SetVFSubSampling(subsampling);
2410       mSlicerManagers[index]->GetSlicer(i)->SetVFScale(scale);
2411       mSlicerManagers[index]->GetSlicer(i)->SetVFWidth(width);
2412       mSlicerManagers[index]->GetSlicer(i)->SetVFColor(r,g,b);
2413       if (log > 0)
2414         mSlicerManagers[index]->GetSlicer(i)->SetVFLog(1);
2415       else
2416         mSlicerManagers[index]->GetSlicer(i)->SetVFLog(0);
2417     }
2418   }
2419 }
2420 //------------------------------------------------------------------------------
2421
2422
2423 //------------------------------------------------------------------------------
2424 void vvMainWindow::SetOverlayProperty(int color, int linked, double window, double level)
2425 {
2426   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2427   if (mSlicerManagers[index]->GetSlicer(0)->GetOverlay()) {
2428     mSlicerManagers[index]->SetOverlayColor(color);
2429     mSlicerManagers[index]->SetColorMap(0);
2430     mSlicerManagers[index]->SetLinkOverlayWindowLevel(linked);
2431     mSlicerManagers[index]->SetOverlayColorWindow(window);
2432     mSlicerManagers[index]->SetOverlayColorLevel(level);
2433     mSlicerManagers[index]->Render();
2434   }
2435 }
2436 //------------------------------------------------------------------------------
2437
2438 //------------------------------------------------------------------------------
2439 void vvMainWindow::SetFusionProperty(int opacity, int thresOpacity, int colormap,double window, double level, bool showLegend)
2440 {
2441   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2442   if (mSlicerManagers[index]->GetSlicer(0)->GetFusion()) {
2443     mSlicerManagers[index]->SetFusionColorMap(colormap);
2444     mSlicerManagers[index]->SetFusionOpacity(opacity);
2445     mSlicerManagers[index]->SetFusionThresholdOpacity(thresOpacity);
2446     mSlicerManagers[index]->SetFusionWindow(window);
2447     mSlicerManagers[index]->SetFusionLevel(level);
2448     mSlicerManagers[index]->SetFusionShowLegend(showLegend);
2449     mSlicerManagers[index]->SetColorMap(0);
2450     mSlicerManagers[index]->Render();
2451   }
2452 }
2453 //------------------------------------------------------------------------------
2454
2455
2456 //------------------------------------------------------------------------------
2457 void vvMainWindow::SelectFusionSequence()
2458 {
2459   //get the index of the slicer manager of the main sequence (CT)
2460   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2461   //check if one overlay image is already associated
2462   for (int child = 0; child < DataTree->topLevelItem(index)->childCount(); child++)
2463     if ( (DataTree->topLevelItem(index)->child(child)->data(1,Qt::UserRole).toString() == "fusion") ||
2464       (DataTree->topLevelItem(index)->child(child)->data(1,Qt::UserRole).toString() == "fusionSequence") ) {
2465         QString error = "Cannot add more than one compared image\n";
2466         error += "Please remove first ";
2467         error += DataTree->topLevelItem(index)->child(child)->data(COLUMN_IMAGE_NAME,Qt::DisplayRole).toString();
2468         QMessageBox::information(this,tr("Problem adding compared image !"),error);
2469         return;
2470     }
2471
2472     QString Extensions = EXTENSIONS;
2473     Extensions += ";;All Files (*)";
2474     QStringList files = QFileDialog::getOpenFileNames(this,tr("Load Overlay image sequence"),mInputPathName,Extensions);
2475     if (files.isEmpty())
2476       return;
2477
2478     std::vector<std::string> vecFileNames;
2479     for (int i = 0; i < files.size(); i++) {
2480       vecFileNames.push_back(files[i].toStdString());
2481     }
2482
2483     //associate the secondary sequence (US) to the main one
2484     AddFusionSequence(index,vecFileNames,vvImageReader::MERGEDWITHTIME);
2485 }
2486 //------------------------------------------------------------------------------
2487
2488
2489 //------------------------------------------------------------------------------
2490 void vvMainWindow::SelectFusionSequenceCorrespondances() {
2491
2492   //make sure the index is right?
2493   //in the end, I should attach the temporal data to the right sequence!
2494   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2495   //in case the other sequence got selected, make sure we select the primary sequence
2496   if ( (!mSlicerManagers[index]->GetSlicer(0)->GetFusion()) && mSlicerManagers[index]->GetFusionSequenceIndexOfLinkedManager()>=0 ) {
2497     index = mSlicerManagers[index]->GetFusionSequenceIndexOfLinkedManager();
2498   }
2499
2500   //open a dialog box to find a file
2501   //QString Extensions = EXTENSIONS;
2502   QString Extensions = ";;All Files (*)";
2503   QString fileName = QFileDialog::getOpenFileName(this,tr("Load respiratory signal for fused sequence"),mInputPathName,Extensions);
2504   if (fileName.isNull())
2505     return;
2506
2507   //read it as a vector of values
2508   vnl_vector<double> tmpVect;
2509
2510   std::ifstream file;
2511   file.open(fileName.toStdString().c_str());
2512   tmpVect.read_ascii(file);
2513   file.close();
2514
2515   //if compatible with the fused image sequence (number of entries = nb of entries in main sequence + nb of entries in joint sequence), enable the temporalSync
2516   bool signalOK = true;
2517   unsigned nbFrameMain = mSlicerManagers[index]->GetImage()->GetTransform().size();
2518   unsigned nbFrameSecondary = mSlicerManagers[index]->GetFusionSequenceNbFrames();
2519 std::cout<<"nbFrameMain = "<<nbFrameMain<<", nbFrameSecondary= "<<nbFrameSecondary<<", signal size: "<<tmpVect.size()<<std::endl;
2520   std::vector<unsigned> temporalCorrespondances;
2521   if ( tmpVect.size() == nbFrameMain + nbFrameSecondary ) {
2522     for (unsigned i=0 ; i<tmpVect.size() ; i++) {
2523       if (i<nbFrameMain) { //first part of the file: i -> index in secondary seq.
2524         if ( tmpVect(i)<nbFrameSecondary ) temporalCorrespondances.push_back(tmpVect(i));
2525         else { signalOK=false; break; } //pointing outside the secondary sequence...
2526       }
2527       else { //first part of the file -> index in secondary seq.
2528         if ( tmpVect(i)<nbFrameMain ) temporalCorrespondances.push_back(tmpVect(i));
2529         else { signalOK=false; break; } //pointing outside the secondary sequence...
2530       }
2531     }
2532   }
2533   else {signalOK=false;}
2534   if (!signalOK) {//else, send a message to signal the failure...
2535     QString error = "The provided temporal correspondances is invalid - check tooltip.\n";
2536     error += "Ignoring file: " + fileName;
2537     QMessageBox::information(this,tr("Problem adding temporal correspondances!"),error);
2538     return;
2539   }
2540   else {
2541     //for convenience, associate this sequence to both the current slicer manager, and to the linked one
2542     mSlicerManagers[index]->SetFusionSequenceCorrespondances(temporalCorrespondances);
2543     mSlicerManagers[ mSlicerManagers[index]->GetFusionSequenceIndexOfLinkedManager() ]->SetFusionSequenceCorrespondances(temporalCorrespondances);
2544     overlayPanel->enableFusionSequenceTemporalSync();
2545   }
2546
2547 }
2548 //------------------------------------------------------------------------------
2549
2550
2551 //------------------------------------------------------------------------------
2552 //when this function is called index is the slicer manager index corresponding to the main sequence (CT)
2553 //the files behind fileNames points to the data for the secondary sequence
2554 void vvMainWindow::AddFusionSequence(int index, std::vector<std::string> fileNames, vvImageReader::LoadedImageType type)
2555 {
2556   QString file(fileNames[0].c_str());
2557   if (QFile::exists(file))
2558   {
2559     mInputPathName = itksys::SystemTools::GetFilenamePath(file.toStdString()).c_str();
2560     itk::ImageIOBase::Pointer reader = itk::ImageIOFactory::CreateImageIO(
2561       file.toStdString().c_str(), itk::ImageIOFactory::ReadMode);
2562     std::sort (fileNames.begin(), fileNames.end());//make sure the files are sorted.
