vv/vvMainWindow.cxx

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