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://oncora1.lyon.fnclcc.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
  25 // VV include
  26 #include "vvMainWindow.h"
  27 #include "vvHelpDialog.h"
  28 #include "vvDocumentation.h"
  29 #include "vvProgressDialog.h"
  30 #include "vvQDicomSeriesSelector.h"
  31 #include "vvSlicerManager.h"
  32 #include "clitkImageCommon.h"
  33 #include "vvSlicer.h"
  34 #include "vvInteractorStyleNavigator.h"
  35 #include "vvImageWriter.h"
  36 #include "vvSegmentationDialog.h"
  37 #include "vvSurfaceViewerDialog.h"
  38 #include "vvDeformationDialog.h"
  39 #include "vvImageWarp.h"
  40 #include "vvUtils.h"
  41 #include "vvMaximumIntensityProjection.h"
  42 #include "vvMidPosition.h"
  43 #include "vvMesh.h"
  44 #include "vvStructSelector.h"
  45 #include "vvMeshReader.h"
  46 #include "vvConstants.h"
  47 #include "clitkConfiguration.h"
  48
  49 // ITK include
  50 #include "itkImage.h"
  51 #include "itkImageFileReader.h"
  52 #include "itkByteSwapper.h"
  53 #include "itkCommand.h"
  54 #include "itkNumericSeriesFileNames.h"
  55
  56 // VTK include
  57 #include "vtkImageData.h"
  58 #include "vtkImageActor.h"
  59 #include "vtkCornerAnnotation.h"
  60 #include "vtkRenderWindow.h"
  61 #include "vtkRenderWindowInteractor.h"
  62 #include "vtkRenderer.h"
  63 #include "vtkRendererCollection.h"
  64 #include "vtkWindowToImageFilter.h"
  65 #include "vtkBMPWriter.h"
  66 #include "vtkTIFFWriter.h"
  67 #include "vtkPNMWriter.h"
  68 #include "vtkPNGWriter.h"
  69 #include "vtkJPEGWriter.h"
  70
  71 // Standard includes
  72 #include <iostream>
  73
  74 #define COLUMN_TREE 0
  75 #define COLUMN_UL_VIEW 1
  76 #define COLUMN_UR_VIEW 2
  77 #define COLUMN_DL_VIEW 3
  78 #define COLUMN_DR_VIEW 4
  79 #define COLUMN_CLOSE_IMAGE 5
  80 #define COLUMN_RELOAD_IMAGE 6
  81 #define COLUMN_IMAGE_NAME 7
  82
  83 #define EXTENSIONS "Images ( *.bmp *.png *.jpeg *.jpg *.tif *.mhd *.hdr *.vox *.his *.xdr *.SCAN )"
  84
  85 /*Data Tree values
  86   0,Qt::UserRole full filename
  87   1,Qt::CheckStateRole checkbutton UL View
  88   1,Qt::UserRole overlay, fusion or vector
  89   2,Qt::CheckStateRole checkbutton UR View
  90   3,Qt::CheckStateRole checkbutton DL View
  91   4,Qt::CheckStateRole checkbutton DR View
  92   5,0  short filename
  93   5,Qt::UserRole mSlicerManager id*/
  94
  95 //------------------------------------------------------------------------------
  96 vvMainWindow::vvMainWindow():vvMainWindowBase()
  97 {
  98   setupUi(this); // this sets up the GUI
  99
 100   mInputPathName = "";
 101   mMenuTools = menuTools;
 102   //  mMenuSegmentation = menuSegmentation;
 103   mContextMenu = &contextMenu;
 104   mMenuExperimentalTools = menuExperimental;
 105   mMainWidget = this;
 106   mCurrentTime = -1;
 107   mCurrentSelectedImageId = "";
 108
 109   //Init the contextMenu
 110   this->setContextMenuPolicy(Qt::CustomContextMenu);
 111   contextActions.resize(0);
 112   QAction* actionOpen_new_image = contextMenu.addAction(QIcon(QString::fromUtf8(":/common/icons/fileopen.png")),
 113                                   tr("O&pen new Image"));
 114   actionOpen_new_image->setShortcut(QKeySequence(tr("Ctrl+O")));