2563     reader->SetFileName(fileNames[0].c_str());
2564     reader->ReadImageInformation();
2565     std::string component = reader->GetComponentTypeAsString(reader->GetComponentType());
2566     int dimension = reader->GetNumberOfDimensions();
2567     QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
2568     vvProgressDialog progress("Opening " + file.toStdString());
2569     qApp->processEvents();
2570
2571     std::string filename = itksys::SystemTools::GetFilenameWithoutExtension(file.toStdString()).c_str();
2572
2573     if (mSlicerManagers[index]->SetFusionSequence(fileNames,dimension, component,type)) {
2574       //create an item in the tree with good settings
2575       QTreeWidgetItem *item = new QTreeWidgetItem();
2576       item->setData(0,Qt::UserRole,file.toStdString().c_str());
2577       item->setData(1,Qt::UserRole,tr("fusionSequence"));
2578
2579       QFileInfo fileinfo(file); //Do not show the path
2580       item->setData(COLUMN_IMAGE_NAME,Qt::DisplayRole,fileinfo.fileName());
2581       item->setToolTip(COLUMN_IMAGE_NAME, mSlicerManagers[index]->GetListOfAbsoluteFilePathInOneString("fusionSequence").c_str());
2582       qApp->processEvents();
2583       for (int j = 1; j <= 4; j++) {
2584         item->setData(j,Qt::CheckStateRole,DataTree->topLevelItem(index)->data(j,Qt::CheckStateRole));
2585       }
2586
2587       //Create the buttons for reload and close
2588       qApp->processEvents();
2589       QTreePushButton* cButton = new QTreePushButton;
2590       cButton->setItem(item);
2591       cButton->setColumn(COLUMN_CLOSE_IMAGE);
2592       cButton->setToolTip(tr("close image"));
2593       cButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/exit.png")));
2594       connect(cButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
2595         this,SLOT(CloseImage(QTreeWidgetItem*, int)));
2596
2597       QTreePushButton* rButton = new QTreePushButton;
2598       rButton->setItem(item);
2599       rButton->setColumn(COLUMN_RELOAD_IMAGE);
2600       rButton->setToolTip(tr("reload image"));
2601       rButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/rotateright.png")));
2602       connect(rButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
2603         this,SLOT(ReloadImage(QTreeWidgetItem*, int)));
2604
2605       DataTree->topLevelItem(index)->setExpanded(1);
2606       DataTree->topLevelItem(index)->addChild(item);
2607       DataTree->setItemWidget(item, COLUMN_CLOSE_IMAGE, cButton);
2608       DataTree->setItemWidget(item, COLUMN_RELOAD_IMAGE, rButton);
2609
2610       //store the original transform matrix
2611       int indexParent = GetSlicerIndexFromItem( DataTree->topLevelItem(index) );
2612       mSlicerManagers[indexParent]->SetFusionSequenceMainTransformMatrix( mSlicerManagers[indexParent]->GetSlicer(0)->GetImage()->GetTransform()[0]->GetMatrix() );
2613
2614       //set the id of the image
2615       QString id = DataTree->topLevelItem(index)->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString();
2616       item->setData(COLUMN_IMAGE_NAME,Qt::UserRole,id.toStdString().c_str());
2617       UpdateTree();
2618       qApp->processEvents();
2619
2620       //ImageInfoChanged();
2621
2622       QApplication::restoreOverrideCursor();
2623       // Update the display to update, e.g., the sliders
2624       for(int i=0; i<4; i++)
2625         DisplaySliders(index, i);
2626
2627
2628       //This loads the secondary sequence (US) as an independent sequence
2629       LoadImages(fileNames, type);
2630       //reset the transforms to identity
2631       //FIX -- and set the thickness of the US slices to a large value (necessary for visualization purposes...)
2632       double sp_x, sp_y, sp_z;
2633       mSlicerManagers[indexParent]->GetImage()->GetVTKImages()[0]->GetSpacing(sp_x, sp_y, sp_z);
2634       sp_z = std::max(sp_x, std::max(sp_y, sp_z)) + 0.5; //
2635       for (unsigned i=0 ; i<mSlicerManagers.back()->GetImage()->GetTransform().size() ; i++) {
2636         sp_x = mSlicerManagers.back()->GetImage()->GetVTKImages()[i]->GetSpacing()[0];
2637         sp_y = mSlicerManagers.back()->GetImage()->GetVTKImages()[i]->GetSpacing()[1];
2638         mSlicerManagers.back()->GetImage()->GetVTKImages()[i]->SetSpacing( sp_x, sp_y, sp_z);
2639         mSlicerManagers.back()->GetImage()->GetTransform()[i]->Identity();
2640         mSlicerManagers.back()->GetImage()->GetTransform()[i]->Update();
2641       }
2642
2643       //automatically link both images...
2644       AddLink(mSlicerManagers[indexParent]->GetId().c_str(), mSlicerManagers.back()->GetId().c_str(), false);
2645
2646       //tie the main and secondary sequences by raising flags and informing each another of their respective SlicerManager indices
2647       mSlicerManagers[indexParent]->SetFusionSequenceIndexOfLinkedManager(mSlicerManagers.size()-1);
2648       mSlicerManagers[indexParent]->SetFusionSequenceInvolvmentCode(0); //main sequence
2649       mSlicerManagers.back()->SetFusionSequenceIndexOfLinkedManager(indexParent);
2650       mSlicerManagers.back()->SetFusionSequenceInvolvmentCode(1); //secondary sequence
2651       for (unsigned i=0 ; i<4 ; i++) {
2652         mSlicerManagers.back()->GetSlicer(i)->SetFusionSequenceCode(1); //flag the slicers of the secondary sequence
2653       }
2654
2655     } else {
2656       QApplication::restoreOverrideCursor();
2657       QString error = "Cannot import the new image.\n";
2658       error += mSlicerManagers[index]->GetLastError().c_str();
2659       QMessageBox::information(this,tr("Problem reading image !"),error);
2660     }
2661     WindowLevelChanged();
2662     ImageInfoChanged(); //this internally calls WindowLevelChanged...
2663   }
2664   else {
2665     QMessageBox::information(this,tr("Problem reading fusion sequence !"),"File doesn't exist!");
2666     return;
2667   }
2668
2669 }
2670 //------------------------------------------------------------------------------
2671
2672
2673 //------------------------------------------------------------------------------
2674 //fusionSequenceFrameIndex and fusionSequenceNbFrames are relative to the secondary sequence (US)
2675 void vvMainWindow::SetFusionSequenceProperty(int fusionSequenceFrameIndex, bool spatialSyncFlag, unsigned int fusionSequenceNbFrames, bool temporalSyncFlag)
2676 {
2677   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2678
2679   if (!mSlicerManagers[index]->IsInvolvedInFusionSequence()) return;
2680
2681   //check if the focus moved to the linked sequence, and in this case, select the master sequence instead
2682   if (!mSlicerManagers[index]->IsMainSequenceOfFusionSequence()) {
2683     index = mSlicerManagers[index]->GetFusionSequenceIndexOfLinkedManager();
2684   }
2685   int secondaryIndex = mSlicerManagers[index]->GetFusionSequenceIndexOfLinkedManager();
2686   if (secondaryIndex==-1) return; //this should never happen
2687   if ( (!mSlicerManagers[index]->IsMainSequenceOfFusionSequence()) ||
2688     (!mSlicerManagers[secondaryIndex]->IsSecondarySequenceOfFusionSequence()) )
2689   {return;} //this should never happen, raise an exception?
