vv/vvMainWindow.cxx

   1 /*=========================================================================
   2 Program:   vv                     http://www.creatis.insa-lyon.fr/rio/vv
   3
   4 Authors belong to:
   5 - University of LYON              http://www.universite-lyon.fr/
   6 - Léon Bérard cancer center       http://www.centreleonberard.fr
   7 - CREATIS CNRS laboratory         http://www.creatis.insa-lyon.fr
   8
   9 This software is distributed WITHOUT ANY WARRANTY; without even
  10 the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
  11 PURPOSE.  See the copyright notices for more information.
  12
  13 It is distributed under dual licence
  14
  15 - BSD        See included LICENSE.txt file
  16 - CeCILL-B   http://www.cecill.info/licences/Licence_CeCILL-B_V1-en.html
  17 ===========================================================================**/
  18
  19 #include <algorithm>
  20 #include <QMessageBox>
  21 #include <QInputDialog>
  22 #include <QTimer>
  23 #include "QTreePushButton.h"
  24 #include <QUrl>
  25 #include <QSettings>
  26
  27 // VV include
  28 #include "vvMainWindow.h"
  29 #include "vvHelpDialog.h"
  30 #include "vvRegisterForm.h"
  31 #include "vvDocumentation.h"
  32 #include "vvProgressDialog.h"
  33 #include "vvQDicomSeriesSelector.h"
  34 #include "vvSlicerManager.h"
  35 #include "clitkImageCommon.h"
  36 #include "vvSlicer.h"
  37 #include "vvInteractorStyleNavigator.h"
  38 #include "vvImageWriter.h"
  39 #include "vvSegmentationDialog.h"
  40 #include "vvSurfaceViewerDialog.h"
  41 #include "vvDeformationDialog.h"
  42 #include "vvImageWarp.h"
  43 #include "vvUtils.h"
  44 #include "vvMidPosition.h"
  45 #include "vvMesh.h"
  46 #include "vvStructSelector.h"
  47 #include "vvMeshReader.h"
  48 #include "vvSaveState.h"
  49 #include "vvReadState.h"
  50 #include "clitkConfiguration.h"
  51
  52 // ITK include
  53 #include <itkImage.h>
  54 #include <itkImageFileReader.h>
  55 #include <itkByteSwapper.h>
  56 #include <itkCommand.h>
  57 #include <itkNumericSeriesFileNames.h>
  58
  59 // VTK include
  60 #include <vtkImageData.h>
  61 #include <vtkImageActor.h>
  62 #include <vtkCornerAnnotation.h>
  63 #include <vtkRenderWindow.h>
  64 #include <vtkRenderWindowInteractor.h>
  65 #include <vtkRenderer.h>
  66 #include <vtkRendererCollection.h>
  67 #include <vtkWindowToImageFilter.h>
  68 #include <vtkBMPWriter.h>
  69 #include <vtkTIFFWriter.h>
  70 #include <vtkPNMWriter.h>
  71 #include <vtkPNGWriter.h>
  72 #include <vtkJPEGWriter.h>
  73 #include <vtkGenericMovieWriter.h>
  74 #ifdef CLITK_EXPERIMENTAL
  75 #  include <vvAnimatedGIFWriter.h>
  76 #endif
  77 #ifdef VTK_USE_VIDEO_FOR_WINDOWS
  78 #  include <vtkAVIWriter.h>
  79 #endif
  80 #ifdef VTK_USE_FFMPEG_ENCODER
  81 #  include <vtkFFMPEGWriter.h>
  82 #endif
  83 #ifdef VTK_USE_MPEG2_ENCODER
  84 #  include <vtkMPEG2Writer.h>
  85 #endif
  86 #include <vtkMatrix4x4.h>
  87 #include <vtkTransform.h>
  88
  89 // Standard includes
  90 #include <iostream>
  91 #include <sstream>
  92 #include <iomanip>
  93
  94 #define COLUMN_TREE 0
  95 #define COLUMN_UL_VIEW 1
  96 #define COLUMN_UR_VIEW 2
  97 #define COLUMN_DL_VIEW 3
  98 #define COLUMN_DR_VIEW 4
  99 #define COLUMN_CLOSE_IMAGE 5
 100 #define COLUMN_RELOAD_IMAGE 6
 101 #define COLUMN_IMAGE_NAME 7
 102
 103 #ifdef CLITK_PRIVATE_FEATURES
 104 #define EXTENSIONS "Images ( *.bmp *.png *.jpeg *.jpg *.tif *.mhd *.mha *.hdr *.vox *.his *.xdr *.SCAN *.nii *.nrrd *.nhdr *.refscan *.nii.gz *.usf)"
 105 #else
 106 #define EXTENSIONS "Images ( *.bmp *.png *.jpeg *.jpg *.tif *.mhd *.mha *.hdr *.vox *.his *.xdr *.SCAN *.nii *.nrrd *.nhdr *.refscan *.nii.gz)"
 107 #endif
 108
 109
 110 /*Data Tree values
 111 0,Qt::UserRole full filename
 112 1,Qt::CheckStateRole checkbutton UL View
 113 1,Qt::UserRole overlay, fusion or vector
 114 2,Qt::CheckStateRole checkbutton UR View
 115 3,Qt::CheckStateRole checkbutton DL View
 116 4,Qt::CheckStateRole checkbutton DR View
 117 5,0  short filename
 118 5,Qt::UserRole mSlicerManager id*/
 119
 120 //------------------------------------------------------------------------------
 121 vvMainWindow::vvMainWindow():vvMainWindowBase()
 122 {
 123   setupUi(this); // this sets up the GUI
 124
 125   mInputPathName = "";
 126   mMenuTools = menuTools;
 127   //  mMenuSegmentation = menuSegmentation;
 128   mContextMenu = &contextMenu;
 129   mMenuExperimentalTools = menuExperimental;
 130   mMainWidget = this;
 131   mCurrentTime = -1;
 132   mCurrentSelectedImageId = "";
 133   mCurrentPickedImageId = "";
 134   mCurrentPickedImageIndex = 0;
 135
 136   //Init the contextMenu
 137   this->setContextMenuPolicy(Qt::CustomContextMenu);
 138   contextActions.resize(0);
 139   QAction* actionOpen_new_image = contextMenu.addAction(QIcon(QString::fromUtf8(":/common/icons/fileopen.png")),
 140     tr("O&pen new Image"));
 141   actionOpen_new_image->setShortcut(QKeySequence(tr("Ctrl+O")));
 142   connect(actionOpen_new_image,SIGNAL(triggered()),this,SLOT(OpenImages()));
 143   contextActions.push_back(actionOpen_new_image);
 144   contextMenu.addSeparator();
 145
 146   QAction* actionClose_Image = contextMenu.addAction(QIcon(QString::fromUtf8(":/common/icons/exit.png")),
 147     tr("Close Current Image"));
 148   connect(actionClose_Image,SIGNAL(triggered()),this,SLOT(CloseImage()));
 149   contextActions.push_back(actionClose_Image);
 150
 151   QAction* actionReload_image = contextMenu.addAction(QIcon(QString::fromUtf8(":/common/icons/rotateright.png")),
 152     tr("Reload Current Image"));
 153   connect(actionReload_image,SIGNAL(triggered()),this,SLOT(ReloadImage()));
 154   contextActions.push_back(actionReload_image);
 155
 156   QAction* actionSave_image = contextMenu.addAction(QIcon(QString::fromUtf8(":/common/icons/filesave.png")),
 157     tr("Save Current Image"));
 158   connect(actionSave_image,SIGNAL(triggered()),this,SLOT(SaveAs()));
 159   contextActions.push_back(actionSave_image);
 160
 161   QAction* actionSave_state = contextMenu.addAction(QIcon(QString::fromUtf8(":/common/icons/filesave.png")),
 162     tr("Save Current State"));
 163   connect(actionSave_state,SIGNAL(triggered()),this,SLOT(SaveCurrentState()));
 164   contextActions.push_back(actionSave_state);
 165
 166   QAction* actionRead_state = contextMenu.addAction(QIcon(QString::fromUtf8(":/common/icons/filesave.png")),
 167     tr("Read Saved State"));
 168   connect(actionRead_state,SIGNAL(triggered()),this,SLOT(ReadSavedState()));
 169   contextActions.push_back(actionRead_state);
 170
 171   contextMenu.addSeparator();
 172
 173   contextMenu.addAction(actionAdd_VF_to_current_Image);
 174   contextActions.push_back(actionAdd_VF_to_current_Image);
 175
 176   //QAction* actionAdd_Overlay_to_current_Image = menuOverlay->addAction(QIcon(QString::fromUtf8(":/common/icons/GPSup.png")),
 177   //    tr("Add overlay image to current image"));
 178   contextMenu.addAction(actionAdd_overlay_image_to_current_image);
 179   contextActions.push_back(actionAdd_overlay_image_to_current_image);
 180
 181   contextMenu.addAction(actionAdd_fusion_image);
 182   contextActions.push_back(actionAdd_fusion_image);
 183
 184   contextMenu.addAction(actionAdd_USSequence_toCT);
 185   contextActions.push_back(actionAdd_USSequence_toCT);
 186
 187
 188   contextMenu.addSeparator();
 189   QAction* actionResetMatrix = contextMenu.addAction(QIcon(QString::fromUtf8(":/common/icons/identity.png")),
 190     tr("Reset transformation to identity"));
 191   connect(actionResetMatrix, SIGNAL(triggered()), this,SLOT(ResetTransformationToIdentity()));
 192
 193   // TRIAL DS
 194   /*
 195   QMenu * m = new QMenu(menubar);
 196   m->setTitle("TOTO");
 197   //  m->setObjectName(QString::fromUtf8("TOTOTO"));
 198   contextMenu.addMenu(m);
 199   QAction * a = m->addAction(QIcon(QString::fromUtf8(":/common/icons/GPSup.png")),
 200   tr("BIDON"));
 201   QAction * b = m->addAction(QIcon(QString::fromUtf8(":/common/icons/GPSup.png")),
 202   tr("BIDON2"));
 203   m->addAction(a);
 204   m->addAction(b);
 205   connect(a,SIGNAL(triggered()),this,SLOT(AddFusionImage()));
 206   */
 207
 208   //init the DataTree
 209   mSlicerManagers.resize(0);
 210
 211   QStringList header;
 212   header.append("");
 213   header.append("TL");
 214   header.append("TR");
 215   header.append("BL");
 216   header.append("BR");
 217   header.append("");
 218   header.append("");
 219   header.append("Name");
 220
 221   DataTree->setHeaderLabels(header);
 222   DataTree->resizeColumnToContents(COLUMN_TREE);
 223   DataTree->resizeColumnToContents(COLUMN_UL_VIEW);
 224   DataTree->resizeColumnToContents(COLUMN_UR_VIEW);
 225   DataTree->resizeColumnToContents(COLUMN_DL_VIEW);
 226   DataTree->resizeColumnToContents(COLUMN_DR_VIEW);
 227   DataTree->resizeColumnToContents(COLUMN_CLOSE_IMAGE);
 228   DataTree->resizeColumnToContents(COLUMN_RELOAD_IMAGE);
 229   DataTree->resizeColumnToContents(COLUMN_IMAGE_NAME);
 230
 231   viewMode = 1;
 232   documentation = new vvDocumentation();
 233   help_dialog = new vvHelpDialog();
 234   dicomSeriesSelector = new vvDicomSeriesSelector();
 235
 236   inverseButton->setEnabled(0);
 237   actionAdd_overlay_image_to_current_image->setEnabled(0);
 238   actionSave_As->setEnabled(0);
 239   actionAdd_VF_to_current_Image->setEnabled(0);
 240   actionAdd_fusion_image->setEnabled(0);
 241   actionAdd_USSequence_toCT->setEnabled(0);
 242
 243   //init the sliders
 244   verticalSliders.push_back(NOVerticalSlider);
 245   verticalSliders.push_back(NEVerticalSlider);
 246   verticalSliders.push_back(SOVerticalSlider);
 247   verticalSliders.push_back(SEVerticalSlider);
 248
 249   for (int i =0; i < 4; i++)
 250     verticalSliders[i]->hide();
 251
 252   horizontalSliders.push_back(NOHorizontalSlider);
 253   horizontalSliders.push_back(NEHorizontalSlider);
 254   horizontalSliders.push_back(SOHorizontalSlider);
 255   horizontalSliders.push_back(SEHorizontalSlider);
 256
 257   for (int i =0; i < 4; i++)
 258     horizontalSliders[i]->hide();
 259
 260
 261   connect(NOVerticalSlider,SIGNAL(valueChanged(int)),this,SLOT(NOVerticalSliderChanged()));
 262   connect(NEVerticalSlider,SIGNAL(valueChanged(int)),this,SLOT(NEVerticalSliderChanged()));
 263   connect(SOVerticalSlider,SIGNAL(valueChanged(int)),this,SLOT(SOVerticalSliderChanged()));
 264   connect(SEVerticalSlider,SIGNAL(valueChanged(int)),this,SLOT(SEVerticalSliderChanged()));
 265
 266   connect(NOHorizontalSlider,SIGNAL(valueChanged(int)),this,SLOT(NOHorizontalSliderMoved()));
 267   connect(NEHorizontalSlider,SIGNAL(valueChanged(int)),this,SLOT(NEHorizontalSliderMoved()));
 268   connect(SOHorizontalSlider,SIGNAL(valueChanged(int)),this,SLOT(SOHorizontalSliderMoved()));
 269   connect(SEHorizontalSlider,SIGNAL(valueChanged(int)),this,SLOT(SEHorizontalSliderMoved()));
 270
 271   //connect everything
 272   connect(actionCompute_mid_position_image,SIGNAL(triggered()),this,SLOT(ComputeMidPosition()));
 273   connect(actionDeformable_Registration,SIGNAL(triggered()),this,SLOT(ComputeDeformableRegistration()));
 274   connect(actionWarp_image_with_vector_field,SIGNAL(triggered()),this,SLOT(WarpImage()));
 275   connect(actionLoad_images,SIGNAL(triggered()),this,SLOT(OpenImages()));
 276   connect(actionOpen_Dicom,SIGNAL(triggered()),this,SLOT(OpenDicom()));
 277   connect(actionOpen_Dicom_Struct,SIGNAL(triggered()),this,SLOT(OpenDCStructContour()));
 278   connect(actionOpen_VTK_contour,SIGNAL(triggered()),this,SLOT(OpenVTKContour()));
 279   connect(actionOpen_Multiple_Images_As_One,SIGNAL(triggered()),this,SLOT(MergeImages()));
 280   connect(actionSlice_Image_As_Multiple_Images,SIGNAL(triggered()),this,SLOT(SliceImages()));
 281   connect(actionOpen_Image_With_Time,SIGNAL(triggered()),this,SLOT(OpenImageWithTime()));
 282   connect(actionMerge_images_as_n_dim_t, SIGNAL(triggered()), this, SLOT(MergeImagesWithTime()));
 283   connect(actionSave_As,SIGNAL(triggered()),this,SLOT(SaveAs()));
 284   connect(actionSave_current_state,SIGNAL(triggered()),this,SLOT(SaveCurrentState()));
 285   connect(actionRead_saved_state,SIGNAL(triggered()),this,SLOT(ReadSavedState()));
 286   connect(actionExit,SIGNAL(triggered()),this,SLOT(close()));
 287   connect(actionAdd_VF_to_current_Image,SIGNAL(triggered()),this,SLOT(OpenField()));
 288   connect(actionAdd_fusion_image,SIGNAL(triggered()),this,SLOT(SelectFusionImage()));
 289   connect(actionAdd_overlay_image_to_current_image,SIGNAL(triggered()), this,SLOT(SelectOverlayImage()));
 290   connect(actionAdd_USSequence_toCT,SIGNAL(triggered()), this,SLOT(SelectFusionSequence()));
 291   connect(actionNavigation_Help,SIGNAL(triggered()),this,SLOT(ShowHelpDialog()));
 292   connect(actionDocumentation,SIGNAL(triggered()),this,SLOT(ShowDocumentation()));
 293   connect(actionRegister_vv,SIGNAL(triggered()),this,SLOT(PopupRegisterForm()));
 294
 295   connect(overlayPanel, SIGNAL(FusionSequenceSignalButtonPressed()), this, SLOT(SelectFusionSequenceTemporalSignal()));
 296
 297
 298   ///////////////////////////////////////////////
 299   connect(actionSegmentation,SIGNAL(triggered()),this,SLOT(SegmentationOnCurrentImage()));
 300   connect(actionSurface_Viewer,SIGNAL(triggered()),this,SLOT(SurfaceViewerLaunch()));
 301   ///////////////////////////////////////////////
 302
 303   actionNorth_East_Window->setEnabled(0);
 304   actionNorth_West_Window->setEnabled(0);
 305   actionSouth_East_Window->setEnabled(0);
 306   actionSouth_West_Window->setEnabled(0);
 307
 308   connect(actionNorth_East_Window,SIGNAL(triggered()),this,SLOT(SaveNEScreenshot()));
 309   connect(actionNorth_West_Window,SIGNAL(triggered()),this,SLOT(SaveNOScreenshot()));
 310   connect(actionSouth_East_Window,SIGNAL(triggered()),this,SLOT(SaveSEScreenshot()));
 311   connect(actionSouth_West_Window,SIGNAL(triggered()),this,SLOT(SaveSOScreenshot()));
 312   connect(actionSave_all_slices,SIGNAL(triggered()),this,SLOT(SaveScreenshotAllSlices()));
 313
 314   connect(DataTree,SIGNAL(itemSelectionChanged()),this,SLOT(ImageInfoChanged()));
 315   connect(DataTree,SIGNAL(itemClicked(QTreeWidgetItem*, int)),this,
 316     SLOT(DisplayChanged(QTreeWidgetItem*, int)));
 317
 318   connect(viewButton,SIGNAL(clicked()),this, SLOT(ChangeViewMode()) );
 319   connect(windowSpinBox,SIGNAL(editingFinished()),this,SLOT(WindowLevelEdited()));
 320   connect(levelSpinBox,SIGNAL(editingFinished()),this,SLOT(WindowLevelEdited()));
 321   connect(colorMapComboBox,SIGNAL(currentIndexChanged(int)),this,SLOT(UpdateColorMap()));
 322   connect(presetComboBox,SIGNAL(currentIndexChanged(int)),this,SLOT(UpdateWindowLevel()));
 323   connect(slicingPresetComboBox, SIGNAL(currentIndexChanged(int)),this,SLOT(UpdateSlicingPreset()));
 324   connect(inverseButton,SIGNAL(clicked()),this,SLOT(SwitchWindowLevel()));
 325   connect(applyWindowLevelToAllButton,SIGNAL(clicked()),this,SLOT(ApplyWindowLevelToAllImages()));
 326
 327   connect(this,SIGNAL(customContextMenuRequested(QPoint)),this,SLOT(ShowContextMenu(QPoint)));
 328
 329   connect(linkPanel,SIGNAL(addLink(QString,QString,bool)),this,SLOT(AddLink(QString,QString,bool)));
 330   connect(linkPanel,SIGNAL(removeLink(QString,QString)),this,SLOT(RemoveLink(QString,QString)));
 331   connect(overlayPanel,SIGNAL(VFPropertyUpdated(int,int,int,int,double,double,double)),this,SLOT(SetVFProperty(int,int,int,int,double,double,double)));
 332   connect(overlayPanel,SIGNAL(OverlayPropertyUpdated(int,int,double,double)),
 333     this,SLOT(SetOverlayProperty(int,int,double,double)));
 334   connect(overlayPanel,SIGNAL(FusionPropertyUpdated(int,int,int,double,double, bool)),
 335     this,SLOT(SetFusionProperty(int,int,int,double,double, bool)));
 336   connect(landmarksPanel,SIGNAL(UpdateRenderWindows()),this,SLOT(UpdateRenderWindows()));
 337
 338   connect(overlayPanel,SIGNAL(FusionSequencePropertyUpdated(int, bool, unsigned int, bool)),
 339     this,SLOT(SetFusionSequenceProperty(int, bool,unsigned int, bool)));
 340
 341
 342   playMode = 0;//pause
 343   mFrameRate = 10;
 344   playButton->setEnabled(0);
 345   frameRateLabel->setEnabled(0);
 346   frameRateSpinBox->setEnabled(0);
 347   connect(playButton, SIGNAL(clicked()),this,SLOT(PlayPause()));
 348   connect(frameRateSpinBox, SIGNAL(valueChanged(int)),this,SLOT(ChangeFrameRate(int)));
 349
 350   goToCursorPushButton->setEnabled(0);
 351   connect(goToCursorPushButton, SIGNAL(clicked()),this,SLOT(GoToCursor()));
 352
 353   NOViewWidget->hide();
 354   NEViewWidget->hide();
 355   SOViewWidget->hide();
 356   SEViewWidget->hide();
 357
 358   //Recently opened files
 359   std::list<std::string> recent_files = GetRecentlyOpenedImages();
 360   recentlyOpenedFilesMenu=NULL;
 361   if ( !recent_files.empty() ) {
 362     createRecentlyOpenedFilesMenu();
 363     updateRecentlyOpenedFilesMenu(recent_files);
 364   }
 365
 366   // Adding all new tools (insertion in the menu)
 367   vvToolManager::GetInstance()->InsertToolsInMenu(this);
 368   vvToolManager::GetInstance()->EnableToolsInMenu(this, false);
 369
 370   if (!CLITK_EXPERIMENTAL)
 371     menuExperimental->menuAction()->setVisible(false);
 372
 373
 374   QTimer * timerMemory = new QTimer(this);
 375   //timerMemory->setInterval(5);
 376   connect(timerMemory, SIGNAL(timeout()), this, SLOT(UpdateMemoryUsage()));
 377   timerMemory->start(2000);
 378
 379 }
 380 //------------------------------------------------------------------------------
 381 void vvMainWindow::show()
 382 {
 383   vvMainWindowBase::show();
 384   PopupRegisterForm(true);
 385 }
 386 //------------------------------------------------------------------------------
 387 void vvMainWindow::UpdateMemoryUsage()
 388 {
 389   //  clitk::PrintMemory(true);
 390   if (clitk::GetMemoryUsageInMb() == 0) infoPanel->setMemoryInMb("NA");
 391   else infoPanel->setMemoryInMb(QString::number(clitk::GetMemoryUsageInMb())+" MiB");
 392 }
 393 //------------------------------------------------------------------------------
 394
 395
 396 //------------------------------------------------------------------------------
 397 void vvMainWindow::createRecentlyOpenedFilesMenu()
 398 {
 399   recentlyOpenedFilesMenu = new QMenu("Recently opened files...");
 400   recentlyOpenedFilesMenu->setIcon(QIcon(QString::fromUtf8(":/common/icons/open.png")));
 401   menuFile->insertMenu(actionOpen_Image_With_Time,recentlyOpenedFilesMenu);
 402   menuFile->insertSeparator(actionOpen_Image_With_Time);
 403 }
 404 //------------------------------------------------------------------------------
 405
 406
 407 //------------------------------------------------------------------------------
 408
 409 void vvMainWindow::updateRecentlyOpenedFilesMenu(const std::list<std::string> &recent_files)
 410 {
 411   if(recentlyOpenedFilesMenu==NULL) {
 412     createRecentlyOpenedFilesMenu();
 413   } else {
 414     recentlyOpenedFilesMenu->clear();
 415   }
 416   for (std::list<std::string>::const_iterator i = recent_files.begin(); i!=recent_files.end(); i++) {
 417     QAction* current=new QAction(QIcon(QString::fromUtf8(":/common/icons/open.png")), i->c_str(),this);
 418     recentlyOpenedFilesMenu->addAction(current);
 419     connect(current,SIGNAL(triggered()),this,SLOT(OpenRecentImage()));
 420   }
 421 }
 422 //------------------------------------------------------------------------------
 423
 424
 425 //------------------------------------------------------------------------------
 426 void vvMainWindow::ComputeMidPosition()
 427 {
 428   bool ok;
 429   int index=GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
 430   int ref = QInputDialog::getInteger(this,"Chose reference phase","Reference phase",0,0,\
 431     mSlicerManagers[index]->GetImage()->GetVTKImages().size()-1,1,&ok);
 432   if (ok) {
 433     vvMidPosition midp;
 434     midp.slicer_manager = mSlicerManagers[index];
 435     midp.reference_image_index = ref;
