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 #ifdef CLITK_USE_SYSTEM_GDCM
  51 #include "vvQPacsConnection.h"
  52 #endif
  53 #include "clitkConfiguration.h"
  54
  55 // ITK include
  56 #include <itkImage.h>
  57 #include <itkImageFileReader.h>
  58 #include <itkByteSwapper.h>
  59 #include <itkCommand.h>
  60 #include <itkNumericSeriesFileNames.h>
  61
  62 // VTK include
  63 #include <vtkImageData.h>
  64 #include <vtkImageActor.h>
  65 #include <vtkCornerAnnotation.h>
  66 #include <vtkRenderWindow.h>
  67 #include <vtkRenderWindowInteractor.h>
  68 #include <vtkRenderer.h>
  69 #include <vtkRendererCollection.h>
  70 #include <vtkWindowToImageFilter.h>
  71 #include <vtkBMPWriter.h>
  72 #include <vtkTIFFWriter.h>
  73 #include <vtkPNMWriter.h>
  74 #include <vtkPNGWriter.h>
  75 #include <vtkJPEGWriter.h>
  76 #include <vtkGenericMovieWriter.h>
  77 #ifdef CLITK_EXPERIMENTAL
  78 #  include <vvAnimatedGIFWriter.h>
  79 #endif
  80 #ifdef VTK_USE_VIDEO_FOR_WINDOWS
  81 #  include <vtkAVIWriter.h>
  82 #endif
  83 #ifdef VTK_USE_FFMPEG_ENCODER
  84 #  include <vtkFFMPEGWriter.h>
  85 #endif
  86 #ifdef VTK_USE_MPEG2_ENCODER
  87 #  include <vtkMPEG2Writer.h>
  88 #endif
  89 #include <vtkMatrix4x4.h>
  90 #include <vtkTransform.h>
  91
  92 // Standard includes
  93 #include <iostream>
  94 #include <fstream>
  95 #include <sstream>
  96 #include <iomanip>
  97
  98 #define COLUMN_TREE 0
  99 #define COLUMN_UL_VIEW 1
 100 #define COLUMN_UR_VIEW 2
 101 #define COLUMN_DL_VIEW 3
 102 #define COLUMN_DR_VIEW 4
 103 #define COLUMN_CLOSE_IMAGE 5
 104 #define COLUMN_RELOAD_IMAGE 6
 105 #define COLUMN_IMAGE_NAME 7
 106
 107 #ifdef CLITK_PRIVATE_FEATURES
 108 #define EXTENSIONS "Images ( *.bmp *.png *.jpeg *.jpg *.tif *.mhd *.mha *.hdr *.vox *.his *.xdr *.SCAN *.nii *.nrrd *.nhdr *.refscan *.nii.gz *.usf *.svl)"
 109 #else
 110 #define EXTENSIONS "Images ( *.bmp *.png *.jpeg *.jpg *.tif *.mhd *.mha *.hdr *.vox *.his *.xdr *.SCAN *.nii *.nrrd *.nhdr *.refscan *.nii.gz)"
 111 #endif
 112
 113
 114 /*Data Tree values
 115 0,Qt::UserRole full filename
 116 1,Qt::CheckStateRole checkbutton UL View
 117 1,Qt::UserRole overlay, fusion or vector
 118 2,Qt::CheckStateRole checkbutton UR View
 119 3,Qt::CheckStateRole checkbutton DL View
 120 4,Qt::CheckStateRole checkbutton DR View
 121 5,0  short filename
 122 5,Qt::UserRole mSlicerManager id*/
 123
 124 //------------------------------------------------------------------------------
 125 vvMainWindow::vvMainWindow():vvMainWindowBase()
 126 {
 127   setupUi(this); // this sets up the GUI
 128   setDicomClient();
 129   mInputPathName = "";
 130   mMenuTools = menuTools;
 131   //  mMenuSegmentation = menuSegmentation;
 132   mContextMenu = &contextMenu;
 133   mMenuExperimentalTools = menuExperimental;
 134   mMainWidget = this;
 135   mCurrentTime = -1;
 136   mCurrentSelectedImageId = "";
 137   mCurrentPickedImageId = "";
 138   mCurrentPickedImageIndex = 0;
 139
 140   //Init the contextMenu
 141   this->setContextMenuPolicy(Qt::CustomContextMenu);
 142   contextActions.resize(0);
 143   QAction* actionOpen_new_image = contextMenu.addAction(QIcon(QString::fromUtf8(":/common/icons/fileopen.png")),
 144     tr("O&pen new Image"));
 145   actionOpen_new_image->setShortcut(QKeySequence(tr("Ctrl+O")));
 146   connect(actionOpen_new_image,SIGNAL(triggered()),this,SLOT(OpenImages()));
 147   contextActions.push_back(actionOpen_new_image);
 148   contextMenu.addSeparator();
 149
 150   QAction* actionClose_Image = contextMenu.addAction(QIcon(QString::fromUtf8(":/common/icons/exit.png")),
 151     tr("Close Current Image"));
 152   connect(actionClose_Image,SIGNAL(triggered()),this,SLOT(CloseImage()));
 153   contextActions.push_back(actionClose_Image);
 154
 155   QAction* actionReload_image = contextMenu.addAction(QIcon(QString::fromUtf8(":/common/icons/rotateright.png")),
 156     tr("Reload Current Image"));
 157   connect(actionReload_image,SIGNAL(triggered()),this,SLOT(ReloadImage()));
 158   contextActions.push_back(actionReload_image);
 159
 160   QAction* actionSave_image = contextMenu.addAction(QIcon(QString::fromUtf8(":/common/icons/filesave.png")),
 161     tr("Save Current Image"));
 162   connect(actionSave_image,SIGNAL(triggered()),this,SLOT(SaveAs()));
 163   contextActions.push_back(actionSave_image);
 164
 165   QAction* actionSave_state = contextMenu.addAction(QIcon(QString::fromUtf8(":/common/icons/filesave.png")),
 166     tr("Save Current State"));
 167   connect(actionSave_state,SIGNAL(triggered()),this,SLOT(SaveCurrentState()));
 168   contextActions.push_back(actionSave_state);
 169
 170   QAction* actionRead_state = contextMenu.addAction(QIcon(QString::fromUtf8(":/common/icons/filesave.png")),
 171     tr("Read Saved State"));
 172   connect(actionRead_state,SIGNAL(triggered()),this,SLOT(ReadSavedState()));
 173   contextActions.push_back(actionRead_state);
 174
 175   contextMenu.addSeparator();
 176
 177   contextMenu.addAction(actionAdd_VF_to_current_Image);
 178   contextActions.push_back(actionAdd_VF_to_current_Image);
 179
 180   //QAction* actionAdd_Overlay_to_current_Image = menuOverlay->addAction(QIcon(QString::fromUtf8(":/common/icons/GPSup.png")),
 181   //    tr("Add overlay image to current image"));
 182   contextMenu.addAction(actionAdd_overlay_image_to_current_image);
 183   contextActions.push_back(actionAdd_overlay_image_to_current_image);
 184
 185   contextMenu.addAction(actionAdd_fusion_image);
 186   contextActions.push_back(actionAdd_fusion_image);
 187
 188 #ifdef CLITK_EXPERIMENTAL
 189   contextMenu.addAction(actionAdd_USSequence_toCT);
 190   contextActions.push_back(actionAdd_USSequence_toCT);
 191 #endif
 192
 193
 194   contextMenu.addSeparator();
 195   QAction* actionResetMatrix = contextMenu.addAction(QIcon(QString::fromUtf8(":/common/icons/identity.png")),
 196     tr("Reset transformation to identity"));
 197   connect(actionResetMatrix, SIGNAL(triggered()), this,SLOT(ResetTransformationToIdentity()));
 198
 199   // TRIAL DS
 200   /*
 201   QMenu * m = new QMenu(menubar);
 202   m->setTitle("TOTO");
 203   //  m->setObjectName(QString::fromUtf8("TOTOTO"));
 204   contextMenu.addMenu(m);
 205   QAction * a = m->addAction(QIcon(QString::fromUtf8(":/common/icons/GPSup.png")),
 206   tr("BIDON"));
 207   QAction * b = m->addAction(QIcon(QString::fromUtf8(":/common/icons/GPSup.png")),
 208   tr("BIDON2"));
 209   m->addAction(a);
 210   m->addAction(b);
 211   connect(a,SIGNAL(triggered()),this,SLOT(AddFusionImage()));
 212   */
 213
 214   //init the DataTree
 215   mSlicerManagers.resize(0);
 216
 217   QStringList header;
 218   header.append("");
 219   header.append("TL");
 220   header.append("TR");
 221   header.append("BL");
 222   header.append("BR");
 223   header.append("");
 224   header.append("");
 225   header.append("Name");
 226
 227   DataTree->setHeaderLabels(header);
 228   DataTree->resizeColumnToContents(COLUMN_TREE);
 229   DataTree->resizeColumnToContents(COLUMN_UL_VIEW);
 230   DataTree->resizeColumnToContents(COLUMN_UR_VIEW);
 231   DataTree->resizeColumnToContents(COLUMN_DL_VIEW);
 232   DataTree->resizeColumnToContents(COLUMN_DR_VIEW);
 233   DataTree->resizeColumnToContents(COLUMN_CLOSE_IMAGE);
 234   DataTree->resizeColumnToContents(COLUMN_RELOAD_IMAGE);
 235   DataTree->resizeColumnToContents(COLUMN_IMAGE_NAME);
 236
 237   viewMode = 1;
 238   documentation = new vvDocumentation();
 239   help_dialog = new vvHelpDialog();
 240   dicomSeriesSelector = new vvDicomSeriesSelector();
 241 #ifdef CLITK_USE_SYSTEM_GDCM
 242      PacsConnection = new vvQPacsConnection();
 243 #endif
 244
 245   inverseButton->setEnabled(0);
 246   actionAdd_overlay_image_to_current_image->setEnabled(0);
 247   actionSave_As->setEnabled(0);
 248   actionAdd_VF_to_current_Image->setEnabled(0);
 249   actionAdd_fusion_image->setEnabled(0);
 250   actionAdd_USSequence_toCT->setEnabled(0);
 251
 252   //init the sliders
 253   verticalSliders.push_back(NOVerticalSlider);
 254   verticalSliders.push_back(NEVerticalSlider);
 255   verticalSliders.push_back(SOVerticalSlider);
 256   verticalSliders.push_back(SEVerticalSlider);
 257
 258   for (int i =0; i < 4; i++)
 259     verticalSliders[i]->hide();
 260
 261   horizontalSliders.push_back(NOHorizontalSlider);
 262   horizontalSliders.push_back(NEHorizontalSlider);
 263   horizontalSliders.push_back(SOHorizontalSlider);
 264   horizontalSliders.push_back(SEHorizontalSlider);
 265
 266   for (int i =0; i < 4; i++)
 267     horizontalSliders[i]->hide();
 268
 269
 270   connect(NOVerticalSlider,SIGNAL(valueChanged(int)),this,SLOT(NOVerticalSliderChanged()));
 271   connect(NEVerticalSlider,SIGNAL(valueChanged(int)),this,SLOT(NEVerticalSliderChanged()));
 272   connect(SOVerticalSlider,SIGNAL(valueChanged(int)),this,SLOT(SOVerticalSliderChanged()));
 273   connect(SEVerticalSlider,SIGNAL(valueChanged(int)),this,SLOT(SEVerticalSliderChanged()));
 274
 275   connect(NOHorizontalSlider,SIGNAL(valueChanged(int)),this,SLOT(NOHorizontalSliderMoved()));
 276   connect(NEHorizontalSlider,SIGNAL(valueChanged(int)),this,SLOT(NEHorizontalSliderMoved()));
 277   connect(SOHorizontalSlider,SIGNAL(valueChanged(int)),this,SLOT(SOHorizontalSliderMoved()));
 278   connect(SEHorizontalSlider,SIGNAL(valueChanged(int)),this,SLOT(SEHorizontalSliderMoved()));
 279
 280   //connect everything
 281   connect(actionCompute_mid_position_image,SIGNAL(triggered()),this,SLOT(ComputeMidPosition()));
 282   connect(actionDeformable_Registration,SIGNAL(triggered()),this,SLOT(ComputeDeformableRegistration()));
 283   connect(actionWarp_image_with_vector_field,SIGNAL(triggered()),this,SLOT(WarpImage()));
 284   connect(actionLoad_images,SIGNAL(triggered()),this,SLOT(OpenImages()));
 285   connect(actionOpen_Dicom,SIGNAL(triggered()),this,SLOT(OpenDicom()));
 286   #ifdef CLITK_USE_SYSTEM_GDCM
 287 connect(actionConnect_Pacs,SIGNAL(triggered()),this,SLOT(ConnectPacs()));
 288 #endif
 289   //  connect(actionOpen_Dicom_Struct,SIGNAL(triggered()),this,SLOT(OpenDCStructContour()));
 290   connect(actionOpen_VTK_contour,SIGNAL(triggered()),this,SLOT(OpenVTKContour()));
 291   connect(actionOpen_Multiple_Images_As_One,SIGNAL(triggered()),this,SLOT(MergeImages()));
 292   connect(actionSlice_Image_As_Multiple_Images,SIGNAL(triggered()),this,SLOT(SliceImages()));
 293   connect(actionOpen_Image_With_Time,SIGNAL(triggered()),this,SLOT(OpenImageWithTime()));
 294   connect(actionMerge_images_as_n_dim_t, SIGNAL(triggered()), this, SLOT(MergeImagesWithTime()));
 295   connect(actionSave_As,SIGNAL(triggered()),this,SLOT(SaveAs()));
 296   connect(actionSave_current_state,SIGNAL(triggered()),this,SLOT(SaveCurrentState()));
 297   connect(actionRead_saved_state,SIGNAL(triggered()),this,SLOT(ReadSavedState()));
 298   connect(actionExit,SIGNAL(triggered()),this,SLOT(close()));
 299   connect(actionAdd_VF_to_current_Image,SIGNAL(triggered()),this,SLOT(OpenField()));
 300   connect(actionAdd_fusion_image,SIGNAL(triggered()),this,SLOT(SelectFusionImage()));
 301   connect(actionAdd_overlay_image_to_current_image,SIGNAL(triggered()), this,SLOT(SelectOverlayImage()));
 302   connect(actionAdd_USSequence_toCT,SIGNAL(triggered()), this,SLOT(SelectFusionSequence()));
 303   connect(actionNavigation_Help,SIGNAL(triggered()),this,SLOT(ShowHelpDialog()));
 304   connect(actionDocumentation,SIGNAL(triggered()),this,SLOT(ShowDocumentation()));
 305   connect(actionRegister_vv,SIGNAL(triggered()),this,SLOT(PopupRegisterForm()));
 306
 307   connect(overlayPanel, SIGNAL(FusionSequenceCorrespondancesButtonPressed()), this, SLOT(SelectFusionSequenceCorrespondances()));
 308
 309
 310   ///////////////////////////////////////////////
 311   connect(actionSegmentation,SIGNAL(triggered()),this,SLOT(SegmentationOnCurrentImage()));
 312   connect(actionSurface_Viewer,SIGNAL(triggered()),this,SLOT(SurfaceViewerLaunch()));
 313   ///////////////////////////////////////////////
 314
 315   actionNorth_East_Window->setEnabled(0);
 316   actionNorth_West_Window->setEnabled(0);
 317   actionSouth_East_Window->setEnabled(0);
 318   actionSouth_West_Window->setEnabled(0);
 319
 320   connect(actionNorth_East_Window,SIGNAL(triggered()),this,SLOT(SaveNEScreenshot()));
 321   connect(actionNorth_West_Window,SIGNAL(triggered()),this,SLOT(SaveNOScreenshot()));
 322   connect(actionSouth_East_Window,SIGNAL(triggered()),this,SLOT(SaveSEScreenshot()));
 323   connect(actionSouth_West_Window,SIGNAL(triggered()),this,SLOT(SaveSOScreenshot()));
 324   connect(actionSave_all_slices,SIGNAL(triggered()),this,SLOT(SaveScreenshotAllSlices()));
 325
 326   connect(DataTree,SIGNAL(itemSelectionChanged()),this,SLOT(ImageInfoChanged()));
 327   connect(DataTree,SIGNAL(itemClicked(QTreeWidgetItem*, int)),this,
 328     SLOT(DisplayChanged(QTreeWidgetItem*, int)));
 329
 330   connect(viewButton,SIGNAL(clicked()),this, SLOT(ChangeViewMode()) );
 331   connect(windowSpinBox,SIGNAL(editingFinished()),this,SLOT(WindowLevelEdited()));
 332   connect(levelSpinBox,SIGNAL(editingFinished()),this,SLOT(WindowLevelEdited()));
 333   connect(colorMapComboBox,SIGNAL(currentIndexChanged(int)),this,SLOT(UpdateColorMap()));
 334   connect(presetComboBox,SIGNAL(currentIndexChanged(int)),this,SLOT(UpdateWindowLevel()));
 335   connect(slicingPresetComboBox, SIGNAL(currentIndexChanged(int)),this,SLOT(UpdateSlicingPreset()));
 336   connect(inverseButton,SIGNAL(clicked()),this,SLOT(SwitchWindowLevel()));
 337   connect(applyWindowLevelToAllButton,SIGNAL(clicked()),this,SLOT(ApplyWindowLevelToAllImages()));
 338
 339   connect(this,SIGNAL(customContextMenuRequested(QPoint)),this,SLOT(ShowContextMenu(QPoint)));
 340
 341   connect(linkPanel,SIGNAL(addLink(QString,QString,bool)),this,SLOT(AddLink(QString,QString,bool)));
 342   connect(linkPanel,SIGNAL(removeLink(QString,QString)),this,SLOT(RemoveLink(QString,QString)));
 343   connect(overlayPanel,SIGNAL(VFPropertyUpdated(int,int,int,int,double,double,double)),this,SLOT(SetVFProperty(int,int,int,int,double,double,double)));
 344   connect(overlayPanel,SIGNAL(OverlayPropertyUpdated(int,int,double,double)),
 345     this,SLOT(SetOverlayProperty(int,int,double,double)));
 346   connect(overlayPanel,SIGNAL(FusionPropertyUpdated(int,int,int,double,double, bool)),
 347     this,SLOT(SetFusionProperty(int,int,int,double,double, bool)));
 348   connect(landmarksPanel,SIGNAL(UpdateRenderWindows()),this,SLOT(UpdateRenderWindows()));
 349   connect(landmarksPanel,SIGNAL(SelectedPointChanged()),this,SLOT(GoToLandmark()));
 350
 351   connect(overlayPanel,SIGNAL(FusionSequencePropertyUpdated(int, bool, unsigned int, bool)),
 352     this,SLOT(SetFusionSequenceProperty(int, bool,unsigned int, bool)));
 353
 354
 355   playMode = 0;//pause
 356   mFrameRate = 10;
 357   playButton->setEnabled(0);
 358   frameRateLabel->setEnabled(0);
 359   frameRateSpinBox->setEnabled(0);
 360   connect(playButton, SIGNAL(clicked()),this,SLOT(PlayPause()));
 361   connect(frameRateSpinBox, SIGNAL(valueChanged(int)),this,SLOT(ChangeFrameRate(int)));
 362
 363   goToCursorPushButton->setEnabled(0);
 364   connect(goToCursorPushButton, SIGNAL(clicked()),this,SLOT(GoToCursor()));
 365
 366   NOViewWidget->hide();
 367   NEViewWidget->hide();
 368   SOViewWidget->hide();
 369   SEViewWidget->hide();
 370
 371   //Recently opened files
 372   std::list<std::string> recent_files = GetRecentlyOpenedImages();
 373   recentlyOpenedFilesMenu=NULL;
 374   if ( !recent_files.empty() ) {
 375     createRecentlyOpenedFilesMenu();
 376     updateRecentlyOpenedFilesMenu(recent_files);
 377   }
 378
 379   // Adding all new tools (insertion in the menu)
 380   vvToolManager::GetInstance()->InsertToolsInMenu(this);
 381   vvToolManager::GetInstance()->EnableToolsInMenu(this, false);
 382
 383   if (!CLITK_EXPERIMENTAL)
 384     menuExperimental->menuAction()->setVisible(false);
 385
 386
 387   QTimer * timerMemory = new QTimer(this);
 388   //timerMemory->setInterval(5);
 389   connect(timerMemory, SIGNAL(timeout()), this, SLOT(UpdateMemoryUsage()));
 390   timerMemory->start(2000);
 391
 392 }
 393 //------------------------------------------------------------------------------
 394 void vvMainWindow::show()
 395 {
 396   vvMainWindowBase::show();
 397   PopupRegisterForm(true);
 398 }
 399 //------------------------------------------------------------------------------
 400 void vvMainWindow::UpdateMemoryUsage()
 401 {
 402   //  clitk::PrintMemory(true);
 403   if (clitk::GetMemoryUsageInMb() == 0) infoPanel->setMemoryInMb("NA");
 404   else infoPanel->setMemoryInMb(QString::number(clitk::GetMemoryUsageInMb())+" MiB");
 405 }
 406 //------------------------------------------------------------------------------
 407
 408
 409 //------------------------------------------------------------------------------
 410 void vvMainWindow::createRecentlyOpenedFilesMenu()
 411 {
 412   recentlyOpenedFilesMenu = new QMenu("Recently opened files...");
 413   recentlyOpenedFilesMenu->setIcon(QIcon(QString::fromUtf8(":/common/icons/open.png")));
 414   menuFile->insertMenu(actionOpen_Image_With_Time,recentlyOpenedFilesMenu);
 415   menuFile->insertSeparator(actionOpen_Image_With_Time);
 416 }
 417 //------------------------------------------------------------------------------
 418
 419
 420 //------------------------------------------------------------------------------
 421
 422 void vvMainWindow::updateRecentlyOpenedFilesMenu(const std::list<std::string> &recent_files)
 423 {
 424   if(recentlyOpenedFilesMenu==NULL) {
 425     createRecentlyOpenedFilesMenu();
 426   } else {
 427     recentlyOpenedFilesMenu->clear();
 428   }
 429   for (std::list<std::string>::const_iterator i = recent_files.begin(); i!=recent_files.end(); i++) {
 430     QAction* current=new QAction(QIcon(QString::fromUtf8(":/common/icons/open.png")), i->c_str(),this);
 431     recentlyOpenedFilesMenu->addAction(current);
 432     connect(current,SIGNAL(triggered()),this,SLOT(OpenRecentImage()));
 433   }
 434 }
 435 //------------------------------------------------------------------------------
 436
 437
 438 //------------------------------------------------------------------------------
 439 void vvMainWindow::ComputeMidPosition()
 440 {
 441   bool ok;
 442   int index=GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
 443   int ref = QInputDialog::getInteger(this,"Chose reference phase","Reference phase",0,0,\
 444     mSlicerManagers[index]->GetImage()->GetVTKImages().size()-1,1,&ok);
 445   if (ok) {
 446     vvMidPosition midp;
 447     midp.slicer_manager = mSlicerManagers[index];
 448     midp.reference_image_index = ref;
 449     QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
 450     midp.Update();
 451     if (midp.error)
 452       QMessageBox::warning(this, "Error computing midposition image",midp.error_message.c_str());
 453     else {
 454       QFileInfo info(midp.slicer_manager->GetFileName().c_str());
 455       AddImage(midp.output,info.path().toStdString()+"/"+info.completeBaseName().toStdString()+"_midposition.mhd");
 456     }
 457     QApplication::restoreOverrideCursor();
 458   }
 459 }
 460 //------------------------------------------------------------------------------
 461
 462
 463 //------------------------------------------------------------------------------
 464 void vvMainWindow::AddContour(int image_index, vvMesh::Pointer contour, bool propagation)
 465 {
 466   QTreeWidgetItem *item = new QTreeWidgetItem();
 467   item->setData(0,Qt::UserRole,"filename.vtk");
 468   item->setData(1,Qt::UserRole,tr("contour"));
 469   QBrush brush;
 470   brush.setColor(QColor(contour->r*255,contour->g*255,contour->b*255));
 471   brush.setStyle(Qt::SolidPattern);
 472   item->setData(COLUMN_IMAGE_NAME,Qt::BackgroundRole,brush);
 473   //  item->setData(COLUMN_IMAGE_NAME,Qt::DisplayRole,contour->structure_name.c_str());