2690
2691   if (mSlicerManagers[index]->GetSlicer(0)->GetFusion()) {
2692
2693     //First, if the spatialSync button is unchecked, then reposition the parent sequence (CT) in its original coordinate frame
2694     if ( (!spatialSyncFlag) && (mSlicerManagers[index]->GetFusionSequenceSpatialSyncFlag()) ) {
2695       for ( unsigned i=0 ; i<mSlicerManagers[index]->GetSlicer(0)->GetImage()->GetTransform().size() ; i++ ) {
2696         mSlicerManagers[index]->GetSlicer(0)->GetImage()->GetTransform()[i]->SetMatrix( mSlicerManagers[index]->GetFusionSequenceMainTransformMatrix() );
2697         mSlicerManagers[index]->GetSlicer(0)->GetImage()->GetTransform()[i]->Update();
2698       }
2699
2700       for (int i=0; i<mSlicerManagers[index]->GetNumberOfSlicers(); i++) {
2701         mSlicerManagers[index]->GetSlicer(i)->ForceUpdateDisplayExtent();
2702         mSlicerManagers[index]->GetSlicer(i)->Render();
2703       }
2704     }
2705
2706     //then, update the property values in the slicer manager
2707     mSlicerManagers[index]->SetFusionSequenceLength(fusionSequenceNbFrames);
2708     mSlicerManagers[index]->SetFusionSequenceSpatialSyncFlag(spatialSyncFlag);
2709     mSlicerManagers[index]->SetFusionSequenceTemporalSyncFlag(temporalSyncFlag);
2710     mSlicerManagers[index]->SetFusionSequenceFrameIndex(fusionSequenceFrameIndex);
2711
2712     //select the right frame of the US sequence
2713     mSlicerManagers[index]->SetFusionSequenceTSlice(fusionSequenceFrameIndex); //here, I should only update the overlayed sequence
2714     mSlicerManagers[secondaryIndex]->SetTSlice(fusionSequenceFrameIndex, false); //this should update the secondary sequence (individual version)
2715
2716     //update the horizontal sliders of the main window
2717     overlayPanel->updateFusionSequenceSliderValueFromWindow(fusionSequenceFrameIndex, false);
2718
2719     if (spatialSyncFlag) { //reslice the CT
2720
2721       if (temporalSyncFlag) { //do the temporal synchronisation
2722         int mainSequenceFrameIndex=0;
2723         //estimate the TSlice to set to the CT
2724         unsigned nbFramesMain = mSlicerManagers[index]->GetImage()->GetTransform().size();
2725         mainSequenceFrameIndex = mSlicerManagers[index]->GetFusionSequenceCorrespondances()[ nbFramesMain + fusionSequenceFrameIndex];
2726         //and set it!
2727         mSlicerManagers[index]->SetTSlice(mainSequenceFrameIndex, false);
2728         //warning, there is a loopback, and modification of the TSlice in main sequence forces an update of the TSlice in secondary, etc...
2729       }
2730
2731
2732       //Set the transform matrix of the parent sequence (typically CT / 4DCT)
2733       vtkSmartPointer<vtkMatrix4x4> tmpMat = vtkSmartPointer<vtkMatrix4x4>::New();
2734       vtkMatrix4x4::Invert( mSlicerManagers[index]->GetFusionSequenceInitialTransformMatrixAtFrame(fusionSequenceFrameIndex), tmpMat );
2735       for ( unsigned i=0 ; i<mSlicerManagers[index]->GetSlicer(0)->GetImage()->GetTransform().size() ; i++ ) {
2736         mSlicerManagers[index]->GetSlicer(0)->GetImage()->GetTransform()[i]->SetMatrix( mSlicerManagers[index]->GetFusionSequenceMainTransformMatrix() );
2737         mSlicerManagers[index]->GetSlicer(0)->GetImage()->GetTransform()[i]->PreMultiply();
2738         mSlicerManagers[index]->GetSlicer(0)->GetImage()->GetTransform()[i]->Concatenate( tmpMat );
2739         mSlicerManagers[index]->GetSlicer(0)->GetImage()->GetTransform()[i]->Update();
2740       }
2741
2742       for (int i=0; i<mSlicerManagers[index]->GetNumberOfSlicers(); i++) {
2743         mSlicerManagers[index]->GetSlicer(i)->ForceUpdateDisplayExtent();
2744         mSlicerManagers[index]->GetSlicer(i)->Render();
2745       }
2746
2747     }
2748
2749   }
2750 }
2751 //------------------------------------------------------------------------------
2752
2753
2754 //------------------------------------------------------------------------------
2755 void vvMainWindow::SaveAs()
2756 {
2757   if (DataTree->selectedItems()[0]->data(1,Qt::UserRole).toString() == "vector") {
2758     QMessageBox::warning(this,tr("Unsupported type"),tr("Sorry, saving a vector field is unsupported for the moment"));
2759     return;
2760   }
2761
2762   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2763   int dimension = mSlicerManagers[index]->GetDimension();
2764   QStringList OutputListeFormat;
2765   OutputListeFormat.clear();
2766   if (dimension == 1) {
2767     OutputListeFormat.push_back(".mhd");
2768     OutputListeFormat.push_back(".mha");
2769   }
2770   if (dimension == 2) {
2771     OutputListeFormat.push_back(".bmp");
2772     OutputListeFormat.push_back(".png");
2773     OutputListeFormat.push_back(".jpeg");
2774     OutputListeFormat.push_back(".tif");
2775     OutputListeFormat.push_back(".mhd");
2776     OutputListeFormat.push_back(".mha");
2777     OutputListeFormat.push_back(".hdr");
2778     OutputListeFormat.push_back(".vox");
2779   } else if (dimension == 3) {
2780     OutputListeFormat.push_back(".mhd");
2781     OutputListeFormat.push_back(".mha");
2782     OutputListeFormat.push_back(".nii");
2783     OutputListeFormat.push_back(".nrrd");
2784     OutputListeFormat.push_back(".nhdr");
2785     OutputListeFormat.push_back(".hdr");
2786     OutputListeFormat.push_back(".vox");
2787   } else if (dimension == 4) {
2788     OutputListeFormat.push_back(".mhd");
2789     OutputListeFormat.push_back(".mha");
2790     OutputListeFormat.push_back(".nii");
2791     OutputListeFormat.push_back(".nrrd");
2792     OutputListeFormat.push_back(".nhdr");
2793   }
2794   QString Extensions = "AllFiles(*.*)";
2795   for (int i = 0; i < OutputListeFormat.count(); i++) {
2796     Extensions += ";;Images ( *";
2797     Extensions += OutputListeFormat[i];
2798     Extensions += ")";
2799   }
2800   QString fileName = QFileDialog::getSaveFileName(this,
2801     tr("Save As"),
2802     mSlicerManagers[index]->GetFileName().c_str(),
2803     Extensions);
2804   if (!fileName.isEmpty()) {
2805     std::string fileformat = itksys::SystemTools::GetFilenameLastExtension(fileName.toStdString());
2806     if (OutputListeFormat.contains(
2807       fileformat.c_str())) {
2808         QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
2809         std::string action = "Saving";
2810         vvProgressDialog progress("Saving "+fileName.toStdString());
2811         qApp->processEvents();
2812         vvImageWriter::Pointer writer = vvImageWriter::New();
2813         writer->SetOutputFileName(fileName.toStdString());
2814         writer->SetInput(mSlicerManagers[index]->GetImage());
2815
2816         // Check on transform and prompt user
2817         writer->SetSaveTransform(false);
2818         bool bId = true;
2819         for(int i=0; i<4; i++)
2820           for(int j=0; j<4; j++) {
2821             // TODO SR and BP: check on the list of transforms and not the first only
2822             double elt = mSlicerManagers[index]->GetImage()->GetTransform()[0]->GetMatrix()->GetElement(i,j);
2823             if(i==j && elt!=1.)
2824               bId = false;
2825             if(i!=j && elt!=0.)