 436     QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
 437     midp.Update();
 438     if (midp.error)
 439       QMessageBox::warning(this, "Error computing midposition image",midp.error_message.c_str());
 440     else {
 441       QFileInfo info(midp.slicer_manager->GetFileName().c_str());
 442       AddImage(midp.output,info.path().toStdString()+"/"+info.completeBaseName().toStdString()+"_midposition.mhd");
 443     }
 444     QApplication::restoreOverrideCursor();
 445   }
 446 }
 447 //------------------------------------------------------------------------------
 448
 449
 450 //------------------------------------------------------------------------------
 451 void vvMainWindow::AddContour(int image_index, vvMesh::Pointer contour, bool propagation)
 452 {
 453   QTreeWidgetItem *item = new QTreeWidgetItem();
 454   item->setData(0,Qt::UserRole,"filename.vtk");
 455   item->setData(1,Qt::UserRole,tr("contour"));
 456   QBrush brush;
 457   brush.setColor(QColor(contour->r*255,contour->g*255,contour->b*255));
 458   brush.setStyle(Qt::SolidPattern);
 459   item->setData(COLUMN_IMAGE_NAME,Qt::BackgroundRole,brush);
 460   item->setData(COLUMN_IMAGE_NAME,Qt::DisplayRole,contour->structure_name.c_str());
 461
 462   for (int j = 1; j <= 4; j++)
 463     item->setData(j,Qt::CheckStateRole,DataTree->topLevelItem(image_index)->data(j,Qt::CheckStateRole));
 464
 465   QTreePushButton* cButton = new QTreePushButton;
 466   cButton->setItem(item);
 467   cButton->setColumn(COLUMN_CLOSE_IMAGE);
 468   cButton->setToolTip(tr("close image"));
 469   cButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/exit.png")));
 470   connect(cButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
 471     this,SLOT(CloseImage(QTreeWidgetItem*, int)));
 472
 473   QTreePushButton* rButton = new QTreePushButton;
 474   rButton->setItem(item);
 475   rButton->setColumn(COLUMN_RELOAD_IMAGE);
 476   rButton->setToolTip(tr("reload image"));
 477   rButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/rotateright.png")));
 478   rButton->setEnabled(false);
 479   //Not implemented
 480   //connect(rButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
 481   //this,SLOT(ReloadImage(QTreeWidgetItem*, int)));
 482
 483   DataTree->topLevelItem(image_index)->setExpanded(1);
 484   DataTree->topLevelItem(image_index)->addChild(item);
 485   DataTree->setItemWidget(item, COLUMN_CLOSE_IMAGE, cButton);
 486   DataTree->setItemWidget(item, COLUMN_RELOAD_IMAGE, rButton);
 487   QString id = DataTree->topLevelItem(image_index)->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString();
 488   item->setData(COLUMN_IMAGE_NAME,Qt::UserRole,id.toStdString().c_str());
 489
 490   UpdateTree();
 491   mSlicerManagers[image_index]->AddContour(contour,propagation);
 492   mSlicerManagers[image_index]->Render();
 493 }
 494 //------------------------------------------------------------------------------
 495
 496
 497 //------------------------------------------------------------------------------
 498 void vvMainWindow::OpenVTKContour()
 499 {
 500   if (mSlicerManagers.size() > 0) {
 501     QString Extensions = "Images ( *.vtk *.obj)";
 502     Extensions += ";;All Files (*)";
 503     QString file = QFileDialog::getOpenFileName(this,tr("Open vtkPolyData"),mInputPathName,Extensions);
 504     if (file.isNull())
 505       return;
 506     QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
 507     int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
 508     vvMeshReader reader;
 509     reader.SetImage(mSlicerManagers[index]->GetImage());
 510     reader.SetModeToVTK();
 511     reader.SetFilename(file.toStdString());
 512     reader.Update();
 513     AddContour(index,reader.GetOutput()[0],false);
 514     QApplication::restoreOverrideCursor();
 515   }
 516 }
 517 //------------------------------------------------------------------------------
 518
 519
 520 //------------------------------------------------------------------------------
 521 void vvMainWindow::AddDCStructContour(int index, QString file)
 522 {
 523   vvMeshReader reader;
 524   reader.SetFilename(file.toStdString());
 525   vvStructSelector selector;
 526   selector.SetStructures(reader.GetROINames());
 527   if (!mSlicerManagers[index]->GetVF().IsNull())
 528     selector.EnablePropagationCheckBox();
 529   if (selector.exec()) {
 530     QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
 531     reader.SetSelectedItems(selector.getSelectedItems());
 532     reader.SetImage(mSlicerManagers[index]->GetImage());
 533     if (selector.PropagationEnabled())
 534       reader.SetPropagationVF(mSlicerManagers[index]->GetVF());
 535     reader.Update();
 536     std::vector<vvMesh::Pointer> contours=reader.GetOutput();
 537     for (std::vector<vvMesh::Pointer>::iterator i=contours.begin();
 538       i!=contours.end(); i++)
 539       AddContour(index,*i,selector.PropagationEnabled());
 540     QApplication::restoreOverrideCursor();
 541   }
 542 }
 543
 544 //------------------------------------------------------------------------------
 545 void vvMainWindow::OpenDCStructContour()
 546 {
 547   if (mSlicerManagers.size() > 0) {
 548     QString Extensions = "Dicom Files ( *.dcm RS*)";
 549     Extensions += ";;All Files (*)";
 550     QString file = QFileDialog::getOpenFileName(this,tr("Merge Images"),mInputPathName,Extensions);
 551     if (file.isNull())
 552       return;
 553     int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
 554     AddDCStructContour(index, file);
 555   }
 556 }
 557 //------------------------------------------------------------------------------
 558
 559
 560 //------------------------------------------------------------------------------
 561 void vvMainWindow::ComputeDeformableRegistration()
 562 {
 563   if (mSlicerManagers.size() > 0) {
 564     int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
 565     vvDeformationDialog dialog(index,mSlicerManagers);
 566     if (dialog.exec()) {
 567       std::string base_name=itksys::SystemTools::GetFilenameWithoutExtension(mSlicerManagers[dialog.GetInputFileIndex()]->GetFileName());
 568       AddField(dialog.GetOutput(),dialog.getFieldFile(),dialog.GetInputFileIndex());
 569       WarpImage(dialog.GetSelectedSlicer(),dialog.GetReferenceFrameIndex());
 570     } else
 571       std::cout << "Error or user cancellation while computing deformation field..." << std::endl;
 572   } else QMessageBox::information(this, "Need to open image","You must open an image first.");
 573 }
 574 //------------------------------------------------------------------------------
 575
 576
 577 //------------------------------------------------------------------------------
 578 void vvMainWindow::WarpImage()
 579 {
 580   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
 581   if (!mSlicerManagers[index]->GetVF().IsNull()) {
 582     bool ok;
 583     int ref = QInputDialog::getInteger(this,"Chose reference phase","Reference phase",0,0,\
 584       mSlicerManagers[index]->GetImage()->GetVTKImages().size()-1,1,&ok);
 585     if (ok) {
 586       WarpImage(mSlicerManagers[index],ref);
 587     }
 588   } else
 589     QMessageBox::warning(this,tr("No vector field"),tr("Sorry, can't warp without a vector field"));
 590 }
 591 //------------------------------------------------------------------------------
 592
 593
 594 //------------------------------------------------------------------------------
 595 void vvMainWindow::WarpImage(vvSlicerManager* selected_slicer,int reference_phase)
 596 {
 597   if (!selected_slicer->GetVF().IsNull()) {
 598     QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
 599     QFileInfo info(selected_slicer->GetFileName().c_str());
 600     vvImageWarp warp(selected_slicer->GetImage(),selected_slicer->GetVF(),
 601       reference_phase,this);
 602     if (warp.ComputeWarpedImage()) {
 603       AddImage(warp.GetWarpedImage(),info.path().toStdString()+"/"+info.completeBaseName().toStdString()+"_warped.mhd");
 604       AddImage(warp.GetDiffImage()  ,info.path().toStdString()+"/"+info.completeBaseName().toStdString()+"_diff.mhd");
 605       AddImage(warp.GetJacobianImage()  ,info.path().toStdString()+"/"+info.completeBaseName().toStdString()+"_jacobian.mhd");
 606       QApplication::restoreOverrideCursor();
 607     } else {
 608       QApplication::restoreOverrideCursor();
 609       QMessageBox::warning(this,tr("Different spacings"),tr("The vector field and image spacings must be the same in order to warp."));
 610     }
 611   } else
 612     QMessageBox::warning(this,tr("No vector field"),tr("Sorry, can't warp without a vector field."));
 613 }
 614 //------------------------------------------------------------------------------
 615
 616
 617 //------------------------------------------------------------------------------
 618 vvMainWindow::~vvMainWindow()
 619 {
 620   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
 621     if (mSlicerManagers[i] != NULL)
 622       delete mSlicerManagers[i];
 623   }
 624 }
 625 //------------------------------------------------------------------------------
 626
 627 //------------------------------------------------------------------------------
 628 QTabWidget * vvMainWindow::GetTab()
 629 {
 630   return tabWidget;
 631 }
 632 //------------------------------------------------------------------------------
 633
 634
 635 //------------------------------------------------------------------------------
 636 void vvMainWindow::MergeImages()
 637 {
 638   QString Extensions = EXTENSIONS;
 639   Extensions += ";;All Files (*)";
 640   QStringList files = QFileDialog::getOpenFileNames(this,tr("Merge Images"),mInputPathName,Extensions);
 641   if (files.isEmpty())
 642     return;
 643   mInputPathName = itksys::SystemTools::GetFilenamePath(files[0].toStdString()).c_str();
 644   std::vector<std::string> vector;
 645
 646   unsigned int currentDim = 0;
 647   std::vector<double> currentSpacing;
 648   std::vector<int> currentSize;
 649   std::vector<double> currentOrigin;
 650
 651   for (int i = 0; i < files.size(); i++) {
 652     itk::ImageIOBase::Pointer reader = itk::ImageIOFactory::CreateImageIO(
 653       files[i].toStdString().c_str(), itk::ImageIOFactory::ReadMode);
 654     reader->SetFileName(files[i].toStdString().c_str());
 655     reader->ReadImageInformation();
 656     if (reader)        {
 657       //NOViewWidget->hide();
 658       //NEViewWidget->hide();
 659       //SOViewWidget->hide();
 660       //SEViewWidget->hide();
 661       if (i == 0)
 662         currentDim = reader->GetNumberOfDimensions();
 663       bool IsOk = true;
 664       for (unsigned int j = 0; j < currentDim; j++) {
 665         if (i == 0) {
 666           if (j == 0) {
 667             currentSpacing.resize(currentDim);
 668             currentSize.resize(currentDim);
 669             currentOrigin.resize(currentDim);
 670           }
 671           currentOrigin[j] = reader->GetOrigin(j);
 672           currentSpacing[j] = reader->GetSpacing(j);
 673           currentSize[j] = reader->GetDimensions(j);
 674         } else if (currentDim != reader->GetNumberOfDimensions()
 675           || currentSpacing[j] != reader->GetSpacing(j)
 676           || currentSize[j] != (int)reader->GetDimensions(j)
 677           || currentOrigin[j] != reader->GetOrigin(j)) {
 678             QString error = "Cannot read file (too different from others ";
 679             error += files[i].toStdString().c_str();
 680             QMessageBox::information(this,tr("Reading problem"),error);
 681             IsOk = false;
 682             break;
 683         }
 684       }
 685       if (IsOk)
 686         vector.push_back(files[i].toStdString());
 687     }
 688   }
 689   if (vector.size() > 0)
 690     LoadImages(vector, vvImageReader::MERGED);
 691 }
 692 //------------------------------------------------------------------------------
 693
 694 //------------------------------------------------------------------------------
 695 void vvMainWindow::SliceImages()
 696 {
 697   QString Extensions = EXTENSIONS;
 698   Extensions += ";;All Files (*)";
 699
 700   QStringList files = QFileDialog::getOpenFileNames(this,tr("Slice Images"),mInputPathName,Extensions);
 701   if (files.isEmpty())
 702     return;
 703   mInputPathName = itksys::SystemTools::GetFilenamePath(files[0].toStdString()).c_str();
 704   std::vector<std::string> vector;
 705   for (int i = 0; i < files.size(); i++)
 706     vector.push_back(files[i].toStdString());
 707   LoadImages(vector, vvImageReader::SLICED);
 708 }
 709 //------------------------------------------------------------------------------
 710
 711 //------------------------------------------------------------------------------
 712 void vvMainWindow::MergeImagesWithTime()
 713 {
 714   QString Extensions = EXTENSIONS;
 715   Extensions += ";;All Files (*)";
 716   QStringList files = QFileDialog::getOpenFileNames(this,tr("Merge Images With Time"),mInputPathName,Extensions);
 717   if (files.isEmpty())
 718     return;
 719   mInputPathName = itksys::SystemTools::GetFilenamePath(files[0].toStdString()).c_str();
 720   std::vector<std::string> vector;
 721
 722   for (int i = 0; i < files.size(); i++)
 723     vector.push_back(files[i].toStdString());
 724   sort(vector.begin(),vector.end());
 725   if (vector.size() > 1)
 726     LoadImages(vector, vvImageReader::MERGEDWITHTIME);
 727   else
 728     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.");
 729 }
 730 //------------------------------------------------------------------------------
 731
 732
 733 //------------------------------------------------------------------------------
 734 void vvMainWindow::OpenDicom()
 735 {
 736   std::vector<std::string> files;
 737
 738   std::cout << "dicomSeriesSelector " << std::endl;
 739   if (dicomSeriesSelector->exec() == QDialog::Accepted) {
 740     files = *(dicomSeriesSelector->GetFilenames());
 741     LoadImages(files, vvImageReader::DICOM);
 742   }
 743 }
 744 //------------------------------------------------------------------------------
 745
 746 //------------------------------------------------------------------------------
 747 void vvMainWindow::OpenImages()
 748 {
 749   QString Extensions = EXTENSIONS;
 750   Extensions += ";;All Files (*)";
 751
 752   QStringList files = QFileDialog::getOpenFileNames(this,tr("Load Images"),mInputPathName,Extensions);
 753   if (files.isEmpty())
 754     return;
 755   mInputPathName = itksys::SystemTools::GetFilenamePath(files[0].toStdString()).c_str();
 756   std::vector<std::string> vector;
 757   for (int i = 0; i < files.size(); i++)
 758     vector.push_back(files[i].toStdString());
 759   LoadImages(vector, vvImageReader::IMAGE);
 760 }
 761 //------------------------------------------------------------------------------
 762 void vvMainWindow::OpenRecentImage()
 763 {
 764   QAction * caller = qobject_cast<QAction*>(sender());
 765   std::vector<std::string> images;
 766   images.push_back(caller->text().toStdString());
 767   mInputPathName = itksys::SystemTools::GetFilenamePath(images[0]).c_str();
 768   LoadImages(images, vvImageReader::IMAGE);
 769 }
 770 //------------------------------------------------------------------------------
 771
 772
 773 //------------------------------------------------------------------------------
 774 void vvMainWindow::OpenImageWithTime()
 775 {
 776   QString Extensions = EXTENSIONS;
 777   Extensions += ";;All Files (*)";
 778
 779   QStringList files = QFileDialog::getOpenFileNames(this,tr("Load Images With Time"),mInputPathName,Extensions);
 780   if (files.isEmpty())
 781     return;
 782   mInputPathName = itksys::SystemTools::GetFilenamePath(files[0].toStdString()).c_str();
 783   std::vector<std::string> vector;
 784   for (int i = 0; i < files.size(); i++) {
 785     vector.push_back(files[i].toStdString());
 786   }
 787   LoadImages(vector, vvImageReader::IMAGEWITHTIME);
 788 }
 789 //------------------------------------------------------------------------------
 790
 791
 792 //------------------------------------------------------------------------------
 793 void vvMainWindow::LoadImages(std::vector<std::string> files, vvImageReader::LoadedImageType filetype)
 794 {
 795   //Separate the way to open images and dicoms
 796   int fileSize;
 797   if (filetype == vvImageReader::IMAGE || filetype == vvImageReader::IMAGEWITHTIME)
 798     fileSize = files.size();
 799   else
 800     fileSize = 1;
 801
 802   // For SLICED, we need the number of slices (ndim and #slices)
 803   std::vector<unsigned int> nSlices;
 804   nSlices.resize(files.size());
 805   std::fill(nSlices.begin(), nSlices.end(), 1);
 806   if (filetype == vvImageReader::SLICED) {
 807     for (int i = 0; i < fileSize; i++) {
 808       itk::ImageIOBase::Pointer header = clitk::readImageHeader(files[i]);
 809       QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
 810       if (!header) {
 811         nSlices[i] = 0;
 812         QString error = "Cannot open file \n";
 813         error += files[i].c_str();
 814         QMessageBox::information(this,tr("Reading problem"),error);
 815         return;
 816       }
 817       if (header->GetNumberOfDimensions() < 3) {
 818         nSlices[i] = 0;
 819         QString error = "Dimension problem. Cannot slice \n";
 820         error += files[i].c_str();
 821         QMessageBox::information(this,tr("Reading problem"),error);
 822         return;
 823       }
 824       nSlices[i] = header->GetDimensions( header->GetNumberOfDimensions()-1 );
 825     }
 826   }
 827
 828   //Only add to the list of recently opened files when a single file is opened,
 829   //to avoid polluting the list of recently opened files
 830   if (files.size() == 1) {
 831     QFileInfo finfo=tr(files[0].c_str());
 832     AddToRecentlyOpenedImages(finfo.absoluteFilePath().toStdString());
 833     updateRecentlyOpenedFilesMenu(GetRecentlyOpenedImages());
 834   }
 835   //init the progress events
 836   QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
 837   vvProgressDialog progress("Opening " + files[0],fileSize>1);
 838   qApp->processEvents();
 839
 840   int numberofsuccesulreads=0;
 841   //open images as 1 or multiples
 842   for (int i = 0; i < fileSize; i++) {
 843     progress.SetText("Opening " + files[i]);
 844     progress.SetProgress(i,fileSize);
 845     qApp->processEvents();
 846
 847     for (unsigned int j = 0; j < nSlices[i]; j++) {
 848       //read the image and put it in mSlicerManagers
 849       vvSlicerManager* imageManager = new vvSlicerManager(4);
 850       qApp->processEvents();
 851
 852       bool SetImageSucceed=false;
 853
 854       // Change filename if an image with the same already exist
 855       int number = GetImageDuplicateFilenameNumber(files[i] + std::string("_slice"));
 856
 857       if (filetype == vvImageReader::IMAGE || filetype == vvImageReader::IMAGEWITHTIME || filetype == vvImageReader::SLICED)
 858         SetImageSucceed = imageManager->SetImage(files[i],filetype, number, j);
 859       else {
 860         SetImageSucceed = imageManager->SetImages(files,filetype, number);
 861       }
 862
 863       if (!SetImageSucceed) {
 864         QApplication::restoreOverrideCursor();
 865         QString error = "Cannot open file \n";
 866         error += imageManager->GetLastError().c_str();
 867         QMessageBox::information(this,tr("Reading problem"),error);
 868         delete imageManager;
 869       } else {
 870         mSlicerManagers.push_back(imageManager);
 871
 872         //create an item in the tree with good settings
 873         QTreeWidgetItem *item = new QTreeWidgetItem();
 874         item->setData(0,Qt::UserRole,files[i].c_str());
 875         QFileInfo fileinfo(imageManager->GetFileName().c_str()); //Do not show the path
 876         item->setData(COLUMN_IMAGE_NAME,Qt::DisplayRole,fileinfo.fileName());