 474
 475   for (int j = 1; j <= 4; j++)
 476     item->setData(j,Qt::CheckStateRole,DataTree->topLevelItem(image_index)->data(j,Qt::CheckStateRole));
 477
 478   QTreePushButton* cButton = new QTreePushButton;
 479   cButton->setItem(item);
 480   cButton->setColumn(COLUMN_CLOSE_IMAGE);
 481   cButton->setToolTip(tr("close image"));
 482   cButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/exit.png")));
 483   connect(cButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
 484     this,SLOT(CloseImage(QTreeWidgetItem*, int)));
 485
 486   QTreePushButton* rButton = new QTreePushButton;
 487   rButton->setItem(item);
 488   rButton->setColumn(COLUMN_RELOAD_IMAGE);
 489   rButton->setToolTip(tr("reload image"));
 490   rButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/rotateright.png")));
 491   rButton->setEnabled(false);
 492   //Not implemented
 493   //connect(rButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
 494   //this,SLOT(ReloadImage(QTreeWidgetItem*, int)));
 495
 496   DataTree->topLevelItem(image_index)->setExpanded(1);
 497   DataTree->topLevelItem(image_index)->addChild(item);
 498   DataTree->setItemWidget(item, COLUMN_CLOSE_IMAGE, cButton);
 499   DataTree->setItemWidget(item, COLUMN_RELOAD_IMAGE, rButton);
 500   QString id = DataTree->topLevelItem(image_index)->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString();
 501   item->setData(COLUMN_IMAGE_NAME,Qt::UserRole,id.toStdString().c_str());
 502
 503   UpdateTree();
 504   mSlicerManagers[image_index]->AddContour(contour,propagation);
 505   mSlicerManagers[image_index]->Render();
 506 }
 507 //------------------------------------------------------------------------------
 508
 509
 510 //------------------------------------------------------------------------------
 511 void vvMainWindow::OpenVTKContour()
 512 {
 513   if (mSlicerManagers.size() > 0) {
 514     QString Extensions = "Images ( *.vtk *.obj)";
 515     Extensions += ";;All Files (*)";
 516     QString file = QFileDialog::getOpenFileName(this,tr("Open vtkPolyData"),mInputPathName,Extensions);
 517     if (file.isNull())
 518       return;
 519     QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
 520     int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
 521     vvMeshReader reader;
 522     reader.SetImage(mSlicerManagers[index]->GetImage());
 523     reader.SetModeToVTK();
 524     reader.SetFilename(file.toStdString());
 525     reader.Update();
 526     AddContour(index,reader.GetOutput()[0],false);
 527     QApplication::restoreOverrideCursor();
 528   }
 529 }
 530 //------------------------------------------------------------------------------
 531
 532
 533 //------------------------------------------------------------------------------
 534 void vvMainWindow::AddDCStructContour(int index, QString file)
 535 {
 536   vvMeshReader reader;
 537   reader.SetFilename(file.toStdString());
 538   vvStructSelector selector;
 539   selector.SetStructures(reader.GetROINames());
 540   if (!mSlicerManagers[index]->GetVF().IsNull())
 541     selector.EnablePropagationCheckBox();
 542   if (selector.exec()) {
 543     QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
 544     reader.SetSelectedItems(selector.getSelectedItems());
 545     reader.SetImage(mSlicerManagers[index]->GetImage());
 546     if (selector.PropagationEnabled())
 547       reader.SetPropagationVF(mSlicerManagers[index]->GetVF());
 548     reader.Update();
 549     std::vector<vvMesh::Pointer> contours=reader.GetOutput();
 550     for (std::vector<vvMesh::Pointer>::iterator i=contours.begin();
 551       i!=contours.end(); i++)
 552       AddContour(index,*i,selector.PropagationEnabled());
 553     QApplication::restoreOverrideCursor();
 554   }
 555 }
 556
 557 //------------------------------------------------------------------------------
 558 void vvMainWindow::OpenDCStructContour()
 559 {
 560   if (mSlicerManagers.size() > 0) {
 561     QString Extensions = "Dicom Files ( *.dcm RS*)";
 562     Extensions += ";;All Files (*)";
 563     QString file = QFileDialog::getOpenFileName(this,tr("Merge Images"),mInputPathName,Extensions);
 564     if (file.isNull())
 565       return;
 566     int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
 567     AddDCStructContour(index, file);
 568   }
 569 }
 570 //------------------------------------------------------------------------------
 571
 572
 573 //------------------------------------------------------------------------------
 574 void vvMainWindow::ComputeDeformableRegistration()
 575 {
 576   if (mSlicerManagers.size() > 0) {
 577     int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
 578     vvDeformationDialog dialog(index,mSlicerManagers);
 579     if (dialog.exec()) {
 580       std::string base_name=itksys::SystemTools::GetFilenameWithoutExtension(mSlicerManagers[dialog.GetInputFileIndex()]->GetFileName());
 581       AddField(dialog.GetOutput(),dialog.getFieldFile(),dialog.GetInputFileIndex());
 582       WarpImage(dialog.GetSelectedSlicer(),dialog.GetReferenceFrameIndex());
 583     } else
 584       std::cout << "Error or user cancellation while computing deformation field..." << std::endl;
 585   } else QMessageBox::information(this, "Need to open image","You must open an image first.");
 586 }
 587 //------------------------------------------------------------------------------
 588
 589
 590 //------------------------------------------------------------------------------
 591 void vvMainWindow::WarpImage()
 592 {
 593   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
 594   if (!mSlicerManagers[index]->GetVF().IsNull()) {
 595     bool ok;
 596     int ref = QInputDialog::getInteger(this,"Chose reference phase","Reference phase",0,0,\
 597       mSlicerManagers[index]->GetImage()->GetVTKImages().size()-1,1,&ok);
 598     if (ok) {
 599       WarpImage(mSlicerManagers[index],ref);
 600     }
 601   } else
 602     QMessageBox::warning(this,tr("No vector field"),tr("Sorry, can't warp without a vector field"));
 603 }
 604 //------------------------------------------------------------------------------
 605
 606
 607 //------------------------------------------------------------------------------
 608 void vvMainWindow::WarpImage(vvSlicerManager* selected_slicer,int reference_phase)
 609 {
 610   if (!selected_slicer->GetVF().IsNull()) {
 611     QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
 612     QFileInfo info(selected_slicer->GetFileName().c_str());
 613     vvImageWarp warp(selected_slicer->GetImage(),selected_slicer->GetVF(),
 614       reference_phase,this);
 615     if (warp.ComputeWarpedImage()) {
 616       AddImage(warp.GetWarpedImage(),info.path().toStdString()+"/"+info.completeBaseName().toStdString()+"_warped.mhd");
 617       AddImage(warp.GetDiffImage()  ,info.path().toStdString()+"/"+info.completeBaseName().toStdString()+"_diff.mhd");
 618       AddImage(warp.GetJacobianImage()  ,info.path().toStdString()+"/"+info.completeBaseName().toStdString()+"_jacobian.mhd");
 619       QApplication::restoreOverrideCursor();
 620     } else {
 621       QApplication::restoreOverrideCursor();
 622       QMessageBox::warning(this,tr("Different spacings"),tr("The vector field and image spacings must be the same in order to warp."));
 623     }
 624   } else
 625     QMessageBox::warning(this,tr("No vector field"),tr("Sorry, can't warp without a vector field."));
 626 }
 627 //------------------------------------------------------------------------------
 628
 629
 630 //------------------------------------------------------------------------------
 631 vvMainWindow::~vvMainWindow()
 632 {
 633   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
 634     if (mSlicerManagers[i] != NULL)
 635       delete mSlicerManagers[i];
 636   }
 637 }
 638 //------------------------------------------------------------------------------
 639
 640 //------------------------------------------------------------------------------
 641 QTabWidget * vvMainWindow::GetTab()
 642 {
 643   return tabWidget;
 644 }
 645 //------------------------------------------------------------------------------
 646
 647
 648 //------------------------------------------------------------------------------
 649 void vvMainWindow::MergeImages()
 650 {
 651   QString Extensions = EXTENSIONS;
 652   Extensions += ";;All Files (*)";
 653   QStringList files = QFileDialog::getOpenFileNames(this,tr("Merge Images"),mInputPathName,Extensions);
 654   if (files.isEmpty())
 655     return;
 656   mInputPathName = itksys::SystemTools::GetFilenamePath(files[0].toStdString()).c_str();
 657   std::vector<std::string> vector;
 658
 659   unsigned int currentDim = 0;
 660   std::vector<double> currentSpacing;
 661   std::vector<int> currentSize;
 662   std::vector<double> currentOrigin;
 663
 664   for (int i = 0; i < files.size(); i++) {
 665     itk::ImageIOBase::Pointer reader = itk::ImageIOFactory::CreateImageIO(
 666       files[i].toStdString().c_str(), itk::ImageIOFactory::ReadMode);
 667     reader->SetFileName(files[i].toStdString().c_str());
 668     reader->ReadImageInformation();
 669     if (reader)        {
 670       //NOViewWidget->hide();
 671       //NEViewWidget->hide();
 672       //SOViewWidget->hide();
 673       //SEViewWidget->hide();
 674       if (i == 0)
 675         currentDim = reader->GetNumberOfDimensions();
 676       bool IsOk = true;
 677       for (unsigned int j = 0; j < currentDim; j++) {
 678         if (i == 0) {
 679           if (j == 0) {
 680             currentSpacing.resize(currentDim);
 681             currentSize.resize(currentDim);
 682             currentOrigin.resize(currentDim);
 683           }
 684           currentOrigin[j] = reader->GetOrigin(j);
 685           currentSpacing[j] = reader->GetSpacing(j);
 686           currentSize[j] = reader->GetDimensions(j);
 687         } else if (currentDim != reader->GetNumberOfDimensions()
 688           || currentSpacing[j] != reader->GetSpacing(j)
 689           || currentSize[j] != (int)reader->GetDimensions(j)
 690           || currentOrigin[j] != reader->GetOrigin(j)) {
 691             QString error = "Cannot read file (too different from others ";
 692             error += files[i].toStdString().c_str();
 693             QMessageBox::information(this,tr("Reading problem"),error);
 694             IsOk = false;
 695             break;
 696         }
 697       }
 698       if (IsOk)
 699         vector.push_back(files[i].toStdString());
 700     }
 701   }
 702   if (vector.size() > 0)
 703     LoadImages(vector, vvImageReader::MERGED);
 704 }
 705 //------------------------------------------------------------------------------
 706
 707 //------------------------------------------------------------------------------
 708 void vvMainWindow::SliceImages()
 709 {
 710   QString Extensions = EXTENSIONS;
 711   Extensions += ";;All Files (*)";
 712
 713   QStringList files = QFileDialog::getOpenFileNames(this,tr("Slice Images"),mInputPathName,Extensions);
 714   if (files.isEmpty())
 715     return;
 716   mInputPathName = itksys::SystemTools::GetFilenamePath(files[0].toStdString()).c_str();
 717   std::vector<std::string> vector;
 718   for (int i = 0; i < files.size(); i++)
 719     vector.push_back(files[i].toStdString());
 720   LoadImages(vector, vvImageReader::SLICED);
 721 }
 722 //------------------------------------------------------------------------------
 723
 724 //------------------------------------------------------------------------------
 725 void vvMainWindow::MergeImagesWithTime()
 726 {
 727   QString Extensions = EXTENSIONS;
 728   Extensions += ";;All Files (*)";
 729   QStringList files = QFileDialog::getOpenFileNames(this,tr("Merge Images With Time"),mInputPathName,Extensions);
 730   if (files.isEmpty())
 731     return;
 732   mInputPathName = itksys::SystemTools::GetFilenamePath(files[0].toStdString()).c_str();
 733   std::vector<std::string> vector;
 734
 735   for (int i = 0; i < files.size(); i++)
 736     vector.push_back(files[i].toStdString());
 737   sort(vector.begin(),vector.end());
 738   if (vector.size() > 1)
 739     LoadImages(vector, vvImageReader::MERGEDWITHTIME);
 740   else
 741     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.");
 742 }
 743 //------------------------------------------------------------------------------
 744
 745
 746 //------------------------------------------------------------------------------
 747 void vvMainWindow::OpenDicom()
 748 {
 749   std::vector<std::string> files;
 750
 751   //std::cout << "dicomSeriesSelector " << std::endl;
 752   if (dicomSeriesSelector->exec() == QDialog::Accepted) {
 753     files = *(dicomSeriesSelector->GetFilenames());
 754     LoadImages(files, vvImageReader::DICOM);
 755   }
 756 }
 757 #ifdef CLITK_USE_SYSTEM_GDCM
 758 void vvMainWindow::ConnectPacs()
 759 {
 760   std::vector<std::string> files;
 761
 762   //std::cout << "dicomSeriesSelector " << std::endl;
 763 if (PacsConnection->exec() == QDialog::Accepted) {
 764         files = PacsConnection->getFileNames();
 765     LoadImages(files, vvImageReader::DICOM);
 766   }
 767   }
 768
 769 #endif
 770 //------------------------------------------------------------------------------
 771
 772 //------------------------------------------------------------------------------
 773 void vvMainWindow::OpenImages()
 774 {
 775   QString Extensions = EXTENSIONS;
 776   Extensions += ";;All Files (*)";
 777
 778   QStringList files = QFileDialog::getOpenFileNames(this,tr("Load Images"),mInputPathName,Extensions);
 779   if (files.isEmpty())
 780     return;
 781   mInputPathName = itksys::SystemTools::GetFilenamePath(files[0].toStdString()).c_str();
 782   std::vector<std::string> vector;
 783   for (int i = 0; i < files.size(); i++)
 784     vector.push_back(files[i].toStdString());
 785   LoadImages(vector, vvImageReader::IMAGE);
 786 }
 787 //------------------------------------------------------------------------------
 788 void vvMainWindow::OpenRecentImage()
 789 {
 790   QAction * caller = qobject_cast<QAction*>(sender());
 791   std::vector<std::string> images;
 792   images.push_back(caller->text().toStdString());
 793   mInputPathName = itksys::SystemTools::GetFilenamePath(images[0]).c_str();
 794   LoadImages(images, vvImageReader::IMAGE);
 795 }
 796 //------------------------------------------------------------------------------
 797
 798
 799 //------------------------------------------------------------------------------
 800 void vvMainWindow::OpenImageWithTime()
 801 {
 802   QString Extensions = EXTENSIONS;
 803   Extensions += ";;All Files (*)";
 804
 805   QStringList files = QFileDialog::getOpenFileNames(this,tr("Load Images With Time"),mInputPathName,Extensions);
 806   if (files.isEmpty())
 807     return;
 808   mInputPathName = itksys::SystemTools::GetFilenamePath(files[0].toStdString()).c_str();
 809   std::vector<std::string> vector;
 810   for (int i = 0; i < files.size(); i++) {
 811     vector.push_back(files[i].toStdString());
 812   }
 813   LoadImages(vector, vvImageReader::IMAGEWITHTIME);
 814 }
 815 //------------------------------------------------------------------------------
 816
 817
 818 //------------------------------------------------------------------------------
 819 void vvMainWindow::LoadImages(std::vector<std::string> files, vvImageReader::LoadedImageType filetype)
 820 {
 821   //Separate the way to open images and dicoms
 822   int fileSize;
 823   if (filetype == vvImageReader::IMAGE || filetype == vvImageReader::IMAGEWITHTIME)
 824     fileSize = files.size();
 825   else
 826     fileSize = 1;
 827
 828   // For SLICED, we need the number of slices (ndim and #slices)
 829   std::vector<unsigned int> nSlices;
 830   nSlices.resize(files.size());
 831   std::fill(nSlices.begin(), nSlices.end(), 1);
 832   if (filetype == vvImageReader::SLICED) {
 833     for (int i = 0; i < fileSize; i++) {
 834       itk::ImageIOBase::Pointer header = clitk::readImageHeader(files[i]);
 835       QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
 836       if (!header) {
 837         nSlices[i] = 0;
 838         QString error = "Cannot open file \n";
 839         error += files[i].c_str();
 840         QMessageBox::information(this,tr("Reading problem"),error);
 841         return;
 842       }
 843       if (header->GetNumberOfDimensions() < 3) {
 844         nSlices[i] = 0;
 845         QString error = "Dimension problem. Cannot slice \n";
 846         error += files[i].c_str();
 847         QMessageBox::information(this,tr("Reading problem"),error);
 848         return;
 849       }
 850       nSlices[i] = header->GetDimensions( header->GetNumberOfDimensions()-1 );
 851     }
 852   }
 853
 854   //Only add to the list of recently opened files when a single file is opened,
 855   //to avoid polluting the list of recently opened files
 856   if (files.size() == 1) {
 857     QFileInfo finfo=tr(files[0].c_str());
 858     AddToRecentlyOpenedImages(finfo.absoluteFilePath().toStdString());
 859     updateRecentlyOpenedFilesMenu(GetRecentlyOpenedImages());
 860   }
 861   //init the progress events
 862   QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
 863   vvProgressDialog progress("Opening " + files[0],fileSize>1);
 864   qApp->processEvents();
 865
 866   int numberofsuccesulreads=0;
 867   //open images as 1 or multiples
 868   for (int i = 0; i < fileSize; i++) {
 869     progress.SetText("Opening " + files[i]);
 870     progress.SetProgress(i,fileSize);
 871     qApp->processEvents();
 872
 873     for (unsigned int j = 0; j < nSlices[i]; j++) {
 874       //read the image and put it in mSlicerManagers
 875       vvSlicerManager* imageManager = new vvSlicerManager(4);
 876       qApp->processEvents();
 877
 878       bool SetImageSucceed=false;
 879
 880       // Change filename if an image with the same already exist
 881       int number = GetImageDuplicateFilenameNumber(files[i] + std::string("_slice"));
 882
 883       if (filetype == vvImageReader::IMAGE || filetype == vvImageReader::IMAGEWITHTIME || filetype == vvImageReader::SLICED)
 884         SetImageSucceed = imageManager->SetImage(files[i],filetype, number, j);
 885       else {
 886         SetImageSucceed = imageManager->SetImages(files,filetype, number);
 887       }
 888
 889       if (!SetImageSucceed) {
 890         QApplication::restoreOverrideCursor();
 891         QString error = "Cannot open file \n";
 892         error += imageManager->GetLastError().c_str();
 893         QMessageBox::information(this,tr("Reading problem"),error);
 894         delete imageManager;
 895       } else {
 896         mSlicerManagers.push_back(imageManager);
 897
 898         //create an item in the tree with good settings
 899         QTreeWidgetItem *item = new QTreeWidgetItem();
 900         item->setData(0,Qt::UserRole,files[i].c_str());
 901         QFileInfo fileinfo(imageManager->GetFileName().c_str()); //Do not show the path
 902         item->setData(COLUMN_IMAGE_NAME,Qt::DisplayRole,fileinfo.fileName());
 903         item->setData(1,Qt::UserRole,tr("image"));
 904         item->setToolTip(COLUMN_IMAGE_NAME, imageManager->GetListOfAbsoluteFilePathInOneString("image").c_str());
 905         qApp->processEvents();
 906
 907         //Create the buttons for reload and close
 908         qApp->processEvents();
 909         QTreePushButton* cButton = new QTreePushButton;
 910         cButton->setItem(item);
 911         cButton->setColumn(COLUMN_CLOSE_IMAGE);
 912         cButton->setToolTip(tr("close image"));
 913         cButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/exit.png")));
 914         connect(cButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
 915           this,SLOT(CloseImage(QTreeWidgetItem*, int)));