2826               bId = false;
2827           }
2828           if( !bId ) {
2829             QString warning = "The image has an associated linear transform. Do you want to save it along?";
2830             QMessageBox msgBox(QMessageBox::Warning, tr("Save transform"), warning, 0, this);
2831             msgBox.addButton(tr("Yes"), QMessageBox::AcceptRole);
2832             msgBox.addButton(tr("No"), QMessageBox::RejectRole);
2833             if (msgBox.exec() == QMessageBox::AcceptRole)
2834               writer->SetSaveTransform(true);
2835           }
2836
2837           writer->Update();
2838           QApplication::restoreOverrideCursor();
2839           if (writer->GetLastError().size()) {
2840             QString error = "Saving did not succeed\n";
2841             error += writer->GetLastError().c_str();
2842             QMessageBox::information(this,tr("Saving Problem"),error);
2843             SaveAs();
2844           }
2845     } else {
2846       QString error = fileformat.c_str();
2847       if (error.isEmpty())
2848         error += "no file format specified !";
2849       else
2850         error += " format unknown !!!\n";
2851       QMessageBox::information(this,tr("Saving Problem"),error);
2852       SaveAs();
2853     }
2854   }
2855 }
2856 //------------------------------------------------------------------------------
2857
2858 //------------------------------------------------------------------------------
2859 void vvMainWindow::SaveCurrentState()
2860 {
2861   QString Extensions = "XML Files(*.xml)";
2862   QString fileName = QFileDialog::getSaveFileName(this,
2863     tr("Save Current Window State"),
2864     "",
2865     Extensions);
2866
2867   SaveCurrentStateAs(fileName.toStdString());
2868 }
2869 //------------------------------------------------------------------------------
2870
2871 //------------------------------------------------------------------------------
2872 void vvMainWindow::SaveCurrentStateAs(const std::string& stateFile)
2873 {
2874   vvSaveState save_state;
2875   save_state.Run(this, stateFile);
2876 }
2877
2878 //------------------------------------------------------------------------------
2879 void vvMainWindow::ReadSavedState()
2880 {
2881   QString Extensions = "XML Files(*.xml)";
2882   QString fileName = QFileDialog::getOpenFileName(this,
2883     tr("Load Window State"),
2884     "",
2885     Extensions);
2886
2887   ReadSavedStateFile(fileName.toStdString());
2888 }
2889 //------------------------------------------------------------------------------
2890
2891 //------------------------------------------------------------------------------
2892 void vvMainWindow::ReadSavedStateFile(const std::string& stateFile)
2893 {
2894   vvReadState read_state;
2895   read_state.Run(this, stateFile);
2896 }
2897 //------------------------------------------------------------------------------
2898
2899 //------------------------------------------------------------------------------
2900 void vvMainWindow::LinkAllImages()
2901 {
2902   linkPanel->linkAll();
2903 }
2904
2905 //------------------------------------------------------------------------------
2906 void vvMainWindow::AddLink(QString image1,QString image2,bool fromPanel)
2907 {
2908   if (!fromPanel) {
2909     // delegate to linkPanel if call came from elsewhere...
2910     linkPanel->addLinkFromIds(image1, image2);
2911     return;
2912   }
2913
2914   unsigned int sm1 = 0;
2915   unsigned int sm2 = 0;
2916
2917   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
2918     if (image1.toStdString() == mSlicerManagers[i]->GetId()) {
2919       mSlicerManagers[i]->AddLink(image2.toStdString());
2920       sm1 = i;
2921     }
2922     if (image2.toStdString() == mSlicerManagers[i]->GetId()) {
2923       mSlicerManagers[i]->AddLink(image1.toStdString());
2924       sm2 = i;
2925     }
2926   }
2927
2928   if (linkPanel->isLinkAll())   {
2929     emit UpdateLinkedNavigation(mSlicerManagers[sm1]->GetId(), mSlicerManagers[mCurrentPickedImageIndex], mSlicerManagers[mCurrentPickedImageIndex]->GetSlicer(0));
2930     emit UpdateLinkedNavigation(mSlicerManagers[sm2]->GetId(), mSlicerManagers[mCurrentPickedImageIndex], mSlicerManagers[mCurrentPickedImageIndex]->GetSlicer(0));
2931   } else {
2932     emit UpdateLinkedNavigation(mSlicerManagers[sm2]->GetId(), mSlicerManagers[sm1], mSlicerManagers[sm1]->GetSlicer(0));
2933   }
2934 }
2935
2936 //------------------------------------------------------------------------------
2937
2938
2939 //------------------------------------------------------------------------------
2940 void vvMainWindow::RemoveLink(QString image1,QString image2)
2941 {
2942   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
2943     if (image1.toStdString() == mSlicerManagers[i]->GetId()) {
2944       mSlicerManagers[i]->RemoveLink(image2.toStdString());
2945     }
2946     if (image2.toStdString() == mSlicerManagers[i]->GetId()) {
2947       mSlicerManagers[i]->RemoveLink(image1.toStdString());
2948     }
2949   }
2950 }
2951 //------------------------------------------------------------------------------
2952
2953 //------------------------------------------------------------------------------
2954 void vvMainWindow::ChangeImageWithIndexOffset(vvSlicerManager *sm, int slicer, int offset)
2955 {
2956   if(mSlicerManagers.size()==1)
2957     return;
2958
2959   int index = 0;
2960   while(sm != mSlicerManagers[index])
2961     index++;
2962   index = (index+offset+mSlicerManagers.size()) % mSlicerManagers.size();
2963
2964   QTreeWidgetItem* item = GetItemFromSlicerManager(mSlicerManagers[index]);
2965   item->setData(slicer+1,Qt::CheckStateRole,2);         //change checkbox
2966   CurrentImageChanged(mSlicerManagers[index]->GetId()); //select new image
2967   DisplayChanged(item,slicer+1);
2968 }
2969 //------------------------------------------------------------------------------
2970 void vvMainWindow::HorizontalSliderMoved(int value,int column, int slicer_index)
2971 {
2972   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
2973     if (DataTree->topLevelItem(i)->data(column,Qt::CheckStateRole).toInt() > 1) {
2974       //i is the SlicerManager that is in charge of this slicer.
2975       if (mSlicerManagers[i]->IsInvolvedInFusionSequence()) {
2976         //if the slicerManager is involved in a fusionSequence as the secondary sequence, then update the slider position in the overlay panel and everything accordingly
2977         if (mSlicerManagers[i]->IsSecondarySequenceOfFusionSequence()) {
2978           overlayPanel->updateFusionSequenceSliderValueFromWindow(value, true);
2979         }
2980         else { //if this is the primary sequence that has been modified
2981           if (mSlicerManagers[i]->GetFusionSequenceTemporalSyncFlag()) {
2982             //WARNING: for some obscure reason, there are problems when accessing mSlicerManagers[mSlicerManagers[i]->GetFusionSequenceIndexOfLinkedManager()]->GetFusionSequenceFrameIndex();
2983
2984             int estimatedValue=0;
2985             //estimate a corresponding time index for the secondary (US) sequence, and update it accordingly.
2986             estimatedValue = mSlicerManagers[i]->GetFusionSequenceCorrespondances()[ value ];
2987             //TODO: at the moment, there is a loop in TSlice modifications
2988             //modifying sequence 1 causes seq 2 to update, which in turns update seq1...
2989             //I disable control on seq1 at the moment.