 877         item->setData(1,Qt::UserRole,tr("image"));
 878         item->setToolTip(COLUMN_IMAGE_NAME, imageManager->GetListOfAbsoluteFilePathInOneString("image").c_str());
 879         qApp->processEvents();
 880
 881         //Create the buttons for reload and close
 882         qApp->processEvents();
 883         QTreePushButton* cButton = new QTreePushButton;
 884         cButton->setItem(item);
 885         cButton->setColumn(COLUMN_CLOSE_IMAGE);
 886         cButton->setToolTip(tr("close image"));
 887         cButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/exit.png")));
 888         connect(cButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
 889           this,SLOT(CloseImage(QTreeWidgetItem*, int)));
 890
 891         QTreePushButton* rButton = new QTreePushButton;
 892         rButton->setItem(item);
 893         rButton->setColumn(COLUMN_RELOAD_IMAGE);
 894         rButton->setToolTip(tr("reload image"));
 895         rButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/rotateright.png")));
 896         connect(rButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
 897           this,SLOT(ReloadImage(QTreeWidgetItem*, int)));
 898
 899         DataTree->addTopLevelItem(item);
 900         DataTree->setItemWidget(item, COLUMN_CLOSE_IMAGE, cButton);
 901         DataTree->setItemWidget(item, COLUMN_RELOAD_IMAGE, rButton);
 902
 903         //set the id of the image
 904         QString id = QDir::current().absoluteFilePath(files[i].c_str()) + QString::number(mSlicerManagers.size()-1);
 905         item->setData(COLUMN_IMAGE_NAME,Qt::UserRole,id.toStdString().c_str());
 906         mSlicerManagers.back()->SetId(id.toStdString());
 907
 908         linkPanel->addImage(imageManager->GetFileName(), id.toStdString());
 909
 910         connect(mSlicerManagers.back(), SIGNAL(currentImageChanged(std::string)),
 911           this,SLOT(CurrentImageChanged(std::string)));
 912         connect(mSlicerManagers.back(), SIGNAL(currentPickedImageChanged(std::string)),
 913           this, SLOT(CurrentPickedImageChanged(std::string)));
 914         connect(mSlicerManagers.back(), SIGNAL(UpdatePosition(int, double, double, double, double, double, double, double)),
 915           this,SLOT(MousePositionChanged(int,double, double, double, double, double, double, double)));
 916         connect(mSlicerManagers.back(), SIGNAL(UpdateVector(int, double, double, double, double)),
 917           this, SLOT(VectorChanged(int,double,double,double, double)));
 918         connect(mSlicerManagers.back(), SIGNAL(UpdateOverlay(int, double, double)),
 919           this, SLOT(OverlayChanged(int,double,double)));
 920         connect(mSlicerManagers.back(), SIGNAL(UpdateFusion(int, double)),
 921           this, SLOT(FusionChanged(int,double)));
 922         connect(mSlicerManagers.back(), SIGNAL(WindowLevelChanged()),
 923           this,SLOT(WindowLevelChanged()));
 924         connect(mSlicerManagers.back(), SIGNAL(UpdateSlice(int,int)),
 925           this,SLOT(UpdateSlice(int,int)));
 926         connect(mSlicerManagers.back(), SIGNAL(UpdateTSlice(int, int, int)),
 927           this,SLOT(UpdateTSlice(int, int, int)));
 928         connect(mSlicerManagers.back(), SIGNAL(UpdateTSlice(int, int, int)),
 929           this,SLOT(ImageInfoChanged()));
 930         connect(mSlicerManagers.back(), SIGNAL(UpdateSliceRange(int,int,int,int,int)),
 931           this,SLOT(UpdateSliceRange(int,int,int,int,int)));
 932         connect(mSlicerManagers.back(), SIGNAL(UpdateLinkManager(std::string,int,double,double,double,int)),
 933           this,SLOT(UpdateLinkManager(std::string,int,double,double,double,int)));
 934         connect(mSlicerManagers.back(), SIGNAL(UpdateLinkedNavigation(std::string,vvSlicerManager*,vvSlicer*)),
 935           this,SLOT(UpdateLinkedNavigation(std::string,vvSlicerManager*,vvSlicer*)));
 936         connect(mSlicerManagers.back(), SIGNAL(ChangeImageWithIndexOffset(vvSlicerManager*,int,int)),
 937           this,SLOT(ChangeImageWithIndexOffset(vvSlicerManager*,int,int)));
 938         connect(mSlicerManagers.back(),SIGNAL(LandmarkAdded()),landmarksPanel,SLOT(AddPoint()));
 939
 940         InitSlicers();
 941         numberofsuccesulreads++;
 942       }
 943     }
 944   }
 945   if (numberofsuccesulreads) {
 946     NOViewWidget->show();
 947     NEViewWidget->show();
 948     SOViewWidget->show();
 949     SEViewWidget->show();
 950     UpdateTree();
 951     InitDisplay();
 952     ShowLastImage();
 953
 954     // Try to guess default WindowLevel
 955     double range[2];
 956     mSlicerManagers.back()->GetImage()->GetFirstVTKImageData()->GetScalarRange(range);
 957     if ((range[0] == 0) && (range[1] == 1)) {
 958       presetComboBox->setCurrentIndex(5);// binary
 959     } else {
 960       // TODO
 961     }
 962   }
 963   QApplication::restoreOverrideCursor();
 964 }
 965 //------------------------------------------------------------------------------
 966
 967 //------------------------------------------------------------------------------
 968 void vvMainWindow::UpdateTree()
 969 {
 970   DataTree->resizeColumnToContents(COLUMN_TREE);
 971   DataTree->resizeColumnToContents(COLUMN_UL_VIEW);
 972   DataTree->resizeColumnToContents(COLUMN_UR_VIEW);
 973   DataTree->resizeColumnToContents(COLUMN_DL_VIEW);
 974   DataTree->resizeColumnToContents(COLUMN_DR_VIEW);
 975   DataTree->resizeColumnToContents(COLUMN_IMAGE_NAME);
 976   DataTree->resizeColumnToContents(COLUMN_CLOSE_IMAGE);
 977   DataTree->resizeColumnToContents(COLUMN_RELOAD_IMAGE);
 978 }
 979 //------------------------------------------------------------------------------
 980
 981 //------------------------------------------------------------------------------
 982 void vvMainWindow::CurrentImageChanged(std::string id)
 983 {
 984   if (id == mCurrentSelectedImageId) return; // Do nothing
 985   int selected = 0;
 986   for (int i = 0; i < DataTree->topLevelItemCount(); i++) {
 987     if (DataTree->topLevelItem(i)->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString().toStdString() == id) {
 988       selected = i;
 989     } else {
 990       DataTree->topLevelItem(i)->setSelected(0);
 991     }
 992     for (int child = 0; child < DataTree->topLevelItem(i)->childCount(); child++)
 993       DataTree->topLevelItem(i)->child(child)->setSelected(0);
 994
 995   }
 996   DataTree->topLevelItem(selected)->setSelected(1);
 997   mCurrentSelectedImageId = id;
 998   emit SelectedImageHasChanged(mSlicerManagers[selected]);
 999 }
1000 //------------------------------------------------------------------------------
1001
1002 //------------------------------------------------------------------------------
1003 void vvMainWindow::CurrentPickedImageChanged(std::string id)
1004 {
1005   if (id == mCurrentPickedImageId) return; // Do nothing
1006   int selected = 0;
1007   for (int i = 0; i < DataTree->topLevelItemCount(); i++) {
1008     if (DataTree->topLevelItem(i)->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString().toStdString() == id) {
1009       selected = i;
1010     } else {
1011       DataTree->topLevelItem(i)->setSelected(0);
1012     }
1013     for (int child = 0; child < DataTree->topLevelItem(i)->childCount(); child++)
1014       DataTree->topLevelItem(i)->child(child)->setSelected(0);
1015
1016   }
1017   DataTree->topLevelItem(selected)->setSelected(1);
1018   mCurrentPickedImageId = id;
1019   mCurrentPickedImageIndex = selected;
1020 }
1021 //------------------------------------------------------------------------------
1022
1023 //------------------------------------------------------------------------------
1024 void vvMainWindow::ImageInfoChanged()
1025 {
1026   contextActions[6]->setEnabled(1);
1027   contextActions[5]->setEnabled(1);
1028   actionSave_As->setEnabled(1);
1029   actionAdd_VF_to_current_Image->setEnabled(1);
1030   actionAdd_fusion_image->setEnabled(1);
1031   actionAdd_overlay_image_to_current_image->setEnabled(1);
1032   actionAdd_USSequence_toCT->setEnabled(1);
1033   actionNorth_East_Window->setEnabled(1);
1034   actionNorth_West_Window->setEnabled(1);
1035   actionSouth_East_Window->setEnabled(1);
1036   actionSouth_West_Window->setEnabled(1);
1037   vvToolManager::GetInstance()->EnableToolsInMenu(this, true);
1038   inverseButton->setEnabled(1);
1039
1040   goToCursorPushButton->setEnabled(1);
1041
1042   if (DataTree->selectedItems().size()) {
1043     int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1044
1045     colorMapComboBox->setEnabled(1);
1046     for (int i = 0; i < DataTree->topLevelItem(index)->childCount(); i++) {
1047       if (DataTree->topLevelItem(index)->child(i)->data(1,Qt::UserRole).toString() == "overlay" ||
1048         DataTree->topLevelItem(index)->child(i)->data(1,Qt::UserRole).toString() == "fusion" ||
1049         DataTree->topLevelItem(index)->child(i)->data(1,Qt::UserRole).toString() == "fusionSequence") {
1050           colorMapComboBox->setEnabled(0);
1051           break;
1052       }
1053     }
1054
1055     std::vector<double> origin;
1056     std::vector<double> inputSpacing;
1057     std::vector<int> inputSize;
1058     std::vector<double> sizeMM;
1059     vtkSmartPointer<vtkMatrix4x4> transformation;
1060     int dimension=0;
1061     QString pixelType;
1062     QString inputSizeInBytes;
1063     QString image = DataTree->selectedItems()[0]->data(COLUMN_IMAGE_NAME,Qt::DisplayRole).toString();
1064
1065     int nframes = mSlicerManagers[index]->GetSlicer(0)->GetTMax();
1066
1067     if (nframes > 1 || playMode == 1) {
1068       playButton->setEnabled(1);
1069       frameRateLabel->setEnabled(1);
1070       frameRateSpinBox->setEnabled(1);
1071     } else {
1072       playButton->setEnabled(0);
1073       frameRateLabel->setEnabled(0);
1074       frameRateSpinBox->setEnabled(0);
1075     }
1076
1077     //read image header
1078     int NPixel = 1;
1079
1080     int tSlice = 0;
1081     vvImage::Pointer imageSelected;
1082     if (DataTree->topLevelItem(index) == DataTree->selectedItems()[0]) {
1083       imageSelected = mSlicerManagers[index]->GetSlicer(0)->GetImage();
1084       tSlice = mSlicerManagers[index]->GetSlicer(0)->GetTSlice();
1085     } else if (DataTree->selectedItems()[0]->data(1,Qt::UserRole).toString() == "vector") {
1086       imageSelected = mSlicerManagers[index]->GetSlicer(0)->GetVF();
1087       tSlice = mSlicerManagers[index]->GetSlicer(0)->GetOverlayTSlice();
1088     } else if (DataTree->selectedItems()[0]->data(1,Qt::UserRole).toString() == "overlay") {
1089       imageSelected = mSlicerManagers[index]->GetSlicer(0)->GetOverlay();
1090       tSlice = mSlicerManagers[index]->GetSlicer(0)->GetOverlayTSlice();
1091     } else if (DataTree->selectedItems()[0]->data(1,Qt::UserRole).toString() == "fusion") {
1092       imageSelected = mSlicerManagers[index]->GetSlicer(0)->GetFusion();
1093       tSlice = mSlicerManagers[index]->GetSlicer(0)->GetFusionTSlice();
1094     }
1095     else if (DataTree->selectedItems()[0]->data(1,Qt::UserRole).toString() == "fusionSequence") {
1096       imageSelected = mSlicerManagers[index]->GetSlicer(0)->GetFusion();
1097       tSlice = mSlicerManagers[index]->GetSlicer(0)->GetFusionTSlice();
1098     }
1099     else if (DataTree->selectedItems()[0]->data(1,Qt::UserRole).toString() == "contour") {
1100       imageSelected = mSlicerManagers[index]->GetSlicer(0)->GetImage();
1101       tSlice = mSlicerManagers[index]->GetSlicer(0)->GetTSlice();
1102     }
1103     else {
1104       imageSelected = mSlicerManagers[index]->GetSlicer(0)->GetImage();
1105       tSlice = mSlicerManagers[index]->GetSlicer(0)->GetTSlice();
1106     }
1107
1108     dimension = imageSelected->GetNumberOfDimensions();
1109     origin.resize(dimension);
1110     inputSpacing.resize(dimension);
1111     inputSize.resize(dimension);
1112     sizeMM.resize(dimension);
1113     pixelType = mSlicerManagers[index]->GetImage()->GetScalarTypeAsITKString().c_str();
1114     for (int i = 0; i < dimension; i++) {
1115       origin[i] = imageSelected->GetOrigin()[i];
1116       inputSpacing[i] = imageSelected->GetSpacing()[i];
1117       inputSize[i] = imageSelected->GetSize()[i];
1118       sizeMM[i] = inputSize[i]*inputSpacing[i];
1119       NPixel *= inputSize[i];
1120     }
1121     inputSizeInBytes = GetSizeInBytes(imageSelected->GetActualMemorySize()*1000);
1122
1123     QString dim = QString::number(dimension) + " (";
1124     dim += pixelType + ")";
1125
1126     infoPanel->setFileName(image);
1127     infoPanel->setDimension(dim);
1128     infoPanel->setSizePixel(GetVectorIntAsString(inputSize));
1129     infoPanel->setSizeMM(GetVectorDoubleAsString(sizeMM));
1130     infoPanel->setOrigin(GetVectorDoubleAsString(origin));
1131     infoPanel->setSpacing(GetVectorDoubleAsString(inputSpacing));
1132     infoPanel->setNPixel(QString::number(NPixel)+" ("+inputSizeInBytes+")");
1133
1134     transformation = imageSelected->GetTransform()[tSlice]->GetMatrix();
1135     infoPanel->setTransformation(Get4x4MatrixDoubleAsString(transformation));
1136
1137     landmarksPanel->SetCurrentLandmarks(mSlicerManagers[index]->GetLandmarks(),
1138       mSlicerManagers[index]->GetSlicer(0)->GetImage()->GetVTKImages().size());
1139     landmarksPanel->SetCurrentPath(mInputPathName.toStdString());
1140     landmarksPanel->SetCurrentImage(mSlicerManagers[index]->GetFileName().c_str());
1141
1142     overlayPanel->getCurrentImageName(mSlicerManagers[index]->GetFileName().c_str());
1143     for (int i = 0; i < 4; i++) {
1144       if (DataTree->selectedItems()[0]->data(i+1,Qt::CheckStateRole).toInt() > 0 || i == 3) {
1145         mSlicerManagers[index]->UpdateInfoOnCursorPosition(i);
1146         break;
1147       }
1148     }
1149
1150     infoPanel->setFileName(image);
1151     infoPanel->setDimension(dim);
1152     infoPanel->setSizePixel(GetVectorIntAsString(inputSize));
1153     infoPanel->setSizeMM(GetVectorDoubleAsString(sizeMM));
1154     infoPanel->setOrigin(GetVectorDoubleAsString(origin));
1155     infoPanel->setSpacing(GetVectorDoubleAsString(inputSpacing));
1156     infoPanel->setNPixel(QString::number(NPixel)+" ("+inputSizeInBytes+")");
1157
1158     landmarksPanel->SetCurrentLandmarks(mSlicerManagers[index]->GetLandmarks(),
1159       mSlicerManagers[index]->GetSlicer(0)->GetImage()->GetVTKImages().size());
1160     landmarksPanel->SetCurrentPath(mInputPathName.toStdString());
1161     landmarksPanel->SetCurrentImage(mSlicerManagers[index]->GetFileName().c_str());
1162
1163     overlayPanel->getCurrentImageName(mSlicerManagers[index]->GetFileName().c_str());
1164     for (int i = 0; i < 4; i++) {
1165       if (DataTree->selectedItems()[0]->data(i+1,Qt::CheckStateRole).toInt() > 0 || i == 3) {
1166         mSlicerManagers[index]->UpdateInfoOnCursorPosition(i);
1167         break;
1168       }
1169     }
1170     WindowLevelChanged();
1171
1172     slicingPresetComboBox->setCurrentIndex(mSlicerManagers[index]->GetSlicingPreset());
1173
1174     if (mSlicerManagers[index]->GetSlicer(0)->GetVF()) {
1175       overlayPanel->getVFName(mSlicerManagers[index]->GetVFName().c_str());
1176       overlayPanel->getVFProperty(mSlicerManagers[index]->GetSlicer(0)->GetVFSubSampling(),
1177         mSlicerManagers[index]->GetSlicer(0)->GetVFScale(),
1178         mSlicerManagers[index]->GetSlicer(0)->GetVFLog());
1179     } else {
1180       overlayPanel->getVFName(mSlicerManagers[index]->GetVFName().c_str());
1181       overlayPanel->getVFProperty(-1,-1,-1);
1182     }
1183     if (mSlicerManagers[index]->GetSlicer(0)->GetOverlay()) {
1184       overlayPanel->getOverlayName(mSlicerManagers[index]->GetOverlayName().c_str());
1185     } else {
1186       overlayPanel->getOverlayName(mSlicerManagers[index]->GetOverlayName().c_str());
1187     }
1188
1189     if (mSlicerManagers[index]->GetSlicer(0)->GetFusion()) {
1190       overlayPanel->getFusionName(mSlicerManagers[index]->GetFusionName().c_str());
1191     } else {
1192       overlayPanel->getFusionName(mSlicerManagers[index]->GetFusionName().c_str());
1193     }
1194   }
1195 }
1196 //------------------------------------------------------------------------------
1197
1198 //------------------------------------------------------------------------------
1199 void vvMainWindow::ShowDocumentation()
1200 {
1201   documentation->show();
1202 }
1203 //------------------------------------------------------------------------------
1204
1205 //------------------------------------------------------------------------------
1206 void vvMainWindow::PopupRegisterForm(bool checkCanPush)
1207 {
1208   vvRegisterForm* registerForm = new vvRegisterForm(QUrl("http://www.creatis.insa-lyon.fr/~dsarrut/vvregister/write.php"), getVVSettingsPath(), getSettingsOptionFormat());
1209   if(!checkCanPush) {
1210     registerForm->show();
1211   } else {
1212     if(registerForm->canPush()) {
1213       registerForm->show();
1214       registerForm->acquitPushed();//too bad if there is not internet connection anymore.
1215     }
1216   }
1217 }
1218 //------------------------------------------------------------------------------
1219
1220 //------------------------------------------------------------------------------
1221 void vvMainWindow::ShowHelpDialog()
1222 {
1223   help_dialog->show();
1224 }
1225 //------------------------------------------------------------------------------
1226
1227 //------------------------------------------------------------------------------
1228 void vvMainWindow::ChangeViewMode()
1229 {
1230   typedef struct _SIZE{
1231     QSplitter* splitter;
1232     QList<int> size1, size2;
1233     int cols[3];
1234   }SplitterSize;
1235   SplitterSize sizes[4];
1236   sizes[0].splitter = OSplitter;
1237   sizes[0].size1.push_back(1);
1238   sizes[0].size1.push_back(0);
1239   sizes[0].size2.push_back(1);
1240   sizes[0].size2.push_back(0);
1241   sizes[0].cols[0] = 2;
1242   sizes[0].cols[1] = 3;
1243   sizes[0].cols[2] = 4;
1244
1245   sizes[1].splitter = ESplitter;
1246   sizes[1].size1.push_back(0);
1247   sizes[1].size1.push_back(1);
1248   sizes[1].size2.push_back(1);
1249   sizes[1].size2.push_back(0);
1250   sizes[1].cols[0] = 1;
1251   sizes[1].cols[1] = 3;
1252   sizes[1].cols[2] = 4;
1253
1254   sizes[2].splitter = OSplitter;
1255   sizes[2].size1.push_back(1);
1256   sizes[2].size1.push_back(0);
1257   sizes[2].size2.push_back(0);
1258   sizes[2].size2.push_back(1);
1259   sizes[2].cols[0] = 1;
1260   sizes[2].cols[1] = 2;
1261   sizes[2].cols[2] = 4;
1262
1263   sizes[3].splitter = ESplitter;
1264   sizes[3].size1.push_back(0);
1265   sizes[3].size1.push_back(1);
1266   sizes[3].size2.push_back(0);
1267   sizes[3].size2.push_back(1);
1268   sizes[3].cols[0] = 1;
1269   sizes[3].cols[1] = 2;
1270   sizes[3].cols[2] = 3;
1271
1272   int slicer = mSlicerManagers[mCurrentPickedImageIndex]->GetSelectedSlicer();
1273   if (viewMode == 1) {
1274     if (slicer >= 0) {
1275       viewMode = 0;
1276       splitter_3->setSizes(sizes[slicer].size1);
1277       sizes[slicer].splitter->setSizes(sizes[slicer].size2);
1278       DataTree->setColumnHidden(sizes[slicer].cols[0],1);
1279       DataTree->setColumnHidden(sizes[slicer].cols[1],1);
1280       DataTree->setColumnHidden(sizes[slicer].cols[2],1);
1281     }
1282   } else {
1283     QList<int> size;
1284     if (slicer >= 0) {
1285       viewMode = 1;
1286       size.push_back(1);
1287       size.push_back(1);
1288       splitter_3->setSizes(size);
1289       sizes[slicer].splitter->setSizes(size);
1290       DataTree->setColumnHidden(sizes[slicer].cols[0],0);
1291       DataTree->setColumnHidden(sizes[slicer].cols[1],0);
1292       DataTree->setColumnHidden(sizes[slicer].cols[2],0);
1293     }
1294   }
1295   UpdateRenderWindows();
1296   /*
1297   ** I don't know why but for both resized QVTKWidget we also need to render
1298   ** the associated Slicer to redraw crosses.