 916
 917         QTreePushButton* rButton = new QTreePushButton;
 918         rButton->setItem(item);
 919         rButton->setColumn(COLUMN_RELOAD_IMAGE);
 920         rButton->setToolTip(tr("reload image"));
 921         rButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/rotateright.png")));
 922         connect(rButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
 923           this,SLOT(ReloadImage(QTreeWidgetItem*, int)));
 924
 925         DataTree->addTopLevelItem(item);
 926         DataTree->setItemWidget(item, COLUMN_CLOSE_IMAGE, cButton);
 927         DataTree->setItemWidget(item, COLUMN_RELOAD_IMAGE, rButton);
 928
 929         //set the id of the image
 930         QString id = QDir::current().absoluteFilePath(files[i].c_str()) + QString::number(mSlicerManagers.size()-1);
 931         item->setData(COLUMN_IMAGE_NAME,Qt::UserRole,id.toStdString().c_str());
 932         mSlicerManagers.back()->SetId(id.toStdString());
 933
 934         linkPanel->addImage(imageManager->GetFileName(), id.toStdString());
 935
 936         connect(mSlicerManagers.back(), SIGNAL(currentImageChanged(std::string)),
 937           this,SLOT(CurrentImageChanged(std::string)));
 938         connect(mSlicerManagers.back(), SIGNAL(currentPickedImageChanged(std::string)),
 939           this, SLOT(CurrentPickedImageChanged(std::string)));
 940         connect(mSlicerManagers.back(), SIGNAL(UpdatePosition(int, double, double, double, double, double, double, double)),
 941           this,SLOT(MousePositionChanged(int,double, double, double, double, double, double, double)));
 942         connect(mSlicerManagers.back(), SIGNAL(UpdateVector(int, double, double, double, double)),
 943           this, SLOT(VectorChanged(int,double,double,double, double)));
 944         connect(mSlicerManagers.back(), SIGNAL(UpdateOverlay(int, double, double)),
 945           this, SLOT(OverlayChanged(int,double,double)));
 946         connect(mSlicerManagers.back(), SIGNAL(UpdateFusion(int, double)),
 947           this, SLOT(FusionChanged(int,double)));
 948         connect(mSlicerManagers.back(), SIGNAL(WindowLevelChanged()),
 949           this,SLOT(WindowLevelChanged()));
 950         connect(mSlicerManagers.back(), SIGNAL(UpdateSlice(int,int)),
 951           this,SLOT(UpdateSlice(int,int)));
 952         connect(mSlicerManagers.back(), SIGNAL(UpdateTSlice(int, int, int)),
 953           this,SLOT(UpdateTSlice(int, int, int)));
 954         connect(mSlicerManagers.back(), SIGNAL(UpdateTSlice(int, int, int)),
 955           this,SLOT(ImageInfoChanged()));
 956         connect(mSlicerManagers.back(), SIGNAL(UpdateSliceRange(int,int,int,int,int)),
 957           this,SLOT(UpdateSliceRange(int,int,int,int,int)));
 958         connect(mSlicerManagers.back(), SIGNAL(UpdateLinkManager(std::string,int,double,double,double,int)),
 959           this,SLOT(UpdateLinkManager(std::string,int,double,double,double,int)));
 960         connect(mSlicerManagers.back(), SIGNAL(UpdateLinkedNavigation(std::string,vvSlicerManager*,vvSlicer*)),
 961           this,SLOT(UpdateLinkedNavigation(std::string,vvSlicerManager*,vvSlicer*)));
 962         connect(mSlicerManagers.back(), SIGNAL(ChangeImageWithIndexOffset(vvSlicerManager*,int,int)),
 963           this,SLOT(ChangeImageWithIndexOffset(vvSlicerManager*,int,int)));
 964         connect(mSlicerManagers.back(),SIGNAL(LandmarkAdded()),landmarksPanel,SLOT(AddPoint()));
 965
 966         InitSlicers();
 967         numberofsuccesulreads++;
 968       }
 969     }
 970   }
 971   if (numberofsuccesulreads) {
 972     NOViewWidget->show();
 973     NEViewWidget->show();
 974     SOViewWidget->show();
 975     SEViewWidget->show();
 976     UpdateTree();
 977     InitDisplay();
 978     ShowLastImage();
 979
 980     // Try to guess default WindowLevel
 981     double range[2];
 982     mSlicerManagers.back()->GetImage()->GetFirstVTKImageData()->GetScalarRange(range);
 983     if ((range[0] == 0) && (range[1] == 1)) {
 984       presetComboBox->setCurrentIndex(WL_BINARY);// binary
 985     } else {
 986       // TODO
 987     }
 988   }
 989   QApplication::restoreOverrideCursor();
 990 }
 991 //------------------------------------------------------------------------------
 992
 993 //------------------------------------------------------------------------------
 994 void vvMainWindow::UpdateTree()
 995 {
 996   DataTree->resizeColumnToContents(COLUMN_TREE);
 997   DataTree->resizeColumnToContents(COLUMN_UL_VIEW);
 998   DataTree->resizeColumnToContents(COLUMN_UR_VIEW);
 999   DataTree->resizeColumnToContents(COLUMN_DL_VIEW);
1000   DataTree->resizeColumnToContents(COLUMN_DR_VIEW);
1001   DataTree->resizeColumnToContents(COLUMN_IMAGE_NAME);
1002   DataTree->resizeColumnToContents(COLUMN_CLOSE_IMAGE);
1003   DataTree->resizeColumnToContents(COLUMN_RELOAD_IMAGE);
1004 }
1005 //------------------------------------------------------------------------------
1006
1007 //------------------------------------------------------------------------------
1008 void vvMainWindow::CurrentImageChanged(std::string id)
1009 {
1010   if (id == mCurrentSelectedImageId) return; // Do nothing
1011   int selected = 0;
1012   for (int i = 0; i < DataTree->topLevelItemCount(); i++) {
1013     if (DataTree->topLevelItem(i)->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString().toStdString() == id) {
1014       selected = i;
1015     } else {
1016       DataTree->topLevelItem(i)->setSelected(0);
1017     }
1018     for (int child = 0; child < DataTree->topLevelItem(i)->childCount(); child++)
1019       DataTree->topLevelItem(i)->child(child)->setSelected(0);
1020
1021   }
1022   DataTree->topLevelItem(selected)->setSelected(1);
1023   mCurrentSelectedImageId = id;
1024
1025   landmarksPanel->SetCurrentLandmarks(mSlicerManagers[selected]->GetLandmarks(),
1026                                       mSlicerManagers[selected]->GetTSlice());
1027   landmarksPanel->SetCurrentPath(mInputPathName.toStdString());
1028   landmarksPanel->SetCurrentImage(mSlicerManagers[selected]->GetFileName().c_str());
1029
1030   emit SelectedImageHasChanged(mSlicerManagers[selected]);
1031 }
1032 //------------------------------------------------------------------------------
1033
1034 //------------------------------------------------------------------------------
1035 void vvMainWindow::CurrentPickedImageChanged(std::string id)
1036 {
1037   if (id == mCurrentPickedImageId) return; // Do nothing
1038   int selected = 0;
1039   for (int i = 0; i < DataTree->topLevelItemCount(); i++) {
1040     if (DataTree->topLevelItem(i)->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString().toStdString() == id) {
1041       selected = i;
1042     } else {
1043       DataTree->topLevelItem(i)->setSelected(0);
1044     }
1045     for (int child = 0; child < DataTree->topLevelItem(i)->childCount(); child++)
1046       DataTree->topLevelItem(i)->child(child)->setSelected(0);
1047
1048   }
1049   DataTree->topLevelItem(selected)->setSelected(1);
1050   mCurrentPickedImageId = id;
1051   mCurrentPickedImageIndex = selected;
1052 }
1053 //------------------------------------------------------------------------------
1054
1055 //------------------------------------------------------------------------------
1056 void vvMainWindow::ImageInfoChanged()
1057 {
1058   contextActions[6]->setEnabled(1);
1059   contextActions[5]->setEnabled(1);
1060   actionSave_As->setEnabled(1);
1061   actionAdd_VF_to_current_Image->setEnabled(1);
1062   actionAdd_fusion_image->setEnabled(1);
1063   actionAdd_overlay_image_to_current_image->setEnabled(1);
1064   actionAdd_USSequence_toCT->setEnabled(1);
1065   actionNorth_East_Window->setEnabled(1);
1066   actionNorth_West_Window->setEnabled(1);
1067   actionSouth_East_Window->setEnabled(1);
1068   actionSouth_West_Window->setEnabled(1);
1069   vvToolManager::GetInstance()->EnableToolsInMenu(this, true);
1070   inverseButton->setEnabled(1);
1071
1072   goToCursorPushButton->setEnabled(1);
1073
1074   if (DataTree->selectedItems().size()) {
1075     int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1076
1077     colorMapComboBox->setEnabled(1);
1078     for (int i = 0; i < DataTree->topLevelItem(index)->childCount(); i++) {
1079       if (DataTree->topLevelItem(index)->child(i)->data(1,Qt::UserRole).toString() == "overlay" ||
1080         DataTree->topLevelItem(index)->child(i)->data(1,Qt::UserRole).toString() == "fusion" ||
1081         DataTree->topLevelItem(index)->child(i)->data(1,Qt::UserRole).toString() == "fusionSequence") {
1082           colorMapComboBox->setEnabled(0);
1083           break;
1084       }
1085     }
1086
1087     std::vector<double> origin;
1088     std::vector<double> inputSpacing;
1089     std::vector<int> inputSize;
1090     std::vector<double> sizeMM;
1091     vtkSmartPointer<vtkMatrix4x4> transformation;
1092     int dimension=0;
1093     QString pixelType;
1094     QString inputSizeInBytes;
1095     QString image = DataTree->selectedItems()[0]->data(COLUMN_IMAGE_NAME,Qt::DisplayRole).toString();
1096
1097     int nframes = mSlicerManagers[index]->GetSlicer(0)->GetTMax();
1098
1099     if (nframes > 1 || playMode == 1) {
1100       playButton->setEnabled(1);
1101       frameRateLabel->setEnabled(1);
1102       frameRateSpinBox->setEnabled(1);
1103     } else {
1104       playButton->setEnabled(0);
1105       frameRateLabel->setEnabled(0);
1106       frameRateSpinBox->setEnabled(0);
1107     }
1108
1109     //read image header
1110     int NPixel = 1;
1111
1112     int tSlice = 0;
1113     vvImage::Pointer imageSelected;
1114     if (DataTree->topLevelItem(index) == DataTree->selectedItems()[0]) {
1115       imageSelected = mSlicerManagers[index]->GetSlicer(0)->GetImage();
1116       tSlice = mSlicerManagers[index]->GetSlicer(0)->GetTSlice();
1117     } else if (DataTree->selectedItems()[0]->data(1,Qt::UserRole).toString() == "vector") {
1118       imageSelected = mSlicerManagers[index]->GetSlicer(0)->GetVF();
1119       tSlice = mSlicerManagers[index]->GetSlicer(0)->GetOverlayTSlice();
1120     } else if (DataTree->selectedItems()[0]->data(1,Qt::UserRole).toString() == "overlay") {
1121       imageSelected = mSlicerManagers[index]->GetSlicer(0)->GetOverlay();
1122       tSlice = mSlicerManagers[index]->GetSlicer(0)->GetOverlayTSlice();
1123     } else if (DataTree->selectedItems()[0]->data(1,Qt::UserRole).toString() == "fusion") {
1124       imageSelected = mSlicerManagers[index]->GetSlicer(0)->GetFusion();
1125       tSlice = mSlicerManagers[index]->GetSlicer(0)->GetFusionTSlice();
1126     }
1127     else if (DataTree->selectedItems()[0]->data(1,Qt::UserRole).toString() == "fusionSequence") {
1128       imageSelected = mSlicerManagers[index]->GetSlicer(0)->GetFusion();
1129       tSlice = mSlicerManagers[index]->GetSlicer(0)->GetFusionTSlice();
1130     }
1131     else if (DataTree->selectedItems()[0]->data(1,Qt::UserRole).toString() == "contour") {
1132       imageSelected = mSlicerManagers[index]->GetSlicer(0)->GetImage();
1133       tSlice = mSlicerManagers[index]->GetSlicer(0)->GetTSlice();
1134     }
1135     else {
1136       imageSelected = mSlicerManagers[index]->GetSlicer(0)->GetImage();
1137       tSlice = mSlicerManagers[index]->GetSlicer(0)->GetTSlice();
1138     }
1139
1140     dimension = imageSelected->GetNumberOfDimensions();
1141     origin.resize(dimension);
1142     inputSpacing.resize(dimension);
1143     inputSize.resize(dimension);
1144     sizeMM.resize(dimension);
1145     pixelType = mSlicerManagers[index]->GetImage()->GetScalarTypeAsITKString().c_str();
1146     for (int i = 0; i < dimension; i++) {
1147       origin[i] = imageSelected->GetOrigin()[i];
1148       inputSpacing[i] = imageSelected->GetSpacing()[i];
1149       inputSize[i] = imageSelected->GetSize()[i];
1150       sizeMM[i] = inputSize[i]*inputSpacing[i];
1151       NPixel *= inputSize[i];
1152     }
1153     inputSizeInBytes = GetSizeInBytes(imageSelected->GetActualMemorySize()*1000);
1154
1155     QString dim = QString::number(dimension) + " (";
1156     dim += pixelType + ")";
1157
1158     infoPanel->setFileName(image);
1159     std::string creationImageTimeValue("No creation time");
1160     itk::ExposeMetaData< std::string > (*imageSelected->GetFirstMetaDataDictionary(), "creationImageTime", creationImageTimeValue);
1161     infoPanel->setImageCreationTime(QString(creationImageTimeValue.c_str()));
1162     infoPanel->setDimension(dim);
1163     infoPanel->setSizePixel(GetVectorIntAsString(inputSize));
1164     infoPanel->setSizeMM(GetVectorDoubleAsString(sizeMM));
1165     infoPanel->setOrigin(GetVectorDoubleAsString(origin));
1166     infoPanel->setSpacing(GetVectorDoubleAsString(inputSpacing));
1167     infoPanel->setNPixel(QString::number(NPixel)+" ("+inputSizeInBytes+")");
1168
1169     transformation = imageSelected->GetTransform()[tSlice]->GetMatrix();
1170     infoPanel->setTransformation(Get4x4MatrixDoubleAsString(transformation));
1171
1172     landmarksPanel->SetCurrentLandmarks(mSlicerManagers[index]->GetLandmarks(),
1173                                         mSlicerManagers[index]->GetTSlice());
1174     landmarksPanel->SetCurrentPath(mInputPathName.toStdString());
1175     landmarksPanel->SetCurrentImage(mSlicerManagers[index]->GetFileName().c_str());
1176
1177     overlayPanel->getCurrentImageName(mSlicerManagers[index]->GetFileName().c_str());
1178     for (int i = 0; i < 4; i++) {
1179       if (DataTree->selectedItems()[0]->data(i+1,Qt::CheckStateRole).toInt() > 0 || i == 3) {
1180         mSlicerManagers[index]->UpdateInfoOnCursorPosition(i);
1181         break;
1182       }
1183     }
1184
1185 //     infoPanel->setFileName(image);
1186 //     infoPanel->setDimension(dim);
1187 //     infoPanel->setSizePixel(GetVectorIntAsString(inputSize));
1188 //     infoPanel->setSizeMM(GetVectorDoubleAsString(sizeMM));
1189 //     infoPanel->setOrigin(GetVectorDoubleAsString(origin));
1190 //     infoPanel->setSpacing(GetVectorDoubleAsString(inputSpacing));
1191 //     infoPanel->setNPixel(QString::number(NPixel)+" ("+inputSizeInBytes+")");
1192 //
1193 //     landmarksPanel->SetCurrentLandmarks(mSlicerManagers[index]->GetLandmarks(),
1194 //                                         mSlicerManagers[index]->GetTSlice());
1195 //     landmarksPanel->SetCurrentPath(mInputPathName.toStdString());
1196 //     landmarksPanel->SetCurrentImage(mSlicerManagers[index]->GetFileName().c_str());
1197 //
1198 //     overlayPanel->getCurrentImageName(mSlicerManagers[index]->GetFileName().c_str());
1199 //     for (int i = 0; i < 4; i++) {
1200 //       if (DataTree->selectedItems()[0]->data(i+1,Qt::CheckStateRole).toInt() > 0 || i == 3) {
1201 //         mSlicerManagers[index]->UpdateInfoOnCursorPosition(i);
1202 //         break;
1203 //       }
1204 //     }
1205     WindowLevelChanged();
1206
1207     slicingPresetComboBox->setCurrentIndex(mSlicerManagers[index]->GetSlicingPreset());
1208
1209     if (mSlicerManagers[index]->GetSlicer(0)->GetVF()) {
1210       overlayPanel->getVFName(mSlicerManagers[index]->GetVFName().c_str());
1211       overlayPanel->getVFProperty(mSlicerManagers[index]->GetSlicer(0)->GetVFSubSampling(),
1212         mSlicerManagers[index]->GetSlicer(0)->GetVFScale(),
1213         mSlicerManagers[index]->GetSlicer(0)->GetVFLog());
1214     } else {
1215       overlayPanel->getVFName(mSlicerManagers[index]->GetVFName().c_str());
1216       overlayPanel->getVFProperty(-1,-1,-1);
1217     }
1218     if (mSlicerManagers[index]->GetSlicer(0)->GetOverlay()) {
1219       overlayPanel->getOverlayName(mSlicerManagers[index]->GetOverlayName().c_str());
1220     } else {
1221       overlayPanel->getOverlayName(mSlicerManagers[index]->GetOverlayName().c_str());
1222     }
1223
1224     if (mSlicerManagers[index]->GetSlicer(0)->GetFusion()) {
1225       overlayPanel->getFusionName(mSlicerManagers[index]->GetFusionName().c_str());
1226     } else {
1227       overlayPanel->getFusionName(mSlicerManagers[index]->GetFusionName().c_str());
1228     }
1229   }
1230 }
1231 //------------------------------------------------------------------------------
1232
1233 //------------------------------------------------------------------------------
1234 void vvMainWindow::ShowDocumentation()
1235 {
1236   documentation->show();
1237 }
1238 //------------------------------------------------------------------------------
1239
1240 //------------------------------------------------------------------------------
1241 void vvMainWindow::PopupRegisterForm(bool checkCanPush)
1242 {
1243   vvRegisterForm* registerForm = new vvRegisterForm(QUrl("http://www.creatis.insa-lyon.fr/~dsarrut/vvregister/write.php"), getVVSettingsPath(), getSettingsOptionFormat());
1244   if(!checkCanPush) {
1245     registerForm->show();
1246   } else {
1247     if(registerForm->canPush()) {
1248       registerForm->show();
1249       registerForm->acquitPushed();//too bad if there is not internet connection anymore.
1250     }
1251   }
1252 }
1253 //------------------------------------------------------------------------------
1254
1255 //------------------------------------------------------------------------------
1256 void vvMainWindow::ShowHelpDialog()
1257 {
1258   help_dialog->show();
1259 }
1260 //------------------------------------------------------------------------------
1261
1262 //------------------------------------------------------------------------------
1263 void vvMainWindow::ChangeViewMode()
1264 {
1265   typedef struct _SIZE{
1266     QSplitter* splitter;
1267     QList<int> size1, size2;
1268     int cols[3];
1269   }SplitterSize;
1270   SplitterSize sizes[4];
1271   sizes[0].splitter = OSplitter;
1272   sizes[0].size1.push_back(1);
1273   sizes[0].size1.push_back(0);
1274   sizes[0].size2.push_back(1);
1275   sizes[0].size2.push_back(0);
1276   sizes[0].cols[0] = 2;
1277   sizes[0].cols[1] = 3;
1278   sizes[0].cols[2] = 4;
1279
1280   sizes[1].splitter = ESplitter;
1281   sizes[1].size1.push_back(0);
1282   sizes[1].size1.push_back(1);
1283   sizes[1].size2.push_back(1);
1284   sizes[1].size2.push_back(0);
1285   sizes[1].cols[0] = 1;
1286   sizes[1].cols[1] = 3;
1287   sizes[1].cols[2] = 4;
1288
1289   sizes[2].splitter = OSplitter;
1290   sizes[2].size1.push_back(1);
1291   sizes[2].size1.push_back(0);
1292   sizes[2].size2.push_back(0);
1293   sizes[2].size2.push_back(1);
1294   sizes[2].cols[0] = 1;
1295   sizes[2].cols[1] = 2;
1296   sizes[2].cols[2] = 4;
1297
1298   sizes[3].splitter = ESplitter;
1299   sizes[3].size1.push_back(0);
1300   sizes[3].size1.push_back(1);
1301   sizes[3].size2.push_back(0);
1302   sizes[3].size2.push_back(1);
1303   sizes[3].cols[0] = 1;
1304   sizes[3].cols[1] = 2;
1305   sizes[3].cols[2] = 3;
1306
1307   int slicer = mSlicerManagers[mCurrentPickedImageIndex]->GetSelectedSlicer();
1308   if (viewMode == 1) {
1309     if (slicer >= 0) {
1310       viewMode = 0;
1311       splitter_3->setSizes(sizes[slicer].size1);
1312       sizes[slicer].splitter->setSizes(sizes[slicer].size2);
1313       DataTree->setColumnHidden(sizes[slicer].cols[0],1);
1314       DataTree->setColumnHidden(sizes[slicer].cols[1],1);
1315       DataTree->setColumnHidden(sizes[slicer].cols[2],1);
1316     }
1317   } else {
1318     QList<int> size;
1319     if (slicer >= 0) {
1320       viewMode = 1;
1321       size.push_back(1);
1322       size.push_back(1);
1323       splitter_3->setSizes(size);
1324       sizes[slicer].splitter->setSizes(size);
1325       DataTree->setColumnHidden(sizes[slicer].cols[0],0);
1326       DataTree->setColumnHidden(sizes[slicer].cols[1],0);
1327       DataTree->setColumnHidden(sizes[slicer].cols[2],0);
1328     }
1329   }
1330   UpdateRenderWindows();
1331   /*
1332   ** I don't know why but for both resized QVTKWidget we also need to render
1333   ** the associated Slicer to redraw crosses.