2990             //overlayPanel->updateFusionSequenceSliderValueFromWindow(estimatedValue, true);
2991           }
2992         }
2993       }
2994
2995       for (int j = 0; j < 4; j++) {
2996         mSlicerManagers[i]->SetTSliceInSlicer(value,j);
2997       }
2998       mSlicerManagers[i]->GetSlicer(slicer_index)->Render();
2999       break;
3000     }
3001   }
3002 }
3003 //------------------------------------------------------------------------------
3004
3005
3006 //------------------------------------------------------------------------------
3007 void vvMainWindow::NOHorizontalSliderMoved()
3008 {
3009   // if (mCurrentTime == NOHorizontalSlider->value()) return;
3010   HorizontalSliderMoved(NOHorizontalSlider->value(),COLUMN_UL_VIEW,0);
3011   //  mCurrentTime = NOHorizontalSlider->value();
3012 }
3013 //------------------------------------------------------------------------------
3014
3015
3016 //------------------------------------------------------------------------------
3017 void vvMainWindow::NEHorizontalSliderMoved()
3018 {
3019   // if (mCurrentTime == NEHorizontalSlider->value()) return;
3020   HorizontalSliderMoved(NEHorizontalSlider->value(),COLUMN_UR_VIEW,1);
3021   //  mCurrentTime = NEHorizontalSlider->value();
3022 }
3023 //------------------------------------------------------------------------------
3024
3025
3026 //------------------------------------------------------------------------------
3027 void vvMainWindow::SOHorizontalSliderMoved()
3028 {
3029   // if (mCurrentTime == SOHorizontalSlider->value()) return;
3030   HorizontalSliderMoved(SOHorizontalSlider->value(),COLUMN_DL_VIEW,2);
3031   // mCurrentTime = SOHorizontalSlider->value();
3032 }
3033 //------------------------------------------------------------------------------
3034
3035
3036 //------------------------------------------------------------------------------
3037 void vvMainWindow::SEHorizontalSliderMoved()
3038 {
3039   // if (mCurrentTime == SEHorizontalSlider->value()) return;
3040   HorizontalSliderMoved(SEHorizontalSlider->value(),COLUMN_DR_VIEW,3);
3041   // mCurrentTime = SEHorizontalSlider->value();
3042 }
3043 //------------------------------------------------------------------------------
3044
3045 //------------------------------------------------------------------------------
3046 void vvMainWindow::NOVerticalSliderChanged()
3047 {
3048   static int value=-1;
3049   if (value == NOVerticalSlider->value()) return;
3050   else value = NOVerticalSlider->value();
3051   //  int value = NOVerticalSlider->value();
3052   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
3053     if (DataTree->topLevelItem(i)->data(COLUMN_UL_VIEW,Qt::CheckStateRole).toInt() > 1) {
3054       if (mSlicerManagers[i]->GetSlicer(0)->GetSlice() != value) {
3055         mSlicerManagers[i]->GetSlicer(0)->SetSlice(value);
3056         mSlicerManagers[i]->VerticalSliderHasChanged(0, value);
3057
3058         // If nor Update/Render -> slider not work
3059         // only render = ok navigation, but for contour Update needed but slower ?
3060
3061         mSlicerManagers[i]->UpdateSlice(0);  // <-- DS add this. Not too much update ? YES. but needed for ImageContour ...
3062         //mSlicerManagers[i]->GetSlicer(0)->Render(); // <-- DS add this, needed for contour, seems ok ? not too slow ?
3063       }
3064       break;
3065     }
3066   }
3067 }
3068 //------------------------------------------------------------------------------
3069
3070
3071 //------------------------------------------------------------------------------
3072 void vvMainWindow::NEVerticalSliderChanged()
3073 {
3074   static int value=-1;
3075   if (value == NEVerticalSlider->value()) return;
3076   else value = NEVerticalSlider->value();
3077   //  int value = NEVerticalSlider->value();
3078   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
3079     if (DataTree->topLevelItem(i)->data(COLUMN_UR_VIEW,Qt::CheckStateRole).toInt() > 1) {
3080       if (mSlicerManagers[i]->GetSlicer(1)->GetSlice() != value) {
3081         mSlicerManagers[i]->GetSlicer(1)->SetSlice(value);
3082         mSlicerManagers[i]->VerticalSliderHasChanged(1, value);
3083         mSlicerManagers[i]->UpdateSlice(1);
3084         //mSlicerManagers[i]->GetSlicer(1)->Render(); // <-- DS add this, needed for contour, seems ok ? not too slow ?
3085       }
3086       break;
3087     }
3088   }
3089 }
3090 //------------------------------------------------------------------------------
3091
3092
3093 //------------------------------------------------------------------------------
3094 void vvMainWindow::SOVerticalSliderChanged()
3095 {
3096   static int value=-1;
3097   if (value == SOVerticalSlider->value()) return;
3098   else value = SOVerticalSlider->value();
3099   //int value = SOVerticalSlider->value();
3100   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
3101     if (DataTree->topLevelItem(i)->data(COLUMN_DL_VIEW,Qt::CheckStateRole).toInt() > 1) {
3102       if (mSlicerManagers[i]->GetSlicer(2)->GetSlice() != value) {
3103         mSlicerManagers[i]->GetSlicer(2)->SetSlice(value);
3104         mSlicerManagers[i]->VerticalSliderHasChanged(2, value);
3105         mSlicerManagers[i]->UpdateSlice(2);
3106         //mSlicerManagers[i]->GetSlicer(2)->Render(); // <-- DS add this, needed for contour, seems ok ? not too slow ?
3107       }
3108       // else { DD("avoid SOVerticalSlider slicer update"); }
3109       break;
3110     }
3111   }
3112 }
3113 //------------------------------------------------------------------------------
3114
3115
3116 //------------------------------------------------------------------------------
3117 void vvMainWindow::SEVerticalSliderChanged()
3118 {
3119   static int value=-1;
3120   if (value == SEVerticalSlider->value()) return;
3121   else value = SEVerticalSlider->value();
3122   // int value = SEVerticalSlider->value();
3123   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
3124     if (DataTree->topLevelItem(i)->data(COLUMN_DR_VIEW,Qt::CheckStateRole).toInt() > 1) {
3125       if (mSlicerManagers[i]->GetSlicer(3)->GetSlice() != value) {
3126         mSlicerManagers[i]->GetSlicer(3)->SetSlice(value);
3127         mSlicerManagers[i]->VerticalSliderHasChanged(3, value);
3128         mSlicerManagers[i]->UpdateSlice(3);
3129         //mSlicerManagers[i]->GetSlicer(3)->Render(); // <-- DS add this, needed for contour, seems ok ? not too slow ?