1299   */
1300   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
1301     //     if (DataTree->topLevelItem(i)->data(COLUMN_UL_VIEW,Qt::CheckStateRole).toInt() > 1)
1302     mSlicerManagers[i]->GetSlicer(0)->Render();
1303     mSlicerManagers[i]->GetSlicer(1)->Render();
1304     //     if (DataTree->topLevelItem(i)->data(COLUMN_DL_VIEW,Qt::CheckStateRole).toInt() > 1)
1305     mSlicerManagers[i]->GetSlicer(2)->Render();
1306     mSlicerManagers[i]->GetSlicer(3)->Render();
1307   }
1308 }
1309 //------------------------------------------------------------------------------
1310
1311 //------------------------------------------------------------------------------
1312 QString vvMainWindow::GetSizeInBytes(unsigned long size)
1313 {
1314   QString result = "";// QString::number(size);
1315   //result += " bytes (";
1316   if (size > 1000000000) {
1317     size /= 1000000000;
1318     result += QString::number(size);
1319     result += "Gb";//)";
1320   } else if (size > 1000000) {
1321     size /= 1000000;
1322     result += QString::number(size);
1323     result += "Mb";//)";
1324   } else if (size > 1000) {
1325     size /= 1000;
1326     result += QString::number(size);
1327     result += "kb";//)";
1328   }
1329   return result;
1330 }
1331 //------------------------------------------------------------------------------
1332
1333 //------------------------------------------------------------------------------
1334 QString vvMainWindow::Get4x4MatrixDoubleAsString(vtkSmartPointer<vtkMatrix4x4> matrix, const int precision)
1335 {
1336   std::ostringstream strmatrix;
1337
1338   // Figure out the number of digits of the integer part of the largest absolute value
1339   // for each column
1340   unsigned width[4];
1341   for (unsigned int j = 0; j < 4; j++){
1342     double absmax = 0.;
1343     for (unsigned int i = 0; i < 4; i++)
1344       absmax = std::max(absmax, vnl_math_abs(matrix->GetElement(i, j)));
1345     unsigned ndigits = (unsigned)std::max(0.,std::log10(absmax))+1;
1346     width[j] = precision+ndigits+3;
1347   }
1348
1349   // Output with correct width, aligned to the right
1350   for (unsigned int i = 0; i < 4; i++) {
1351     for (unsigned int j = 0; j < 4; j++) {
1352       strmatrix.setf(ios::fixed,ios::floatfield);
1353       strmatrix.precision(precision);
1354       strmatrix.fill(' ');
1355       strmatrix.width(width[j]);
1356       strmatrix << std::right << matrix->GetElement(i, j);
1357     }
1358     strmatrix << std::endl;
1359   }
1360   QString result = strmatrix.str().c_str();
1361   return result;
1362 }
1363 //------------------------------------------------------------------------------
1364
1365 //------------------------------------------------------------------------------
1366 QString vvMainWindow::GetVectorDoubleAsString(std::vector<double> vectorDouble)
1367 {
1368   QString result;
1369   for (unsigned int i= 0; i < vectorDouble.size(); i++) {
1370     if (i != 0)
1371       result += " ";
1372     result += QString::number(vectorDouble[i]);
1373   }
1374   return result;
1375 }
1376 //------------------------------------------------------------------------------
1377
1378 //------------------------------------------------------------------------------
1379 QString vvMainWindow::GetVectorIntAsString(std::vector<int> vectorInt)
1380 {
1381   QString result;
1382   for (unsigned int i= 0; i < vectorInt.size(); i++) {
1383     if (i != 0)
1384       result += " ";
1385     result += QString::number(vectorInt[i]);
1386   }
1387   return result;
1388 }
1389 //------------------------------------------------------------------------------
1390
1391 //------------------------------------------------------------------------------
1392 //this actually returns the SlicerManager index!
1393 int vvMainWindow::GetSlicerIndexFromItem(QTreeWidgetItem* item)
1394 {
1395   QString id = item->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString();
1396   for (int i = 0; i < DataTree->topLevelItemCount(); i++) {
1397     if (DataTree->topLevelItem(i)->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString() == id)
1398       return i;
1399   }
1400   return -1;
1401 }
1402 //------------------------------------------------------------------------------
1403
1404 //------------------------------------------------------------------------------
1405 QTreeWidgetItem* vvMainWindow::GetItemFromSlicerManager(vvSlicerManager* sm)
1406 {
1407   QString id = sm->GetId().c_str();
1408   for (int i = 0; i < DataTree->topLevelItemCount(); i++) {
1409     if (DataTree->topLevelItem(i)->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString() == id)
1410       return DataTree->topLevelItem(i);
1411   }
1412   return NULL;
1413 }
1414 //------------------------------------------------------------------------------
1415
1416 //------------------------------------------------------------------------------
1417 void vvMainWindow::DisplayChanged(QTreeWidgetItem *clickedItem, int column)
1418 {
1419   if ( column >= COLUMN_CLOSE_IMAGE || column <= 0)
1420     return;
1421
1422   // Get parent information (might be the same item)
1423   int slicerManagerIndex = GetSlicerIndexFromItem(clickedItem);
1424   QTreeWidgetItem* clickedParentItem = DataTree->topLevelItem(slicerManagerIndex);
1425   vvSlicer* clickedSlicer = mSlicerManagers[slicerManagerIndex]->GetSlicer(column-1);
1426
1427   // Go over the complete item tree (only 2 levels, parents and children)
1428   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
1429     // Trick to avoid redoing twice the job for a key (sr)
1430     mSlicerManagers[i]->GetSlicer(column-1)->GetRenderWindow()->GetInteractor()->SetKeySym("Crap");
1431
1432     QTreeWidgetItem* currentParentItem = DataTree->topLevelItem(i);
1433     if(currentParentItem != clickedParentItem) {
1434       // Not the branch of the clicked item, uncheck all
1435
1436       // Parent
1437       currentParentItem->setData(column,Qt::CheckStateRole, 0);
1438       mSlicerManagers[i]->UpdateSlicer(column-1, false);
1439
1440       // Children
1441       for (int iChild = 0; iChild < currentParentItem->childCount(); iChild++) {
1442         currentParentItem->child(iChild)->setData(column,Qt::CheckStateRole, 0);
1443       }
1444     }
1445     else {
1446       // Branch of the clicked one: get check status from actor visibility in slicer
1447       // and toggle the clicked one
1448
1449       // Parent
1450       bool vis = clickedSlicer->GetActorVisibility("image", 0);
1451       bool draw = clickedSlicer->GetRenderer()->GetDraw();
1452
1453       // Update slicer (after getting visibility)
1454       mSlicerManagers[slicerManagerIndex]->UpdateSlicer(column-1, true);
1455       mSlicerManagers[slicerManagerIndex]->UpdateInfoOnCursorPosition(column-1);
1456       DisplaySliders(slicerManagerIndex, column-1);
1457       if(clickedParentItem == clickedItem) {
1458         // Toggle
1459         vis = !draw || !vis;
1460       }
1461       clickedSlicer->SetActorVisibility("image", 0, vis);
1462       clickedParentItem->setData(column, Qt::CheckStateRole, vis?2:0);
1463
1464       // Children
1465       std::map<std::string, int> actorTypeCounts;
1466       for (int iChild = 0; iChild < clickedParentItem->childCount(); iChild++) {
1467         QTreeWidgetItem* currentChildItem = clickedParentItem->child(iChild);
1468         std::string actorType = currentChildItem->data(1,Qt::UserRole).toString().toStdString();
1469         vis = clickedSlicer->GetActorVisibility(actorType, actorTypeCounts[actorType]);
1470         if(currentChildItem == clickedItem) {
1471           // Toggle or force visibility if it was not on this branch so far
1472           vis = !draw || !vis;
1473           clickedSlicer->SetActorVisibility(actorType, actorTypeCounts[actorType], vis);
1474         }
1475         currentChildItem->setData(column, Qt::CheckStateRole, vis?2:0);
1476         actorTypeCounts[actorType]++;
1477       }
1478     }
1479   }
1480
1481   clickedSlicer->Render();
1482 }
1483 //------------------------------------------------------------------------------
1484
1485 void vvMainWindow::InitSlicers()
1486 {
1487   if (mSlicerManagers.size()) {
1488     mSlicerManagers.back()->GenerateDefaultLookupTable();
1489
1490     mSlicerManagers.back()->SetSlicerWindow(0,NOViewWidget->GetRenderWindow());
1491     mSlicerManagers.back()->SetSlicerWindow(1,NEViewWidget->GetRenderWindow());
1492     mSlicerManagers.back()->SetSlicerWindow(2,SOViewWidget->GetRenderWindow());
1493     mSlicerManagers.back()->SetSlicerWindow(3,SEViewWidget->GetRenderWindow());
1494   }
1495 }
1496
1497 //------------------------------------------------------------------------------
1498 void vvMainWindow::InitDisplay()
1499 {
1500   if (mSlicerManagers.size()) {
1501     //BE CAREFUL : this is absolutely necessary to set the interactor style
1502     //in order to have the same style instanciation for all SlicerManagers in
1503     // a same window
1504     for (int j = 0; j < 4; j++) {
1505       vvInteractorStyleNavigator* style = vvInteractorStyleNavigator::New();
1506       style->SetAutoAdjustCameraClippingRange(1);
1507       bool AlreadySelected = false;
1508       for (int i = 0; i < DataTree->topLevelItemCount(); i++) {
1509         mSlicerManagers[i]->SetInteractorStyleNavigator(j,style);
1510
1511         //select the image only if previous are not selected
1512         if (DataTree->topLevelItem(i)->data(j+1,Qt::CheckStateRole).toInt() > 1) {
1513           mSlicerManagers[i]->UpdateSlicer(j,1);
1514           AlreadySelected = true;
1515         } else if (i == DataTree->topLevelItemCount()-1 && !AlreadySelected) {
1516           if (DataTree->selectedItems().size() == 0)
1517             DataTree->topLevelItem(i)->setSelected(1);
1518           DataTree->topLevelItem(i)->setData(j+1,Qt::CheckStateRole,2);
1519           mSlicerManagers[i]->UpdateSlicer(j,1);
1520           DisplaySliders(i,j);
1521         } else {
1522           DataTree->topLevelItem(i)->setData(j+1,Qt::CheckStateRole,0);
1523           mSlicerManagers[i]->UpdateSlicer(j,0);
1524         }
1525       }
1526       style->Delete();
1527     }
1528   }
1529 }
1530 //------------------------------------------------------------------------------
1531
1532 //------------------------------------------------------------------------------
1533 void vvMainWindow::DisplaySliders(int slicer, int window)
1534 {
1535   if(!mSlicerManagers[slicer]->GetSlicer(window)->GetRenderer()->GetDraw())
1536     return;
1537
1538   int range[2];
1539   mSlicerManagers[slicer]->GetSlicer(window)->GetSliceRange(range);
1540   int position = mSlicerManagers[slicer]->GetSlicer(window)->GetSlice();
1541   if (range[1]>0)
1542     verticalSliders[window]->show();
1543   else
1544     verticalSliders[window]->hide();
1545   verticalSliders[window]->setRange(range[0],range[1]);
1546   verticalSliders[window]->setValue(position);
1547
1548   int tRange[2];
1549   tRange[0] = 0;
1550   tRange[1] = mSlicerManagers[slicer]->GetSlicer(window)->GetTMax();
1551   if (tRange[1]>0)
1552     horizontalSliders[window]->show();
1553   else
1554     horizontalSliders[window]->hide();
1555   horizontalSliders[window]->setRange(tRange[0],tRange[1]);
1556   int tPosition = mSlicerManagers[slicer]->GetSlicer(window)->GetMaxCurrentTSlice();
1557   horizontalSliders[window]->setValue(tPosition);
1558 }
1559 //------------------------------------------------------------------------------
1560
1561 //------------------------------------------------------------------------------
1562 void vvMainWindow::CloseImage(QTreeWidgetItem* item, int column)
1563 {
1564   int index = GetSlicerIndexFromItem(item);
1565
1566   if (DataTree->topLevelItem(index) != item) {
1567     QString warning = "Do you really want to close the overlay : ";
1568     warning += item->data(COLUMN_IMAGE_NAME,Qt::DisplayRole).toString();
1569     QMessageBox msgBox(QMessageBox::Warning, tr("Close Overlay"),
1570       warning, 0, this);
1571     msgBox.addButton(tr("Close"), QMessageBox::AcceptRole);
1572     msgBox.addButton(tr("Cancel"), QMessageBox::RejectRole);
1573     if (msgBox.exec() == QMessageBox::AcceptRole) {
1574       std::string overlay_type=item->data(1,Qt::UserRole).toString().toStdString();
1575       int overlay_index=0;
1576       for (int child = 0; child < DataTree->topLevelItem(index)->childCount(); child++) {
1577         if (DataTree->topLevelItem(index)->\
1578           child(child)->data(1,Qt::UserRole).toString().toStdString() == overlay_type)
1579           overlay_index++;
1580         if (DataTree->topLevelItem(index)->child(child) == item) break;
1581       }
1582       if (overlay_type=="fusionSequence") {
1583         //removing the overlay sequence in a fusion sequence visualization mode
1584         //TODO: remove the synchronization (transform matrices, etc...)
1585
1586         //=> unlink and untie the slicer managers
1587         RemoveLink(mSlicerManagers[index]->GetId().c_str(), mSlicerManagers[mSlicerManagers[index]->GetFusionSequenceIndexOfLinkedManager()]->GetId().c_str());
1588         mSlicerManagers[index]->SetFusionSequenceInvolvmentCode(-1);
1589         mSlicerManagers[mSlicerManagers[index]->GetFusionSequenceIndexOfLinkedManager()]->SetFusionSequenceInvolvmentCode(-1);
1590
1591       }
1592       mSlicerManagers[index]->RemoveActor(overlay_type, overlay_index-1);
1593       mSlicerManagers[index]->SetColorMap(0);
1594       DataTree->topLevelItem(index)->takeChild(DataTree->topLevelItem(index)->indexOfChild(item));
1595       mSlicerManagers[index]->Render();
1596     }
1597   } else if (DataTree->topLevelItemCount() <= 1) {
1598     QString warning = "Do you really want to close the image : ";
1599     warning += item->data(COLUMN_IMAGE_NAME,Qt::DisplayRole).toString();
1600     warning += "\nThis is the last image, you're about to close vv !!!";
1601     QMessageBox msgBox(QMessageBox::Warning, tr("Close Image"),
1602       warning, 0, this);
1603     msgBox.addButton(tr("Close vv"), QMessageBox::AcceptRole);
1604     msgBox.addButton(tr("Cancel"), QMessageBox::RejectRole);
1605     if (msgBox.exec() == QMessageBox::AcceptRole) {
1606       this->close();
1607     }
1608   } else {
1609     QString warning = "Do you really want to close the image : ";
1610     warning += item->data(COLUMN_IMAGE_NAME,Qt::DisplayRole).toString();
1611     QMessageBox msgBox(QMessageBox::Warning, tr("Close Image"),
1612       warning, 0, this);
1613     msgBox.addButton(tr("Close"), QMessageBox::AcceptRole);
1614     msgBox.addButton(tr("Cancel"), QMessageBox::RejectRole);
1615     if (msgBox.exec() == QMessageBox::AcceptRole) {
1616
1617       // Tell tools that we close an image
1618       emit AnImageIsBeingClosed(mSlicerManagers[index]);
1619
1620       std::vector<vvSlicerManager*>::iterator Manageriter = mSlicerManagers.begin();
1621       DataTree->takeTopLevelItem(index);
1622       for (int i = 0; i < index; i++) {
1623         Manageriter++;
1624       }
1625       linkPanel->removeImage(index);
1626       mSlicerManagers[index]->RemoveActors();
1627
1628       //if the slicer manager was involved in a fusion sequence visualization...
1629       if ( item->data(1,Qt::UserRole).toString().toStdString() == "fusionSequence" ) {
1630         //TODO
1631         //make sure both SlicerManager exit the FusionSequence visualization mode
1632         //disable the temporal and spatial sync? make sure we reset the spatial transforms to their initial states...
1633         mSlicerManagers[index]->SetFusionSequenceInvolvmentCode(-1);
1634         mSlicerManagers[mSlicerManagers[index]->GetFusionSequenceIndexOfLinkedManager()]->SetFusionSequenceInvolvmentCode(-1);
1635       }
1636
1637       //remove the slicer manager
1638       delete mSlicerManagers[index];
1639       mSlicerManagers.erase(Manageriter);
1640
1641       //
1642       InitDisplay();
1643     }
1644   }
1645   ImageInfoChanged();
1646 }
1647 //------------------------------------------------------------------------------
1648
1649 //------------------------------------------------------------------------------
1650 void vvMainWindow::ReloadImage(QTreeWidgetItem* item, int column)
1651 {
1652   // int index = GetSlicerIndexFromItem(item);
1653   //   QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
1654   //   if (item->data(1,Qt::UserRole).toString() == "vector")
1655   //     mSlicerManagers[index]->ReloadVF();
1656   //   else
1657   //     mSlicerManagers[index]->Reload();
1658
1659   //   QApplication::restoreOverrideCursor();
1660   int index = GetSlicerIndexFromItem(item);
1661   QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
1662   QString role=item->data(1,Qt::UserRole).toString();
1663   if ( role == "vector") {
1664     mSlicerManagers[index]->ReloadVF();
1665   }
1666   else if (role == "overlay") {
1667     mSlicerManagers[index]->ReloadOverlay();
1668   }
1669   else if (role == "fusion") {
1670     mSlicerManagers[index]->ReloadFusion();
1671   }
1672   else if (role == "fusionSequence") {
1673     //both versions of the secondary sequence must be updated.
1674     mSlicerManagers[index]->ReloadFusionSequence();
1675     mSlicerManagers[mSlicerManagers[index]->GetFusionSequenceIndexOfLinkedManager()]->Reload();
1676   }
1677   else {
1678     mSlicerManagers[index]->Reload();
1679     //if we update the secondary sequence, then the overlay of the main sequence should also be updated
1680     if (mSlicerManagers[index]->IsSecondarySequenceOfFusionSequence()) mSlicerManagers[mSlicerManagers[index]->GetFusionSequenceIndexOfLinkedManager()]->ReloadFusionSequence();
1681   }
1682   // Update view and info
1683   ImageInfoChanged();
1684   mSlicerManagers[index]->Render();
1685   QApplication::restoreOverrideCursor();
1686 }
1687 //------------------------------------------------------------------------------
1688
1689 //------------------------------------------------------------------------------
1690 void vvMainWindow::MousePositionChanged(int visibility,double x, double y, double z, double X, double Y, double Z , double value)
1691 {
1692   infoPanel->setCurrentInfo(visibility,x,y,z,X,Y,Z,value);
1693 }
1694 //------------------------------------------------------------------------------
1695
1696 //------------------------------------------------------------------------------
1697 void vvMainWindow::VectorChanged(int visibility,double x, double y, double z, double value)
1698 {
1699   overlayPanel->getCurrentVectorInfo(visibility,x,y,z,value);
1700 }
1701 //------------------------------------------------------------------------------
1702
1703 //------------------------------------------------------------------------------
1704 void vvMainWindow::OverlayChanged(int visibility, double valueOver, double valueRef)
1705 {
1706   overlayPanel->getCurrentOverlayInfo(visibility,valueOver, valueRef);
1707 }
1708 //------------------------------------------------------------------------------
1709
1710 //------------------------------------------------------------------------------
1711 void vvMainWindow::FusionChanged(int visibility, double value)
1712 {
1713   overlayPanel->getCurrentFusionInfo(visibility,value);
1714 }
1715 //------------------------------------------------------------------------------
1716
1717 //------------------------------------------------------------------------------
1718 //called when AddOverlayImage, AddFusionSequence
1719 //or when UpdateWindowLevel() is called ; when slicerManager emits WindowLevelChanged
1720 //when ImageInfoChanged() is called
1721 void vvMainWindow::WindowLevelChanged()
1722 {
1723   // Base image
1724   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1725   if(index==-1) return;
1726   windowSpinBox->setValue(mSlicerManagers[index]->GetColorWindow());
1727   levelSpinBox->setValue(mSlicerManagers[index]->GetColorLevel());
1728   colorMapComboBox->setCurrentIndex(mSlicerManagers[index]->GetColorMap());
1729   presetComboBox->setCurrentIndex(mSlicerManagers[index]->GetPreset());
1730
1731   // Overlay image
1732   if (mSlicerManagers[index]->GetSlicer(0)->GetOverlay())
1733     overlayPanel->getOverlayProperty(mSlicerManagers[index]->GetOverlayColor(),
1734     mSlicerManagers[index]->GetLinkOverlayWindowLevel(),
1735     mSlicerManagers[index]->GetOverlayColorWindow(),
1736     mSlicerManagers[index]->GetOverlayColorLevel());
1737   else
1738     overlayPanel->getOverlayProperty(-1,0,0.,0.);
1739
1740   // Fusion & SequenceFusion image
1741   if (mSlicerManagers[index]->GetSlicer(0)->GetFusion()) {
1742     overlayPanel->getFusionProperty(mSlicerManagers[index]->GetFusionOpacity(),
1743       mSlicerManagers[index]->GetFusionThresholdOpacity(),
1744       mSlicerManagers[index]->GetFusionColorMap(),
1745       mSlicerManagers[index]->GetFusionWindow(),
1746       mSlicerManagers[index]->GetFusionLevel());
1747     if (mSlicerManagers[index]->IsMainSequenceOfFusionSequence()) {
1748       overlayPanel->getFusionSequenceProperty(mSlicerManagers[index]->GetFusionSequenceFrameIndex(),
1749         mSlicerManagers[index]->GetFusionSequenceSpatialSyncFlag(),
1750         mSlicerManagers[index]->GetFusionSequenceNbFrames(),
1751         mSlicerManagers[index]->GetFusionSequenceTemporalSyncFlag());
1752     }
1753   }
1754   else if ( mSlicerManagers[index]->IsSecondarySequenceOfFusionSequence() ) {
1755     //if the image is involved in a fusion sequence, preserve the overlay panel!