 115   connect(actionOpen_new_image,SIGNAL(triggered()),this,SLOT(OpenImages()));
 116   contextActions.push_back(actionOpen_new_image);
 117   contextMenu.addSeparator();
 118
 119   QAction* actionClose_Image = contextMenu.addAction(QIcon(QString::fromUtf8(":/common/icons/exit.png")),
 120                                tr("Close Current Image"));
 121   connect(actionClose_Image,SIGNAL(triggered()),this,SLOT(CloseImage()));
 122   contextActions.push_back(actionClose_Image);
 123
 124   QAction* actionReload_image = contextMenu.addAction(QIcon(QString::fromUtf8(":/common/icons/rotateright.png")),
 125                                 tr("Reload Current Image"));
 126   connect(actionReload_image,SIGNAL(triggered()),this,SLOT(ReloadImage()));
 127   contextActions.push_back(actionReload_image);
 128
 129   QAction* actionSave_image = contextMenu.addAction(QIcon(QString::fromUtf8(":/common/icons/filesave.png")),
 130                               tr("Save Current Image"));
 131   connect(actionSave_image,SIGNAL(triggered()),this,SLOT(SaveAs()));
 132   contextActions.push_back(actionSave_image);
 133
 134   contextMenu.addSeparator();
 135
 136   contextMenu.addAction(actionAdd_VF_to_current_Image);
 137   contextActions.push_back(actionAdd_VF_to_current_Image);
 138
 139   QAction* actionAdd_Overlay_to_current_Image = menuOverlay->addAction(QIcon(QString::fromUtf8(":/common/icons/GPSup.png")),
 140       tr("Add overlay image to current image"));
 141   contextMenu.addAction(actionAdd_Overlay_to_current_Image);
 142   contextActions.push_back(actionAdd_Overlay_to_current_Image);
 143
 144   connect(actionAdd_Overlay_to_current_Image,SIGNAL(triggered()), this,SLOT(SelectOverlayImage()));
 145
 146   contextMenu.addAction(actionAdd_fusion_image);
 147   connect(actionAdd_fusion_image,SIGNAL(triggered()),this,SLOT(SelectFusionImage()));
 148   contextActions.push_back(actionAdd_fusion_image);
 149
 150   // TRIAL DS
 151   /*
 152   QMenu * m = new QMenu(menubar);
 153   m->setTitle("TOTO");
 154   //  m->setObjectName(QString::fromUtf8("TOTOTO"));
 155   contextMenu.addMenu(m);
 156   QAction * a = m->addAction(QIcon(QString::fromUtf8(":/common/icons/GPSup.png")),
 157                      tr("BIDON"));
 158   QAction * b = m->addAction(QIcon(QString::fromUtf8(":/common/icons/GPSup.png")),
 159                      tr("BIDON2"));
 160   m->addAction(a);
 161   m->addAction(b);
 162   connect(a,SIGNAL(triggered()),this,SLOT(AddFusionImage()));
 163   */
 164
 165   //init the DataTree
 166   mSlicerManagers.resize(0);
 167
 168   QStringList header;
 169   header.append("");
 170   header.append("TL");
 171   header.append("TR");
 172   header.append("BL");
 173   header.append("BR");
 174   header.append("");
 175   header.append("");
 176   header.append("Name");
 177
 178   DataTree->setHeaderLabels(header);
 179   DataTree->resizeColumnToContents(COLUMN_TREE);
 180   DataTree->resizeColumnToContents(COLUMN_UL_VIEW);
 181   DataTree->resizeColumnToContents(COLUMN_UR_VIEW);
 182   DataTree->resizeColumnToContents(COLUMN_DL_VIEW);
 183   DataTree->resizeColumnToContents(COLUMN_DR_VIEW);
 184   DataTree->resizeColumnToContents(COLUMN_CLOSE_IMAGE);