3130       }
3131       break;
3132     }
3133   }
3134 }
3135 //------------------------------------------------------------------------------
3136
3137
3138 //------------------------------------------------------------------------------
3139 void vvMainWindow::UpdateSlice(int slicer, int slice)
3140 {
3141   // DD("vvMainWindow::UpdateSlice");
3142   //   DD(slicer);
3143   //   DD(slice);
3144   if (slicer == 0) {
3145     //    if (slice != NOVerticalSlider->value())
3146     NOVerticalSlider->setValue(slice);
3147   } else {
3148     if (slicer == 1)
3149       NEVerticalSlider->setValue(slice);
3150     else {
3151       if (slicer == 2)
3152         SOVerticalSlider->setValue(slice);
3153       else {
3154         if (slicer == 3)
3155           SEVerticalSlider->setValue(slice);
3156       }
3157     }
3158   }
3159   // DD("vvMainWindow:UpdateSlice END");
3160 }
3161 //------------------------------------------------------------------------------
3162
3163
3164 //------------------------------------------------------------------------------
3165 void vvMainWindow::UpdateTSlice(int slicer, int slice, int code)
3166 {
3167   //FusionSequence: the slider value should be updated for slicers which show the same sequence as requested
3168   bool doUpdate=false;
3169   if (code==-1) doUpdate=true;
3170   else {
3171     for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
3172       if (DataTree->topLevelItem(i)->data(slicer+1,Qt::CheckStateRole).toInt() > 1) {
3173         //i is the active SlicerManager
3174         if (mSlicerManagers[i]->GetFusionSequenceInvolvmentCode()==code) doUpdate=true;
3175         break;
3176       }
3177     }
3178   }
3179   if (!doUpdate) return;
3180
3181   switch (slicer) {
3182   case 0:
3183     if (NOHorizontalSlider->value()==slice) return;
3184     NOHorizontalSlider->setValue(slice);
3185     break;
3186   case 1:
3187     if (NEHorizontalSlider->value()==slice) return;
3188     NEHorizontalSlider->setValue(slice);
3189     break;
3190   case 2:
3191     if (SOHorizontalSlider->value()==slice) return;
3192     SOHorizontalSlider->setValue(slice);
3193     break;
3194   case 3:
3195     if (SEHorizontalSlider->value()==slice) return;
3196     SEHorizontalSlider->setValue(slice);
3197     break;
3198   }
3199 }
3200 //------------------------------------------------------------------------------
3201
3202
3203 //------------------------------------------------------------------------------
3204 void vvMainWindow::UpdateSliceRange(int slicer, int min, int max, int tmin, int tmax)
3205 {
3206   //int position = int((min+max)/2);
3207   int position = mSlicerManagers[mCurrentPickedImageIndex]->GetSlicer(slicer)->GetSlice();
3208   if (slicer == 0) {
3209     NOVerticalSlider->setRange(min,max);
3210     NOHorizontalSlider->setRange(tmin,tmax);
3211     NOVerticalSlider->setValue(position);
3212   } else if (slicer == 1) {
3213     NEVerticalSlider->setRange(min,max);
3214     NEHorizontalSlider->setRange(tmin,tmax);
3215     NEVerticalSlider->setValue(position);
3216   } else if (slicer == 2) {
3217     SOVerticalSlider->setRange(min,max);
3218     SOHorizontalSlider->setRange(tmin,tmax);
3219     SOVerticalSlider->setValue(position);
3220   } else if (slicer == 3) {
3221     SEVerticalSlider->setRange(min,max);
3222     SEHorizontalSlider->setRange(tmin,tmax);
3223     SEVerticalSlider->setValue(position);
3224   }
3225 }
3226 //------------------------------------------------------------------------------
3227
3228
3229 //------------------------------------------------------------------------------
3230 void vvMainWindow::SaveNOScreenshot()
3231 {
3232   SaveScreenshot(NOViewWidget);
3233 }
3234 //------------------------------------------------------------------------------
3235
3236
3237 //------------------------------------------------------------------------------
3238 void vvMainWindow::SaveNEScreenshot()
3239 {
3240   SaveScreenshot(NEViewWidget);
3241 }
3242 //------------------------------------------------------------------------------
3243
3244
3245 //------------------------------------------------------------------------------
3246 void vvMainWindow::SaveSOScreenshot()
3247 {
3248   SaveScreenshot(SOViewWidget);
3249 }
3250 //------------------------------------------------------------------------------
3251
3252
3253 //------------------------------------------------------------------------------
3254 void vvMainWindow::SaveSEScreenshot()
3255 {
3256   SaveScreenshot(SEViewWidget);
3257 }
3258 //------------------------------------------------------------------------------
3259
3260
3261 //------------------------------------------------------------------------------
3262 void vvMainWindow::SaveScreenshotAllSlices()
3263 {
3264   QVTKWidget *widget = NOViewWidget;
3265
3266   int index = 0;// GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
3267   vvSlicerManager * SM = mSlicerManagers[index];
3268   vvImage * image = SM->GetImage();
3269   vvSlicer * slicer = SM->GetSlicer(0);
3270   int orientation = slicer->GetOrientation();
3271   int nbSlices = image->GetSize()[orientation];
3272   vtkSmartPointer<vtkRenderWindow>  renderWindow = widget->GetRenderWindow();
3273
3274   // Select filename base
3275   QString filename = QFileDialog::getSaveFileName(this,
3276     tr("Save As (filename will be completed by slice number)"),
3277     itksys::SystemTools::GetFilenamePath(mSlicerManagers[index]->GetFileName()).c_str(),
3278     "Images( *.png);;Images( *.jpg)");
3279
3280   // Loop on slices
3281   for(int i=0; i<nbSlices; i++) {
3282     // Change the slice
3283     slicer->SetSlice(i); // -> change the slice of the current slicer
3284     SM->UpdateSlice(0); // --> this one emit UpdateSlice
3285     QCoreApplication::flush(); // -> needed to force display of contours
3286
3287     // Screenshot
3288     vtkSmartPointer<vtkWindowToImageFilter> windowToImageFilter = vtkSmartPointer<vtkWindowToImageFilter>::New();
3289     windowToImageFilter->SetInput(renderWindow);
3290     windowToImageFilter->SetMagnification(1);
3291     windowToImageFilter->SetInputBufferTypeToRGBA(); //also record the alpha (transparency) channel
3292     windowToImageFilter->Update();
3293
3294     vtkSmartPointer<vtkPNGWriter> writer = vtkSmartPointer<vtkPNGWriter>::New();
3295     std::string fn = itksys::SystemTools::GetFilenameWithoutLastExtension(filename.toStdString());
3296     std::string num = clitk::toString(i);
3297     if (i<10) num = "0"+num;
3298     if (i<100) num = "0"+num;
3299     if (i<1000) num = "0"+num;
3300
3301     fn = itksys::SystemTools::GetFilenamePath(filename.toStdString()) + "/"+ fn
3302       + "_" + num + itksys::SystemTools::GetFilenameLastExtension(filename.toStdString());
3303     writer->SetFileName(fn.c_str());
3304     writer->SetInput(windowToImageFilter->GetOutput());
3305     writer->Write();
3306   }
3307 }
3308 //------------------------------------------------------------------------------
3309
3310
3311 //------------------------------------------------------------------------------
3312 void vvMainWindow::SaveScreenshot(QVTKWidget *widget)
3313 {
3314   QString Extensions = "Images( *.png);;";
3315   Extensions += "Images( *.jpg);;";
3316   Extensions += "Images( *.bmp);;";
3317   Extensions += "Images( *.tif);;";
3318   Extensions += "Images( *.ppm)";
3319 #if defined(VTK_USE_FFMPEG_ENCODER) || defined(VTK_USE_VIDEO_FOR_WINDOWS)
3320   Extensions += ";;Video( *.avi)";
3321 #endif
3322 #ifdef VTK_USE_MPEG2_ENCODER
3323   Extensions += ";;Video( *.mpg)";
3324 #endif
3325 #ifdef CLITK_EXPERIMENTAL
3326   Extensions += ";;Video( *.gif)";
3327 #endif
3328
3329   int smIndex=GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
3330   QString fileName = QFileDialog::getSaveFileName(this,
3331     tr("Save As"),
3332     itksys::SystemTools::GetFilenamePath(mSlicerManagers[smIndex]->GetFileName()).c_str(),
3333     Extensions);
3334