1756     int ind = mSlicerManagers[index]->GetFusionSequenceIndexOfLinkedManager();
1757     overlayPanel->getFusionProperty(mSlicerManagers[ind]->GetFusionOpacity(),
1758       mSlicerManagers[ind]->GetFusionThresholdOpacity(),
1759       mSlicerManagers[ind]->GetFusionColorMap(),
1760       mSlicerManagers[ind]->GetFusionWindow(),
1761       mSlicerManagers[ind]->GetFusionLevel());
1762     overlayPanel->getFusionSequenceProperty(mSlicerManagers[ind]->GetFusionSequenceFrameIndex(),
1763       mSlicerManagers[ind]->GetFusionSequenceSpatialSyncFlag(),
1764       mSlicerManagers[ind]->GetFusionSequenceNbFrames(),
1765       mSlicerManagers[ind]->GetFusionSequenceTemporalSyncFlag());
1766   }
1767   else
1768   {
1769     overlayPanel->getFusionProperty(-1, -1, -1, -1, -1);
1770     overlayPanel->getFusionSequenceProperty(-1, false, 0, false);
1771   }
1772 }
1773 //------------------------------------------------------------------------------
1774
1775 //------------------------------------------------------------------------------
1776 void vvMainWindow::WindowLevelEdited()
1777 {
1778   presetComboBox->setCurrentIndex(6);
1779   UpdateWindowLevel();
1780 }
1781 //------------------------------------------------------------------------------
1782
1783 //------------------------------------------------------------------------------
1784 void vvMainWindow::SetWindowLevel(double w, double l)
1785 {
1786   windowSpinBox->setValue(w);
1787   levelSpinBox->setValue(l);
1788   presetComboBox->setCurrentIndex(6);
1789   colorMapComboBox->setCurrentIndex(0);
1790   UpdateWindowLevel();
1791 }
1792 //------------------------------------------------------------------------------
1793
1794 //------------------------------------------------------------------------------
1795 void vvMainWindow::UpdateWindowLevel()
1796 {
1797   if (DataTree->selectedItems().size()) {
1798     if (presetComboBox->currentIndex() == 7) //For ventilation
1799       colorMapComboBox->setCurrentIndex(5);
1800     int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1801     mSlicerManagers[index]->SetColorWindow(windowSpinBox->value());
1802     mSlicerManagers[index]->SetColorLevel(levelSpinBox->value());
1803     mSlicerManagers[index]->SetPreset(presetComboBox->currentIndex());
1804     mSlicerManagers[index]->Render();
1805     WindowLevelChanged();
1806   }
1807 }
1808 //------------------------------------------------------------------------------
1809
1810 //------------------------------------------------------------------------------
1811 void vvMainWindow::UpdateSlicingPreset()
1812 {
1813   if (DataTree->selectedItems().size()) {
1814     int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1815     mSlicerManagers[index]->SetSlicingPreset(vvSlicerManager::SlicingPresetType(slicingPresetComboBox->currentIndex()));
1816   }
1817 }
1818 //------------------------------------------------------------------------------
1819
1820 //------------------------------------------------------------------------------
1821 void vvMainWindow::UpdateColorMap()
1822 {
1823   if (DataTree->selectedItems().size()) {
1824     int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1825     mSlicerManagers[index]->SetColorMap(colorMapComboBox->currentIndex());
1826     mSlicerManagers[index]->Render();
1827   }
1828 }
1829 //------------------------------------------------------------------------------
1830 void vvMainWindow::SwitchWindowLevel()
1831 {
1832   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1833   int window = mSlicerManagers[index]->GetColorWindow();
1834   presetComboBox->setCurrentIndex(6);
1835   windowSpinBox->setValue(-window);
1836   UpdateWindowLevel();
1837 }
1838 //------------------------------------------------------------------------------
1839
1840 //------------------------------------------------------------------------------
1841 void vvMainWindow::ApplyWindowLevelToAllImages()
1842 {
1843   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1844   if(index==-1) return;
1845   double window = mSlicerManagers[index]->GetColorWindow();
1846   double level = mSlicerManagers[index]->GetColorLevel();
1847
1848   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
1849     if (mSlicerManagers[i] == NULL)
1850       continue;
1851     mSlicerManagers[i]->SetColorWindow(window);
1852     mSlicerManagers[i]->SetColorLevel(level);
1853     mSlicerManagers[i]->SetPreset(6);
1854     mSlicerManagers[i]->Render();
1855   }
1856 }
1857 //------------------------------------------------------------------------------
1858
1859 //------------------------------------------------------------------------------
1860 void vvMainWindow::ApplyWindowToSetOfImages(double window, unsigned int indexMin, unsigned int indexMax)
1861 {
1862   for (unsigned int i = indexMin; i <= indexMax && i < mSlicerManagers.size(); i++) {
1863     if (mSlicerManagers[i] == NULL)
1864       continue;
1865     mSlicerManagers[i]->SetColorWindow(window);
1866     mSlicerManagers[i]->SetPreset(6);
1867     mSlicerManagers[i]->Render();
1868   }
1869 }
1870 //------------------------------------------------------------------------------
1871
1872 //------------------------------------------------------------------------------
1873 void vvMainWindow::ApplyLevelToSetOfImages(double level, unsigned int indexMin, unsigned int indexMax)
1874 {
1875   for (unsigned int i = indexMin; i <= indexMax && i < mSlicerManagers.size(); i++) {
1876     if (mSlicerManagers[i] == NULL)
1877       continue;
1878     mSlicerManagers[i]->SetColorLevel(level);
1879     mSlicerManagers[i]->SetPreset(6);
1880     mSlicerManagers[i]->Render();
1881   }
1882 }
1883 //------------------------------------------------------------------------------
1884
1885 //------------------------------------------------------------------------------
1886 void vvMainWindow::UpdateLinkManager(std::string id, int slicer, double x, double y, double z, int temps)
1887 {
1888   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
1889     if (mSlicerManagers[i]->GetId() == id) {
1890       mSlicerManagers[i]->GetSlicer(slicer)->SetCurrentPosition(x,y,z,temps);
1891       mSlicerManagers[i]->UpdateViews(0,slicer);
1892       break;
1893     }
1894   }
1895 }
1896 //------------------------------------------------------------------------------
1897
1898 //------------------------------------------------------------------------------
1899 void vvMainWindow::UpdateLinkedNavigation(std::string id, vvSlicerManager * sm, vvSlicer* refSlicer)
1900 {
1901   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
1902     if (id == mSlicerManagers[i]->GetId()) {
1903       mSlicerManagers[i]->UpdateLinkedNavigation(refSlicer);
1904     }
1905   }
1906 }
1907 //------------------------------------------------------------------------------
1908
1909 //------------------------------------------------------------------------------
1910 void vvMainWindow::ShowContextMenu(QPoint point)
1911 {
1912   if (!DataTree->selectedItems().size()) {
1913     contextActions[1]->setEnabled(0);
1914     contextActions[2]->setEnabled(0);
1915     contextActions[3]->setEnabled(0);
1916     contextActions[4]->setEnabled(0);
1917     contextActions[5]->setEnabled(0);
1918     contextActions[6]->setEnabled(0);
1919   } else {
1920     int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1921     contextActions[1]->setEnabled(1);
1922     contextActions[2]->setEnabled(
1923       DataTree->itemWidget(DataTree->selectedItems()[0],
1924       COLUMN_RELOAD_IMAGE)->isEnabled());
1925     contextActions[3]->setEnabled(1);
1926     contextActions[5]->setEnabled(1);
1927     contextActions[6]->setEnabled(1);
1928
1929     if (mSlicerManagers[index]->GetDimension() < 3)
1930       contextActions[4]->setEnabled(0);
1931     else
1932       contextActions[4]->setEnabled(1);
1933   }
1934   contextMenu.exec(QCursor::pos());
1935 }
1936 //------------------------------------------------------------------------------
1937
1938 //------------------------------------------------------------------------------
1939 void vvMainWindow::CloseImage()
1940 {
1941   CloseImage(DataTree->selectedItems()[0],0);
1942 }
1943 //------------------------------------------------------------------------------
1944
1945 //------------------------------------------------------------------------------
1946 void vvMainWindow::ReloadImage()
1947 {
1948   ReloadImage(DataTree->selectedItems()[0],0);
1949 }
1950 //------------------------------------------------------------------------------
1951
1952 //------------------------------------------------------------------------------
1953 void vvMainWindow::SelectOverlayImage()
1954 {
1955   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1956
1957   //check if one overlay image is added
1958   for (int child = 0; child < DataTree->topLevelItem(index)->childCount(); child++)
1959     if (DataTree->topLevelItem(index)->child(child)->data(1,Qt::UserRole).toString() == "overlay") {
1960       QString error = "Cannot add more than one compared image\n";
1961       error += "Please remove first ";
1962       error += DataTree->topLevelItem(index)->child(child)->data(COLUMN_IMAGE_NAME,Qt::DisplayRole).toString();
1963       QMessageBox::information(this,tr("Problem adding compared image !"),error);
1964       return;
1965     }
1966
1967     QString Extensions = EXTENSIONS;
1968     Extensions += ";;All Files (*)";
1969     QStringList files = QFileDialog::getOpenFileNames(this,tr("Load Overlay image"),mInputPathName,Extensions);
1970     if (files.isEmpty())
1971       return;
1972
1973     std::vector<std::string> vecFileNames;
1974     for (int i = 0; i < files.size(); i++) {
1975       vecFileNames.push_back(files[i].toStdString());
1976     }
1977     AddOverlayImage(index,vecFileNames,vvImageReader::IMAGE);
1978 }
1979 //------------------------------------------------------------------------------
1980
1981 //------------------------------------------------------------------------------
1982 void vvMainWindow::AddOverlayImage(int index, std::vector<std::string> fileNames, vvImageReader::LoadedImageType type)
1983 {
1984   QString file(fileNames[0].c_str());
1985   if (QFile::exists(file))
1986   {
1987     mInputPathName = itksys::SystemTools::GetFilenamePath(file.toStdString()).c_str();
1988     itk::ImageIOBase::Pointer reader = itk::ImageIOFactory::CreateImageIO(
1989       file.toStdString().c_str(), itk::ImageIOFactory::ReadMode);
1990     reader->SetFileName(fileNames[0].c_str());
1991     reader->ReadImageInformation();
1992     std::string component = reader->GetComponentTypeAsString(reader->GetComponentType());
1993     int dimension = reader->GetNumberOfDimensions();
1994     QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
1995     vvProgressDialog progress("Opening " + file.toStdString());
1996     qApp->processEvents();
1997
1998     std::string filename = itksys::SystemTools::GetFilenameWithoutExtension(file.toStdString()).c_str();
1999     if (mSlicerManagers[index]->SetOverlay(fileNames,dimension, component,type)) {
2000       //create an item in the tree with good settings
2001       QTreeWidgetItem *item = new QTreeWidgetItem();
2002       item->setData(0,Qt::UserRole,file.toStdString().c_str());
2003       item->setData(1,Qt::UserRole,tr("overlay"));
2004       QFileInfo fileinfo(file); //Do not show the path
2005       item->setData(COLUMN_IMAGE_NAME,Qt::DisplayRole,fileinfo.fileName());
2006       item->setToolTip(COLUMN_IMAGE_NAME, mSlicerManagers[index]->GetListOfAbsoluteFilePathInOneString("overlay").c_str());
2007       qApp->processEvents();
2008
2009       for (int j = 1; j <= 4; j++) {
2010         item->setData(j,Qt::CheckStateRole,DataTree->topLevelItem(index)->data(j,Qt::CheckStateRole));
2011       }
2012
2013       //Create the buttons for reload and close
2014       qApp->processEvents();
2015       QTreePushButton* cButton = new QTreePushButton;
2016       cButton->setItem(item);
2017       cButton->setColumn(COLUMN_CLOSE_IMAGE);
2018       cButton->setToolTip(tr("close image"));
2019       cButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/exit.png")));
2020       connect(cButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
2021         this,SLOT(CloseImage(QTreeWidgetItem*, int)));
2022
2023       QTreePushButton* rButton = new QTreePushButton;
2024       rButton->setItem(item);
2025       rButton->setColumn(COLUMN_RELOAD_IMAGE);
2026       rButton->setToolTip(tr("reload image"));
2027       rButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/rotateright.png")));
2028       connect(rButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
2029         this,SLOT(ReloadImage(QTreeWidgetItem*, int)));
2030
2031       DataTree->topLevelItem(index)->setExpanded(1);
2032       DataTree->topLevelItem(index)->addChild(item);
2033       DataTree->setItemWidget(item, COLUMN_CLOSE_IMAGE, cButton);
2034       DataTree->setItemWidget(item, COLUMN_RELOAD_IMAGE, rButton);
2035
2036       //set the id of the image
2037       QString id = DataTree->topLevelItem(index)->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString();
2038       item->setData(COLUMN_IMAGE_NAME,Qt::UserRole,id.toStdString().c_str());
2039       UpdateTree();
2040       qApp->processEvents();
2041       ImageInfoChanged();
2042       QApplication::restoreOverrideCursor();
2043
2044       // Update the display to update, e.g., the sliders
2045       for(int i=0; i<4; i++)
2046         DisplaySliders(index, i);
2047     } else {
2048       QApplication::restoreOverrideCursor();
2049       QString error = "Cannot import the new image.\n";
2050       error += mSlicerManagers[index]->GetLastError().c_str();
2051       QMessageBox::information(this,tr("Problem reading image !"),error);
2052     }
2053     WindowLevelChanged();
2054   }
2055   else
2056     QMessageBox::information(this,tr("Problem reading Overlay !"),"File doesn't exist!");
2057 }
2058 //------------------------------------------------------------------------------
2059
2060
2061 //------------------------------------------------------------------------------
2062 void vvMainWindow::AddROI(int index, QString file)
2063 {
2064   /*
2065   // Get slice manager
2066
2067   // Load image
2068
2069   vvImageReader * mReader = new vvImageReader;
2070   mReader->SetInputFilename(filename.toStdString());
2071   mReader->Update(IMAGE);
2072   if (mReader->GetLastError().size() != 0) {
2073   std::cerr << "Error while reading " << filename.toStdString() << std::endl;
2074   QString error = "Cannot open file \n";
2075   error += mReader->GetLastError().c_str();
2076   QMessageBox::information(this,tr("Reading problem"),error);
2077   delete mReader;
2078   return;
2079   }
2080   vvImage::Pointer roi = mReader->GetOutput();
2081
2082   // Create roi in new tool
2083   vvToolStructureSetManager::AddImage(mCurrentSlicerManager, roi);
2084   */
2085 }
2086 //------------------------------------------------------------------------------
2087
2088 //------------------------------------------------------------------------------
2089 void vvMainWindow::SelectFusionImage()
2090 {
2091   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2092
2093   //check if one fusion image is added
2094   for (int child = 0; child < DataTree->topLevelItem(index)->childCount(); child++)
2095     if ( (DataTree->topLevelItem(index)->child(child)->data(1,Qt::UserRole).toString() == "fusion") ||
2096       (DataTree->topLevelItem(index)->child(child)->data(1,Qt::UserRole).toString() == "fusionSequence") ) {
2097         QString error = "Cannot add more than one fusion image\n";
2098         error += "Please remove first ";
2099         error += DataTree->topLevelItem(index)->child(child)->data(COLUMN_IMAGE_NAME,Qt::DisplayRole).toString();
2100         QMessageBox::information(this,tr("Problem adding fusion image !"),error);
2101         return;
2102     }
2103
2104     QString Extensions = EXTENSIONS;
2105     Extensions += ";;All Files (*)";
2106     QString file = QFileDialog::getOpenFileName(this,tr("Load Fusion image"),mInputPathName,Extensions);
2107     if (!file.isEmpty())
2108       AddFusionImage(index,file);
2109 }
2110 //------------------------------------------------------------------------------
2111
2112 //------------------------------------------------------------------------------
2113 void vvMainWindow::ResetTransformationToIdentity()
2114 {
2115   std::string actorType = DataTree->selectedItems()[0]->data(1,Qt::UserRole).toString().toStdString();
2116   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2117   mSlicerManagers[index]->ResetTransformationToIdentity(actorType);
2118   ImageInfoChanged();
2119 }
2120 //------------------------------------------------------------------------------
2121
2122 //------------------------------------------------------------------------------
2123 void vvMainWindow::AddFusionImage(int index, QString file)
2124 {
2125   if (QFile::exists(file))
2126   {
2127     mInputPathName = itksys::SystemTools::GetFilenamePath(file.toStdString()).c_str();
2128     itk::ImageIOBase::Pointer reader = itk::ImageIOFactory::CreateImageIO(
2129       file.toStdString().c_str(), itk::ImageIOFactory::ReadMode);
2130     reader->SetFileName(file.toStdString().c_str());
2131     reader->ReadImageInformation();
2132     std::string component = reader->GetComponentTypeAsString(reader->GetComponentType());
2133     if (reader) {
2134       QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
2135       vvProgressDialog progress("Opening fusion");
2136       qApp->processEvents();
2137
2138       std::string filename = itksys::SystemTools::GetFilenameWithoutExtension(file.toStdString()).c_str();
2139       if (mSlicerManagers[index]->SetFusion(file.toStdString(),
2140         reader->GetNumberOfDimensions(), component)) {
2141           //create an item in the tree with good settings
2142           QTreeWidgetItem *item = new QTreeWidgetItem();
2143           item->setData(0,Qt::UserRole,file.toStdString().c_str());
2144           item->setData(1,Qt::UserRole,tr("fusion"));
2145           QFileInfo fileinfo(filename.c_str()); //Do not show the path
2146           item->setData(COLUMN_IMAGE_NAME,Qt::DisplayRole,fileinfo.fileName());
2147           item->setToolTip(COLUMN_IMAGE_NAME, mSlicerManagers[index]->GetListOfAbsoluteFilePathInOneString("fusion").c_str());
2148           qApp->processEvents();
2149
2150           for (int j = 1; j <= 4; j++) {
2151             item->setData(j,Qt::CheckStateRole,DataTree->topLevelItem(index)->data(j,Qt::CheckStateRole));
2152           }
2153
2154           //Create the buttons for reload and close
2155           qApp->processEvents();
2156           QTreePushButton* cButton = new QTreePushButton;
2157           cButton->setItem(item);
2158           cButton->setColumn(COLUMN_CLOSE_IMAGE);
2159           cButton->setToolTip(tr("close image"));
2160           cButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/exit.png")));
2161           connect(cButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
2162             this,SLOT(CloseImage(QTreeWidgetItem*, int)));
2163
2164           QTreePushButton* rButton = new QTreePushButton;
2165           rButton->setItem(item);
2166           rButton->setColumn(COLUMN_RELOAD_IMAGE);
2167           rButton->setToolTip(tr("reload image"));
2168           rButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/rotateright.png")));
2169           connect(rButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
2170             this,SLOT(ReloadImage(QTreeWidgetItem*, int)));
2171
2172           DataTree->topLevelItem(index)->setExpanded(1);
2173           DataTree->topLevelItem(index)->addChild(item);
2174           DataTree->setItemWidget(item, COLUMN_CLOSE_IMAGE, cButton);
2175           DataTree->setItemWidget(item, COLUMN_RELOAD_IMAGE, rButton);
2176
2177           //set the id of the image
2178           QString id = DataTree->topLevelItem(index)->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString();
2179           item->setData(COLUMN_IMAGE_NAME,Qt::UserRole,id.toStdString().c_str());
2180           UpdateTree();
2181           qApp->processEvents();
2182           ImageInfoChanged();
2183           QApplication::restoreOverrideCursor();
2184       } else {
2185         QApplication::restoreOverrideCursor();
2186         QString error = "Cannot import the new image.\n";
2187         error += mSlicerManagers[index]->GetLastError().c_str();
2188         QMessageBox::information(this,tr("Problem reading image !"),error);
2189       }
2190     } else {
2191       QString error = "Cannot import the new image.\n";
2192       QMessageBox::information(this,tr("Problem reading image !"),error);
2193     }
2194   }
2195   else
2196     QMessageBox::information(this,tr("Problem reading Fusion !"),"File doesn't exist!");
2197 }
2198 //------------------------------------------------------------------------------
2199
2200
2201 //------------------------------------------------------------------------------
2202 void vvMainWindow::OpenField()
2203 {
2204   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2205   //check if a vector field has already been added
2206   for (int child = 0; child < DataTree->topLevelItem(index)->childCount(); child++)
2207     if (DataTree->topLevelItem(index)->child(child)->data(1,Qt::UserRole).toString() == "vector") {
2208       QString error = "Cannot add more than one vector field\n";
2209       error += "Please remove first ";
2210       error += DataTree->topLevelItem(index)->child(child)->data(COLUMN_IMAGE_NAME,Qt::DisplayRole).toString();
2211       QMessageBox::information(this,tr("Problem adding vector field!"),error);
2212       return;
2213     }
2214
2215     QString Extensions = "Images ( *.mhd)";
2216     Extensions += ";;Images ( *.mha)";
2217     Extensions += ";;VF Images ( *.vf)";