 185   DataTree->resizeColumnToContents(COLUMN_RELOAD_IMAGE);
 186   DataTree->resizeColumnToContents(COLUMN_IMAGE_NAME);
 187
 188   viewMode = 1;
 189   documentation = new vvDocumentation();
 190   help_dialog = new vvHelpDialog();
 191   dicomSeriesSelector = new vvDicomSeriesSelector();
 192
 193   inverseButton->setEnabled(0);
 194   actionAdd_Overlay_to_current_Image->setEnabled(0);
 195   actionSave_As->setEnabled(0);
 196   actionAdd_VF_to_current_Image->setEnabled(0);
 197   actionAdd_fusion_image->setEnabled(0);
 198
 199   //init the sliders
 200   verticalSliders.push_back(NOVerticalSlider);
 201   verticalSliders.push_back(NEVerticalSlider);
 202   verticalSliders.push_back(SOVerticalSlider);
 203   verticalSliders.push_back(SEVerticalSlider);
 204
 205   for (int i =0; i < 4; i++)
 206     verticalSliders[i]->hide();
 207
 208   horizontalSliders.push_back(NOHorizontalSlider);
 209   horizontalSliders.push_back(NEHorizontalSlider);
 210   horizontalSliders.push_back(SOHorizontalSlider);
 211   horizontalSliders.push_back(SEHorizontalSlider);
 212
 213   for (int i =0; i < 4; i++)
 214     horizontalSliders[i]->hide();
 215
 216
 217   connect(NOVerticalSlider,SIGNAL(valueChanged(int)),this,SLOT(NOVerticalSliderChanged()));
 218   connect(NEVerticalSlider,SIGNAL(valueChanged(int)),this,SLOT(NEVerticalSliderChanged()));
 219   connect(SOVerticalSlider,SIGNAL(valueChanged(int)),this,SLOT(SOVerticalSliderChanged()));
 220   connect(SEVerticalSlider,SIGNAL(valueChanged(int)),this,SLOT(SEVerticalSliderChanged()));
 221
 222   connect(NOHorizontalSlider,SIGNAL(valueChanged(int)),this,SLOT(NOHorizontalSliderMoved()));
 223   connect(NEHorizontalSlider,SIGNAL(valueChanged(int)),this,SLOT(NEHorizontalSliderMoved()));
 224   connect(SOHorizontalSlider,SIGNAL(valueChanged(int)),this,SLOT(SOHorizontalSliderMoved()));
 225   connect(SEHorizontalSlider,SIGNAL(valueChanged(int)),this,SLOT(SEHorizontalSliderMoved()));
 226
 227   //connect everything
 228   connect(actionMaximum_Intensity_Projection,SIGNAL(triggered()),this,SLOT(ComputeMIP()));
 229   connect(actionCompute_mid_position_image,SIGNAL(triggered()),this,SLOT(ComputeMidPosition()));
 230   connect(actionDeformable_Registration,SIGNAL(triggered()),this,SLOT(ComputeDeformableRegistration()));
 231   connect(actionWarp_image_with_vector_field,SIGNAL(triggered()),this,SLOT(WarpImage()));
 232   connect(actionLoad_images,SIGNAL(triggered()),this,SLOT(OpenImages()));
 233   connect(actionOpen_Dicom,SIGNAL(triggered()),this,SLOT(OpenDicom()));
 234   connect(actionOpen_Dicom_Struct,SIGNAL(triggered()),this,SLOT(OpenDCStructContour()));
 235   connect(actionOpen_VTK_contour,SIGNAL(triggered()),this,SLOT(OpenVTKContour()));
 236   connect(actionOpen_Multiple_Images_As_One,SIGNAL(triggered()),this,SLOT(MergeImages()));
 237   connect(actionSlice_Image_As_Multiple_Images,SIGNAL(triggered()),this,SLOT(SliceImages()));
 238   connect(actionOpen_Image_With_Time,SIGNAL(triggered()),this,SLOT(OpenImageWithTime()));
 239   connect(actionMerge_images_as_n_dim_t, SIGNAL(triggered()), this, SLOT(MergeImagesWithTime()));
 240   connect(actionSave_As,SIGNAL(triggered()),this,SLOT(SaveAs()));