1334   */
1335   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
1336     //     if (DataTree->topLevelItem(i)->data(COLUMN_UL_VIEW,Qt::CheckStateRole).toInt() > 1)
1337     mSlicerManagers[i]->GetSlicer(0)->Render();
1338     mSlicerManagers[i]->GetSlicer(1)->Render();
1339     //     if (DataTree->topLevelItem(i)->data(COLUMN_DL_VIEW,Qt::CheckStateRole).toInt() > 1)
1340     mSlicerManagers[i]->GetSlicer(2)->Render();
1341     mSlicerManagers[i]->GetSlicer(3)->Render();
1342   }
1343 }
1344 //------------------------------------------------------------------------------
1345
1346 //------------------------------------------------------------------------------
1347 QString vvMainWindow::GetSizeInBytes(unsigned long size)
1348 {
1349   QString result = "";// QString::number(size);
1350   //result += " bytes (";
1351   if (size > 1000000000) {
1352     size /= 1000000000;
1353     result += QString::number(size);
1354     result += "Gb";//)";
1355   } else if (size > 1000000) {
1356     size /= 1000000;
1357     result += QString::number(size);
1358     result += "Mb";//)";
1359   } else if (size > 1000) {
1360     size /= 1000;
1361     result += QString::number(size);
1362     result += "kb";//)";
1363   }
1364   return result;
1365 }
1366 //------------------------------------------------------------------------------
1367
1368 //------------------------------------------------------------------------------
1369 QString vvMainWindow::Get4x4MatrixDoubleAsString(vtkSmartPointer<vtkMatrix4x4> matrix, const int precision)
1370 {
1371   std::ostringstream strmatrix;
1372
1373   // Figure out the number of digits of the integer part of the largest absolute value
1374   // for each column
1375   unsigned width[4];
1376   for (unsigned int j = 0; j < 4; j++){
1377     double absmax = 0.;
1378     for (unsigned int i = 0; i < 4; i++)
1379       absmax = std::max(absmax, vnl_math_abs(matrix->GetElement(i, j)));
1380     unsigned ndigits = (unsigned)std::max(0.,std::log10(absmax))+1;
1381     width[j] = precision+ndigits+3;
1382   }
1383
1384   // Output with correct width, aligned to the right
1385   for (unsigned int i = 0; i < 4; i++) {
1386     for (unsigned int j = 0; j < 4; j++) {
1387       strmatrix.setf(ios::fixed,ios::floatfield);
1388       strmatrix.precision(precision);
1389       strmatrix.fill(' ');
1390       strmatrix.width(width[j]);
1391       strmatrix << std::right << matrix->GetElement(i, j);
1392     }
1393     strmatrix << std::endl;
1394   }
1395   QString result = strmatrix.str().c_str();
1396   return result;
1397 }
1398 //------------------------------------------------------------------------------
1399
1400 //------------------------------------------------------------------------------
1401 QString vvMainWindow::GetVectorDoubleAsString(std::vector<double> vectorDouble)
1402 {
1403   QString result;
1404   for (unsigned int i= 0; i < vectorDouble.size(); i++) {
1405     if (i != 0)
1406       result += " ";
1407     result += QString::number(vectorDouble[i]);
1408   }
1409   return result;
1410 }
1411 //------------------------------------------------------------------------------
1412
1413 //------------------------------------------------------------------------------
1414 QString vvMainWindow::GetVectorIntAsString(std::vector<int> vectorInt)
1415 {
1416   QString result;
1417   for (unsigned int i= 0; i < vectorInt.size(); i++) {
1418     if (i != 0)
1419       result += " ";
1420     result += QString::number(vectorInt[i]);
1421   }
1422   return result;
1423 }
1424 //------------------------------------------------------------------------------
1425
1426 //------------------------------------------------------------------------------
1427 //this actually returns the SlicerManager index!
1428 int vvMainWindow::GetSlicerIndexFromItem(QTreeWidgetItem* item)
1429 {
1430   QString id = item->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString();
1431   for (int i = 0; i < DataTree->topLevelItemCount(); i++) {
1432     if (DataTree->topLevelItem(i)->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString() == id)
1433       return i;
1434   }
1435   return -1;
1436 }
1437 //------------------------------------------------------------------------------
1438
1439 //------------------------------------------------------------------------------
1440 QTreeWidgetItem* vvMainWindow::GetItemFromSlicerManager(vvSlicerManager* sm)
1441 {
1442   QString id = sm->GetId().c_str();
1443   for (int i = 0; i < DataTree->topLevelItemCount(); i++) {
1444     if (DataTree->topLevelItem(i)->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString() == id)
1445       return DataTree->topLevelItem(i);
1446   }
1447   return NULL;
1448 }
1449 //------------------------------------------------------------------------------
1450
1451 //------------------------------------------------------------------------------
1452 void vvMainWindow::DisplayChanged(QTreeWidgetItem *clickedItem, int column)
1453 {
1454   if ( column >= COLUMN_CLOSE_IMAGE || column <= 0)
1455     return;
1456
1457   // Get parent information (might be the same item)
1458   int slicerManagerIndex = GetSlicerIndexFromItem(clickedItem);
1459   QTreeWidgetItem* clickedParentItem = DataTree->topLevelItem(slicerManagerIndex);
1460   vvSlicer* clickedSlicer = mSlicerManagers[slicerManagerIndex]->GetSlicer(column-1);
1461
1462   // Go over the complete item tree (only 2 levels, parents and children)
1463   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
1464     // Trick to avoid redoing twice the job for a key (sr)
1465     mSlicerManagers[i]->GetSlicer(column-1)->GetRenderWindow()->GetInteractor()->SetKeySym("Crap");
1466
1467     QTreeWidgetItem* currentParentItem = DataTree->topLevelItem(i);
1468     if(currentParentItem != clickedParentItem) {
1469       // Not the branch of the clicked item, uncheck all
1470
1471       // Parent
1472       currentParentItem->setData(column,Qt::CheckStateRole, 0);
1473       mSlicerManagers[i]->UpdateSlicer(column-1, false);
1474
1475       // Children
1476       for (int iChild = 0; iChild < currentParentItem->childCount(); iChild++) {
1477         currentParentItem->child(iChild)->setData(column,Qt::CheckStateRole, 0);
1478       }
1479     }
1480     else {
1481       // Branch of the clicked one: get check status from actor visibility in slicer
1482       // and toggle the clicked one
1483
1484       // Parent
1485       bool vis = clickedSlicer->GetActorVisibility("image", 0);
1486       bool draw = clickedSlicer->GetRenderer()->GetDraw();
1487
1488       // Update slicer (after getting visibility)
1489       mSlicerManagers[slicerManagerIndex]->UpdateSlicer(column-1, true);
1490       mSlicerManagers[slicerManagerIndex]->UpdateInfoOnCursorPosition(column-1);
1491       DisplaySliders(slicerManagerIndex, column-1);
1492       if(clickedParentItem == clickedItem) {
1493         // Toggle
1494         vis = !draw || !vis;
1495       }
1496       clickedSlicer->SetActorVisibility("image", 0, vis);
1497       clickedParentItem->setData(column, Qt::CheckStateRole, vis?2:0);
1498
1499       // Children
1500       std::map<std::string, int> actorTypeCounts;
1501       for (int iChild = 0; iChild < clickedParentItem->childCount(); iChild++) {
1502         QTreeWidgetItem* currentChildItem = clickedParentItem->child(iChild);
1503         std::string actorType = currentChildItem->data(1,Qt::UserRole).toString().toStdString();
1504         vis = clickedSlicer->GetActorVisibility(actorType, actorTypeCounts[actorType]);
1505         if(currentChildItem == clickedItem) {
1506           // Toggle or force visibility if it was not on this branch so far
1507           vis = !draw || !vis;
1508           clickedSlicer->SetActorVisibility(actorType, actorTypeCounts[actorType], vis);
1509         }
1510         currentChildItem->setData(column, Qt::CheckStateRole, vis?2:0);
1511         actorTypeCounts[actorType]++;
1512       }
1513     }
1514   }
1515
1516   clickedSlicer->Render();
1517 }
1518 //------------------------------------------------------------------------------
1519
1520 void vvMainWindow::InitSlicers()
1521 {
1522   if (mSlicerManagers.size()) {
1523     mSlicerManagers.back()->GenerateDefaultLookupTable();
1524
1525     mSlicerManagers.back()->SetSlicerWindow(0,NOViewWidget->GetRenderWindow());
1526     mSlicerManagers.back()->SetSlicerWindow(1,NEViewWidget->GetRenderWindow());
1527     mSlicerManagers.back()->SetSlicerWindow(2,SOViewWidget->GetRenderWindow());
1528     mSlicerManagers.back()->SetSlicerWindow(3,SEViewWidget->GetRenderWindow());
1529   }
1530 }
1531
1532 //------------------------------------------------------------------------------
1533 void vvMainWindow::InitDisplay()
1534 {
1535   if (mSlicerManagers.size()) {
1536     //BE CAREFUL : this is absolutely necessary to set the interactor style
1537     //in order to have the same style instanciation for all SlicerManagers in
1538     // a same window
1539     for (int j = 0; j < 4; j++) {
1540       vvInteractorStyleNavigator* style = vvInteractorStyleNavigator::New();
1541       style->SetAutoAdjustCameraClippingRange(1);
1542       bool AlreadySelected = false;
1543       for (int i = 0; i < DataTree->topLevelItemCount(); i++) {
1544         mSlicerManagers[i]->SetInteractorStyleNavigator(j,style);
1545
1546         //select the image only if previous are not selected
1547         if (DataTree->topLevelItem(i)->data(j+1,Qt::CheckStateRole).toInt() > 1) {
1548           mSlicerManagers[i]->UpdateSlicer(j,1);
1549           AlreadySelected = true;
1550         } else if (i == DataTree->topLevelItemCount()-1 && !AlreadySelected) {
1551           if (DataTree->selectedItems().size() == 0)
1552             DataTree->topLevelItem(i)->setSelected(1);
1553           DataTree->topLevelItem(i)->setData(j+1,Qt::CheckStateRole,2);
1554           mSlicerManagers[i]->UpdateSlicer(j,1);
1555           DisplaySliders(i,j);
1556         } else {
1557           DataTree->topLevelItem(i)->setData(j+1,Qt::CheckStateRole,0);
1558           mSlicerManagers[i]->UpdateSlicer(j,0);
1559         }
1560       }
1561       style->Delete();
1562     }
1563   }
1564 }
1565 //------------------------------------------------------------------------------
1566
1567 //------------------------------------------------------------------------------
1568 void vvMainWindow::DisplaySliders(int slicer, int window)
1569 {
1570   if(!mSlicerManagers[slicer]->GetSlicer(window)->GetRenderer()->GetDraw())
1571     return;
1572
1573   int range[2];
1574   mSlicerManagers[slicer]->GetSlicer(window)->GetSliceRange(range);
1575   int position = mSlicerManagers[slicer]->GetSlicer(window)->GetSlice();
1576   if (range[1]>0)
1577     verticalSliders[window]->show();
1578   else
1579     verticalSliders[window]->hide();
1580   verticalSliders[window]->setRange(range[0],range[1]);
1581   verticalSliders[window]->setValue(position);
1582
1583   int tRange[2];
1584   tRange[0] = 0;
1585   tRange[1] = mSlicerManagers[slicer]->GetSlicer(window)->GetTMax();
1586   if (tRange[1]>0)
1587     horizontalSliders[window]->show();
1588   else
1589     horizontalSliders[window]->hide();
1590   horizontalSliders[window]->setRange(tRange[0],tRange[1]);
1591   int tPosition = mSlicerManagers[slicer]->GetSlicer(window)->GetMaxCurrentTSlice();
1592   horizontalSliders[window]->setValue(tPosition);
1593 }
1594 //------------------------------------------------------------------------------
1595
1596 //------------------------------------------------------------------------------
1597 void vvMainWindow::CloseImage(QTreeWidgetItem* item, int column)
1598 {
1599   int index = GetSlicerIndexFromItem(item);
1600
1601   if (DataTree->topLevelItem(index) != item) {
1602     QString warning = "Do you really want to close the overlay : ";
1603     warning += item->data(COLUMN_IMAGE_NAME,Qt::DisplayRole).toString();
1604     QMessageBox msgBox(QMessageBox::Warning, tr("Close Overlay"),
1605       warning, 0, this);
1606     msgBox.addButton(tr("Close"), QMessageBox::AcceptRole);
1607     msgBox.addButton(tr("Cancel"), QMessageBox::RejectRole);
1608     if (msgBox.exec() == QMessageBox::AcceptRole) {
1609       std::string overlay_type=item->data(1,Qt::UserRole).toString().toStdString();
1610       int overlay_index=0;
1611       for (int child = 0; child < DataTree->topLevelItem(index)->childCount(); child++) {
1612         if (DataTree->topLevelItem(index)->\
1613           child(child)->data(1,Qt::UserRole).toString().toStdString() == overlay_type)
1614           overlay_index++;
1615         if (DataTree->topLevelItem(index)->child(child) == item) break;
1616       }
1617       if (overlay_type=="fusionSequence") {
1618         //removing the overlay sequence in a fusion sequence visualization mode
1619         //reset the transforms
1620         overlayPanel->getFusionSequenceProperty(-1, false, 0, false);
1621
1622         //unlink and untie the slicer managers
1623         RemoveLink(mSlicerManagers[index]->GetId().c_str(), mSlicerManagers[mSlicerManagers[index]->GetFusionSequenceIndexOfLinkedManager()]->GetId().c_str());
1624         mSlicerManagers[index]->SetFusionSequenceInvolvmentCode(-1);
1625         mSlicerManagers[mSlicerManagers[index]->GetFusionSequenceIndexOfLinkedManager()]->SetFusionSequenceInvolvmentCode(-1);
1626         for (unsigned i=0 ; i<4 ; i++) {
1627             mSlicerManagers[index]->GetSlicer(i)->SetFusionSequenceCode(-1);
1628             mSlicerManagers[mSlicerManagers[index]->GetFusionSequenceIndexOfLinkedManager()]->GetSlicer(i)->SetFusionSequenceCode(-1);
1629         }
1630
1631       }
1632       mSlicerManagers[index]->RemoveActor(overlay_type, overlay_index-1);
1633       mSlicerManagers[index]->SetColorMap(0);
1634       DataTree->topLevelItem(index)->takeChild(DataTree->topLevelItem(index)->indexOfChild(item));
1635       mSlicerManagers[index]->Render();
1636     }
1637   } else if (DataTree->topLevelItemCount() <= 1) {
1638     QString warning = "Do you really want to close the image : ";
1639     warning += item->data(COLUMN_IMAGE_NAME,Qt::DisplayRole).toString();
1640     warning += "\nThis is the last image, you're about to close vv !!!";
1641     QMessageBox msgBox(QMessageBox::Warning, tr("Close Image"),
1642       warning, 0, this);
1643     msgBox.addButton(tr("Close vv"), QMessageBox::AcceptRole);
1644     msgBox.addButton(tr("Cancel"), QMessageBox::RejectRole);
1645     if (msgBox.exec() == QMessageBox::AcceptRole) {
1646       this->close();
1647     }
1648   } else {
1649     QString warning = "Do you really want to close the image : ";
1650     warning += item->data(COLUMN_IMAGE_NAME,Qt::DisplayRole).toString();
1651     QMessageBox msgBox(QMessageBox::Warning, tr("Close Image"),
1652       warning, 0, this);
1653     msgBox.addButton(tr("Close"), QMessageBox::AcceptRole);
1654     msgBox.addButton(tr("Cancel"), QMessageBox::RejectRole);
1655     if (msgBox.exec() == QMessageBox::AcceptRole) {
1656
1657       // Tell tools that we close an image
1658       emit AnImageIsBeingClosed(mSlicerManagers[index]);
1659
1660       std::vector<vvSlicerManager*>::iterator Manageriter = mSlicerManagers.begin();
1661       DataTree->takeTopLevelItem(index);
1662       for (int i = 0; i < index; i++) {
1663         Manageriter++;
1664       }
1665       //if the slicer manager was involved in a fusion sequence visualization...
1666       if ( mSlicerManagers[index]->IsInvolvedInFusionSequence() ) {
1667         //in both cases, close the overlay: find it... and close it
1668         //ideally, I should duplicate the code, and avoid calling CloseImage, since this pops up another interactive box
1669         QTreeWidgetItem* overlayItem;
1670         if (mSlicerManagers[index]->IsMainSequenceOfFusionSequence()) {
1671           for (unsigned i=0 ; i<item->childCount() ; i++) {
1672             overlayItem = item->child(i);
1673             this->CloseImage( overlayItem, 0 );
1674           }
1675         }
1676         else {
1677           QTreeWidgetItem* linkedItem = this->GetItemFromSlicerManager( mSlicerManagers[mSlicerManagers[index]->GetFusionSequenceIndexOfLinkedManager()] );
1678           for (unsigned i=0 ; i<linkedItem->childCount() ; i++) {
1679             overlayItem = linkedItem->child(i);
1680             this->CloseImage( overlayItem, 0 );
1681           }
1682         }
1683
1684         /* -- this is normally already done when closing the overlay.
1685         //reset the transforms
1686         overlayPanel->getFusionSequenceProperty(-1, false, 0, false);
1687
1688         //unlink and untie the slicer managers
1689         RemoveLink(mSlicerManagers[index]->GetId().c_str(), mSlicerManagers[mSlicerManagers[index]->GetFusionSequenceIndexOfLinkedManager()]->GetId().c_str());
1690         mSlicerManagers[index]->SetFusionSequenceInvolvmentCode(-1);
1691         mSlicerManagers[mSlicerManagers[index]->GetFusionSequenceIndexOfLinkedManager()]->SetFusionSequenceInvolvmentCode(-1);
1692         for (unsigned i=0 ; i<4 ; i++) {
1693             mSlicerManagers[index]->GetSlicer(i)->SetFusionSequenceCode(-1);
1694             mSlicerManagers[mSlicerManagers[index]->GetFusionSequenceIndexOfLinkedManager()]->GetSlicer(i)->SetFusionSequenceCode(-1);
1695         }
1696         */
1697       }
1698
1699       linkPanel->removeImage(index);
1700       mSlicerManagers[index]->RemoveActors();
1701
1702       //remove the slicer manager
1703       delete mSlicerManagers[index];
1704       mSlicerManagers.erase(Manageriter);
1705
1706       //
1707       InitDisplay();
1708     }
1709   }
1710   ImageInfoChanged();
1711 }
1712 //------------------------------------------------------------------------------
1713
1714 //------------------------------------------------------------------------------
1715 void vvMainWindow::ReloadImage(QTreeWidgetItem* item, int column)
1716 {
1717   // int index = GetSlicerIndexFromItem(item);
1718   //   QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
1719   //   if (item->data(1,Qt::UserRole).toString() == "vector")
1720   //     mSlicerManagers[index]->ReloadVF();
1721   //   else
1722   //     mSlicerManagers[index]->Reload();
1723
1724   //   QApplication::restoreOverrideCursor();
1725   int index = GetSlicerIndexFromItem(item);
1726   QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
1727   QString role=item->data(1,Qt::UserRole).toString();
1728   if ( role == "vector") {
1729     mSlicerManagers[index]->ReloadVF();
1730   }
1731   else if (role == "overlay") {
1732     mSlicerManagers[index]->ReloadOverlay();
1733   }
1734   else if (role == "fusion") {
1735     mSlicerManagers[index]->ReloadFusion();
1736   }
1737   else if (role == "fusionSequence") {
1738     //both versions of the secondary sequence must be updated.
1739     mSlicerManagers[index]->ReloadFusionSequence();
1740     mSlicerManagers[mSlicerManagers[index]->GetFusionSequenceIndexOfLinkedManager()]->Reload();
1741   }
1742   else {
1743     mSlicerManagers[index]->Reload();
1744     //if we update the secondary sequence, then the overlay of the main sequence should also be updated
1745     if (mSlicerManagers[index]->IsSecondarySequenceOfFusionSequence()) mSlicerManagers[mSlicerManagers[index]->GetFusionSequenceIndexOfLinkedManager()]->ReloadFusionSequence();
1746   }
1747   // Update view and info
1748   ImageInfoChanged();
1749   mSlicerManagers[index]->Render();
1750   QApplication::restoreOverrideCursor();
1751 }
1752 //------------------------------------------------------------------------------
1753
1754 //------------------------------------------------------------------------------
1755 void vvMainWindow::MousePositionChanged(int visibility,double x, double y, double z, double X, double Y, double Z , double value)
1756 {
1757   infoPanel->setCurrentInfo(visibility,x,y,z,X,Y,Z,value);
1758 }
1759 //------------------------------------------------------------------------------
1760
1761 //------------------------------------------------------------------------------
1762 void vvMainWindow::VectorChanged(int visibility,double x, double y, double z, double value)
1763 {
1764   overlayPanel->getCurrentVectorInfo(visibility,x,y,z,value);
1765 }
1766 //------------------------------------------------------------------------------
1767
1768 //------------------------------------------------------------------------------
1769 void vvMainWindow::OverlayChanged(int visibility, double valueOver, double valueRef)
1770 {
1771   overlayPanel->getCurrentOverlayInfo(visibility,valueOver, valueRef);
1772 }
1773 //------------------------------------------------------------------------------
1774
1775 //------------------------------------------------------------------------------
1776 void vvMainWindow::FusionChanged(int visibility, double value)
1777 {
1778   overlayPanel->getCurrentFusionInfo(visibility,value);
1779 }
1780 //------------------------------------------------------------------------------
1781
1782 //------------------------------------------------------------------------------
1783 //called when AddOverlayImage, AddFusionSequence
1784 //or when UpdateWindowLevel() is called ; when slicerManager emits WindowLevelChanged
1785 //when ImageInfoChanged() is called
1786 void vvMainWindow::WindowLevelChanged()
1787 {
1788   // Base image
1789   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1790   if(index==-1) return;
1791   windowSpinBox->setValue(mSlicerManagers[index]->GetColorWindow());
1792   levelSpinBox->setValue(mSlicerManagers[index]->GetColorLevel());
1793   colorMapComboBox->setCurrentIndex(mSlicerManagers[index]->GetColorMap());
1794   presetComboBox->setCurrentIndex(mSlicerManagers[index]->GetPreset());
1795
1796   // Overlay image
1797   if (mSlicerManagers[index]->GetSlicer(0)->GetOverlay())
1798     overlayPanel->getOverlayProperty(mSlicerManagers[index]->GetOverlayColor(),
1799     mSlicerManagers[index]->GetLinkOverlayWindowLevel(),
1800     mSlicerManagers[index]->GetOverlayColorWindow(),
1801     mSlicerManagers[index]->GetOverlayColorLevel());
1802   else
1803     overlayPanel->getOverlayProperty(-1,0,0.,0.);
1804
1805   // Fusion & SequenceFusion image
1806   if (mSlicerManagers[index]->GetSlicer(0)->GetFusion()) {
1807     overlayPanel->getFusionProperty(mSlicerManagers[index]->GetFusionOpacity(),
1808       mSlicerManagers[index]->GetFusionThresholdOpacity(),
1809       mSlicerManagers[index]->GetFusionColorMap(),
1810       mSlicerManagers[index]->GetFusionWindow(),
1811       mSlicerManagers[index]->GetFusionLevel());
1812     if (mSlicerManagers[index]->IsMainSequenceOfFusionSequence()) {
1813       overlayPanel->getFusionSequenceProperty(mSlicerManagers[index]->GetFusionSequenceFrameIndex(),
1814         mSlicerManagers[index]->GetFusionSequenceSpatialSyncFlag(),
1815         mSlicerManagers[index]->GetFusionSequenceNbFrames(),
1816         mSlicerManagers[index]->GetFusionSequenceTemporalSyncFlag());
1817     }
1818   }
1819   else if ( mSlicerManagers[index]->IsSecondarySequenceOfFusionSequence() ) {
1820     //if the image is involved in a fusion sequence, preserve the overlay panel!