2218     Extensions += ";;nii Images ( *.nii)";
2219     Extensions += ";;nrrd Images ( *.nrrd)";
2220     Extensions += ";;nhdr Images ( *.nhdr)";
2221     Extensions += ";;All Files (*)";
2222     QString file = QFileDialog::getOpenFileName(this,tr("Load deformation field"),mInputPathName,Extensions);
2223     if (!file.isEmpty())
2224       AddField(file,index);
2225 }
2226 //------------------------------------------------------------------------------
2227
2228
2229 //------------------------------------------------------------------------------
2230 void vvMainWindow::AddFieldEntry(QString filename,int index,bool from_disk)
2231 {
2232   //create an item in the tree with good settings
2233   QTreeWidgetItem *item = new QTreeWidgetItem();
2234   item->setData(0,Qt::UserRole,filename.toStdString().c_str());
2235   item->setData(1,Qt::UserRole,tr("vector"));
2236   QFileInfo fileinfo(filename); //Do not show the path
2237   item->setData(COLUMN_IMAGE_NAME,Qt::DisplayRole,fileinfo.fileName());
2238   item->setToolTip(COLUMN_IMAGE_NAME, mSlicerManagers[index]->GetListOfAbsoluteFilePathInOneString("vector").c_str());
2239   qApp->processEvents();
2240
2241   for (int j = 1; j <= 4; j++) {
2242     item->setData(j,Qt::CheckStateRole,DataTree->topLevelItem(index)->data(j,Qt::CheckStateRole));
2243   }
2244
2245   //Create the buttons for reload and close
2246   qApp->processEvents();
2247   QTreePushButton* cButton = new QTreePushButton;
2248   cButton->setItem(item);
2249   cButton->setColumn(COLUMN_CLOSE_IMAGE);
2250   cButton->setToolTip(tr("close vector field"));
2251   cButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/exit.png")));
2252   connect(cButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
2253     this,SLOT(CloseImage(QTreeWidgetItem*, int)));
2254
2255   QTreePushButton* rButton = new QTreePushButton;
2256   rButton->setItem(item);
2257   rButton->setColumn(COLUMN_RELOAD_IMAGE);
2258   rButton->setToolTip(tr("reload vector field"));
2259   rButton->setEnabled(from_disk);
2260   rButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/rotateright.png")));
2261   connect(rButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
2262     this,SLOT(ReloadImage(QTreeWidgetItem*, int)));
2263
2264   DataTree->topLevelItem(index)->setExpanded(1);
2265   DataTree->topLevelItem(index)->addChild(item);
2266   DataTree->setItemWidget(item, COLUMN_RELOAD_IMAGE, rButton);
2267   DataTree->setItemWidget(item, COLUMN_CLOSE_IMAGE, cButton);
2268
2269   //set the id of the image
2270   QString id = DataTree->topLevelItem(index)->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString();
2271   item->setData(COLUMN_IMAGE_NAME,Qt::UserRole,id.toStdString().c_str());
2272   UpdateTree();
2273   qApp->processEvents();
2274   ImageInfoChanged();
2275   QApplication::restoreOverrideCursor();
2276 }
2277 //------------------------------------------------------------------------------
2278
2279
2280 //------------------------------------------------------------------------------
2281 void vvMainWindow::AddField(vvImage::Pointer vf,QString file,int index)
2282 {
2283   QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
2284   vvSlicerManager* imageManager = mSlicerManagers[index];
2285   if (imageManager->SetVF(vf,file.toStdString())) {
2286     AddFieldEntry(file,index,false);
2287   } else {
2288     QString error = "Cannot import the vector field for this image.\n";
2289     error += imageManager->GetLastError().c_str();
2290     QMessageBox::information(this,tr("Problem reading VF !"),error);
2291   }
2292   QApplication::restoreOverrideCursor();
2293 }
2294 //------------------------------------------------------------------------------
2295
2296
2297 //------------------------------------------------------------------------------
2298 void vvMainWindow::AddField(QString file,int index)
2299 {
2300   if (QFile::exists(file)) {
2301     mInputPathName = itksys::SystemTools::GetFilenamePath(file.toStdString()).c_str();
2302
2303     //init the progress events
2304     QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
2305     vvProgressDialog progress("Opening " + file.toStdString());
2306     qApp->processEvents();
2307
2308     //read the vector and put it in the current mSlicerManager
2309     vvSlicerManager* imageManager = mSlicerManagers[index];
2310     qApp->processEvents();
2311
2312     std::string filename = itksys::SystemTools::GetFilenameWithoutExtension(file.toStdString()).c_str();
2313     if (imageManager->SetVF(file.toStdString())) {
2314       imageManager->Render();
2315       AddFieldEntry(file,index,true);
2316     } else {
2317       QApplication::restoreOverrideCursor();
2318       QString error = "Cannot import the vector field for this image.\n";
2319       error += imageManager->GetLastError().c_str();
2320       QMessageBox::information(this,tr("Problem reading VF !"),error);
2321     }
2322   } else
2323     QMessageBox::information(this,tr("Problem reading VF !"),"File doesn't exist!");
2324
2325 }
2326 //------------------------------------------------------------------------------
2327
2328
2329 //------------------------------------------------------------------------------
2330 void vvMainWindow::SetVFProperty(int subsampling, int scale, int log, int width, double r, double g, double b)
2331 {
2332   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2333   if (mSlicerManagers[index]->GetSlicer(0)->GetVF()) {
2334     for (int i = 0; i < 4; i++) {
2335       mSlicerManagers[index]->GetSlicer(i)->SetVFSubSampling(subsampling);
2336       mSlicerManagers[index]->GetSlicer(i)->SetVFScale(scale);
2337       mSlicerManagers[index]->GetSlicer(i)->SetVFWidth(width);
2338       mSlicerManagers[index]->GetSlicer(i)->SetVFColor(r,g,b);
2339       if (log > 0)
2340         mSlicerManagers[index]->GetSlicer(i)->SetVFLog(1);
2341       else
2342         mSlicerManagers[index]->GetSlicer(i)->SetVFLog(0);
2343     }
2344   }
2345 }
2346 //------------------------------------------------------------------------------
2347
2348
2349 //------------------------------------------------------------------------------
2350 void vvMainWindow::SetOverlayProperty(int color, int linked, double window, double level)
2351 {
2352   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2353   if (mSlicerManagers[index]->GetSlicer(0)->GetOverlay()) {
2354     mSlicerManagers[index]->SetOverlayColor(color);
2355     mSlicerManagers[index]->SetColorMap(0);
2356     mSlicerManagers[index]->SetLinkOverlayWindowLevel(linked);
2357     mSlicerManagers[index]->SetOverlayColorWindow(window);
2358     mSlicerManagers[index]->SetOverlayColorLevel(level);
2359     mSlicerManagers[index]->Render();
2360   }
2361 }
2362 //------------------------------------------------------------------------------
2363
2364 //------------------------------------------------------------------------------
2365 void vvMainWindow::SetFusionProperty(int opacity, int thresOpacity, int colormap,double window, double level, bool showLegend)
2366 {
2367   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2368   if (mSlicerManagers[index]->GetSlicer(0)->GetFusion()) {
2369     mSlicerManagers[index]->SetFusionColorMap(colormap);
2370     mSlicerManagers[index]->SetFusionOpacity(opacity);
2371     mSlicerManagers[index]->SetFusionThresholdOpacity(thresOpacity);
2372     mSlicerManagers[index]->SetFusionWindow(window);
2373     mSlicerManagers[index]->SetFusionLevel(level);
2374     mSlicerManagers[index]->SetFusionShowLegend(showLegend);
2375     mSlicerManagers[index]->SetColorMap(0);
2376     mSlicerManagers[index]->Render();
2377   }
2378 }
2379 //------------------------------------------------------------------------------
2380
2381
2382 //------------------------------------------------------------------------------
2383 void vvMainWindow::SelectFusionSequence()
2384 {
2385   //get the index of the slicer manager of the main sequence (CT)
2386   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2387   //check if one overlay image is already associated
2388   for (int child = 0; child < DataTree->topLevelItem(index)->childCount(); child++)
2389     if ( (DataTree->topLevelItem(index)->child(child)->data(1,Qt::UserRole).toString() == "fusion") ||
2390       (DataTree->topLevelItem(index)->child(child)->data(1,Qt::UserRole).toString() == "fusionSequence") ) {
2391         QString error = "Cannot add more than one compared image\n";
2392         error += "Please remove first ";
2393         error += DataTree->topLevelItem(index)->child(child)->data(COLUMN_IMAGE_NAME,Qt::DisplayRole).toString();
2394         QMessageBox::information(this,tr("Problem adding compared image !"),error);
2395         return;
2396     }
2397
2398     QString Extensions = EXTENSIONS;
2399     Extensions += ";;All Files (*)";
2400     QStringList files = QFileDialog::getOpenFileNames(this,tr("Load Overlay image sequence"),mInputPathName,Extensions);
2401     if (files.isEmpty())
2402       return;
2403
2404     std::vector<std::string> vecFileNames;
2405     for (int i = 0; i < files.size(); i++) {
2406       vecFileNames.push_back(files[i].toStdString());
2407     }
2408
2409     //associate the secondary sequence (US) to the main one
2410     AddFusionSequence(index,vecFileNames,vvImageReader::MERGEDWITHTIME);
2411 }
2412 //------------------------------------------------------------------------------
2413
2414
2415 //------------------------------------------------------------------------------
2416 void vvMainWindow::SelectFusionSequenceTemporalSignal() {
2417
2418   //make sure the index is right?
2419   //in the end, I should attach the temporal data to the right sequence!
2420   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2421   //in case the other sequence got selected, make sure we select the primary sequence
2422   if ( (!mSlicerManagers[index]->GetSlicer(0)->GetFusion()) && mSlicerManagers[index]->GetFusionSequenceIndexOfLinkedManager()>=0 ) {
2423     index = mSlicerManagers[index]->GetFusionSequenceIndexOfLinkedManager();
2424   }
2425
2426   //open a dialog box to find a file
2427   QString Extensions = EXTENSIONS;
2428   Extensions += ";;All Files (*)";
2429   QString fileName = QFileDialog::getOpenFileName(this,tr("Load respiratory signal for fused sequence"),mInputPathName,Extensions);
2430   if (fileName.isNull())
2431     return;
2432
2433   //read it as a vector of values
2434   std::vector<double> signal;
2435   //...TODO, look for itk functions that can do that... vnl in the worst case.
2436   signal.push_back(1);signal.push_back(2);
2437
2438   //TODO: instead: if the loaded signal is longer, just crop it...
2439   //this allows loading only the first few frames when testing.
2440   //->maybe raise a message that this behavior may be unsafe...
2441
2442   //if compatible with the fused image sequence (number of images = number of entries), enable the temporalSync
2443   if ( signal.size() >= mSlicerManagers[index]->GetFusionSequenceNbFrames()) {
2444     //for convenience, associate this sequence to both the current slicer manager, and to the linked one
2445     mSlicerManagers[index]->SetFusionSequenceTemporalSignal(signal);
2446     mSlicerManagers[ mSlicerManagers[index]->GetFusionSequenceIndexOfLinkedManager() ]->SetFusionSequenceTemporalSignal(signal);
2447     overlayPanel->enableFusionSequenceTemporalSync();
2448     QMessageBox::information(this,tr("Adding signal"),"would add the signal from file: "+ fileName);
2449   }
2450   else {//else, send a message to signal the failure...
2451     QString error = "The provided signal doesn't have the same duration as the sequence\n";
2452     error += "Ignoring file: " + fileName;
2453     QMessageBox::information(this,tr("Problem adding signal!"),error);
2454     return;
2455   }
2456
2457 }
2458 //------------------------------------------------------------------------------
2459
2460
2461 //------------------------------------------------------------------------------
2462 //when this function is called index is the slicer manager index corresponding to the main sequence (CT)
2463 //the files behind fileNames points to the data for the secondary sequence
2464 void vvMainWindow::AddFusionSequence(int index, std::vector<std::string> fileNames, vvImageReader::LoadedImageType type)
2465 {
2466   QString file(fileNames[0].c_str());
2467   if (QFile::exists(file))
2468   {
2469     mInputPathName = itksys::SystemTools::GetFilenamePath(file.toStdString()).c_str();
2470     itk::ImageIOBase::Pointer reader = itk::ImageIOFactory::CreateImageIO(
2471       file.toStdString().c_str(), itk::ImageIOFactory::ReadMode);
2472     reader->SetFileName(fileNames[0].c_str());
2473     reader->ReadImageInformation();
2474     std::string component = reader->GetComponentTypeAsString(reader->GetComponentType());
2475     int dimension = reader->GetNumberOfDimensions();
2476     QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
2477     vvProgressDialog progress("Opening " + file.toStdString());
2478     qApp->processEvents();
2479
2480     std::string filename = itksys::SystemTools::GetFilenameWithoutExtension(file.toStdString()).c_str();
2481
2482     if (mSlicerManagers[index]->SetFusionSequence(fileNames,dimension, component,type)) {
2483       //create an item in the tree with good settings
2484       QTreeWidgetItem *item = new QTreeWidgetItem();
2485       item->setData(0,Qt::UserRole,file.toStdString().c_str());
2486       item->setData(1,Qt::UserRole,tr("fusionSequence"));
2487
2488       QFileInfo fileinfo(file); //Do not show the path
2489       item->setData(COLUMN_IMAGE_NAME,Qt::DisplayRole,fileinfo.fileName());
2490       item->setToolTip(COLUMN_IMAGE_NAME, mSlicerManagers[index]->GetListOfAbsoluteFilePathInOneString("fusionSequence").c_str());
2491       qApp->processEvents();
2492       for (int j = 1; j <= 4; j++) {
2493         item->setData(j,Qt::CheckStateRole,DataTree->topLevelItem(index)->data(j,Qt::CheckStateRole));
2494       }
2495
2496       //Create the buttons for reload and close
2497       qApp->processEvents();
2498       QTreePushButton* cButton = new QTreePushButton;
2499       cButton->setItem(item);
2500       cButton->setColumn(COLUMN_CLOSE_IMAGE);
2501       cButton->setToolTip(tr("close image"));
2502       cButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/exit.png")));
2503       connect(cButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
2504         this,SLOT(CloseImage(QTreeWidgetItem*, int)));
2505
2506       QTreePushButton* rButton = new QTreePushButton;
2507       rButton->setItem(item);
2508       rButton->setColumn(COLUMN_RELOAD_IMAGE);
2509       rButton->setToolTip(tr("reload image"));
2510       rButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/rotateright.png")));
2511       connect(rButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
2512         this,SLOT(ReloadImage(QTreeWidgetItem*, int)));
2513
2514       DataTree->topLevelItem(index)->setExpanded(1);
2515       DataTree->topLevelItem(index)->addChild(item);
2516       DataTree->setItemWidget(item, COLUMN_CLOSE_IMAGE, cButton);
2517       DataTree->setItemWidget(item, COLUMN_RELOAD_IMAGE, rButton);
2518
2519       //store the original transform matrix
2520       int indexParent = GetSlicerIndexFromItem( DataTree->topLevelItem(index) );
2521       mSlicerManagers[indexParent]->SetFusionSequenceMainTransformMatrix( mSlicerManagers[indexParent]->GetSlicer(0)->GetImage()->GetTransform()[0]->GetMatrix() );
2522
2523       //set the id of the image
2524       QString id = DataTree->topLevelItem(index)->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString();
2525       item->setData(COLUMN_IMAGE_NAME,Qt::UserRole,id.toStdString().c_str());
2526       UpdateTree();
2527       qApp->processEvents();
2528
2529       //ImageInfoChanged();
2530
2531       QApplication::restoreOverrideCursor();
2532       // Update the display to update, e.g., the sliders
2533       for(int i=0; i<4; i++)
2534         DisplaySliders(index, i);
2535
2536
2537       //This loads the secondary sequence (US) as an independent sequence
2538       LoadImages(fileNames, type);
2539       //reset the transforms to identiy
2540       for (unsigned i=0 ; i<mSlicerManagers.back()->GetImage()->GetTransform().size() ; i++) {
2541         mSlicerManagers.back()->GetImage()->GetTransform()[i]->Identity();
2542         mSlicerManagers.back()->GetImage()->GetTransform()[i]->Update();
2543       }
2544
2545       //automatically link both images...
2546       AddLink(mSlicerManagers[indexParent]->GetId().c_str(), mSlicerManagers.back()->GetId().c_str(), false);
2547
2548       //tie the main and secondary sequences by raising flags and informing each another of their respective SlicerManager indices
2549       mSlicerManagers[indexParent]->SetFusionSequenceIndexOfLinkedManager(mSlicerManagers.size()-1);
2550       mSlicerManagers[indexParent]->SetFusionSequenceInvolvmentCode(0); //main sequence
2551       mSlicerManagers.back()->SetFusionSequenceIndexOfLinkedManager(indexParent);
2552       mSlicerManagers.back()->SetFusionSequenceInvolvmentCode(1); //secondary sequence
2553       for (unsigned i=0 ; i<4 ; i++) {
2554         mSlicerManagers.back()->GetSlicer(i)->SetFusionSequenceCode(1); //flag the slicers of the secondary sequence
2555       }
2556
2557     } else {
2558       QApplication::restoreOverrideCursor();
2559       QString error = "Cannot import the new image.\n";
2560       error += mSlicerManagers[index]->GetLastError().c_str();
2561       QMessageBox::information(this,tr("Problem reading image !"),error);
2562     }
2563     //WindowLevelChanged();
2564     ImageInfoChanged(); //this internally calls WindowLevelChanged...
2565   }
2566   else {
2567     QMessageBox::information(this,tr("Problem reading fusion sequence !"),"File doesn't exist!");
2568     return;
2569   }
2570
2571 }
2572 //------------------------------------------------------------------------------
2573
2574
2575 //------------------------------------------------------------------------------
2576 //fusionSequenceFrameIndex and fusionSequenceNbFrames are relative to the secondary sequence (US)
2577 void vvMainWindow::SetFusionSequenceProperty(int fusionSequenceFrameIndex, bool spatialSyncFlag, unsigned int fusionSequenceNbFrames, bool temporalSyncFlag)
2578 {
2579   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2580
2581   if (!mSlicerManagers[index]->IsInvolvedInFusionSequence()) return;
2582
2583   //check if the focus moved to the linked sequence, and in this case, select the master sequence instead
2584   if (!mSlicerManagers[index]->IsMainSequenceOfFusionSequence()) {
2585     index = mSlicerManagers[index]->GetFusionSequenceIndexOfLinkedManager();
2586   }
2587   int secondaryIndex = mSlicerManagers[index]->GetFusionSequenceIndexOfLinkedManager();
2588   if (secondaryIndex==-1) return; //this should never happen
2589   if ( (!mSlicerManagers[index]->IsMainSequenceOfFusionSequence()) ||
2590     (!mSlicerManagers[secondaryIndex]->IsSecondarySequenceOfFusionSequence()) )
2591   {return;} //this should never happen, raise an exception?
2592
2593   if (mSlicerManagers[index]->GetSlicer(0)->GetFusion()) {
2594
2595     //First, if the spatialSync button is unchecked, then reposition the parent sequence (CT) in its original coordinate frame
2596     if ( (!spatialSyncFlag) && (mSlicerManagers[index]->GetFusionSequenceSpatialSyncFlag()) ) {
2597       for ( unsigned i=0 ; i<mSlicerManagers[index]->GetSlicer(0)->GetImage()->GetTransform().size() ; i++ ) {
2598         mSlicerManagers[index]->GetSlicer(0)->GetImage()->GetTransform()[i]->SetMatrix( mSlicerManagers[index]->GetFusionSequenceMainTransformMatrix() );
2599         mSlicerManagers[index]->GetSlicer(0)->GetImage()->GetTransform()[i]->Update();
2600       }
2601
2602       for (int i=0; i<mSlicerManagers[index]->GetNumberOfSlicers(); i++) {
2603         mSlicerManagers[index]->GetSlicer(i)->ForceUpdateDisplayExtent();
2604         mSlicerManagers[index]->GetSlicer(i)->Render();
2605       }
2606     }
2607
2608     //then, update the property values in the slicer manager
2609     mSlicerManagers[index]->SetFusionSequenceLength(fusionSequenceNbFrames);
2610     mSlicerManagers[index]->SetFusionSequenceSpatialSyncFlag(spatialSyncFlag);
2611     mSlicerManagers[index]->SetFusionSequenceTemporalSyncFlag(temporalSyncFlag);
2612     mSlicerManagers[index]->SetFusionSequenceFrameIndex(fusionSequenceFrameIndex);
2613
2614     //select the right frame of the US sequence
2615     mSlicerManagers[index]->SetFusionSequenceTSlice(fusionSequenceFrameIndex); //here, I should only update the overlayed sequence
2616     mSlicerManagers[secondaryIndex]->SetTSlice(fusionSequenceFrameIndex, false); //this should update the secondary sequence (individual version)
2617
2618     //update the horizontal sliders of the main window
2619     overlayPanel->updateFusionSequenceSliderValueFromWindow(fusionSequenceFrameIndex, false);
2620
2621     if (spatialSyncFlag) { //reslice the CT
2622
2623       if (temporalSyncFlag) { //do the temporal synchronisation
2624         //TODO: add the temporal synchronisation stuff
2625         //if the button is checked, get the phase of the requested US frame from the available signal
2626         //and select the corresponding one in the CT. (check the one just before, and the one just after, and select the closest)
2627
2628         //TODO: do it also the other way around, when modifying the time index related to CT, select a close frame
2629         //this should not be done here directly, but the code should be inspired from the one here
2630         //->find a good US frame such that when calling this function with this US frame, it produces the expected result
2631
2632
2633         //TODO: select the right CT image to display
2634         int mainSequenceFrameIndex=0;
2635         //estimate the TSlice to set to the CT
2636
2637         //and set it!