 241   connect(actionExit,SIGNAL(triggered()),this,SLOT(close()));
 242   connect(actionAdd_VF_to_current_Image,SIGNAL(triggered()),this,SLOT(OpenField()));
 243   connect(actionNavigation_Help,SIGNAL(triggered()),this,SLOT(ShowHelpDialog()));
 244   connect(actionDocumentation,SIGNAL(triggered()),this,SLOT(ShowDocumentation()));
 245
 246   ///////////////////////////////////////////////
 247   connect(actionSegmentation,SIGNAL(triggered()),this,SLOT(SegmentationOnCurrentImage()));
 248   connect(actionSurface_Viewer,SIGNAL(triggered()),this,SLOT(SurfaceViewerLaunch()));
 249   ///////////////////////////////////////////////
 250
 251   actionNorth_East_Window->setEnabled(0);
 252   actionNorth_West_Window->setEnabled(0);
 253   actionSouth_East_Window->setEnabled(0);
 254   actionSouth_West_Window->setEnabled(0);
 255
 256   connect(actionNorth_East_Window,SIGNAL(triggered()),this,SLOT(SaveNEScreenshot()));
 257   connect(actionNorth_West_Window,SIGNAL(triggered()),this,SLOT(SaveNOScreenshot()));
 258   connect(actionSouth_East_Window,SIGNAL(triggered()),this,SLOT(SaveSEScreenshot()));
 259   connect(actionSouth_West_Window,SIGNAL(triggered()),this,SLOT(SaveSOScreenshot()));
 260
 261   connect(DataTree,SIGNAL(itemSelectionChanged()),this,SLOT(ImageInfoChanged()));
 262   connect(DataTree,SIGNAL(itemClicked(QTreeWidgetItem*, int)),this,
 263           SLOT(DisplayChanged(QTreeWidgetItem*, int)));
 264
 265   connect(viewButton,SIGNAL(clicked()),this, SLOT(ChangeViewMode()) );
 266   connect(windowSpinBox,SIGNAL(editingFinished()),this,SLOT(WindowLevelEdited()));
 267   connect(levelSpinBox,SIGNAL(editingFinished()),this,SLOT(WindowLevelEdited()));
 268   connect(colorMapComboBox,SIGNAL(currentIndexChanged(int)),this,SLOT(UpdateColorMap()));
 269   connect(presetComboBox,SIGNAL(currentIndexChanged(int)),this,SLOT(UpdateWindowLevel()));
 270   connect(inverseButton,SIGNAL(clicked()),this,SLOT(SwitchWindowLevel()));
 271
 272
 273   connect(this,SIGNAL(customContextMenuRequested(QPoint)),this,SLOT(ShowContextMenu(QPoint)));
 274
 275   connect(linkPanel,SIGNAL(addLink(QString,QString)),this,SLOT(AddLink(QString,QString)));
 276   connect(linkPanel,SIGNAL(removeLink(QString,QString)),this,SLOT(RemoveLink(QString,QString)));
 277   connect(overlayPanel,SIGNAL(VFPropertyUpdated(int,int,int,int)),this,SLOT(SetVFProperty(int,int,int,int)));
 278   connect(overlayPanel,SIGNAL(OverlayPropertyUpdated(int)),this,SLOT(SetOverlayProperty(int)));
 279   connect(overlayPanel,SIGNAL(FusionPropertyUpdated(int,int,double,double)),
 280           this,SLOT(SetFusionProperty(int,int,double,double)));
 281   connect(landmarksPanel,SIGNAL(UpdateRenderWindows()),this,SLOT(UpdateRenderWindows()));
 282
 283   playMode = 0;//pause
 284   mFrameRate = 10;
 285   playButton->setEnabled(0);
 286   frameRateLabel->setEnabled(0);
 287   frameRateSpinBox->setEnabled(0);
 288   connect(playButton, SIGNAL(clicked()),this,SLOT(PlayPause()));
 289   connect(frameRateSpinBox, SIGNAL(valueChanged(int)),this,SLOT(ChangeFrameRate(int)));
 290
 291   goToCursorPushButton->setEnabled(0);
 292   connect(goToCursorPushButton, SIGNAL(clicked()),this,SLOT(GoToCursor()));
 293
 294   NOViewWidget->hide();