1821     int ind = mSlicerManagers[index]->GetFusionSequenceIndexOfLinkedManager();
1822     overlayPanel->getFusionProperty(mSlicerManagers[ind]->GetFusionOpacity(),
1823       mSlicerManagers[ind]->GetFusionThresholdOpacity(),
1824       mSlicerManagers[ind]->GetFusionColorMap(),
1825       mSlicerManagers[ind]->GetFusionWindow(),
1826       mSlicerManagers[ind]->GetFusionLevel());
1827     overlayPanel->getFusionSequenceProperty(mSlicerManagers[ind]->GetFusionSequenceFrameIndex(),
1828       mSlicerManagers[ind]->GetFusionSequenceSpatialSyncFlag(),
1829       mSlicerManagers[ind]->GetFusionSequenceNbFrames(),
1830       mSlicerManagers[ind]->GetFusionSequenceTemporalSyncFlag());
1831   }
1832   else
1833   {
1834     overlayPanel->getFusionProperty(-1, -1, -1, -1, -1);
1835     overlayPanel->getFusionSequenceProperty(-1, false, 0, false);
1836   }
1837 }
1838 //------------------------------------------------------------------------------
1839
1840 //------------------------------------------------------------------------------
1841 void vvMainWindow::WindowLevelEdited()
1842 {
1843   presetComboBox->setCurrentIndex(WL_USER);
1844   UpdateWindowLevel();
1845 }
1846 //------------------------------------------------------------------------------
1847
1848 //------------------------------------------------------------------------------
1849 void vvMainWindow::SetWindowLevel(double w, double l)
1850 {
1851   windowSpinBox->setValue(w);
1852   levelSpinBox->setValue(l);
1853   presetComboBox->setCurrentIndex(WL_USER);
1854   colorMapComboBox->setCurrentIndex(0);
1855   UpdateWindowLevel();
1856 }
1857 //------------------------------------------------------------------------------
1858
1859 //------------------------------------------------------------------------------
1860 void vvMainWindow::UpdateWindowLevel()
1861 {
1862   if (DataTree->selectedItems().size()) {
1863     if (presetComboBox->currentIndex() == WL_VENTILATION) //For ventilation
1864       colorMapComboBox->setCurrentIndex(5);
1865     int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1866     mSlicerManagers[index]->SetColorWindow(windowSpinBox->value());
1867     mSlicerManagers[index]->SetColorLevel(levelSpinBox->value());
1868     mSlicerManagers[index]->SetPreset(presetComboBox->currentIndex());
1869     mSlicerManagers[index]->Render();
1870     WindowLevelChanged();
1871   }
1872 }
1873 //------------------------------------------------------------------------------
1874
1875 //------------------------------------------------------------------------------
1876 void vvMainWindow::UpdateSlicingPreset()
1877 {
1878   if (DataTree->selectedItems().size()) {
1879     int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1880     mSlicerManagers[index]->SetSlicingPreset(vvSlicerManager::SlicingPresetType(slicingPresetComboBox->currentIndex()));
1881   }
1882 }
1883 //------------------------------------------------------------------------------
1884
1885 //------------------------------------------------------------------------------
1886 void vvMainWindow::UpdateColorMap()
1887 {
1888   if (DataTree->selectedItems().size()) {
1889     int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1890     mSlicerManagers[index]->SetColorMap(colorMapComboBox->currentIndex());
1891     mSlicerManagers[index]->Render();
1892   }
1893 }
1894 //------------------------------------------------------------------------------
1895 void vvMainWindow::SwitchWindowLevel()
1896 {
1897   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1898   int window = mSlicerManagers[index]->GetColorWindow();
1899   presetComboBox->setCurrentIndex(WL_USER);
1900   windowSpinBox->setValue(-window);
1901   UpdateWindowLevel();
1902 }
1903 //------------------------------------------------------------------------------
1904
1905 //------------------------------------------------------------------------------
1906 void vvMainWindow::ApplyWindowLevelToAllImages()
1907 {
1908   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1909   if(index==-1) return;
1910   double window = mSlicerManagers[index]->GetColorWindow();
1911   double level = mSlicerManagers[index]->GetColorLevel();
1912
1913   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
1914     if (mSlicerManagers[i] == NULL)
1915       continue;
1916     mSlicerManagers[i]->SetColorWindow(window);
1917     mSlicerManagers[i]->SetColorLevel(level);
1918     mSlicerManagers[i]->SetPreset(WL_USER);
1919     mSlicerManagers[i]->Render();
1920   }
1921 }
1922 //------------------------------------------------------------------------------
1923
1924 //------------------------------------------------------------------------------
1925 void vvMainWindow::ApplyWindowToSetOfImages(double window, unsigned int indexMin, unsigned int indexMax)
1926 {
1927   for (unsigned int i = indexMin; i <= indexMax && i < mSlicerManagers.size(); i++) {
1928     if (mSlicerManagers[i] == NULL)
1929       continue;
1930     mSlicerManagers[i]->SetColorWindow(window);
1931     mSlicerManagers[i]->SetPreset(WL_USER);
1932     mSlicerManagers[i]->Render();
1933   }
1934 }
1935 //------------------------------------------------------------------------------
1936
1937 //------------------------------------------------------------------------------
1938 void vvMainWindow::ApplyLevelToSetOfImages(double level, unsigned int indexMin, unsigned int indexMax)
1939 {
1940   for (unsigned int i = indexMin; i <= indexMax && i < mSlicerManagers.size(); i++) {
1941     if (mSlicerManagers[i] == NULL)
1942       continue;
1943     mSlicerManagers[i]->SetColorLevel(level);
1944     mSlicerManagers[i]->SetPreset(WL_USER);
1945     mSlicerManagers[i]->Render();
1946   }
1947 }
1948 //------------------------------------------------------------------------------
1949
1950 //------------------------------------------------------------------------------
1951 void vvMainWindow::UpdateLinkManager(std::string id, int slicer, double x, double y, double z, int temps)
1952 {
1953   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
1954     if (mSlicerManagers[i]->GetId() == id) {
1955       mSlicerManagers[i]->GetSlicer(slicer)->SetCurrentPosition(x,y,z,temps);
1956       mSlicerManagers[i]->UpdateViews(0,slicer);
1957       break;
1958     }
1959   }
1960 }
1961 //------------------------------------------------------------------------------
1962
1963 //------------------------------------------------------------------------------
1964 void vvMainWindow::UpdateLinkedNavigation(std::string id, vvSlicerManager * sm, vvSlicer* refSlicer)
1965 {
1966   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
1967     if (id == mSlicerManagers[i]->GetId()) {
1968       mSlicerManagers[i]->UpdateLinkedNavigation(refSlicer);
1969     }
1970   }
1971 }
1972 //------------------------------------------------------------------------------
1973
1974 //------------------------------------------------------------------------------
1975 void vvMainWindow::ShowContextMenu(QPoint point)
1976 {
1977   if (!DataTree->selectedItems().size()) {
1978     contextActions[1]->setEnabled(0);
1979     contextActions[2]->setEnabled(0);
1980     contextActions[3]->setEnabled(0);
1981     contextActions[4]->setEnabled(0);
1982     contextActions[5]->setEnabled(0);
1983     contextActions[6]->setEnabled(0);
1984   } else {
1985     int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1986     contextActions[1]->setEnabled(1);
1987     contextActions[2]->setEnabled(
1988       DataTree->itemWidget(DataTree->selectedItems()[0],
1989       COLUMN_RELOAD_IMAGE)->isEnabled());
1990     contextActions[3]->setEnabled(1);
1991     contextActions[5]->setEnabled(1);
1992     contextActions[6]->setEnabled(1);
1993
1994     if (mSlicerManagers[index]->GetDimension() < 3)
1995       contextActions[4]->setEnabled(0);
1996     else
1997       contextActions[4]->setEnabled(1);
1998   }
1999   contextMenu.exec(QCursor::pos());
2000 }
2001 //------------------------------------------------------------------------------
2002
2003 //------------------------------------------------------------------------------
2004 void vvMainWindow::CloseImage()
2005 {
2006   CloseImage(DataTree->selectedItems()[0],0);
2007 }
2008 //------------------------------------------------------------------------------
2009
2010 //------------------------------------------------------------------------------
2011 void vvMainWindow::ReloadImage()
2012 {
2013   ReloadImage(DataTree->selectedItems()[0],0);
2014 }
2015 //------------------------------------------------------------------------------
2016
2017 //------------------------------------------------------------------------------
2018 void vvMainWindow::SelectOverlayImage()
2019 {
2020   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2021
2022   //check if one overlay image is added
2023   for (int child = 0; child < DataTree->topLevelItem(index)->childCount(); child++)
2024     if (DataTree->topLevelItem(index)->child(child)->data(1,Qt::UserRole).toString() == "overlay") {
2025       QString error = "Cannot add more than one compared image\n";
2026       error += "Please remove first ";
2027       error += DataTree->topLevelItem(index)->child(child)->data(COLUMN_IMAGE_NAME,Qt::DisplayRole).toString();
2028       QMessageBox::information(this,tr("Problem adding compared image !"),error);
2029       return;
2030     }
2031
2032     QString Extensions = EXTENSIONS;
2033     Extensions += ";;All Files (*)";
2034     QStringList files = QFileDialog::getOpenFileNames(this,tr("Load Overlay image"),mInputPathName,Extensions);
2035     if (files.isEmpty())
2036       return;
2037
2038     std::vector<std::string> vecFileNames;
2039     for (int i = 0; i < files.size(); i++) {
2040       vecFileNames.push_back(files[i].toStdString());
2041     }
2042     AddOverlayImage(index,vecFileNames,vvImageReader::IMAGE);
2043 }
2044 //------------------------------------------------------------------------------
2045
2046 //------------------------------------------------------------------------------
2047 void vvMainWindow::AddOverlayImage(int index, std::vector<std::string> fileNames, vvImageReader::LoadedImageType type)
2048 {
2049   QString file(fileNames[0].c_str());
2050   if (QFile::exists(file))
2051   {
2052     mInputPathName = itksys::SystemTools::GetFilenamePath(file.toStdString()).c_str();
2053     itk::ImageIOBase::Pointer reader = itk::ImageIOFactory::CreateImageIO(
2054       file.toStdString().c_str(), itk::ImageIOFactory::ReadMode);
2055     reader->SetFileName(fileNames[0].c_str());
2056     reader->ReadImageInformation();
2057     std::string component = reader->GetComponentTypeAsString(reader->GetComponentType());
2058     int dimension = reader->GetNumberOfDimensions();
2059     QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
2060     vvProgressDialog progress("Opening " + file.toStdString());
2061     qApp->processEvents();
2062
2063     std::string filename = itksys::SystemTools::GetFilenameWithoutExtension(file.toStdString()).c_str();
2064     if (mSlicerManagers[index]->SetOverlay(fileNames,dimension, component,type)) {
2065       //create an item in the tree with good settings
2066       QTreeWidgetItem *item = new QTreeWidgetItem();
2067       item->setData(0,Qt::UserRole,file.toStdString().c_str());
2068       item->setData(1,Qt::UserRole,tr("overlay"));
2069       QFileInfo fileinfo(file); //Do not show the path
2070       item->setData(COLUMN_IMAGE_NAME,Qt::DisplayRole,fileinfo.fileName());
2071       item->setToolTip(COLUMN_IMAGE_NAME, mSlicerManagers[index]->GetListOfAbsoluteFilePathInOneString("overlay").c_str());
2072       qApp->processEvents();
2073
2074       for (int j = 1; j <= 4; j++) {
2075         item->setData(j,Qt::CheckStateRole,DataTree->topLevelItem(index)->data(j,Qt::CheckStateRole));
2076       }
2077
2078       //Create the buttons for reload and close
2079       qApp->processEvents();
2080       QTreePushButton* cButton = new QTreePushButton;
2081       cButton->setItem(item);
2082       cButton->setColumn(COLUMN_CLOSE_IMAGE);
2083       cButton->setToolTip(tr("close image"));
2084       cButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/exit.png")));
2085       connect(cButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
2086         this,SLOT(CloseImage(QTreeWidgetItem*, int)));
2087
2088       QTreePushButton* rButton = new QTreePushButton;
2089       rButton->setItem(item);
2090       rButton->setColumn(COLUMN_RELOAD_IMAGE);
2091       rButton->setToolTip(tr("reload image"));
2092       rButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/rotateright.png")));
2093       connect(rButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
2094         this,SLOT(ReloadImage(QTreeWidgetItem*, int)));
2095
2096       DataTree->topLevelItem(index)->setExpanded(1);
2097       DataTree->topLevelItem(index)->addChild(item);
2098       DataTree->setItemWidget(item, COLUMN_CLOSE_IMAGE, cButton);
2099       DataTree->setItemWidget(item, COLUMN_RELOAD_IMAGE, rButton);
2100
2101       //set the id of the image
2102       QString id = DataTree->topLevelItem(index)->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString();
2103       item->setData(COLUMN_IMAGE_NAME,Qt::UserRole,id.toStdString().c_str());
2104       UpdateTree();
2105       qApp->processEvents();
2106       ImageInfoChanged();
2107       QApplication::restoreOverrideCursor();
2108
2109       // Update the display to update, e.g., the sliders
2110       for(int i=0; i<4; i++)
2111         DisplaySliders(index, i);
2112     } else {
2113       QApplication::restoreOverrideCursor();
2114       QString error = "Cannot import the new image.\n";
2115       error += mSlicerManagers[index]->GetLastError().c_str();
2116       QMessageBox::information(this,tr("Problem reading image !"),error);
2117     }
2118     WindowLevelChanged();
2119   }
2120   else
2121     QMessageBox::information(this,tr("Problem reading Overlay !"),"File doesn't exist!");
2122 }
2123 //------------------------------------------------------------------------------
2124
2125
2126 //------------------------------------------------------------------------------
2127 void vvMainWindow::AddROI(int index, QString file)
2128 {
2129   /*
2130   // Get slice manager
2131
2132   // Load image
2133
2134   vvImageReader * mReader = new vvImageReader;
2135   mReader->SetInputFilename(filename.toStdString());
2136   mReader->Update(IMAGE);
2137   if (mReader->GetLastError().size() != 0) {
2138   std::cerr << "Error while reading " << filename.toStdString() << std::endl;
2139   QString error = "Cannot open file \n";
2140   error += mReader->GetLastError().c_str();
2141   QMessageBox::information(this,tr("Reading problem"),error);
2142   delete mReader;
2143   return;
2144   }
2145   vvImage::Pointer roi = mReader->GetOutput();
2146
2147   // Create roi in new tool
2148   vvToolStructureSetManager::AddImage(mCurrentSlicerManager, roi);
2149   */
2150 }
2151 //------------------------------------------------------------------------------
2152
2153 //------------------------------------------------------------------------------
2154 void vvMainWindow::SelectFusionImage()
2155 {
2156   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2157
2158   //check if one fusion image is added
2159   for (int child = 0; child < DataTree->topLevelItem(index)->childCount(); child++)
2160     if ( (DataTree->topLevelItem(index)->child(child)->data(1,Qt::UserRole).toString() == "fusion") ||
2161       (DataTree->topLevelItem(index)->child(child)->data(1,Qt::UserRole).toString() == "fusionSequence") ) {
2162         QString error = "Cannot add more than one fusion image\n";
2163         error += "Please remove first ";
2164         error += DataTree->topLevelItem(index)->child(child)->data(COLUMN_IMAGE_NAME,Qt::DisplayRole).toString();
2165         QMessageBox::information(this,tr("Problem adding fusion image !"),error);
2166         return;
2167     }
2168
2169     QString Extensions = EXTENSIONS;
2170     Extensions += ";;All Files (*)";
2171     QStringList files = QFileDialog::getOpenFileNames(this,tr("Load Fusion image"),mInputPathName,Extensions);
2172     if (files.isEmpty())
2173       return;
2174
2175     std::vector<std::string> vecFileNames;
2176     for (int i = 0; i < files.size(); i++) {
2177       vecFileNames.push_back(files[i].toStdString());
2178     }
2179     AddFusionImage(index,vecFileNames,vvImageReader::IMAGE);
2180 }
2181 //------------------------------------------------------------------------------
2182
2183 //------------------------------------------------------------------------------
2184 void vvMainWindow::ResetTransformationToIdentity()
2185 {
2186   std::string actorType = DataTree->selectedItems()[0]->data(1,Qt::UserRole).toString().toStdString();
2187   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2188   mSlicerManagers[index]->ResetTransformationToIdentity(actorType);
2189   ImageInfoChanged();
2190 }
2191 //------------------------------------------------------------------------------
2192
2193 //------------------------------------------------------------------------------
2194 void vvMainWindow::AddFusionImage(int index, std::vector<std::string> fileNames, vvImageReader::LoadedImageType type)
2195 {
2196   QString file(fileNames[0].c_str());
2197   if (QFile::exists(file))
2198   {
2199     mInputPathName = itksys::SystemTools::GetFilenamePath(file.toStdString()).c_str();
2200     itk::ImageIOBase::Pointer reader = itk::ImageIOFactory::CreateImageIO(
2201       file.toStdString().c_str(), itk::ImageIOFactory::ReadMode);
2202     reader->SetFileName(fileNames[0].c_str());
2203     reader->ReadImageInformation();
2204     std::string component = reader->GetComponentTypeAsString(reader->GetComponentType());
2205     int dimension = reader->GetNumberOfDimensions();
2206     QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
2207     vvProgressDialog progress("Opening fusion");
2208     qApp->processEvents();
2209
2210     std::string filename = itksys::SystemTools::GetFilenameWithoutExtension(file.toStdString()).c_str();
2211     if (mSlicerManagers[index]->SetFusion(fileNames,dimension, component,type)) {
2212       //create an item in the tree with good settings
2213       QTreeWidgetItem *item = new QTreeWidgetItem();
2214       item->setData(0,Qt::UserRole,file.toStdString().c_str());
2215       item->setData(1,Qt::UserRole,tr("fusion"));
2216       QFileInfo fileinfo(file); //Do not show the path
2217           item->setData(COLUMN_IMAGE_NAME,Qt::DisplayRole,fileinfo.fileName());
2218           item->setToolTip(COLUMN_IMAGE_NAME, mSlicerManagers[index]->GetListOfAbsoluteFilePathInOneString("fusion").c_str());
2219           qApp->processEvents();
2220
2221       for (int j = 1; j <= 4; j++) {
2222         item->setData(j,Qt::CheckStateRole,DataTree->topLevelItem(index)->data(j,Qt::CheckStateRole));
2223       }
2224
2225       //Create the buttons for reload and close
2226       qApp->processEvents();
2227       QTreePushButton* cButton = new QTreePushButton;
2228       cButton->setItem(item);
2229       cButton->setColumn(COLUMN_CLOSE_IMAGE);
2230       cButton->setToolTip(tr("close image"));
2231       cButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/exit.png")));
2232       connect(cButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
2233         this,SLOT(CloseImage(QTreeWidgetItem*, int)));
2234
2235       QTreePushButton* rButton = new QTreePushButton;
2236       rButton->setItem(item);
2237       rButton->setColumn(COLUMN_RELOAD_IMAGE);
2238       rButton->setToolTip(tr("reload image"));
2239       rButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/rotateright.png")));
2240       connect(rButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
2241         this,SLOT(ReloadImage(QTreeWidgetItem*, int)));
2242
2243       DataTree->topLevelItem(index)->setExpanded(1);
2244       DataTree->topLevelItem(index)->addChild(item);
2245       DataTree->setItemWidget(item, COLUMN_CLOSE_IMAGE, cButton);
2246       DataTree->setItemWidget(item, COLUMN_RELOAD_IMAGE, rButton);
2247
2248       //set the id of the image
2249       QString id = DataTree->topLevelItem(index)->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString();
2250       item->setData(COLUMN_IMAGE_NAME,Qt::UserRole,id.toStdString().c_str());
2251       UpdateTree();
2252       qApp->processEvents();
2253       ImageInfoChanged();
2254       QApplication::restoreOverrideCursor();
2255
2256       // Update the display to update, e.g., the sliders
2257       for(int i=0; i<4; i++)
2258         DisplaySliders(index, i);
2259     } else {
2260       QApplication::restoreOverrideCursor();
2261       QString error = "Cannot import the new image.\n";
2262       error += mSlicerManagers[index]->GetLastError().c_str();
2263       QMessageBox::information(this,tr("Problem reading image !"),error);
2264     }
2265     WindowLevelChanged();
2266   }
2267   else
2268     QMessageBox::information(this,tr("Problem reading Fusion !"),"File doesn't exist!");
2269 }
2270 //------------------------------------------------------------------------------
2271 //------------------------------------------------------------------------------
2272 void vvMainWindow::AddLandmarks(int index, std::vector<std::string> files)
2273 {
2274     if (!landmarksPanel->LoadFromFile(files))
2275       QMessageBox::information(this,tr("Problem reading Landmarks !"),"File doesn't exist!");
2276
2277     landmarksPanel->SetCurrentPath(mInputPathName.toStdString());
2278     landmarksPanel->SetCurrentImage(mSlicerManagers[index]->GetFileName().c_str());
2279 }
2280
2281 //------------------------------------------------------------------------------
2282 void vvMainWindow::OpenField()
2283 {
2284   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2285   //check if a vector field has already been added
2286   for (int child = 0; child < DataTree->topLevelItem(index)->childCount(); child++)
2287     if (DataTree->topLevelItem(index)->child(child)->data(1,Qt::UserRole).toString() == "vector") {
2288       QString error = "Cannot add more than one vector field\n";
2289       error += "Please remove first ";
2290       error += DataTree->topLevelItem(index)->child(child)->data(COLUMN_IMAGE_NAME,Qt::DisplayRole).toString();
2291       QMessageBox::information(this,tr("Problem adding vector field!"),error);
2292       return;
2293     }
2294
2295     QString Extensions = "Images ( *.mhd)";
2296     Extensions += ";;Images ( *.mha)";
2297     Extensions += ";;VF Images ( *.vf)";
2298     Extensions += ";;nii Images ( *.nii)";
2299     Extensions += ";;nrrd Images ( *.nrrd)";
2300     Extensions += ";;nhdr Images ( *.nhdr)";