2638         mSlicerManagers[index]->SetTSlice(mainSequenceFrameIndex, false);
2639       }
2640
2641
2642       //Set the transform matrix of the parent sequence (typically CT / 4DCT)
2643       vtkSmartPointer<vtkMatrix4x4> tmpMat = vtkSmartPointer<vtkMatrix4x4>::New();
2644       vtkMatrix4x4::Invert( mSlicerManagers[index]->GetFusionSequenceInitialTransformMatrixAtFrame(fusionSequenceFrameIndex), tmpMat );
2645       for ( unsigned i=0 ; i<mSlicerManagers[index]->GetSlicer(0)->GetImage()->GetTransform().size() ; i++ ) {
2646         mSlicerManagers[index]->GetSlicer(0)->GetImage()->GetTransform()[i]->SetMatrix( mSlicerManagers[index]->GetFusionSequenceMainTransformMatrix() );
2647         mSlicerManagers[index]->GetSlicer(0)->GetImage()->GetTransform()[i]->PreMultiply();
2648         mSlicerManagers[index]->GetSlicer(0)->GetImage()->GetTransform()[i]->Concatenate( tmpMat );
2649         mSlicerManagers[index]->GetSlicer(0)->GetImage()->GetTransform()[i]->Update();
2650       }
2651
2652       for (int i=0; i<mSlicerManagers[index]->GetNumberOfSlicers(); i++) {
2653         mSlicerManagers[index]->GetSlicer(i)->ForceUpdateDisplayExtent();
2654         mSlicerManagers[index]->GetSlicer(i)->Render();
2655       }
2656
2657     }
2658
2659   }
2660 }
2661 //------------------------------------------------------------------------------
2662
2663
2664 //------------------------------------------------------------------------------
2665 void vvMainWindow::SaveAs()
2666 {
2667   if (DataTree->selectedItems()[0]->data(1,Qt::UserRole).toString() == "vector") {
2668     QMessageBox::warning(this,tr("Unsupported type"),tr("Sorry, saving a vector field is unsupported for the moment"));
2669     return;
2670   }
2671
2672   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2673   int dimension = mSlicerManagers[index]->GetDimension();
2674   QStringList OutputListeFormat;
2675   OutputListeFormat.clear();
2676   if (dimension == 1) {
2677     OutputListeFormat.push_back(".mhd");
2678     OutputListeFormat.push_back(".mha");
2679   }
2680   if (dimension == 2) {
2681     OutputListeFormat.push_back(".bmp");
2682     OutputListeFormat.push_back(".png");
2683     OutputListeFormat.push_back(".jpeg");
2684     OutputListeFormat.push_back(".tif");
2685     OutputListeFormat.push_back(".mhd");
2686     OutputListeFormat.push_back(".mha");
2687     OutputListeFormat.push_back(".hdr");
2688     OutputListeFormat.push_back(".vox");
2689   } else if (dimension == 3) {
2690     OutputListeFormat.push_back(".mhd");
2691     OutputListeFormat.push_back(".mha");
2692     OutputListeFormat.push_back(".nii");
2693     OutputListeFormat.push_back(".nrrd");
2694     OutputListeFormat.push_back(".nhdr");
2695     OutputListeFormat.push_back(".hdr");
2696     OutputListeFormat.push_back(".vox");
2697   } else if (dimension == 4) {
2698     OutputListeFormat.push_back(".mhd");
2699     OutputListeFormat.push_back(".mha");
2700     OutputListeFormat.push_back(".nii");
2701     OutputListeFormat.push_back(".nrrd");
2702     OutputListeFormat.push_back(".nhdr");
2703   }
2704   QString Extensions = "AllFiles(*.*)";
2705   for (int i = 0; i < OutputListeFormat.count(); i++) {
2706     Extensions += ";;Images ( *";
2707     Extensions += OutputListeFormat[i];
2708     Extensions += ")";
2709   }
2710   QString fileName = QFileDialog::getSaveFileName(this,
2711     tr("Save As"),
2712     mSlicerManagers[index]->GetFileName().c_str(),
2713     Extensions);
2714   if (!fileName.isEmpty()) {
2715     std::string fileformat = itksys::SystemTools::GetFilenameLastExtension(fileName.toStdString());
2716     if (OutputListeFormat.contains(
2717       fileformat.c_str())) {
2718         QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
2719         std::string action = "Saving";
2720         vvProgressDialog progress("Saving "+fileName.toStdString());
2721         qApp->processEvents();
2722         vvImageWriter::Pointer writer = vvImageWriter::New();
2723         writer->SetOutputFileName(fileName.toStdString());
2724         writer->SetInput(mSlicerManagers[index]->GetImage());
2725
2726         // Check on transform and prompt user
2727         writer->SetSaveTransform(false);
2728         bool bId = true;
2729         for(int i=0; i<4; i++)
2730           for(int j=0; j<4; j++) {
2731             // TODO SR and BP: check on the list of transforms and not the first only
2732             double elt = mSlicerManagers[index]->GetImage()->GetTransform()[0]->GetMatrix()->GetElement(i,j);
2733             if(i==j && elt!=1.)
2734               bId = false;
2735             if(i!=j && elt!=0.)
2736               bId = false;
2737           }
2738           if( !bId ) {
2739             QString warning = "The image has an associated linear transform. Do you want to save it along?";
2740             QMessageBox msgBox(QMessageBox::Warning, tr("Save transform"), warning, 0, this);
2741             msgBox.addButton(tr("Yes"), QMessageBox::AcceptRole);
2742             msgBox.addButton(tr("No"), QMessageBox::RejectRole);
2743             if (msgBox.exec() == QMessageBox::AcceptRole)
2744               writer->SetSaveTransform(true);
2745           }
2746
2747           writer->Update();
2748           QApplication::restoreOverrideCursor();
2749           if (writer->GetLastError().size()) {
2750             QString error = "Saving did not succeed\n";
2751             error += writer->GetLastError().c_str();
2752             QMessageBox::information(this,tr("Saving Problem"),error);
2753             SaveAs();
2754           }
2755     } else {
2756       QString error = fileformat.c_str();
2757       if (error.isEmpty())
2758         error += "no file format specified !";
2759       else
2760         error += " format unknown !!!\n";
2761       QMessageBox::information(this,tr("Saving Problem"),error);
2762       SaveAs();
2763     }
2764   }
2765 }
2766 //------------------------------------------------------------------------------
2767
2768 //------------------------------------------------------------------------------
2769 void vvMainWindow::SaveCurrentState()
2770 {
2771   QString Extensions = "XML Files(*.xml)";
2772   QString fileName = QFileDialog::getSaveFileName(this,
2773     tr("Save Current Window State"),
2774     "",
2775     Extensions);
2776
2777   SaveCurrentStateAs(fileName.toStdString());
2778 }
2779 //------------------------------------------------------------------------------
2780
2781 //------------------------------------------------------------------------------
2782 void vvMainWindow::SaveCurrentStateAs(const std::string& stateFile)
2783 {
2784   vvSaveState save_state;
2785   save_state.Run(this, stateFile);
2786 }
2787
2788 //------------------------------------------------------------------------------
2789 void vvMainWindow::ReadSavedState()
2790 {
2791   QString Extensions = "XML Files(*.xml)";
2792   QString fileName = QFileDialog::getOpenFileName(this,
2793     tr("Load Window State"),
2794     "",
2795     Extensions);
2796
2797   ReadSavedStateFile(fileName.toStdString());
2798 }
2799 //------------------------------------------------------------------------------
2800
2801 //------------------------------------------------------------------------------
2802 void vvMainWindow::ReadSavedStateFile(const std::string& stateFile)
2803 {
2804   vvReadState read_state;
2805   read_state.Run(this, stateFile);
2806 }
2807 //------------------------------------------------------------------------------
2808
2809 //------------------------------------------------------------------------------
2810 void vvMainWindow::LinkAllImages()
2811 {
2812   linkPanel->linkAll();
2813 }
2814
2815 //------------------------------------------------------------------------------
2816 void vvMainWindow::AddLink(QString image1,QString image2,bool fromPanel)
2817 {
2818   if (!fromPanel) {
2819     // delegate to linkPanel if call came from elsewhere...
2820     linkPanel->addLinkFromIds(image1, image2);
2821     return;
2822   }
2823
2824   unsigned int sm1 = 0;
2825   unsigned int sm2 = 0;
2826
2827   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
2828     if (image1.toStdString() == mSlicerManagers[i]->GetId()) {
2829       mSlicerManagers[i]->AddLink(image2.toStdString());
2830       sm1 = i;
2831     }
2832     if (image2.toStdString() == mSlicerManagers[i]->GetId()) {
2833       mSlicerManagers[i]->AddLink(image1.toStdString());
2834       sm2 = i;
2835     }
2836   }
2837
2838   if (linkPanel->isLinkAll())   {
2839     emit UpdateLinkedNavigation(mSlicerManagers[sm1]->GetId(), mSlicerManagers[mCurrentPickedImageIndex], mSlicerManagers[mCurrentPickedImageIndex]->GetSlicer(0));
2840     emit UpdateLinkedNavigation(mSlicerManagers[sm2]->GetId(), mSlicerManagers[mCurrentPickedImageIndex], mSlicerManagers[mCurrentPickedImageIndex]->GetSlicer(0));
2841   } else {
2842     emit UpdateLinkedNavigation(mSlicerManagers[sm2]->GetId(), mSlicerManagers[sm1], mSlicerManagers[sm1]->GetSlicer(0));
2843   }
2844 }
2845
2846 //------------------------------------------------------------------------------
2847
2848
2849 //------------------------------------------------------------------------------
2850 void vvMainWindow::RemoveLink(QString image1,QString image2)
2851 {
2852   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
2853     if (image1.toStdString() == mSlicerManagers[i]->GetId()) {
2854       mSlicerManagers[i]->RemoveLink(image2.toStdString());
2855     }
2856     if (image2.toStdString() == mSlicerManagers[i]->GetId()) {
2857       mSlicerManagers[i]->RemoveLink(image1.toStdString());
2858     }
2859   }
2860 }
2861 //------------------------------------------------------------------------------
2862
2863 //------------------------------------------------------------------------------
2864 void vvMainWindow::ChangeImageWithIndexOffset(vvSlicerManager *sm, int slicer, int offset)
2865 {
2866   if(mSlicerManagers.size()==1)
2867     return;
2868
2869   int index = 0;
2870   while(sm != mSlicerManagers[index])
2871     index++;
2872   index = (index+offset+mSlicerManagers.size()) % mSlicerManagers.size();
2873
2874   QTreeWidgetItem* item = GetItemFromSlicerManager(mSlicerManagers[index]);
2875   item->setData(slicer+1,Qt::CheckStateRole,2);         //change checkbox
2876   CurrentImageChanged(mSlicerManagers[index]->GetId()); //select new image
2877   DisplayChanged(item,slicer+1);
2878 }
2879 //------------------------------------------------------------------------------
2880 void vvMainWindow::HorizontalSliderMoved(int value,int column, int slicer_index)
2881 {
2882   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
2883     if (DataTree->topLevelItem(i)->data(column,Qt::CheckStateRole).toInt() > 1) {
2884       //i is the SlicerManager that is in charge of this slicer.
2885       if (mSlicerManagers[i]->IsInvolvedInFusionSequence()) {
2886         //if the slicerManager is involved in a fusionSequence as the secondary sequence, then update the slider position in the overlay panel and everything accordingly
2887         if (mSlicerManagers[i]->IsSecondarySequenceOfFusionSequence()) {
2888           overlayPanel->updateFusionSequenceSliderValueFromWindow(value, true);
2889         }
2890         else { //if this is the primary sequence that has been modified
2891           if (mSlicerManagers[i]->GetFusionSequenceTemporalSyncFlag()) {
2892             //WARNING: for some obscure reason, there are problems when accessing mSlicerManagers[mSlicerManagers[i]->GetFusionSequenceIndexOfLinkedManager()]->GetFusionSequenceFrameIndex();
2893
2894             //int estimatedValue=mSlicerManagers[mSlicerManagers[i]->GetFusionSequenceIndexOfLinkedManager()]->GetFusionSequenceFrameIndex();
2895             int estimatedValue=0;
2896             //TODO: if temporal sync is active
2897             //estimate a corresponding time index for the secondary (US) sequence, and update it accordingly.
2898             //estimatedValue = ...
2899             overlayPanel->updateFusionSequenceSliderValueFromWindow(estimatedValue, true);
2900           }
2901         }
2902       }
2903
2904       for (int j = 0; j < 4; j++) {
2905         mSlicerManagers[i]->SetTSliceInSlicer(value,j);
2906       }
2907       mSlicerManagers[i]->GetSlicer(slicer_index)->Render();
2908       break;
2909     }
2910   }
2911 }
2912 //------------------------------------------------------------------------------
2913
2914
2915 //------------------------------------------------------------------------------
2916 void vvMainWindow::NOHorizontalSliderMoved()
2917 {
2918   // if (mCurrentTime == NOHorizontalSlider->value()) return;
2919   HorizontalSliderMoved(NOHorizontalSlider->value(),COLUMN_UL_VIEW,0);
2920   //  mCurrentTime = NOHorizontalSlider->value();
2921 }
2922 //------------------------------------------------------------------------------
2923
2924
2925 //------------------------------------------------------------------------------
2926 void vvMainWindow::NEHorizontalSliderMoved()
2927 {
2928   // if (mCurrentTime == NEHorizontalSlider->value()) return;
2929   HorizontalSliderMoved(NEHorizontalSlider->value(),COLUMN_UR_VIEW,1);
2930   //  mCurrentTime = NEHorizontalSlider->value();
2931 }
2932 //------------------------------------------------------------------------------
2933
2934
2935 //------------------------------------------------------------------------------
2936 void vvMainWindow::SOHorizontalSliderMoved()
2937 {
2938   // if (mCurrentTime == SOHorizontalSlider->value()) return;
2939   HorizontalSliderMoved(SOHorizontalSlider->value(),COLUMN_DL_VIEW,2);
2940   // mCurrentTime = SOHorizontalSlider->value();
2941 }
2942 //------------------------------------------------------------------------------
2943
2944
2945 //------------------------------------------------------------------------------
2946 void vvMainWindow::SEHorizontalSliderMoved()
2947 {
2948   // if (mCurrentTime == SEHorizontalSlider->value()) return;
2949   HorizontalSliderMoved(SEHorizontalSlider->value(),COLUMN_DR_VIEW,3);
2950   // mCurrentTime = SEHorizontalSlider->value();
2951 }
2952 //------------------------------------------------------------------------------
2953
2954 //------------------------------------------------------------------------------
2955 void vvMainWindow::NOVerticalSliderChanged()
2956 {
2957   static int value=-1;
2958   if (value == NOVerticalSlider->value()) return;
2959   else value = NOVerticalSlider->value();
2960   //  int value = NOVerticalSlider->value();
2961   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
2962     if (DataTree->topLevelItem(i)->data(COLUMN_UL_VIEW,Qt::CheckStateRole).toInt() > 1) {
2963       if (mSlicerManagers[i]->GetSlicer(0)->GetSlice() != value) {
2964         mSlicerManagers[i]->GetSlicer(0)->SetSlice(value);
2965         mSlicerManagers[i]->VerticalSliderHasChanged(0, value);
2966
2967         // If nor Update/Render -> slider not work
2968         // only render = ok navigation, but for contour Update needed but slower ?
2969
2970         mSlicerManagers[i]->UpdateSlice(0);  // <-- DS add this. Not too much update ? YES. but needed for ImageContour ...
2971         //mSlicerManagers[i]->GetSlicer(0)->Render(); // <-- DS add this, needed for contour, seems ok ? not too slow ?
2972       }
2973       break;
2974     }
2975   }
2976 }
2977 //------------------------------------------------------------------------------
2978
2979
2980 //------------------------------------------------------------------------------
2981 void vvMainWindow::NEVerticalSliderChanged()
2982 {
2983   static int value=-1;
2984   if (value == NEVerticalSlider->value()) return;
2985   else value = NEVerticalSlider->value();
2986   //  int value = NEVerticalSlider->value();
2987   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
2988     if (DataTree->topLevelItem(i)->data(COLUMN_UR_VIEW,Qt::CheckStateRole).toInt() > 1) {
2989       if (mSlicerManagers[i]->GetSlicer(1)->GetSlice() != value) {
2990         mSlicerManagers[i]->GetSlicer(1)->SetSlice(value);
2991         mSlicerManagers[i]->VerticalSliderHasChanged(1, value);
2992         mSlicerManagers[i]->UpdateSlice(1);
2993         //mSlicerManagers[i]->GetSlicer(1)->Render(); // <-- DS add this, needed for contour, seems ok ? not too slow ?
2994       }
2995       break;
2996     }
2997   }
2998 }
2999 //------------------------------------------------------------------------------
3000
3001
3002 //------------------------------------------------------------------------------
3003 void vvMainWindow::SOVerticalSliderChanged()
3004 {
3005   static int value=-1;
3006   if (value == SOVerticalSlider->value()) return;
3007   else value = SOVerticalSlider->value();
3008   //int value = SOVerticalSlider->value();
3009   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
3010     if (DataTree->topLevelItem(i)->data(COLUMN_DL_VIEW,Qt::CheckStateRole).toInt() > 1) {
3011       if (mSlicerManagers[i]->GetSlicer(2)->GetSlice() != value) {
3012         mSlicerManagers[i]->GetSlicer(2)->SetSlice(value);
3013         mSlicerManagers[i]->VerticalSliderHasChanged(2, value);
3014         mSlicerManagers[i]->UpdateSlice(2);
3015         //mSlicerManagers[i]->GetSlicer(2)->Render(); // <-- DS add this, needed for contour, seems ok ? not too slow ?
3016       }
3017       // else { DD("avoid SOVerticalSlider slicer update"); }
3018       break;
3019     }
3020   }
3021 }
3022 //------------------------------------------------------------------------------
3023
3024
3025 //------------------------------------------------------------------------------
3026 void vvMainWindow::SEVerticalSliderChanged()
3027 {
3028   static int value=-1;
3029   if (value == SEVerticalSlider->value()) return;
3030   else value = SEVerticalSlider->value();
3031   // int value = SEVerticalSlider->value();
3032   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
3033     if (DataTree->topLevelItem(i)->data(COLUMN_DR_VIEW,Qt::CheckStateRole).toInt() > 1) {
3034       if (mSlicerManagers[i]->GetSlicer(3)->GetSlice() != value) {
3035         mSlicerManagers[i]->GetSlicer(3)->SetSlice(value);
3036         mSlicerManagers[i]->VerticalSliderHasChanged(3, value);
3037         mSlicerManagers[i]->UpdateSlice(3);
3038         //mSlicerManagers[i]->GetSlicer(3)->Render(); // <-- DS add this, needed for contour, seems ok ? not too slow ?