3335   if (!fileName.isEmpty()) {
3336     vtkSmartPointer<vtkWindowToImageFilter> w2i = vtkSmartPointer<vtkWindowToImageFilter>::New();
3337     w2i->SetInput(widget->GetRenderWindow());
3338     w2i->Update();
3339     vtkImageData *image = w2i->GetOutput();
3340
3341     std::string ext(itksys::SystemTools::GetFilenameLastExtension(fileName.toStdString()));
3342
3343     // Image
3344     vtkImageWriter *imgwriter = NULL;
3345     if (ext==".bmp")
3346       imgwriter = vtkBMPWriter::New();
3347     else if (ext==".tif")
3348       imgwriter = vtkTIFFWriter::New();
3349     else if (ext==".ppm")
3350       imgwriter = vtkPNMWriter::New();
3351     else if (ext==".png")
3352       imgwriter = vtkPNGWriter::New();
3353     else if (ext==".jpg")
3354       imgwriter = vtkJPEGWriter::New();
3355
3356     // Snapshot image if not null
3357     if(imgwriter!=NULL) {
3358       imgwriter->SetInput(image);
3359       imgwriter->SetFileName(fileName.toStdString().c_str());
3360       imgwriter->Write();
3361       return;
3362     }
3363
3364     // Video
3365     vtkGenericMovieWriter *vidwriter = NULL;
3366 #if CLITK_EXPERIMENTAL == 1
3367     if (ext==".gif") {
3368       vvAnimatedGIFWriter *gif = vvAnimatedGIFWriter::New();
3369       vidwriter = gif;
3370
3371       // FPS
3372       bool ok;
3373       int fps = QInputDialog::getInteger(this, tr("Number of frames per second"),
3374         tr("FPS:"), 5, 0, 1000, 1, &ok);
3375       if(ok)
3376         gif->SetRate(fps);
3377
3378       // Loops
3379       int loops = QInputDialog::getInteger(this, tr("Loops"),
3380         tr("Number of loops (0 means infinite):"), 0, 0, 1000000000, 1, &ok);
3381       if(ok)
3382         gif->SetLoops(loops);
3383
3384       // Dithering
3385       QString msg = "Would you like to activate dithering?";
3386       QMessageBox msgBox(QMessageBox::Question, tr("Dithering"),msg, 0, this);
3387       msgBox.addButton(tr("Yes"), QMessageBox::AcceptRole);
3388       msgBox.addButton(tr("No"), QMessageBox::RejectRole);
3389       gif->SetDither(msgBox.exec() == QMessageBox::AcceptRole);
3390     }
3391 #endif
3392 #ifdef VTK_USE_VIDEO_FOR_WINDOWS
3393     if (ext==".avi") {
3394       vtkAVIWriter *mpg = vtkAVIWriter::New();
3395       vidwriter = mpg;
3396       mpg->SetQuality(2);
3397       bool ok;
3398       int fps = QInputDialog::getInteger(this, tr("Number of frames per second"),
3399         tr("FPS:"), 5, 0, 1024, 1, &ok);
3400       if(!ok)
3401         fps = 5;
3402       mpg->SetRate(fps);
3403     }
3404 #endif
3405 #ifdef VTK_USE_FFMPEG_ENCODER
3406     if (ext==".avi") {
3407       vtkFFMPEGWriter *mpg = vtkFFMPEGWriter::New();
3408       vidwriter = mpg;
3409       mpg->SetQuality(2);
3410       bool ok;
3411       int fps = QInputDialog::getInteger(this, tr("Number of frames per second"),
3412         tr("FPS:"), 5, 0, 1024, 1, &ok);
3413       if(!ok)
3414         fps = 5;
3415       mpg->SetRate(fps);
3416       mpg->SetBitRateTolerance(int(ceil(12.0*1024*1024/fps)));
3417     }
3418 #endif
3419 #ifdef VTK_USE_MPEG2_ENCODER
3420     if (ext==".mpg") {
3421       vtkMPEG2Writer *mpg = vtkMPEG2Writer::New();
3422       vidwriter = mpg;
3423     }
3424 #endif
3425
3426     // Take video if not null
3427     if(vidwriter!=NULL){
3428       vidwriter->SetInput(image);
3429       vidwriter->SetFileName(fileName.toStdString().c_str());
3430       vidwriter->Start();
3431       int nSlice = mSlicerManagers[smIndex]->GetSlicer(0)->GetTMax();
3432       for(int i=0; i<=nSlice; i++) {
3433         mSlicerManagers[smIndex]->SetNextTSlice(0);
3434         vtkSmartPointer<vtkWindowToImageFilter> w2i = vtkSmartPointer<vtkWindowToImageFilter>::New();
3435         w2i->SetInput(widget->GetRenderWindow());
3436         w2i->Update();
3437         vidwriter->SetInput(w2i->GetOutput());
3438         vidwriter->Write();
3439       }
3440       vidwriter->End();
3441       vidwriter->Delete();
3442       return;
3443     }
3444
3445     QMessageBox::information(this,tr("Problem saving screenshot !"),tr("Cannot save image.\nPlease set a file extension !!!"));
3446   }
3447 }
3448 //------------------------------------------------------------------------------
3449
3450
3451 //------------------------------------------------------------------------------
3452 void vvMainWindow::GoToCursor()
3453 {
3454   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
3455   for (int column = 1; column < 5; column++) {
3456     if (DataTree->selectedItems()[0]->data(column,Qt::CheckStateRole).toInt() > 1) {
3457       double* cursorPos = mSlicerManagers[index]->GetSlicer(column-1)->GetCursorPosition();
3458       mSlicerManagers[index]->GetSlicer(column-1)->SetCurrentPosition(
3459         cursorPos[0],cursorPos[1],cursorPos[2],cursorPos[3]);
3460       mSlicerManagers[index]->UpdateViews(1,column-1);
3461       mSlicerManagers[index]->UpdateLinked(column-1);
3462       break;
3463     }
3464   }
3465 }
3466 //------------------------------------------------------------------------------
3467
3468 //------------------------------------------------------------------------------
3469 void vvMainWindow::GoToLandmark()
3470 {
3471   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
3472   for (int column = 1; column < 5; column++) {
3473     if (DataTree->selectedItems()[0]->data(column,Qt::CheckStateRole).toInt() > 1) {
3474       double* cursorPos = landmarksPanel->GetSelectedPoint();
3475       mSlicerManagers[index]->GetSlicer(column-1)->SetCurrentPosition(
3476         cursorPos[0],cursorPos[1],cursorPos[2],cursorPos[3]);
3477       mSlicerManagers[index]->UpdateViews(1,column-1);
3478       mSlicerManagers[index]->UpdateLinked(column-1);
3479       break;
3480     }
3481   }
3482 }
3483 //------------------------------------------------------------------------------
3484
3485 //------------------------------------------------------------------------------
3486 void vvMainWindow::PlayPause()
3487 {
3488   if (playMode) {
3489     playMode = 0;
3490     playButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/player_play.png")));
3491     ImageInfoChanged();
3492     return;
3493   } else {
3494     int image_number=DataTree->topLevelItemCount();
3495     bool has_temporal;
3496     for (int i=0; i<image_number; i++)
3497       if (mSlicerManagers[i]->GetSlicer(0)->GetTMax() > 0) {
3498         has_temporal=true;
3499         break;
3500       }
3501       if (has_temporal) {
3502         playMode = 1;
3503         playButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/player_pause.png")));
3504         QTimer::singleShot(1000/mFrameRate, this, SLOT(PlayNext()));
3505       }
3506   }
3507 }
3508 //------------------------------------------------------------------------------
3509
3510 //------------------------------------------------------------------------------
3511 void vvMainWindow::PlayNext()
3512 {
3513   if (playMode && !this->isHidden()) {
3514     int image_number=DataTree->topLevelItemCount();
3515     ///Only play one slicer per SM, and only if the SM is being displayed
3516     for (int i=0; i<image_number; i++)
3517       for (int j=0; j<4; j++)
3518         if (mSlicerManagers[i]->GetSlicer(0)->GetTMax() > 0 &&
3519           DataTree->topLevelItem(i)->data(j+1,Qt::CheckStateRole).toInt() > 0) {
3520             mSlicerManagers[i]->SetNextTSlice(j);
3521             break;
3522         }
3523         QTimer::singleShot(1000/mFrameRate, this, SLOT(PlayNext()));
3524   }
3525 }
3526 //------------------------------------------------------------------------------
3527
3528 void vvMainWindow::ShowLastImage()
3529 {
3530   if (mSlicerManagers.size() > 1) {
3531     QTreeWidgetItem * item=DataTree->topLevelItem(DataTree->topLevelItemCount()-1);
3532     CurrentImageChanged(mSlicerManagers.back()->GetId()); //select new image
3533     item->setData(1,Qt::CheckStateRole,2); //show the new image in the first panel
3534     DisplayChanged(item,1);
3535   }