2301     Extensions += ";;All Files (*)";
2302     QString file = QFileDialog::getOpenFileName(this,tr("Load deformation field"),mInputPathName,Extensions);
2303     if (!file.isEmpty())
2304       AddField(file,index);
2305 }
2306 //------------------------------------------------------------------------------
2307
2308
2309 //------------------------------------------------------------------------------
2310 void vvMainWindow::AddFieldEntry(QString filename,int index,bool from_disk)
2311 {
2312   //create an item in the tree with good settings
2313   QTreeWidgetItem *item = new QTreeWidgetItem();
2314   item->setData(0,Qt::UserRole,filename.toStdString().c_str());
2315   item->setData(1,Qt::UserRole,tr("vector"));
2316   QFileInfo fileinfo(filename); //Do not show the path
2317   item->setData(COLUMN_IMAGE_NAME,Qt::DisplayRole,fileinfo.fileName());
2318   item->setToolTip(COLUMN_IMAGE_NAME, mSlicerManagers[index]->GetListOfAbsoluteFilePathInOneString("vector").c_str());
2319   qApp->processEvents();
2320
2321   for (int j = 1; j <= 4; j++) {
2322     item->setData(j,Qt::CheckStateRole,DataTree->topLevelItem(index)->data(j,Qt::CheckStateRole));
2323   }
2324
2325   //Create the buttons for reload and close
2326   qApp->processEvents();
2327   QTreePushButton* cButton = new QTreePushButton;
2328   cButton->setItem(item);
2329   cButton->setColumn(COLUMN_CLOSE_IMAGE);
2330   cButton->setToolTip(tr("close vector field"));
2331   cButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/exit.png")));
2332   connect(cButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
2333     this,SLOT(CloseImage(QTreeWidgetItem*, int)));
2334
2335   QTreePushButton* rButton = new QTreePushButton;
2336   rButton->setItem(item);
2337   rButton->setColumn(COLUMN_RELOAD_IMAGE);
2338   rButton->setToolTip(tr("reload vector field"));
2339   rButton->setEnabled(from_disk);
2340   rButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/rotateright.png")));
2341   connect(rButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
2342     this,SLOT(ReloadImage(QTreeWidgetItem*, int)));
2343
2344   DataTree->topLevelItem(index)->setExpanded(1);
2345   DataTree->topLevelItem(index)->addChild(item);
2346   DataTree->setItemWidget(item, COLUMN_RELOAD_IMAGE, rButton);
2347   DataTree->setItemWidget(item, COLUMN_CLOSE_IMAGE, cButton);
2348
2349   //set the id of the image
2350   QString id = DataTree->topLevelItem(index)->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString();
2351   item->setData(COLUMN_IMAGE_NAME,Qt::UserRole,id.toStdString().c_str());
2352   UpdateTree();
2353   qApp->processEvents();
2354   ImageInfoChanged();
2355   QApplication::restoreOverrideCursor();
2356 }
2357 //------------------------------------------------------------------------------
2358
2359
2360 //------------------------------------------------------------------------------
2361 void vvMainWindow::AddField(vvImage::Pointer vf,QString file,int index)
2362 {
2363   QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
2364   vvSlicerManager* imageManager = mSlicerManagers[index];
2365   if (imageManager->SetVF(vf,file.toStdString())) {
2366     AddFieldEntry(file,index,false);
2367   } else {
2368     QString error = "Cannot import the vector field for this image.\n";
2369     error += imageManager->GetLastError().c_str();
2370     QMessageBox::information(this,tr("Problem reading VF !"),error);
2371   }
2372   QApplication::restoreOverrideCursor();
2373 }
2374 //------------------------------------------------------------------------------
2375
2376
2377 //------------------------------------------------------------------------------
2378 void vvMainWindow::AddField(QString file,int index)
2379 {
2380   if (QFile::exists(file)) {
2381     mInputPathName = itksys::SystemTools::GetFilenamePath(file.toStdString()).c_str();
2382
2383     //init the progress events
2384     QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
2385     vvProgressDialog progress("Opening " + file.toStdString());
2386     qApp->processEvents();
2387
2388     //read the vector and put it in the current mSlicerManager
2389     vvSlicerManager* imageManager = mSlicerManagers[index];
2390     qApp->processEvents();
2391
2392     std::string filename = itksys::SystemTools::GetFilenameWithoutExtension(file.toStdString()).c_str();
2393     if (imageManager->SetVF(file.toStdString())) {
2394       imageManager->Render();
2395       AddFieldEntry(file,index,true);
2396     } else {
2397       QApplication::restoreOverrideCursor();
2398       QString error = "Cannot import the vector field for this image.\n";
2399       error += imageManager->GetLastError().c_str();
2400       QMessageBox::information(this,tr("Problem reading VF !"),error);
2401     }
2402   } else
2403     QMessageBox::information(this,tr("Problem reading VF !"),"File doesn't exist!");
2404
2405 }
2406 //------------------------------------------------------------------------------
2407
2408
2409 //------------------------------------------------------------------------------
2410 void vvMainWindow::SetVFProperty(int subsampling, int scale, int log, int width, double r, double g, double b)
2411 {
2412   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2413   if (mSlicerManagers[index]->GetSlicer(0)->GetVF()) {
2414     for (int i = 0; i < 4; i++) {
2415       mSlicerManagers[index]->GetSlicer(i)->SetVFSubSampling(subsampling);
2416       mSlicerManagers[index]->GetSlicer(i)->SetVFScale(scale);
2417       mSlicerManagers[index]->GetSlicer(i)->SetVFWidth(width);
2418       mSlicerManagers[index]->GetSlicer(i)->SetVFColor(r,g,b);
2419       if (log > 0)
2420         mSlicerManagers[index]->GetSlicer(i)->SetVFLog(1);
2421       else
2422         mSlicerManagers[index]->GetSlicer(i)->SetVFLog(0);
2423     }
2424   }
2425 }
2426 //------------------------------------------------------------------------------
2427
2428
2429 //------------------------------------------------------------------------------
2430 void vvMainWindow::SetOverlayProperty(int color, int linked, double window, double level)
2431 {
2432   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2433   if (mSlicerManagers[index]->GetSlicer(0)->GetOverlay()) {
2434     mSlicerManagers[index]->SetOverlayColor(color);
2435     mSlicerManagers[index]->SetColorMap(0);
2436     mSlicerManagers[index]->SetLinkOverlayWindowLevel(linked);
2437     mSlicerManagers[index]->SetOverlayColorWindow(window);
2438     mSlicerManagers[index]->SetOverlayColorLevel(level);
2439     mSlicerManagers[index]->Render();
2440   }
2441 }
2442 //------------------------------------------------------------------------------
2443
2444 //------------------------------------------------------------------------------
2445 void vvMainWindow::SetFusionProperty(int opacity, int thresOpacity, int colormap,double window, double level, bool showLegend)
2446 {
2447   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2448   if (mSlicerManagers[index]->GetSlicer(0)->GetFusion()) {
2449     mSlicerManagers[index]->SetFusionColorMap(colormap);
2450     mSlicerManagers[index]->SetFusionOpacity(opacity);
2451     mSlicerManagers[index]->SetFusionThresholdOpacity(thresOpacity);
2452     mSlicerManagers[index]->SetFusionWindow(window);
2453     mSlicerManagers[index]->SetFusionLevel(level);
2454     mSlicerManagers[index]->SetFusionShowLegend(showLegend);
2455     mSlicerManagers[index]->SetColorMap(0);
2456     mSlicerManagers[index]->Render();
2457   }
2458 }
2459 //------------------------------------------------------------------------------
2460
2461
2462 //------------------------------------------------------------------------------
2463 void vvMainWindow::SelectFusionSequence()
2464 {
2465   //get the index of the slicer manager of the main sequence (CT)
2466   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2467   //check if one overlay image is already associated
2468   for (int child = 0; child < DataTree->topLevelItem(index)->childCount(); child++)
2469     if ( (DataTree->topLevelItem(index)->child(child)->data(1,Qt::UserRole).toString() == "fusion") ||
2470       (DataTree->topLevelItem(index)->child(child)->data(1,Qt::UserRole).toString() == "fusionSequence") ) {
2471         QString error = "Cannot add more than one compared image\n";
2472         error += "Please remove first ";
2473         error += DataTree->topLevelItem(index)->child(child)->data(COLUMN_IMAGE_NAME,Qt::DisplayRole).toString();
2474         QMessageBox::information(this,tr("Problem adding compared image !"),error);
2475         return;
2476     }
2477
2478     QString Extensions = EXTENSIONS;
2479     Extensions += ";;All Files (*)";
2480     QStringList files = QFileDialog::getOpenFileNames(this,tr("Load Overlay image sequence"),mInputPathName,Extensions);
2481     if (files.isEmpty())
2482       return;
2483
2484     std::vector<std::string> vecFileNames;
2485     for (int i = 0; i < files.size(); i++) {
2486       vecFileNames.push_back(files[i].toStdString());
2487     }
2488
2489     //associate the secondary sequence (US) to the main one
2490     AddFusionSequence(index,vecFileNames,vvImageReader::MERGEDWITHTIME);
2491 }
2492 //------------------------------------------------------------------------------
2493
2494
2495 //------------------------------------------------------------------------------
2496 void vvMainWindow::SelectFusionSequenceCorrespondances() {
2497
2498   //make sure the index is right?
2499   //in the end, I should attach the temporal data to the right sequence!
2500   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2501   //in case the other sequence got selected, make sure we select the primary sequence
2502   if ( (!mSlicerManagers[index]->GetSlicer(0)->GetFusion()) && mSlicerManagers[index]->GetFusionSequenceIndexOfLinkedManager()>=0 ) {
2503     index = mSlicerManagers[index]->GetFusionSequenceIndexOfLinkedManager();
2504   }
2505
2506   //open a dialog box to find a file
2507   //QString Extensions = EXTENSIONS;
2508   QString Extensions = ";;All Files (*)";
2509   QString fileName = QFileDialog::getOpenFileName(this,tr("Load respiratory signal for fused sequence"),mInputPathName,Extensions);
2510   if (fileName.isNull())
2511     return;
2512
2513   //read it as a vector of values
2514   vnl_vector<double> tmpVect;
2515
2516   std::ifstream file;
2517   file.open(fileName.toStdString().c_str());
2518   tmpVect.read_ascii(file);
2519   file.close();
2520
2521   //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
2522   bool signalOK = true;
2523   unsigned nbFrameMain = mSlicerManagers[index]->GetImage()->GetTransform().size();
2524   unsigned nbFrameSecondary = mSlicerManagers[index]->GetFusionSequenceNbFrames();
2525 std::cout<<"nbFrameMain = "<<nbFrameMain<<", nbFrameSecondary= "<<nbFrameSecondary<<", signal size: "<<tmpVect.size()<<std::endl;
2526   std::vector<unsigned> temporalCorrespondances;
2527   if ( tmpVect.size() == nbFrameMain + nbFrameSecondary ) {
2528     for (unsigned i=0 ; i<tmpVect.size() ; i++) {
2529       if (i<nbFrameMain) { //first part of the file: i -> index in secondary seq.
2530         if ( tmpVect(i)<nbFrameSecondary ) temporalCorrespondances.push_back(tmpVect(i));
2531         else { signalOK=false; break; } //pointing outside the secondary sequence...
2532       }
2533       else { //first part of the file -> index in secondary seq.
2534         if ( tmpVect(i)<nbFrameMain ) temporalCorrespondances.push_back(tmpVect(i));
2535         else { signalOK=false; break; } //pointing outside the secondary sequence...
2536       }
2537     }
2538   }
2539   else {signalOK=false;}
2540   if (!signalOK) {//else, send a message to signal the failure...
2541     QString error = "The provided temporal correspondances is invalid - check tooltip.\n";
2542     error += "Ignoring file: " + fileName;
2543     QMessageBox::information(this,tr("Problem adding temporal correspondances!"),error);
2544     return;
2545   }
2546   else {
2547     //for convenience, associate this sequence to both the current slicer manager, and to the linked one
2548     mSlicerManagers[index]->SetFusionSequenceCorrespondances(temporalCorrespondances);
2549     mSlicerManagers[ mSlicerManagers[index]->GetFusionSequenceIndexOfLinkedManager() ]->SetFusionSequenceCorrespondances(temporalCorrespondances);
2550     overlayPanel->enableFusionSequenceTemporalSync();
2551   }
2552
2553 }
2554 //------------------------------------------------------------------------------
2555
2556
2557 //------------------------------------------------------------------------------
2558 //when this function is called index is the slicer manager index corresponding to the main sequence (CT)
2559 //the files behind fileNames points to the data for the secondary sequence
2560 void vvMainWindow::AddFusionSequence(int index, std::vector<std::string> fileNames, vvImageReader::LoadedImageType type)
2561 {
2562   QString file(fileNames[0].c_str());
2563   if (QFile::exists(file))
2564   {
2565     mInputPathName = itksys::SystemTools::GetFilenamePath(file.toStdString()).c_str();
2566     itk::ImageIOBase::Pointer reader = itk::ImageIOFactory::CreateImageIO(
2567       file.toStdString().c_str(), itk::ImageIOFactory::ReadMode);
2568     std::sort (fileNames.begin(), fileNames.end());//make sure the files are sorted.
2569     reader->SetFileName(fileNames[0].c_str());
2570     reader->ReadImageInformation();
2571     std::string component = reader->GetComponentTypeAsString(reader->GetComponentType());
2572     int dimension = reader->GetNumberOfDimensions();
2573     QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
2574     vvProgressDialog progress("Opening " + file.toStdString());
2575     qApp->processEvents();
2576
2577     std::string filename = itksys::SystemTools::GetFilenameWithoutExtension(file.toStdString()).c_str();
2578
2579     if (mSlicerManagers[index]->SetFusionSequence(fileNames,dimension, component,type)) {
2580       //create an item in the tree with good settings
2581       QTreeWidgetItem *item = new QTreeWidgetItem();
2582       item->setData(0,Qt::UserRole,file.toStdString().c_str());
2583       item->setData(1,Qt::UserRole,tr("fusionSequence"));
2584
2585       QFileInfo fileinfo(file); //Do not show the path
2586       item->setData(COLUMN_IMAGE_NAME,Qt::DisplayRole,fileinfo.fileName());
2587       item->setToolTip(COLUMN_IMAGE_NAME, mSlicerManagers[index]->GetListOfAbsoluteFilePathInOneString("fusionSequence").c_str());
2588       qApp->processEvents();
2589       for (int j = 1; j <= 4; j++) {
2590         item->setData(j,Qt::CheckStateRole,DataTree->topLevelItem(index)->data(j,Qt::CheckStateRole));
2591       }
2592
2593       //Create the buttons for reload and close
2594       qApp->processEvents();
2595       QTreePushButton* cButton = new QTreePushButton;
2596       cButton->setItem(item);
2597       cButton->setColumn(COLUMN_CLOSE_IMAGE);
2598       cButton->setToolTip(tr("close image"));
2599       cButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/exit.png")));
2600       connect(cButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
2601         this,SLOT(CloseImage(QTreeWidgetItem*, int)));
2602
2603       QTreePushButton* rButton = new QTreePushButton;
2604       rButton->setItem(item);
2605       rButton->setColumn(COLUMN_RELOAD_IMAGE);
2606       rButton->setToolTip(tr("reload image"));
2607       rButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/rotateright.png")));
2608       connect(rButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
2609         this,SLOT(ReloadImage(QTreeWidgetItem*, int)));
2610
2611       DataTree->topLevelItem(index)->setExpanded(1);
2612       DataTree->topLevelItem(index)->addChild(item);
2613       DataTree->setItemWidget(item, COLUMN_CLOSE_IMAGE, cButton);
2614       DataTree->setItemWidget(item, COLUMN_RELOAD_IMAGE, rButton);
2615
2616       //store the original transform matrix
2617       int indexParent = GetSlicerIndexFromItem( DataTree->topLevelItem(index) );
2618       mSlicerManagers[indexParent]->SetFusionSequenceMainTransformMatrix( mSlicerManagers[indexParent]->GetSlicer(0)->GetImage()->GetTransform()[0]->GetMatrix() );
2619
2620       //set the id of the image
2621       QString id = DataTree->topLevelItem(index)->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString();
2622       item->setData(COLUMN_IMAGE_NAME,Qt::UserRole,id.toStdString().c_str());
2623       UpdateTree();
2624       qApp->processEvents();
2625
2626       //ImageInfoChanged();
2627
2628       QApplication::restoreOverrideCursor();
2629       // Update the display to update, e.g., the sliders
2630       for(int i=0; i<4; i++)
2631         DisplaySliders(index, i);
2632
2633
2634       //This loads the secondary sequence (US) as an independent sequence
2635       LoadImages(fileNames, type);
2636       //reset the transforms to identity
2637       //FIX -- and set the thickness of the US slices to a large value (necessary for visualization purposes...)
2638       double sp_x, sp_y, sp_z;
2639       mSlicerManagers[indexParent]->GetImage()->GetVTKImages()[0]->GetSpacing(sp_x, sp_y, sp_z);
2640       sp_z = std::max(sp_x, std::max(sp_y, sp_z)) + 0.5; //
2641       for (unsigned i=0 ; i<mSlicerManagers.back()->GetImage()->GetTransform().size() ; i++) {
2642         sp_x = mSlicerManagers.back()->GetImage()->GetVTKImages()[i]->GetSpacing()[0];
2643         sp_y = mSlicerManagers.back()->GetImage()->GetVTKImages()[i]->GetSpacing()[1];
2644         mSlicerManagers.back()->GetImage()->GetVTKImages()[i]->SetSpacing( sp_x, sp_y, sp_z);
2645         mSlicerManagers.back()->GetImage()->GetTransform()[i]->Identity();
2646         mSlicerManagers.back()->GetImage()->GetTransform()[i]->Update();
2647       }
2648
2649       //automatically link both images...
2650       AddLink(mSlicerManagers[indexParent]->GetId().c_str(), mSlicerManagers.back()->GetId().c_str(), false);
2651
2652       //tie the main and secondary sequences by raising flags and informing each another of their respective SlicerManager indices
2653       mSlicerManagers[indexParent]->SetFusionSequenceIndexOfLinkedManager(mSlicerManagers.size()-1);
2654       mSlicerManagers[indexParent]->SetFusionSequenceInvolvmentCode(0); //main sequence
2655       mSlicerManagers.back()->SetFusionSequenceIndexOfLinkedManager(indexParent);
2656       mSlicerManagers.back()->SetFusionSequenceInvolvmentCode(1); //secondary sequence
2657       for (unsigned i=0 ; i<4 ; i++) {
2658         mSlicerManagers.back()->GetSlicer(i)->SetFusionSequenceCode(1); //flag the slicers of the secondary sequence
2659       }
2660
2661     } else {
2662       QApplication::restoreOverrideCursor();
2663       QString error = "Cannot import the new image.\n";
2664       error += mSlicerManagers[index]->GetLastError().c_str();
2665       QMessageBox::information(this,tr("Problem reading image !"),error);
2666     }
2667     WindowLevelChanged();
2668     ImageInfoChanged(); //this internally calls WindowLevelChanged...
2669   }
2670   else {
2671     QMessageBox::information(this,tr("Problem reading fusion sequence !"),"File doesn't exist!");
2672     return;
2673   }
2674
2675 }
2676 //------------------------------------------------------------------------------
2677
2678
2679 //------------------------------------------------------------------------------
2680 //fusionSequenceFrameIndex and fusionSequenceNbFrames are relative to the secondary sequence (US)
2681 void vvMainWindow::SetFusionSequenceProperty(int fusionSequenceFrameIndex, bool spatialSyncFlag, unsigned int fusionSequenceNbFrames, bool temporalSyncFlag)
2682 {
2683   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2684
2685   if (!mSlicerManagers[index]->IsInvolvedInFusionSequence()) return;
2686
2687   //check if the focus moved to the linked sequence, and in this case, select the master sequence instead
2688   if (!mSlicerManagers[index]->IsMainSequenceOfFusionSequence()) {
2689     index = mSlicerManagers[index]->GetFusionSequenceIndexOfLinkedManager();
2690   }
2691   int secondaryIndex = mSlicerManagers[index]->GetFusionSequenceIndexOfLinkedManager();
2692   if (secondaryIndex==-1) return; //this should never happen
2693   if ( (!mSlicerManagers[index]->IsMainSequenceOfFusionSequence()) ||
2694     (!mSlicerManagers[secondaryIndex]->IsSecondarySequenceOfFusionSequence()) )
2695   {return;} //this should never happen, raise an exception?
2696
2697   if (mSlicerManagers[index]->GetSlicer(0)->GetFusion()) {
2698
2699     //First, if the spatialSync button is unchecked, then reposition the parent sequence (CT) in its original coordinate frame
2700     if ( (!spatialSyncFlag) && (mSlicerManagers[index]->GetFusionSequenceSpatialSyncFlag()) ) {
2701       for ( unsigned i=0 ; i<mSlicerManagers[index]->GetSlicer(0)->GetImage()->GetTransform().size() ; i++ ) {
2702         mSlicerManagers[index]->GetSlicer(0)->GetImage()->GetTransform()[i]->SetMatrix( mSlicerManagers[index]->GetFusionSequenceMainTransformMatrix() );
2703         mSlicerManagers[index]->GetSlicer(0)->GetImage()->GetTransform()[i]->Update();
2704       }
2705
2706       for (int i=0; i<mSlicerManagers[index]->GetNumberOfSlicers(); i++) {
2707         mSlicerManagers[index]->GetSlicer(i)->ForceUpdateDisplayExtent();
2708         mSlicerManagers[index]->GetSlicer(i)->Render();
2709       }
2710     }
2711
2712     //then, update the property values in the slicer manager
2713     mSlicerManagers[index]->SetFusionSequenceLength(fusionSequenceNbFrames);
2714     mSlicerManagers[index]->SetFusionSequenceSpatialSyncFlag(spatialSyncFlag);
2715     mSlicerManagers[index]->SetFusionSequenceTemporalSyncFlag(temporalSyncFlag);
2716     mSlicerManagers[index]->SetFusionSequenceFrameIndex(fusionSequenceFrameIndex);
2717
2718     //select the right frame of the US sequence
2719     mSlicerManagers[index]->SetFusionSequenceTSlice(fusionSequenceFrameIndex); //here, I should only update the overlayed sequence
2720     mSlicerManagers[secondaryIndex]->SetTSlice(fusionSequenceFrameIndex, false); //this should update the secondary sequence (individual version)
2721
2722     //update the horizontal sliders of the main window
2723     overlayPanel->updateFusionSequenceSliderValueFromWindow(fusionSequenceFrameIndex, false);
2724
2725     if (spatialSyncFlag) { //reslice the CT
2726
2727       if (temporalSyncFlag) { //do the temporal synchronisation
2728         int mainSequenceFrameIndex=0;
2729         //estimate the TSlice to set to the CT
2730         unsigned nbFramesMain = mSlicerManagers[index]->GetImage()->GetTransform().size();
2731         mainSequenceFrameIndex = mSlicerManagers[index]->GetFusionSequenceCorrespondances()[ nbFramesMain + fusionSequenceFrameIndex];
2732         //and set it!
