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