3536 }
3537
3538 //------------------------------------------------------------------------------
3539 void vvMainWindow::UpdateRenderWindows()
3540 {
3541   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
3542     mSlicerManagers[i]->GetSlicer(0)->UpdateLandmarks();
3543     mSlicerManagers[i]->GetSlicer(1)->UpdateLandmarks();
3544     mSlicerManagers[i]->GetSlicer(2)->UpdateLandmarks();
3545     mSlicerManagers[i]->GetSlicer(3)->UpdateLandmarks();
3546   }
3547   if (NOViewWidget->GetRenderWindow()) NOViewWidget->GetRenderWindow()->Render();
3548   if (NEViewWidget->GetRenderWindow()) NEViewWidget->GetRenderWindow()->Render();
3549   if (SOViewWidget->GetRenderWindow()) SOViewWidget->GetRenderWindow()->Render();
3550   if (SEViewWidget->GetRenderWindow()) SEViewWidget->GetRenderWindow()->Render();
3551 }
3552 //------------------------------------------------------------------------------
3553
3554 //------------------------------------------------------------------------------
3555 void vvMainWindow::SegmentationOnCurrentImage()
3556 {
3557   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
3558
3559   vvSegmentationDialog segmentation;
3560   segmentation.SetImage(mSlicerManagers[index]->GetSlicer(0)->GetImage());
3561   segmentation.exec();
3562 }
3563 //------------------------------------------------------------------------------
3564
3565 void vvMainWindow::SurfaceViewerLaunch()
3566 {
3567   vvSurfaceViewerDialog surfaceViewer;
3568   surfaceViewer.exec();
3569 }
3570 //------------------------------------------------------------------------------
3571
3572
3573 //------------------------------------------------------------------------------
3574 int vvMainWindow::GetImageDuplicateFilenameNumber(std::string filename)
3575 {
3576   int number=0;
3577   for(unsigned int l=0; l<mSlicerManagers.size(); l++) {
3578     vvSlicerManager * v = mSlicerManagers[l];
3579     if (v->GetBaseFileName() ==
3580       vtksys::SystemTools::GetFilenameName(vtksys::SystemTools::GetFilenameWithoutLastExtension(filename))) {
3581         number = std::max(number, v->GetBaseFileNameNumber()+1);
3582     }
3583   }
3584   return number;
3585 }
3586 //------------------------------------------------------------------------------
3587
3588
3589 //------------------------------------------------------------------------------
3590 vvSlicerManager* vvMainWindow::AddImage(vvImage::Pointer image,std::string filename)
3591 {
3592   // Change filename if another image exist with the same name
3593   int number = GetImageDuplicateFilenameNumber(filename);
3594
3595   // Create new SliceManager
3596   vvSlicerManager* slicer_manager = new vvSlicerManager(4);
3597   slicer_manager->SetImage(image);//, IMAGE, number);
3598   //  filename = filename+"_"+clitk::toString(number);
3599   slicer_manager->SetFilename(filename, number);
3600   mSlicerManagers.push_back(slicer_manager);
3601
3602   //create an item in the tree with good settings
3603   QTreeWidgetItem *item = new QTreeWidgetItem();
3604   item->setData(0,Qt::UserRole,slicer_manager->GetFileName().c_str());//files[i].c_str());
3605   item->setData(1,Qt::UserRole,tr("image"));
3606   item->setData(COLUMN_IMAGE_NAME,Qt::DisplayRole,slicer_manager->GetFileName().c_str());//filename.c_str());
3607   qApp->processEvents();
3608
3609   for (int j = 1; j <= 4; j++) item->setData(j,Qt::CheckStateRole,1);
3610
3611   //Create the buttons for reload and close
3612   qApp->processEvents();
3613   QTreePushButton* cButton = new QTreePushButton;
3614   cButton->setItem(item);
3615   cButton->setColumn(COLUMN_CLOSE_IMAGE);
3616   cButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/exit.png")));
3617   connect(cButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
3618     this,SLOT(CloseImage(QTreeWidgetItem*, int)));
3619
3620   QTreePushButton* rButton = new QTreePushButton;
3621   rButton->setItem(item);
3622   rButton->setColumn(COLUMN_RELOAD_IMAGE);
3623   rButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/rotateright.png")));
3624   rButton->setEnabled(0);
3625   connect(rButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
3626     this,SLOT(ReloadImage(QTreeWidgetItem*, int)));
3627
3628   DataTree->addTopLevelItem(item);
3629   DataTree->setItemWidget(item, COLUMN_CLOSE_IMAGE, cButton);
3630   DataTree->setItemWidget(item, COLUMN_RELOAD_IMAGE, rButton);
3631
3632   //set the id of the image
3633   QString id = QDir::current().absoluteFilePath(slicer_manager->GetFileName().c_str()) + QString::number(mSlicerManagers.size()-1);
3634   item->setData(COLUMN_IMAGE_NAME,Qt::UserRole,id.toStdString().c_str());
3635   mSlicerManagers.back()->SetId(id.toStdString());
3636
3637   linkPanel->addImage(slicer_manager->GetFileName().c_str()// filename
3638     , id.toStdString());
3639
3640   connect(mSlicerManagers.back(), SIGNAL(currentImageChanged(std::string)),
3641     this, SLOT(CurrentImageChanged(std::string)));
3642   connect(mSlicerManagers.back(), SIGNAL(currentPickedImageChanged(std::string)),
3643     this, SLOT(CurrentPickedImageChanged(std::string)));
3644   connect(mSlicerManagers.back(), SIGNAL(UpdatePosition(int, double, double, double, double, double, double, double)),
3645     this, SLOT(MousePositionChanged(int,double, double, double, double, double, double, double)));
3646   connect(mSlicerManagers.back(), SIGNAL(UpdateVector(int, double, double, double, double)),
3647     this, SLOT(VectorChanged(int,double,double,double, double)));
3648   connect(mSlicerManagers.back(), SIGNAL(UpdateOverlay(int, double, double)),
3649     this, SLOT(OverlayChanged(int,double,double)));
3650   connect(mSlicerManagers.back(), SIGNAL(UpdateFusion(int, double)),
3651     this, SLOT(FusionChanged(int,double)));
3652   //connect(mSlicerManagers.back(), SIGNAL(UpdateFusionSequence(int, bool, unsigned int)),
3653   //  this, SLOT(FusionSequenceChanged(int, bool, unsigned int)));
3654   connect(mSlicerManagers.back(), SIGNAL(WindowLevelChanged()),
3655     this,SLOT(WindowLevelChanged()));
3656   connect(mSlicerManagers.back(), SIGNAL(UpdateSlice(int,int)),
3657     this,SLOT(UpdateSlice(int,int)));
3658   connect(mSlicerManagers.back(), SIGNAL(UpdateTSlice(int, int, int)),
3659     this,SLOT(UpdateTSlice(int, int, int)));
3660   connect(mSlicerManagers.back(), SIGNAL(UpdateTSlice(int, int, int)),
3661     this,SLOT(ImageInfoChanged()));
3662   connect(mSlicerManagers.back(), SIGNAL(UpdateSliceRange(int,int,int,int,int)),
3663     this,SLOT(UpdateSliceRange(int,int,int,int,int)));
3664   connect(mSlicerManagers.back(), SIGNAL(UpdateLinkManager(std::string,int,double,double,double,int)),
3665     this,SLOT(UpdateLinkManager(std::string,int,double,double,double,int)));
3666   connect(mSlicerManagers.back(), SIGNAL(UpdateLinkedNavigation(std::string,vvSlicerManager*,vvSlicer*)),
3667     this,SLOT(UpdateLinkedNavigation(std::string,vvSlicerManager*,vvSlicer*)));
3668   connect(mSlicerManagers.back(), SIGNAL(ChangeImageWithIndexOffset(vvSlicerManager*,int,int)),
3669     this,SLOT(ChangeImageWithIndexOffset(vvSlicerManager*,int,int)));
3670   connect(mSlicerManagers.back(), SIGNAL(LandmarkAdded()),landmarksPanel,SLOT(AddPoint()));
3671
3672
3673   UpdateTree();
3674   qApp->processEvents();
3675   InitSlicers();
3676   ShowLastImage();
3677   InitDisplay();
3678   qApp->processEvents();
3679
3680   // End
3681   ImageInfoChanged();
3682   return slicer_manager;
3683 }
3684 //------------------------------------------------------------------------------
3685
3686
3687 //------------------------------------------------------------------------------
3688 void vvMainWindow::UpdateCurrentSlicer()
3689 {
3690   int index = -1;
3691   if (DataTree->selectedItems().size() > 0) {
3692     index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
3693   }
3694   mSlicerManagerCurrentIndex = index;
3695 }
3696 //------------------------------------------------------------------------------
3697