3039       }
3040       break;
3041     }
3042   }
3043 }
3044 //------------------------------------------------------------------------------
3045
3046
3047 //------------------------------------------------------------------------------
3048 void vvMainWindow::UpdateSlice(int slicer, int slice)
3049 {
3050   // DD("vvMainWindow::UpdateSlice");
3051   //   DD(slicer);
3052   //   DD(slice);
3053   if (slicer == 0) {
3054     //    if (slice != NOVerticalSlider->value())
3055     NOVerticalSlider->setValue(slice);
3056   } else {
3057     if (slicer == 1)
3058       NEVerticalSlider->setValue(slice);
3059     else {
3060       if (slicer == 2)
3061         SOVerticalSlider->setValue(slice);
3062       else {
3063         if (slicer == 3)
3064           SEVerticalSlider->setValue(slice);
3065       }
3066     }
3067   }
3068   // DD("vvMainWindow:UpdateSlice END");
3069 }
3070 //------------------------------------------------------------------------------
3071
3072
3073 //------------------------------------------------------------------------------
3074 void vvMainWindow::UpdateTSlice(int slicer, int slice, int code)
3075 {
3076   //FusionSequence: the slider value should be updated for slicers which show the same sequence as requested
3077   bool doUpdate=false;
3078   if (code==-1) doUpdate=true;
3079   else {
3080     for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
3081       if (DataTree->topLevelItem(i)->data(slicer+1,Qt::CheckStateRole).toInt() > 1) {
3082         //i is the active SlicerManager
3083         if (mSlicerManagers[i]->GetFusionSequenceInvolvmentCode()==code) doUpdate=true;
3084         break;
3085       }
3086     }
3087   }
3088   if (!doUpdate) return;
3089
3090   switch (slicer) {
3091   case 0:
3092     if (NOHorizontalSlider->value()==slice) return;
3093     NOHorizontalSlider->setValue(slice);
3094     break;
3095   case 1:
3096     if (NEHorizontalSlider->value()==slice) return;
3097     NEHorizontalSlider->setValue(slice);
3098     break;
3099   case 2:
3100     if (SOHorizontalSlider->value()==slice) return;
3101     SOHorizontalSlider->setValue(slice);
3102     break;
3103   case 3:
3104     if (SEHorizontalSlider->value()==slice) return;
3105     SEHorizontalSlider->setValue(slice);
3106     break;
3107   }
3108 }
3109 //------------------------------------------------------------------------------
3110
3111
3112 //------------------------------------------------------------------------------
3113 void vvMainWindow::UpdateSliceRange(int slicer, int min, int max, int tmin, int tmax)
3114 {
3115   //int position = int((min+max)/2);
3116   int position = mSlicerManagers[mCurrentPickedImageIndex]->GetSlicer(slicer)->GetSlice();
3117   if (slicer == 0) {
3118     NOVerticalSlider->setRange(min,max);
3119     NOHorizontalSlider->setRange(tmin,tmax);
3120     NOVerticalSlider->setValue(position);
3121   } else if (slicer == 1) {
3122     NEVerticalSlider->setRange(min,max);
3123     NEHorizontalSlider->setRange(tmin,tmax);
3124     NEVerticalSlider->setValue(position);
3125   } else if (slicer == 2) {
3126     SOVerticalSlider->setRange(min,max);
3127     SOHorizontalSlider->setRange(tmin,tmax);
3128     SOVerticalSlider->setValue(position);
3129   } else if (slicer == 3) {
3130     SEVerticalSlider->setRange(min,max);
3131     SEHorizontalSlider->setRange(tmin,tmax);
3132     SEVerticalSlider->setValue(position);
3133   }
3134 }
3135 //------------------------------------------------------------------------------
3136
3137
3138 //------------------------------------------------------------------------------
3139 void vvMainWindow::SaveNOScreenshot()
3140 {
3141   SaveScreenshot(NOViewWidget);
3142 }
3143 //------------------------------------------------------------------------------
3144
3145
3146 //------------------------------------------------------------------------------
3147 void vvMainWindow::SaveNEScreenshot()
3148 {
3149   SaveScreenshot(NEViewWidget);
3150 }
3151 //------------------------------------------------------------------------------
3152
3153
3154 //------------------------------------------------------------------------------
3155 void vvMainWindow::SaveSOScreenshot()
3156 {
3157   SaveScreenshot(SOViewWidget);
3158 }
3159 //------------------------------------------------------------------------------
3160
3161
3162 //------------------------------------------------------------------------------
3163 void vvMainWindow::SaveSEScreenshot()
3164 {
3165   SaveScreenshot(SEViewWidget);
3166 }
3167 //------------------------------------------------------------------------------
3168
3169
3170 //------------------------------------------------------------------------------
3171 void vvMainWindow::SaveScreenshotAllSlices()
3172 {
3173   QVTKWidget *widget = NOViewWidget;
3174
3175   int index = 0;// GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
3176   vvSlicerManager * SM = mSlicerManagers[index];
3177   vvImage * image = SM->GetImage();
3178   vvSlicer * slicer = SM->GetSlicer(0);
3179   int orientation = slicer->GetOrientation();
3180   int nbSlices = image->GetSize()[orientation];
3181   vtkSmartPointer<vtkRenderWindow>  renderWindow = widget->GetRenderWindow();
3182
3183   // Select filename base
3184   QString filename = QFileDialog::getSaveFileName(this,
3185     tr("Save As (filename will be completed by slice number)"),
3186     itksys::SystemTools::GetFilenamePath(mSlicerManagers[index]->GetFileName()).c_str(),
3187     "Images( *.png);;Images( *.jpg)");
3188
3189   // Loop on slices
3190   for(int i=0; i<nbSlices; i++) {
3191     // Change the slice
3192     slicer->SetSlice(i); // -> change the slice of the current slicer
3193     SM->UpdateSlice(0); // --> this one emit UpdateSlice
3194     QCoreApplication::flush(); // -> needed to force display of contours
3195
3196     // Screenshot
3197     vtkSmartPointer<vtkWindowToImageFilter> windowToImageFilter = vtkSmartPointer<vtkWindowToImageFilter>::New();
3198     windowToImageFilter->SetInput(renderWindow);
3199     windowToImageFilter->SetMagnification(1);
3200     windowToImageFilter->SetInputBufferTypeToRGBA(); //also record the alpha (transparency) channel
3201     windowToImageFilter->Update();
3202
3203     vtkSmartPointer<vtkPNGWriter> writer = vtkSmartPointer<vtkPNGWriter>::New();
3204     std::string fn = itksys::SystemTools::GetFilenameWithoutLastExtension(filename.toStdString());
3205     std::string num = clitk::toString(i);
3206     if (i<10) num = "0"+num;
3207     if (i<100) num = "0"+num;
3208     if (i<1000) num = "0"+num;
3209
3210     fn = itksys::SystemTools::GetFilenamePath(filename.toStdString()) + "/"+ fn
3211       + "_" + num + itksys::SystemTools::GetFilenameLastExtension(filename.toStdString());
3212     writer->SetFileName(fn.c_str());
3213     writer->SetInput(windowToImageFilter->GetOutput());
3214     writer->Write();
3215   }
3216 }
3217 //------------------------------------------------------------------------------
3218
3219
3220 //------------------------------------------------------------------------------
3221 void vvMainWindow::SaveScreenshot(QVTKWidget *widget)
3222 {
3223   QString Extensions = "Images( *.png);;";
3224   Extensions += "Images( *.jpg);;";
3225   Extensions += "Images( *.bmp);;";
3226   Extensions += "Images( *.tif);;";
3227   Extensions += "Images( *.ppm)";
3228 #if defined(VTK_USE_FFMPEG_ENCODER) || defined(VTK_USE_VIDEO_FOR_WINDOWS)
3229   Extensions += ";;Video( *.avi)";
3230 #endif
3231 #ifdef VTK_USE_MPEG2_ENCODER
3232   Extensions += ";;Video( *.mpg)";
3233 #endif
3234 #ifdef CLITK_EXPERIMENTAL
3235   Extensions += ";;Video( *.gif)";
3236 #endif
3237
3238   int smIndex=GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
3239   QString fileName = QFileDialog::getSaveFileName(this,
3240     tr("Save As"),
3241     itksys::SystemTools::GetFilenamePath(mSlicerManagers[smIndex]->GetFileName()).c_str(),
3242     Extensions);
3243
3244   if (!fileName.isEmpty()) {
3245     vtkSmartPointer<vtkWindowToImageFilter> w2i = vtkSmartPointer<vtkWindowToImageFilter>::New();
3246     w2i->SetInput(widget->GetRenderWindow());
3247     w2i->Update();
3248     vtkImageData *image = w2i->GetOutput();
3249
3250     std::string ext(itksys::SystemTools::GetFilenameLastExtension(fileName.toStdString()));
3251
3252     // Image
3253     vtkImageWriter *imgwriter = NULL;
3254     if (ext==".bmp")
3255       imgwriter = vtkBMPWriter::New();
3256     else if (ext==".tif")
3257       imgwriter = vtkTIFFWriter::New();
3258     else if (ext==".ppm")
3259       imgwriter = vtkPNMWriter::New();
3260     else if (ext==".png")
3261       imgwriter = vtkPNGWriter::New();
3262     else if (ext==".jpg")
3263       imgwriter = vtkJPEGWriter::New();
3264
3265     // Snapshot image if not null
3266     if(imgwriter!=NULL) {
3267       imgwriter->SetInput(image);
3268       imgwriter->SetFileName(fileName.toStdString().c_str());
3269       imgwriter->Write();
3270       return;
3271     }
3272
3273     // Video
3274     vtkGenericMovieWriter *vidwriter = NULL;
3275 #if CLITK_EXPERIMENTAL == 1
3276     if (ext==".gif") {
3277       vvAnimatedGIFWriter *gif = vvAnimatedGIFWriter::New();
3278       vidwriter = gif;
3279
3280       // FPS
3281       bool ok;
3282       int fps = QInputDialog::getInteger(this, tr("Number of frames per second"),
3283         tr("FPS:"), 5, 0, 1000, 1, &ok);
3284       if(ok)
3285         gif->SetRate(fps);
3286
3287       // Loops
3288       int loops = QInputDialog::getInteger(this, tr("Loops"),
3289         tr("Number of loops (0 means infinite):"), 0, 0, 1000000000, 1, &ok);
3290       if(ok)
3291         gif->SetLoops(loops);
3292
3293       // Dithering
3294       QString msg = "Would you like to activate dithering?";
3295       QMessageBox msgBox(QMessageBox::Question, tr("Dithering"),msg, 0, this);
3296       msgBox.addButton(tr("Yes"), QMessageBox::AcceptRole);
3297       msgBox.addButton(tr("No"), QMessageBox::RejectRole);
3298       gif->SetDither(msgBox.exec() == QMessageBox::AcceptRole);
3299     }
3300 #endif
3301 #ifdef VTK_USE_VIDEO_FOR_WINDOWS
3302     if (ext==".avi") {
3303       vtkAVIWriter *mpg = vtkAVIWriter::New();
3304       vidwriter = mpg;
3305       mpg->SetQuality(2);
3306       bool ok;
3307       int fps = QInputDialog::getInteger(this, tr("Number of frames per second"),
3308         tr("FPS:"), 5, 0, 1024, 1, &ok);
3309       if(!ok)
3310         fps = 5;
3311       mpg->SetRate(fps);
3312     }
3313 #endif
3314 #ifdef VTK_USE_FFMPEG_ENCODER
3315     if (ext==".avi") {
3316       vtkFFMPEGWriter *mpg = vtkFFMPEGWriter::New();
3317       vidwriter = mpg;
3318       mpg->SetQuality(2);
3319       bool ok;
3320       int fps = QInputDialog::getInteger(this, tr("Number of frames per second"),
3321         tr("FPS:"), 5, 0, 1024, 1, &ok);
3322       if(!ok)
3323         fps = 5;
3324       mpg->SetRate(fps);
3325       mpg->SetBitRateTolerance(int(ceil(12.0*1024*1024/fps)));
3326     }
3327 #endif
3328 #ifdef VTK_USE_MPEG2_ENCODER
3329     if (ext==".mpg") {
3330       vtkMPEG2Writer *mpg = vtkMPEG2Writer::New();
3331       vidwriter = mpg;
3332     }
3333 #endif
3334
3335     // Take video if not null
3336     if(vidwriter!=NULL){
3337       vidwriter->SetInput(image);
3338       vidwriter->SetFileName(fileName.toStdString().c_str());
3339       vidwriter->Start();
3340       int nSlice = mSlicerManagers[smIndex]->GetSlicer(0)->GetTMax();
3341       for(int i=0; i<=nSlice; i++) {
3342         mSlicerManagers[smIndex]->SetNextTSlice(0);
3343         vtkSmartPointer<vtkWindowToImageFilter> w2i = vtkSmartPointer<vtkWindowToImageFilter>::New();
3344         w2i->SetInput(widget->GetRenderWindow());
3345         w2i->Update();
3346         vidwriter->SetInput(w2i->GetOutput());
3347         vidwriter->Write();
3348       }
3349       vidwriter->End();
3350       vidwriter->Delete();
3351       return;
3352     }
3353
3354     QMessageBox::information(this,tr("Problem saving screenshot !"),tr("Cannot save image.\nPlease set a file extension !!!"));
3355   }
3356 }
3357 //------------------------------------------------------------------------------
3358
3359
3360 //------------------------------------------------------------------------------
3361 void vvMainWindow::GoToCursor()
3362 {
3363   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
3364   for (int column = 1; column < 5; column++) {
3365     if (DataTree->selectedItems()[0]->data(column,Qt::CheckStateRole).toInt() > 1) {
3366       double* cursorPos = mSlicerManagers[index]->GetSlicer(column-1)->GetCursorPosition();
3367       mSlicerManagers[index]->GetSlicer(column-1)->SetCurrentPosition(
3368         cursorPos[0],cursorPos[1],cursorPos[2],cursorPos[3]);
3369       mSlicerManagers[index]->UpdateViews(1,column-1);
3370       mSlicerManagers[index]->UpdateLinked(column-1);
3371       break;
3372     }
3373   }
3374 }
3375 //------------------------------------------------------------------------------
3376
3377 //------------------------------------------------------------------------------
3378 void vvMainWindow::PlayPause()
3379 {
3380   if (playMode) {
3381     playMode = 0;
3382     playButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/player_play.png")));
3383     ImageInfoChanged();
3384     return;
3385   } else {
3386     int image_number=DataTree->topLevelItemCount();
3387     bool has_temporal;
3388     for (int i=0; i<image_number; i++)
3389       if (mSlicerManagers[i]->GetSlicer(0)->GetTMax() > 0) {
3390         has_temporal=true;
3391         break;
3392       }
3393       if (has_temporal) {
3394         playMode = 1;
3395         playButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/player_pause.png")));
3396         QTimer::singleShot(1000/mFrameRate, this, SLOT(PlayNext()));
3397       }
3398   }
3399 }
3400 //------------------------------------------------------------------------------
3401
3402 //------------------------------------------------------------------------------
3403 void vvMainWindow::PlayNext()
3404 {
3405   if (playMode && !this->isHidden()) {
3406     int image_number=DataTree->topLevelItemCount();
3407     ///Only play one slicer per SM, and only if the SM is being displayed
3408     for (int i=0; i<image_number; i++)
3409       for (int j=0; j<4; j++)
3410         if (mSlicerManagers[i]->GetSlicer(0)->GetTMax() > 0 &&
3411           DataTree->topLevelItem(i)->data(j+1,Qt::CheckStateRole).toInt() > 0) {
3412             mSlicerManagers[i]->SetNextTSlice(j);
3413             break;
3414         }
3415         QTimer::singleShot(1000/mFrameRate, this, SLOT(PlayNext()));
3416   }
3417 }
3418 //------------------------------------------------------------------------------
3419
3420 void vvMainWindow::ShowLastImage()
3421 {
3422   if (mSlicerManagers.size() > 1) {
3423     QTreeWidgetItem * item=DataTree->topLevelItem(DataTree->topLevelItemCount()-1);
3424     CurrentImageChanged(mSlicerManagers.back()->GetId()); //select new image
3425     item->setData(1,Qt::CheckStateRole,2); //show the new image in the first panel
3426     DisplayChanged(item,1);
3427   }
3428 }
3429
3430 //------------------------------------------------------------------------------
3431 void vvMainWindow::UpdateRenderWindows()
3432 {
3433   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
3434     mSlicerManagers[i]->GetSlicer(0)->UpdateLandmarks();
3435     mSlicerManagers[i]->GetSlicer(1)->UpdateLandmarks();
3436     mSlicerManagers[i]->GetSlicer(2)->UpdateLandmarks();
3437     mSlicerManagers[i]->GetSlicer(3)->UpdateLandmarks();
3438   }
3439   if (NOViewWidget->GetRenderWindow()) NOViewWidget->GetRenderWindow()->Render();
3440   if (NEViewWidget->GetRenderWindow()) NEViewWidget->GetRenderWindow()->Render();
3441   if (SOViewWidget->GetRenderWindow()) SOViewWidget->GetRenderWindow()->Render();
3442   if (SEViewWidget->GetRenderWindow()) SEViewWidget->GetRenderWindow()->Render();
3443 }
3444 //------------------------------------------------------------------------------
3445
3446 //------------------------------------------------------------------------------
3447 void vvMainWindow::SegmentationOnCurrentImage()
3448 {
3449   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
3450
3451   vvSegmentationDialog segmentation;
3452   segmentation.SetImage(mSlicerManagers[index]->GetSlicer(0)->GetImage());
3453   segmentation.exec();
3454 }
3455 //------------------------------------------------------------------------------
3456
3457 void vvMainWindow::SurfaceViewerLaunch()
3458 {
3459   vvSurfaceViewerDialog surfaceViewer;
3460   surfaceViewer.exec();
3461 }
3462 //------------------------------------------------------------------------------
3463
3464
3465 //------------------------------------------------------------------------------
3466 int vvMainWindow::GetImageDuplicateFilenameNumber(std::string filename)
3467 {
3468   int number=0;
3469   for(unsigned int l=0; l<mSlicerManagers.size(); l++) {
3470     vvSlicerManager * v = mSlicerManagers[l];
3471     if (v->GetBaseFileName() ==
3472       vtksys::SystemTools::GetFilenameName(vtksys::SystemTools::GetFilenameWithoutLastExtension(filename))) {
3473         number = std::max(number, v->GetBaseFileNameNumber()+1);
3474     }
3475   }
3476   return number;
3477 }
3478 //------------------------------------------------------------------------------
3479
3480
3481 //------------------------------------------------------------------------------
3482 vvSlicerManager* vvMainWindow::AddImage(vvImage::Pointer image,std::string filename)
3483 {
3484   // Change filename if another image exist with the same name
3485   int number = GetImageDuplicateFilenameNumber(filename);
3486
3487   // Create new SliceManager
3488   vvSlicerManager* slicer_manager = new vvSlicerManager(4);
3489   slicer_manager->SetImage(image);//, IMAGE, number);
3490   //  filename = filename+"_"+clitk::toString(number);
3491   slicer_manager->SetFilename(filename, number);
3492   mSlicerManagers.push_back(slicer_manager);
3493
3494   //create an item in the tree with good settings
3495   QTreeWidgetItem *item = new QTreeWidgetItem();
3496   item->setData(0,Qt::UserRole,slicer_manager->GetFileName().c_str());//files[i].c_str());
3497   item->setData(1,Qt::UserRole,tr("image"));
3498   item->setData(COLUMN_IMAGE_NAME,Qt::DisplayRole,slicer_manager->GetFileName().c_str());//filename.c_str());
3499   qApp->processEvents();
3500
3501   for (int j = 1; j <= 4; j++) item->setData(j,Qt::CheckStateRole,1);
3502
3503   //Create the buttons for reload and close
3504   qApp->processEvents();
3505   QTreePushButton* cButton = new QTreePushButton;
3506   cButton->setItem(item);
3507   cButton->setColumn(COLUMN_CLOSE_IMAGE);
3508   cButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/exit.png")));
3509   connect(cButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
3510     this,SLOT(CloseImage(QTreeWidgetItem*, int)));
3511
3512   QTreePushButton* rButton = new QTreePushButton;
3513   rButton->setItem(item);
3514   rButton->setColumn(COLUMN_RELOAD_IMAGE);
3515   rButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/rotateright.png")));
3516   rButton->setEnabled(0);
3517   connect(rButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
3518     this,SLOT(ReloadImage(QTreeWidgetItem*, int)));
3519
3520   DataTree->addTopLevelItem(item);
3521   DataTree->setItemWidget(item, COLUMN_CLOSE_IMAGE, cButton);
3522   DataTree->setItemWidget(item, COLUMN_RELOAD_IMAGE, rButton);
3523
3524   //set the id of the image
3525   QString id = QDir::current().absoluteFilePath(slicer_manager->GetFileName().c_str()) + QString::number(mSlicerManagers.size()-1);
3526   item->setData(COLUMN_IMAGE_NAME,Qt::UserRole,id.toStdString().c_str());
3527   mSlicerManagers.back()->SetId(id.toStdString());
3528
3529   linkPanel->addImage(slicer_manager->GetFileName().c_str()// filename
3530     , id.toStdString());
3531
3532   connect(mSlicerManagers.back(), SIGNAL(currentImageChanged(std::string)),
3533     this, SLOT(CurrentImageChanged(std::string)));
3534   connect(mSlicerManagers.back(), SIGNAL(currentPickedImageChanged(std::string)),
3535     this, SLOT(CurrentPickedImageChanged(std::string)));
3536   connect(mSlicerManagers.back(), SIGNAL(UpdatePosition(int, double, double, double, double, double, double, double)),
3537     this, SLOT(MousePositionChanged(int,double, double, double, double, double, double, double)));
3538   connect(mSlicerManagers.back(), SIGNAL(UpdateVector(int, double, double, double, double)),
3539     this, SLOT(VectorChanged(int,double,double,double, double)));
3540   connect(mSlicerManagers.back(), SIGNAL(UpdateOverlay(int, double, double)),
3541     this, SLOT(OverlayChanged(int,double,double)));
3542   connect(mSlicerManagers.back(), SIGNAL(UpdateFusion(int, double)),
3543     this, SLOT(FusionChanged(int,double)));
3544   //connect(mSlicerManagers.back(), SIGNAL(UpdateFusionSequence(int, bool, unsigned int)),
3545   //  this, SLOT(FusionSequenceChanged(int, bool, unsigned int)));
3546   connect(mSlicerManagers.back(), SIGNAL(WindowLevelChanged()),
3547     this,SLOT(WindowLevelChanged()));
3548   connect(mSlicerManagers.back(), SIGNAL(UpdateSlice(int,int)),
3549     this,SLOT(UpdateSlice(int,int)));
3550   connect(mSlicerManagers.back(), SIGNAL(UpdateTSlice(int, int, int)),
3551     this,SLOT(UpdateTSlice(int, int, int)));
3552   connect(mSlicerManagers.back(), SIGNAL(UpdateTSlice(int, int, int)),
3553     this,SLOT(ImageInfoChanged()));
3554   connect(mSlicerManagers.back(), SIGNAL(UpdateSliceRange(int,int,int,int,int)),
3555     this,SLOT(UpdateSliceRange(int,int,int,int,int)));
3556   connect(mSlicerManagers.back(), SIGNAL(UpdateLinkManager(std::string,int,double,double,double,int)),
3557     this,SLOT(UpdateLinkManager(std::string,int,double,double,double,int)));
3558   connect(mSlicerManagers.back(), SIGNAL(UpdateLinkedNavigation(std::string,vvSlicerManager*,vvSlicer*)),
3559     this,SLOT(UpdateLinkedNavigation(std::string,vvSlicerManager*,vvSlicer*)));
3560   connect(mSlicerManagers.back(), SIGNAL(ChangeImageWithIndexOffset(vvSlicerManager*,int,int)),
3561     this,SLOT(ChangeImageWithIndexOffset(vvSlicerManager*,int,int)));
3562   connect(mSlicerManagers.back(), SIGNAL(LandmarkAdded()),landmarksPanel,SLOT(AddPoint()));
3563
3564
3565   UpdateTree();
3566   qApp->processEvents();
3567   InitSlicers();
3568   ShowLastImage();
3569   InitDisplay();
3570   qApp->processEvents();
3571
3572   // End
3573   ImageInfoChanged();
3574   return slicer_manager;
3575 }
3576 //------------------------------------------------------------------------------
3577
3578
3579 //------------------------------------------------------------------------------
3580 void vvMainWindow::UpdateCurrentSlicer()
3581 {
3582   int index = -1;
3583   if (DataTree->selectedItems().size() > 0) {
3584     index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
3585   }
3586   mSlicerManagerCurrentIndex = index;
3587 }
3588 //------------------------------------------------------------------------------
3589