2733         mSlicerManagers[index]->SetTSlice(mainSequenceFrameIndex, false);
2734         //warning, there is a loopback, and modification of the TSlice in main sequence forces an update of the TSlice in secondary, etc...
2735       }
2736
2737
2738       //Set the transform matrix of the parent sequence (typically CT / 4DCT)
2739       vtkSmartPointer<vtkMatrix4x4> tmpMat = vtkSmartPointer<vtkMatrix4x4>::New();
2740       vtkMatrix4x4::Invert( mSlicerManagers[index]->GetFusionSequenceInitialTransformMatrixAtFrame(fusionSequenceFrameIndex), tmpMat );
2741       for ( unsigned i=0 ; i<mSlicerManagers[index]->GetSlicer(0)->GetImage()->GetTransform().size() ; i++ ) {
2742         mSlicerManagers[index]->GetSlicer(0)->GetImage()->GetTransform()[i]->SetMatrix( mSlicerManagers[index]->GetFusionSequenceMainTransformMatrix() );
2743         mSlicerManagers[index]->GetSlicer(0)->GetImage()->GetTransform()[i]->PreMultiply();
2744         mSlicerManagers[index]->GetSlicer(0)->GetImage()->GetTransform()[i]->Concatenate( tmpMat );
2745         mSlicerManagers[index]->GetSlicer(0)->GetImage()->GetTransform()[i]->Update();
2746       }
2747
2748       for (int i=0; i<mSlicerManagers[index]->GetNumberOfSlicers(); i++) {
2749         mSlicerManagers[index]->GetSlicer(i)->ForceUpdateDisplayExtent();
2750         mSlicerManagers[index]->GetSlicer(i)->Render();
2751       }
2752
2753     }
2754
2755   }
2756 }
2757 //------------------------------------------------------------------------------
2758
2759
2760 //------------------------------------------------------------------------------
2761 void vvMainWindow::SaveAs()
2762 {
2763   if (DataTree->selectedItems()[0]->data(1,Qt::UserRole).toString() == "vector") {
2764     QMessageBox::warning(this,tr("Unsupported type"),tr("Sorry, saving a vector field is unsupported for the moment"));
2765     return;
2766   }
2767
2768   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2769   int dimension = mSlicerManagers[index]->GetDimension();
2770   QStringList OutputListeFormat;
2771   OutputListeFormat.clear();
2772   if (dimension == 1) {
2773     OutputListeFormat.push_back(".mhd");
2774     OutputListeFormat.push_back(".mha");
2775   }
2776   if (dimension == 2) {
2777     OutputListeFormat.push_back(".bmp");
2778     OutputListeFormat.push_back(".png");
2779     OutputListeFormat.push_back(".jpeg");
2780     OutputListeFormat.push_back(".tif");
2781     OutputListeFormat.push_back(".mhd");
2782     OutputListeFormat.push_back(".mha");
2783     OutputListeFormat.push_back(".hdr");
2784     OutputListeFormat.push_back(".vox");
2785   } else if (dimension == 3) {
2786     OutputListeFormat.push_back(".mhd");
2787     OutputListeFormat.push_back(".mha");
2788     OutputListeFormat.push_back(".nii");
2789     OutputListeFormat.push_back(".nrrd");
2790     OutputListeFormat.push_back(".nhdr");
2791     OutputListeFormat.push_back(".hdr");
2792     OutputListeFormat.push_back(".vox");
2793   } else if (dimension == 4) {
2794     OutputListeFormat.push_back(".mhd");
2795     OutputListeFormat.push_back(".mha");
2796     OutputListeFormat.push_back(".nii");
2797     OutputListeFormat.push_back(".nrrd");
2798     OutputListeFormat.push_back(".nhdr");
2799   }
2800   QString Extensions = "AllFiles(*.*)";
2801   for (int i = 0; i < OutputListeFormat.count(); i++) {
2802     Extensions += ";;Images ( *";
2803     Extensions += OutputListeFormat[i];
2804     Extensions += ")";
2805   }
2806   QString fileName = QFileDialog::getSaveFileName(this,
2807     tr("Save As"),
2808     mSlicerManagers[index]->GetFileName().c_str(),
2809     Extensions);
2810   if (!fileName.isEmpty()) {
2811     std::string fileformat = itksys::SystemTools::GetFilenameLastExtension(fileName.toStdString());
2812     if (OutputListeFormat.contains(
2813       fileformat.c_str())) {
2814         QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
2815         std::string action = "Saving";
2816         vvProgressDialog progress("Saving "+fileName.toStdString());
2817         qApp->processEvents();
2818         vvImageWriter::Pointer writer = vvImageWriter::New();
2819         writer->SetOutputFileName(fileName.toStdString());
2820         writer->SetInput(mSlicerManagers[index]->GetImage());
2821
2822         // Check on transform and prompt user
2823         writer->SetSaveTransform(false);
2824         bool bId = true;
2825         for(int i=0; i<4; i++)
2826           for(int j=0; j<4; j++) {
2827             // TODO SR and BP: check on the list of transforms and not the first only
2828             double elt = mSlicerManagers[index]->GetImage()->GetTransform()[0]->GetMatrix()->GetElement(i,j);
2829             if(i==j && elt!=1.)
2830               bId = false;
2831             if(i!=j && elt!=0.)
2832               bId = false;
2833           }
2834           if( !bId ) {
2835             QString warning = "The image has an associated linear transform. Do you want to save it along?";
2836             QMessageBox msgBox(QMessageBox::Warning, tr("Save transform"), warning, 0, this);
2837             msgBox.addButton(tr("Yes"), QMessageBox::AcceptRole);
2838             msgBox.addButton(tr("No"), QMessageBox::RejectRole);
2839             if (msgBox.exec() == QMessageBox::AcceptRole)
2840               writer->SetSaveTransform(true);
2841           }
2842
2843           writer->Update();
2844           QApplication::restoreOverrideCursor();
2845           if (writer->GetLastError().size()) {
2846             QString error = "Saving did not succeed\n";
2847             error += writer->GetLastError().c_str();
2848             QMessageBox::information(this,tr("Saving Problem"),error);
2849             SaveAs();
2850           }
2851     } else {
2852       QString error = fileformat.c_str();
2853       if (error.isEmpty())
2854         error += "no file format specified !";
2855       else
2856         error += " format unknown !!!\n";
2857       QMessageBox::information(this,tr("Saving Problem"),error);
2858       SaveAs();
2859     }
2860   }
2861 }
2862 //------------------------------------------------------------------------------
2863
2864 //------------------------------------------------------------------------------
2865 void vvMainWindow::SaveCurrentState()
2866 {
2867   QString Extensions = "XML Files(*.xml)";
2868   QString fileName = QFileDialog::getSaveFileName(this,
2869     tr("Save Current Window State"),
2870     "",
2871     Extensions);
2872
2873   SaveCurrentStateAs(fileName.toStdString());
2874 }
2875 //------------------------------------------------------------------------------
2876
2877 //------------------------------------------------------------------------------
2878 void vvMainWindow::SaveCurrentStateAs(const std::string& stateFile)
2879 {
2880   vvSaveState save_state;
2881   save_state.Run(this, stateFile);
2882 }
2883
2884 //------------------------------------------------------------------------------
2885 void vvMainWindow::ReadSavedState()
2886 {
2887   QString Extensions = "XML Files(*.xml)";
2888   QString fileName = QFileDialog::getOpenFileName(this,
2889     tr("Load Window State"),
2890     "",
2891     Extensions);
2892
2893   ReadSavedStateFile(fileName.toStdString());
2894 }
2895 //------------------------------------------------------------------------------
2896
2897 //------------------------------------------------------------------------------
2898 void vvMainWindow::ReadSavedStateFile(const std::string& stateFile)
2899 {
2900   vvReadState read_state;
2901   read_state.Run(this, stateFile);
2902 }
2903 //------------------------------------------------------------------------------
2904
2905 //------------------------------------------------------------------------------
2906 void vvMainWindow::LinkAllImages()
2907 {
2908   linkPanel->linkAll();
2909 }
2910
2911 //------------------------------------------------------------------------------
2912 void vvMainWindow::AddLink(QString image1,QString image2,bool fromPanel)
2913 {
2914   if (!fromPanel) {
2915     // delegate to linkPanel if call came from elsewhere...
2916     linkPanel->addLinkFromIds(image1, image2);
2917     return;
2918   }
2919
2920   unsigned int sm1 = 0;
2921   unsigned int sm2 = 0;
2922
2923   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
2924     if (image1.toStdString() == mSlicerManagers[i]->GetId()) {
2925       mSlicerManagers[i]->AddLink(image2.toStdString());
2926       sm1 = i;
2927     }
2928     if (image2.toStdString() == mSlicerManagers[i]->GetId()) {
2929       mSlicerManagers[i]->AddLink(image1.toStdString());
2930       sm2 = i;
2931     }
2932   }
2933
2934   if (linkPanel->isLinkAll())   {
2935     emit UpdateLinkedNavigation(mSlicerManagers[sm1]->GetId(), mSlicerManagers[mCurrentPickedImageIndex], mSlicerManagers[mCurrentPickedImageIndex]->GetSlicer(0));
2936     emit UpdateLinkedNavigation(mSlicerManagers[sm2]->GetId(), mSlicerManagers[mCurrentPickedImageIndex], mSlicerManagers[mCurrentPickedImageIndex]->GetSlicer(0));
2937   } else {
2938     emit UpdateLinkedNavigation(mSlicerManagers[sm2]->GetId(), mSlicerManagers[sm1], mSlicerManagers[sm1]->GetSlicer(0));
2939   }
2940 }
2941
2942 //------------------------------------------------------------------------------
2943
2944
2945 //------------------------------------------------------------------------------
2946 void vvMainWindow::RemoveLink(QString image1,QString image2)
2947 {
2948   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
2949     if (image1.toStdString() == mSlicerManagers[i]->GetId()) {
2950       mSlicerManagers[i]->RemoveLink(image2.toStdString());
2951     }
2952     if (image2.toStdString() == mSlicerManagers[i]->GetId()) {
2953       mSlicerManagers[i]->RemoveLink(image1.toStdString());
2954     }
2955   }
2956 }
2957 //------------------------------------------------------------------------------
2958
2959 //------------------------------------------------------------------------------
2960 void vvMainWindow::ChangeImageWithIndexOffset(vvSlicerManager *sm, int slicer, int offset)
2961 {
2962   if(mSlicerManagers.size()==1)
2963     return;
2964
2965   int index = 0;
2966   while(sm != mSlicerManagers[index])
2967     index++;
2968   index = (index+offset+mSlicerManagers.size()) % mSlicerManagers.size();
2969
2970   QTreeWidgetItem* item = GetItemFromSlicerManager(mSlicerManagers[index]);
2971   item->setData(slicer+1,Qt::CheckStateRole,2);         //change checkbox
2972   CurrentImageChanged(mSlicerManagers[index]->GetId()); //select new image
2973   DisplayChanged(item,slicer+1);
2974 }
2975 //------------------------------------------------------------------------------
2976 void vvMainWindow::HorizontalSliderMoved(int value,int column, int slicer_index)
2977 {
2978   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
2979     if (DataTree->topLevelItem(i)->data(column,Qt::CheckStateRole).toInt() > 1) {
2980       //i is the SlicerManager that is in charge of this slicer.
2981       if (mSlicerManagers[i]->IsInvolvedInFusionSequence()) {
2982         //if the slicerManager is involved in a fusionSequence as the secondary sequence, then update the slider position in the overlay panel and everything accordingly
2983         if (mSlicerManagers[i]->IsSecondarySequenceOfFusionSequence()) {
2984           overlayPanel->updateFusionSequenceSliderValueFromWindow(value, true);
2985         }
2986         else { //if this is the primary sequence that has been modified
2987           if (mSlicerManagers[i]->GetFusionSequenceTemporalSyncFlag()) {
2988             //WARNING: for some obscure reason, there are problems when accessing mSlicerManagers[mSlicerManagers[i]->GetFusionSequenceIndexOfLinkedManager()]->GetFusionSequenceFrameIndex();
2989
2990             int estimatedValue=0;
2991             //estimate a corresponding time index for the secondary (US) sequence, and update it accordingly.
2992             estimatedValue = mSlicerManagers[i]->GetFusionSequenceCorrespondances()[ value ];
2993             //TODO: at the moment, there is a loop in TSlice modifications
2994             //modifying sequence 1 causes seq 2 to update, which in turns update seq1...
2995             //I disable control on seq1 at the moment.
2996             //overlayPanel->updateFusionSequenceSliderValueFromWindow(estimatedValue, true);
2997           }
2998         }
2999       }
3000
3001       for (int j = 0; j < 4; j++) {
3002         mSlicerManagers[i]->SetTSliceInSlicer(value,j);
3003       }
3004       mSlicerManagers[i]->GetSlicer(slicer_index)->Render();
3005       break;
3006     }
3007   }
3008 }
3009 //------------------------------------------------------------------------------
3010
3011
3012 //------------------------------------------------------------------------------
3013 void vvMainWindow::NOHorizontalSliderMoved()
3014 {
3015   // if (mCurrentTime == NOHorizontalSlider->value()) return;
3016   HorizontalSliderMoved(NOHorizontalSlider->value(),COLUMN_UL_VIEW,0);
3017   //  mCurrentTime = NOHorizontalSlider->value();
3018 }
3019 //------------------------------------------------------------------------------
3020
3021
3022 //------------------------------------------------------------------------------
3023 void vvMainWindow::NEHorizontalSliderMoved()
3024 {
3025   // if (mCurrentTime == NEHorizontalSlider->value()) return;
3026   HorizontalSliderMoved(NEHorizontalSlider->value(),COLUMN_UR_VIEW,1);
3027   //  mCurrentTime = NEHorizontalSlider->value();
3028 }
3029 //------------------------------------------------------------------------------
3030
3031
3032 //------------------------------------------------------------------------------
3033 void vvMainWindow::SOHorizontalSliderMoved()
3034 {
3035   // if (mCurrentTime == SOHorizontalSlider->value()) return;
3036   HorizontalSliderMoved(SOHorizontalSlider->value(),COLUMN_DL_VIEW,2);
3037   // mCurrentTime = SOHorizontalSlider->value();
3038 }
3039 //------------------------------------------------------------------------------
3040
3041
3042 //------------------------------------------------------------------------------
3043 void vvMainWindow::SEHorizontalSliderMoved()
3044 {
3045   // if (mCurrentTime == SEHorizontalSlider->value()) return;
3046   HorizontalSliderMoved(SEHorizontalSlider->value(),COLUMN_DR_VIEW,3);
3047   // mCurrentTime = SEHorizontalSlider->value();
3048 }
3049 //------------------------------------------------------------------------------
3050
3051 //------------------------------------------------------------------------------
3052 void vvMainWindow::NOVerticalSliderChanged()
3053 {
3054   static int value=-1;
3055   if (value == NOVerticalSlider->value()) return;
3056   else value = NOVerticalSlider->value();
3057   //  int value = NOVerticalSlider->value();
3058   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
3059     if (DataTree->topLevelItem(i)->data(COLUMN_UL_VIEW,Qt::CheckStateRole).toInt() > 1) {
3060       if (mSlicerManagers[i]->GetSlicer(0)->GetSlice() != value) {
3061         mSlicerManagers[i]->GetSlicer(0)->SetSlice(value);
3062         mSlicerManagers[i]->VerticalSliderHasChanged(0, value);
3063
3064         // If nor Update/Render -> slider not work
3065         // only render = ok navigation, but for contour Update needed but slower ?
3066
3067         mSlicerManagers[i]->UpdateSlice(0);  // <-- DS add this. Not too much update ? YES. but needed for ImageContour ...
3068         //mSlicerManagers[i]->GetSlicer(0)->Render(); // <-- DS add this, needed for contour, seems ok ? not too slow ?
3069       }
3070       break;
3071     }
3072   }
3073 }
3074 //------------------------------------------------------------------------------
3075
3076
3077 //------------------------------------------------------------------------------
3078 void vvMainWindow::NEVerticalSliderChanged()
3079 {
3080   static int value=-1;
3081   if (value == NEVerticalSlider->value()) return;
3082   else value = NEVerticalSlider->value();
3083   //  int value = NEVerticalSlider->value();
3084   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
3085     if (DataTree->topLevelItem(i)->data(COLUMN_UR_VIEW,Qt::CheckStateRole).toInt() > 1) {
3086       if (mSlicerManagers[i]->GetSlicer(1)->GetSlice() != value) {
3087         mSlicerManagers[i]->GetSlicer(1)->SetSlice(value);
3088         mSlicerManagers[i]->VerticalSliderHasChanged(1, value);
3089         mSlicerManagers[i]->UpdateSlice(1);
3090         //mSlicerManagers[i]->GetSlicer(1)->Render(); // <-- DS add this, needed for contour, seems ok ? not too slow ?
3091       }
3092       break;
3093     }
3094   }
3095 }
3096 //------------------------------------------------------------------------------
3097
3098
3099 //------------------------------------------------------------------------------
3100 void vvMainWindow::SOVerticalSliderChanged()
3101 {
3102   static int value=-1;
3103   if (value == SOVerticalSlider->value()) return;
3104   else value = SOVerticalSlider->value();
3105   //int value = SOVerticalSlider->value();
3106   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
3107     if (DataTree->topLevelItem(i)->data(COLUMN_DL_VIEW,Qt::CheckStateRole).toInt() > 1) {
3108       if (mSlicerManagers[i]->GetSlicer(2)->GetSlice() != value) {
3109         mSlicerManagers[i]->GetSlicer(2)->SetSlice(value);
3110         mSlicerManagers[i]->VerticalSliderHasChanged(2, value);
3111         mSlicerManagers[i]->UpdateSlice(2);
3112         //mSlicerManagers[i]->GetSlicer(2)->Render(); // <-- DS add this, needed for contour, seems ok ? not too slow ?
3113       }
3114       // else { DD("avoid SOVerticalSlider slicer update"); }
3115       break;
3116     }
3117   }
3118 }
3119 //------------------------------------------------------------------------------
3120
3121
3122 //------------------------------------------------------------------------------
3123 void vvMainWindow::SEVerticalSliderChanged()
3124 {
3125   static int value=-1;
3126   if (value == SEVerticalSlider->value()) return;
3127   else value = SEVerticalSlider->value();
3128   // int value = SEVerticalSlider->value();
3129   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
3130     if (DataTree->topLevelItem(i)->data(COLUMN_DR_VIEW,Qt::CheckStateRole).toInt() > 1) {
3131       if (mSlicerManagers[i]->GetSlicer(3)->GetSlice() != value) {
3132         mSlicerManagers[i]->GetSlicer(3)->SetSlice(value);
3133         mSlicerManagers[i]->VerticalSliderHasChanged(3, value);
3134         mSlicerManagers[i]->UpdateSlice(3);
3135         //mSlicerManagers[i]->GetSlicer(3)->Render(); // <-- DS add this, needed for contour, seems ok ? not too slow ?
3136       }
3137       break;
3138     }
3139   }
3140 }
3141 //------------------------------------------------------------------------------
3142
3143
3144 //------------------------------------------------------------------------------
3145 void vvMainWindow::UpdateSlice(int slicer, int slice)
3146 {
3147   // DD("vvMainWindow::UpdateSlice");
3148   //   DD(slicer);
3149   //   DD(slice);
3150   if (slicer == 0) {
3151     //    if (slice != NOVerticalSlider->value())
3152     NOVerticalSlider->setValue(slice);
3153   } else {
3154     if (slicer == 1)
3155       NEVerticalSlider->setValue(slice);
3156     else {
3157       if (slicer == 2)
3158         SOVerticalSlider->setValue(slice);
3159       else {
3160         if (slicer == 3)
3161           SEVerticalSlider->setValue(slice);
3162       }
3163     }
3164   }
3165   // DD("vvMainWindow:UpdateSlice END");
3166 }
3167 //------------------------------------------------------------------------------
3168
3169
3170 //------------------------------------------------------------------------------
3171 void vvMainWindow::UpdateTSlice(int slicer, int slice, int code)
3172 {
3173   //FusionSequence: the slider value should be updated for slicers which show the same sequence as requested
3174   bool doUpdate=false;
3175   if (code==-1) doUpdate=true;
3176   else {
3177     for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
3178       if (DataTree->topLevelItem(i)->data(slicer+1,Qt::CheckStateRole).toInt() > 1) {
3179         //i is the active SlicerManager
3180         if (mSlicerManagers[i]->GetFusionSequenceInvolvmentCode()==code) doUpdate=true;
3181         break;
3182       }
3183     }
3184   }
3185   if (!doUpdate) return;
3186
3187   switch (slicer) {
3188   case 0:
3189     if (NOHorizontalSlider->value()==slice) return;
3190     NOHorizontalSlider->setValue(slice);
3191     break;
3192   case 1:
3193     if (NEHorizontalSlider->value()==slice) return;
3194     NEHorizontalSlider->setValue(slice);
3195     break;
3196   case 2:
3197     if (SOHorizontalSlider->value()==slice) return;
3198     SOHorizontalSlider->setValue(slice);
3199     break;
3200   case 3:
3201     if (SEHorizontalSlider->value()==slice) return;
3202     SEHorizontalSlider->setValue(slice);
3203     break;
3204   }
3205 }
3206 //------------------------------------------------------------------------------
3207
3208
3209 //------------------------------------------------------------------------------
3210 void vvMainWindow::UpdateSliceRange(int slicer, int min, int max, int tmin, int tmax)
3211 {
3212   //int position = int((min+max)/2);
3213   int position = mSlicerManagers[mCurrentPickedImageIndex]->GetSlicer(slicer)->GetSlice();
3214   if (slicer == 0) {
3215     NOVerticalSlider->setRange(min,max);
3216     NOHorizontalSlider->setRange(tmin,tmax);
3217     NOVerticalSlider->setValue(position);
3218   } else if (slicer == 1) {
3219     NEVerticalSlider->setRange(min,max);
3220     NEHorizontalSlider->setRange(tmin,tmax);
3221     NEVerticalSlider->setValue(position);
3222   } else if (slicer == 2) {
3223     SOVerticalSlider->setRange(min,max);
3224     SOHorizontalSlider->setRange(tmin,tmax);
3225     SOVerticalSlider->setValue(position);
3226   } else if (slicer == 3) {
3227     SEVerticalSlider->setRange(min,max);
3228     SEHorizontalSlider->setRange(tmin,tmax);
3229     SEVerticalSlider->setValue(position);
3230   }
3231 }
3232 //------------------------------------------------------------------------------
3233
3234
3235 //------------------------------------------------------------------------------
3236 void vvMainWindow::SaveNOScreenshot()
3237 {
3238   SaveScreenshot(NOViewWidget);
3239 }
3240 //------------------------------------------------------------------------------
3241
3242
3243 //------------------------------------------------------------------------------
3244 void vvMainWindow::SaveNEScreenshot()
3245 {
3246   SaveScreenshot(NEViewWidget);
3247 }
3248 //------------------------------------------------------------------------------
3249
3250
3251 //------------------------------------------------------------------------------
3252 void vvMainWindow::SaveSOScreenshot()
3253 {
3254   SaveScreenshot(SOViewWidget);
3255 }
3256 //------------------------------------------------------------------------------
3257
3258
3259 //------------------------------------------------------------------------------
3260 void vvMainWindow::SaveSEScreenshot()
3261 {
3262   SaveScreenshot(SEViewWidget);
3263 }
3264 //------------------------------------------------------------------------------
3265
3266
3267 //------------------------------------------------------------------------------
3268 void vvMainWindow::SaveScreenshotAllSlices()
3269 {
3270   QVTKWidget *widget = NOViewWidget;
3271
3272   int index = 0;// GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
3273   vvSlicerManager * SM = mSlicerManagers[index];
3274   vvImage * image = SM->GetImage();
3275   vvSlicer * slicer = SM->GetSlicer(0);
3276   int orientation = slicer->GetOrientation();
3277   int nbSlices = image->GetSize()[orientation];
3278   vtkSmartPointer<vtkRenderWindow>  renderWindow = widget->GetRenderWindow();
3279
3280   // Select filename base
3281   QString filename = QFileDialog::getSaveFileName(this,
3282     tr("Save As (filename will be completed by slice number)"),
3283     itksys::SystemTools::GetFilenamePath(mSlicerManagers[index]->GetFileName()).c_str(),
3284     "Images( *.png);;Images( *.jpg)");
3285
3286   // Loop on slices
3287   for(int i=0; i<nbSlices; i++) {
3288     // Change the slice
3289     slicer->SetSlice(i); // -> change the slice of the current slicer
3290     SM->UpdateSlice(0); // --> this one emit UpdateSlice
3291     QCoreApplication::flush(); // -> needed to force display of contours
3292
3293     // Screenshot
3294     vtkSmartPointer<vtkWindowToImageFilter> windowToImageFilter = vtkSmartPointer<vtkWindowToImageFilter>::New();
3295     windowToImageFilter->SetInput(renderWindow);
3296     windowToImageFilter->SetMagnification(1);
3297     windowToImageFilter->SetInputBufferTypeToRGBA(); //also record the alpha (transparency) channel
3298     windowToImageFilter->Update();
3299
3300     vtkSmartPointer<vtkPNGWriter> writer = vtkSmartPointer<vtkPNGWriter>::New();
3301     std::string fn = itksys::SystemTools::GetFilenameWithoutLastExtension(filename.toStdString());
3302     std::string num = clitk::toString(i);
3303     if (i<10) num = "0"+num;
3304     if (i<100) num = "0"+num;
3305     if (i<1000) num = "0"+num;
3306
3307     fn = itksys::SystemTools::GetFilenamePath(filename.toStdString()) + "/"+ fn
3308       + "_" + num + itksys::SystemTools::GetFilenameLastExtension(filename.toStdString());
3309     writer->SetFileName(fn.c_str());
3310     writer->SetInput(windowToImageFilter->GetOutput());
3311     writer->Write();
3312   }
3313 }
3314 //------------------------------------------------------------------------------
3315
3316
3317 //------------------------------------------------------------------------------
3318 void vvMainWindow::SaveScreenshot(QVTKWidget *widget)
3319 {
3320   QString Extensions = "Images( *.png);;";
3321   Extensions += "Images( *.jpg);;";
3322   Extensions += "Images( *.bmp);;";
3323   Extensions += "Images( *.tif);;";
3324   Extensions += "Images( *.ppm)";
3325 #if defined(VTK_USE_FFMPEG_ENCODER) || defined(VTK_USE_VIDEO_FOR_WINDOWS)
3326   Extensions += ";;Video( *.avi)";
3327 #endif
3328 #ifdef VTK_USE_MPEG2_ENCODER
3329   Extensions += ";;Video( *.mpg)";
3330 #endif
3331 #ifdef CLITK_EXPERIMENTAL
3332   Extensions += ";;Video( *.gif)";
3333 #endif
3334
3335   int smIndex=GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
3336   QString fileName = QFileDialog::getSaveFileName(this,
3337     tr("Save As"),
3338     itksys::SystemTools::GetFilenamePath(mSlicerManagers[smIndex]->GetFileName()).c_str(),
3339     Extensions);
3340
3341   if (!fileName.isEmpty()) {
3342     vtkSmartPointer<vtkWindowToImageFilter> w2i = vtkSmartPointer<vtkWindowToImageFilter>::New();
3343     w2i->SetInput(widget->GetRenderWindow());
3344     w2i->Update();
3345     vtkImageData *image = w2i->GetOutput();
3346
3347     std::string ext(itksys::SystemTools::GetFilenameLastExtension(fileName.toStdString()));
3348
3349     // Image
3350     vtkImageWriter *imgwriter = NULL;
3351     if (ext==".bmp")
3352       imgwriter = vtkBMPWriter::New();
3353     else if (ext==".tif")
3354       imgwriter = vtkTIFFWriter::New();
3355     else if (ext==".ppm")
3356       imgwriter = vtkPNMWriter::New();
3357     else if (ext==".png")
3358       imgwriter = vtkPNGWriter::New();
3359     else if (ext==".jpg")
3360       imgwriter = vtkJPEGWriter::New();
3361
3362     // Snapshot image if not null
3363     if(imgwriter!=NULL) {
3364       imgwriter->SetInput(image);
3365       imgwriter->SetFileName(fileName.toStdString().c_str());
3366       imgwriter->Write();
3367       return;
3368     }
3369
3370     // Video
3371     vtkGenericMovieWriter *vidwriter = NULL;
3372 #if CLITK_EXPERIMENTAL == 1
3373     if (ext==".gif") {
3374       vvAnimatedGIFWriter *gif = vvAnimatedGIFWriter::New();
3375       vidwriter = gif;
3376
3377       // FPS
3378       bool ok;
3379       int fps = QInputDialog::getInteger(this, tr("Number of frames per second"),
3380         tr("FPS:"), 5, 0, 1000, 1, &ok);
3381       if(ok)
3382         gif->SetRate(fps);
3383
3384       // Loops
3385       int loops = QInputDialog::getInteger(this, tr("Loops"),
3386         tr("Number of loops (0 means infinite):"), 0, 0, 1000000000, 1, &ok);
3387       if(ok)
3388         gif->SetLoops(loops);
3389
3390       // Dithering
3391       QString msg = "Would you like to activate dithering?";
3392       QMessageBox msgBox(QMessageBox::Question, tr("Dithering"),msg, 0, this);
3393       msgBox.addButton(tr("Yes"), QMessageBox::AcceptRole);
3394       msgBox.addButton(tr("No"), QMessageBox::RejectRole);
3395       gif->SetDither(msgBox.exec() == QMessageBox::AcceptRole);
3396     }
3397 #endif
3398 #ifdef VTK_USE_VIDEO_FOR_WINDOWS
3399     if (ext==".avi") {
3400       vtkAVIWriter *mpg = vtkAVIWriter::New();
3401       vidwriter = mpg;
3402       mpg->SetQuality(2);
3403       bool ok;
3404       int fps = QInputDialog::getInteger(this, tr("Number of frames per second"),
3405         tr("FPS:"), 5, 0, 1024, 1, &ok);
3406       if(!ok)
3407         fps = 5;
3408       mpg->SetRate(fps);
3409     }
3410 #endif
3411 #ifdef VTK_USE_FFMPEG_ENCODER
3412     if (ext==".avi") {
3413       vtkFFMPEGWriter *mpg = vtkFFMPEGWriter::New();
3414       vidwriter = mpg;
3415       mpg->SetQuality(2);
3416       bool ok;
3417       int fps = QInputDialog::getInteger(this, tr("Number of frames per second"),
3418         tr("FPS:"), 5, 0, 1024, 1, &ok);
3419       if(!ok)
3420         fps = 5;
3421       mpg->SetRate(fps);
3422       mpg->SetBitRateTolerance(int(ceil(12.0*1024*1024/fps)));
3423     }
3424 #endif
3425 #ifdef VTK_USE_MPEG2_ENCODER
3426     if (ext==".mpg") {
3427       vtkMPEG2Writer *mpg = vtkMPEG2Writer::New();
3428       vidwriter = mpg;
3429     }
3430 #endif
3431
3432     // Take video if not null
3433     if(vidwriter!=NULL){
3434       vidwriter->SetInput(image);
3435       vidwriter->SetFileName(fileName.toStdString().c_str());
3436       vidwriter->Start();
3437       int nSlice = mSlicerManagers[smIndex]->GetSlicer(0)->GetTMax();
3438       for(int i=0; i<=nSlice; i++) {
3439         mSlicerManagers[smIndex]->SetNextTSlice(0);
3440         vtkSmartPointer<vtkWindowToImageFilter> w2i = vtkSmartPointer<vtkWindowToImageFilter>::New();
3441         w2i->SetInput(widget->GetRenderWindow());
3442         w2i->Update();
3443         vidwriter->SetInput(w2i->GetOutput());
3444         vidwriter->Write();
3445       }
3446       vidwriter->End();
3447       vidwriter->Delete();
3448       return;
3449     }
3450
3451     QMessageBox::information(this,tr("Problem saving screenshot !"),tr("Cannot save image.\nPlease set a file extension !!!"));
3452   }
3453 }
3454 //------------------------------------------------------------------------------
3455
3456
3457 //------------------------------------------------------------------------------
3458 void vvMainWindow::GoToCursor()
3459 {
3460   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
3461   for (int column = 1; column < 5; column++) {
3462     if (DataTree->selectedItems()[0]->data(column,Qt::CheckStateRole).toInt() > 1) {
3463       double* cursorPos = mSlicerManagers[index]->GetSlicer(column-1)->GetCursorPosition();
3464       mSlicerManagers[index]->GetSlicer(column-1)->SetCurrentPosition(
3465         cursorPos[0],cursorPos[1],cursorPos[2],cursorPos[3]);
3466       mSlicerManagers[index]->UpdateViews(1,column-1);
3467       mSlicerManagers[index]->UpdateLinked(column-1);
3468       break;
3469     }
3470   }
3471 }
3472 //------------------------------------------------------------------------------
3473
3474 //------------------------------------------------------------------------------
3475 void vvMainWindow::GoToLandmark()
3476 {
3477   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
3478   for (int column = 1; column < 5; column++) {
3479     if (DataTree->selectedItems()[0]->data(column,Qt::CheckStateRole).toInt() > 1) {
3480       double* cursorPos = landmarksPanel->GetSelectedPoint();
3481       mSlicerManagers[index]->GetSlicer(column-1)->SetCurrentPosition(
3482         cursorPos[0],cursorPos[1],cursorPos[2],cursorPos[3]);
3483       mSlicerManagers[index]->UpdateViews(1,column-1);
3484       mSlicerManagers[index]->UpdateLinked(column-1);
3485       break;
3486     }
3487   }
3488 }
3489 //------------------------------------------------------------------------------
3490
3491 //------------------------------------------------------------------------------
3492 void vvMainWindow::PlayPause()
3493 {
3494   if (playMode) {
3495     playMode = 0;
3496     playButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/player_play.png")));
3497     ImageInfoChanged();
3498     return;
3499   } else {
3500     int image_number=DataTree->topLevelItemCount();
3501     bool has_temporal;
3502     for (int i=0; i<image_number; i++)
3503       if (mSlicerManagers[i]->GetSlicer(0)->GetTMax() > 0) {
3504         has_temporal=true;
3505         break;
3506       }
3507       if (has_temporal) {
3508         playMode = 1;
3509         playButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/player_pause.png")));
3510         QTimer::singleShot(1000/mFrameRate, this, SLOT(PlayNext()));
3511       }
3512   }
3513 }
3514 //------------------------------------------------------------------------------
3515
3516 //------------------------------------------------------------------------------
3517 void vvMainWindow::PlayNext()
3518 {
3519   if (playMode && !this->isHidden()) {
3520     int image_number=DataTree->topLevelItemCount();
3521     ///Only play one slicer per SM, and only if the SM is being displayed
3522     for (int i=0; i<image_number; i++)
3523       for (int j=0; j<4; j++)
3524         if (mSlicerManagers[i]->GetSlicer(0)->GetTMax() > 0 &&
3525           DataTree->topLevelItem(i)->data(j+1,Qt::CheckStateRole).toInt() > 0) {
3526             mSlicerManagers[i]->SetNextTSlice(j);
3527             break;
3528         }
3529         QTimer::singleShot(1000/mFrameRate, this, SLOT(PlayNext()));
3530   }
3531 }
3532 //------------------------------------------------------------------------------
3533
3534 void vvMainWindow::ShowLastImage()
3535 {
3536   if (mSlicerManagers.size() > 1) {
3537     QTreeWidgetItem * item=DataTree->topLevelItem(DataTree->topLevelItemCount()-1);
3538     CurrentImageChanged(mSlicerManagers.back()->GetId()); //select new image
3539     item->setData(1,Qt::CheckStateRole,2); //show the new image in the first panel
3540     DisplayChanged(item,1);
3541   }
3542 }
3543
3544 //------------------------------------------------------------------------------
3545 void vvMainWindow::UpdateRenderWindows()
3546 {
3547   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
3548     mSlicerManagers[i]->GetSlicer(0)->UpdateLandmarks();
3549     mSlicerManagers[i]->GetSlicer(1)->UpdateLandmarks();
3550     mSlicerManagers[i]->GetSlicer(2)->UpdateLandmarks();
3551     mSlicerManagers[i]->GetSlicer(3)->UpdateLandmarks();
3552   }
3553   if (NOViewWidget->GetRenderWindow()) NOViewWidget->GetRenderWindow()->Render();
3554   if (NEViewWidget->GetRenderWindow()) NEViewWidget->GetRenderWindow()->Render();
3555   if (SOViewWidget->GetRenderWindow()) SOViewWidget->GetRenderWindow()->Render();
3556   if (SEViewWidget->GetRenderWindow()) SEViewWidget->GetRenderWindow()->Render();
3557 }
3558 //------------------------------------------------------------------------------
3559
3560 //------------------------------------------------------------------------------
3561 void vvMainWindow::SegmentationOnCurrentImage()
3562 {
3563   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
3564
3565   vvSegmentationDialog segmentation;
3566   segmentation.SetImage(mSlicerManagers[index]->GetSlicer(0)->GetImage());
3567   segmentation.exec();
3568 }
3569 //------------------------------------------------------------------------------
3570
3571 void vvMainWindow::SurfaceViewerLaunch()
3572 {
3573   vvSurfaceViewerDialog surfaceViewer;
3574   surfaceViewer.exec();
3575 }
3576 //------------------------------------------------------------------------------
3577
3578
3579 //------------------------------------------------------------------------------
3580 int vvMainWindow::GetImageDuplicateFilenameNumber(std::string filename)
3581 {
3582   int number=0;
3583   for(unsigned int l=0; l<mSlicerManagers.size(); l++) {
3584     vvSlicerManager * v = mSlicerManagers[l];
3585     if (v->GetBaseFileName() ==
3586       vtksys::SystemTools::GetFilenameName(vtksys::SystemTools::GetFilenameWithoutLastExtension(filename))) {
3587         number = std::max(number, v->GetBaseFileNameNumber()+1);
3588     }
3589   }
3590   return number;
3591 }
3592 //------------------------------------------------------------------------------
3593
3594
3595 //------------------------------------------------------------------------------
3596 vvSlicerManager* vvMainWindow::AddImage(vvImage::Pointer image,std::string filename)
3597 {
3598   // Change filename if another image exist with the same name
3599   int number = GetImageDuplicateFilenameNumber(filename);
3600
3601   // Create new SliceManager
3602   vvSlicerManager* slicer_manager = new vvSlicerManager(4);
3603   slicer_manager->SetImage(image);//, IMAGE, number);
3604   //  filename = filename+"_"+clitk::toString(number);
3605   slicer_manager->SetFilename(filename, number);
3606   mSlicerManagers.push_back(slicer_manager);
3607
3608   //create an item in the tree with good settings
3609   QTreeWidgetItem *item = new QTreeWidgetItem();
3610   item->setData(0,Qt::UserRole,slicer_manager->GetFileName().c_str());//files[i].c_str());
3611   item->setData(1,Qt::UserRole,tr("image"));
3612   item->setData(COLUMN_IMAGE_NAME,Qt::DisplayRole,slicer_manager->GetFileName().c_str());//filename.c_str());
3613   qApp->processEvents();
3614
3615   for (int j = 1; j <= 4; j++) item->setData(j,Qt::CheckStateRole,1);
3616
3617   //Create the buttons for reload and close
3618   qApp->processEvents();
3619   QTreePushButton* cButton = new QTreePushButton;
3620   cButton->setItem(item);
3621   cButton->setColumn(COLUMN_CLOSE_IMAGE);
3622   cButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/exit.png")));
3623   connect(cButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
3624     this,SLOT(CloseImage(QTreeWidgetItem*, int)));
3625
3626   QTreePushButton* rButton = new QTreePushButton;
3627   rButton->setItem(item);
3628   rButton->setColumn(COLUMN_RELOAD_IMAGE);
3629   rButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/rotateright.png")));
3630   rButton->setEnabled(0);
3631   connect(rButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
3632     this,SLOT(ReloadImage(QTreeWidgetItem*, int)));
3633
3634   DataTree->addTopLevelItem(item);
3635   DataTree->setItemWidget(item, COLUMN_CLOSE_IMAGE, cButton);
3636   DataTree->setItemWidget(item, COLUMN_RELOAD_IMAGE, rButton);
3637
3638   //set the id of the image
3639   QString id = QDir::current().absoluteFilePath(slicer_manager->GetFileName().c_str()) + QString::number(mSlicerManagers.size()-1);
3640   item->setData(COLUMN_IMAGE_NAME,Qt::UserRole,id.toStdString().c_str());
3641   mSlicerManagers.back()->SetId(id.toStdString());
3642
3643   linkPanel->addImage(slicer_manager->GetFileName().c_str()// filename
3644     , id.toStdString());
3645
3646   connect(mSlicerManagers.back(), SIGNAL(currentImageChanged(std::string)),
3647     this, SLOT(CurrentImageChanged(std::string)));
3648   connect(mSlicerManagers.back(), SIGNAL(currentPickedImageChanged(std::string)),
3649     this, SLOT(CurrentPickedImageChanged(std::string)));
3650   connect(mSlicerManagers.back(), SIGNAL(UpdatePosition(int, double, double, double, double, double, double, double)),
3651     this, SLOT(MousePositionChanged(int,double, double, double, double, double, double, double)));
3652   connect(mSlicerManagers.back(), SIGNAL(UpdateVector(int, double, double, double, double)),
3653     this, SLOT(VectorChanged(int,double,double,double, double)));
3654   connect(mSlicerManagers.back(), SIGNAL(UpdateOverlay(int, double, double)),
3655     this, SLOT(OverlayChanged(int,double,double)));
3656   connect(mSlicerManagers.back(), SIGNAL(UpdateFusion(int, double)),
3657     this, SLOT(FusionChanged(int,double)));
3658   //connect(mSlicerManagers.back(), SIGNAL(UpdateFusionSequence(int, bool, unsigned int)),
3659   //  this, SLOT(FusionSequenceChanged(int, bool, unsigned int)));
3660   connect(mSlicerManagers.back(), SIGNAL(WindowLevelChanged()),
3661     this,SLOT(WindowLevelChanged()));
3662   connect(mSlicerManagers.back(), SIGNAL(UpdateSlice(int,int)),
3663     this,SLOT(UpdateSlice(int,int)));
3664   connect(mSlicerManagers.back(), SIGNAL(UpdateTSlice(int, int, int)),
3665     this,SLOT(UpdateTSlice(int, int, int)));
3666   connect(mSlicerManagers.back(), SIGNAL(UpdateTSlice(int, int, int)),
3667     this,SLOT(ImageInfoChanged()));
3668   connect(mSlicerManagers.back(), SIGNAL(UpdateSliceRange(int,int,int,int,int)),
3669     this,SLOT(UpdateSliceRange(int,int,int,int,int)));
3670   connect(mSlicerManagers.back(), SIGNAL(UpdateLinkManager(std::string,int,double,double,double,int)),
3671     this,SLOT(UpdateLinkManager(std::string,int,double,double,double,int)));
3672   connect(mSlicerManagers.back(), SIGNAL(UpdateLinkedNavigation(std::string,vvSlicerManager*,vvSlicer*)),
3673     this,SLOT(UpdateLinkedNavigation(std::string,vvSlicerManager*,vvSlicer*)));
3674   connect(mSlicerManagers.back(), SIGNAL(ChangeImageWithIndexOffset(vvSlicerManager*,int,int)),
3675     this,SLOT(ChangeImageWithIndexOffset(vvSlicerManager*,int,int)));
3676   connect(mSlicerManagers.back(), SIGNAL(LandmarkAdded()),landmarksPanel,SLOT(AddPoint()));
3677
3678
3679   UpdateTree();
3680   qApp->processEvents();
3681   InitSlicers();
3682   ShowLastImage();
3683   InitDisplay();
3684   qApp->processEvents();
3685
3686   // End
3687   ImageInfoChanged();
3688   return slicer_manager;
3689 }
3690 //------------------------------------------------------------------------------
3691
3692
3693 //------------------------------------------------------------------------------
3694 void vvMainWindow::UpdateCurrentSlicer()
3695 {
3696   int index = -1;
3697   if (DataTree->selectedItems().size() > 0) {
3698     index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
3699   }
3700   mSlicerManagerCurrentIndex = index;
3701 }
3702 //------------------------------------------------------------------------------
3703