 295   NEViewWidget->hide();
 296   SOViewWidget->hide();
 297   SEViewWidget->hide();
 298
 299   //Recently opened files
 300   std::list<std::string> recent_files = GetRecentlyOpenedImages();
 301   if ( !recent_files.empty() ) {
 302     QMenu * rmenu = new QMenu("Recently opened files...");
 303     rmenu->setIcon(QIcon(QString::fromUtf8(":/common/icons/open.png")));
 304     menuFile->insertMenu(actionOpen_Image_With_Time,rmenu);
 305     menuFile->insertSeparator(actionOpen_Image_With_Time);
 306     for (std::list<std::string>::iterator i = recent_files.begin(); i!=recent_files.end(); i++) {
 307       QAction* current=new QAction(QIcon(QString::fromUtf8(":/common/icons/open.png")),
 308                                    (*i).c_str(),this);
 309       rmenu->addAction(current);
 310       connect(current,SIGNAL(triggered()),this,SLOT(OpenRecentImage()));
 311     }
 312   }
 313
 314   // Adding all new tools (insertion in the menu)
 315   vvToolManager::GetInstance()->InsertToolsInMenu(this);
 316
 317   if (!CLITK_EXPERIMENTAL)
 318     menuExperimental->menuAction()->setVisible(false);
 319 }
 320 //------------------------------------------------------------------------------
 321
 322
 323 //------------------------------------------------------------------------------
 324 void vvMainWindow::ComputeMIP()
 325 {
 326   vvMaximumIntensityProjection mip;
 327   vvSlicerManager* selected_slicer = mSlicerManagers[GetSlicerIndexFromItem(DataTree->selectedItems()[0])];
 328   QFileInfo info(selected_slicer->GetFileName().c_str());
 329   mip.Compute(selected_slicer);
 330   if (!mip.error)
 331     AddImage(mip.GetOutput(),info.path().toStdString()+"/"+info.completeBaseName().toStdString()+"_mip.mhd");
 332 }
 333 //------------------------------------------------------------------------------
 334
 335
 336 //------------------------------------------------------------------------------
 337 void vvMainWindow::ComputeMidPosition()
 338 {
 339   bool ok;
 340   int index=GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
 341   int ref = QInputDialog::getInteger(this,"Chose reference phase","Reference phase",0,0,\
 342                                      mSlicerManagers[index]->GetImage()->GetVTKImages().size()-1,1,&ok);
 343   if (ok) {
 344     vvMidPosition midp;
 345     midp.slicer_manager = mSlicerManagers[index];
 346     midp.reference_image_index = ref;
 347     QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
 348     midp.Update();
 349     if (midp.error)
 350       QMessageBox::warning(this, "Error computing midposition image",midp.error_message.c_str());
 351     else {
 352       QFileInfo info(midp.slicer_manager->GetFileName().c_str());
 353       AddImage(midp.output,info.path().toStdString()+"/"+info.completeBaseName().toStdString()+"_midposition.mhd");
 354     }
 355     QApplication::restoreOverrideCursor();
 356   }
 357 }
 358 //------------------------------------------------------------------------------
 359
 360
 361 //------------------------------------------------------------------------------
 362 void vvMainWindow::AddContour(int image_index, vvMesh::Pointer contour, bool propagation)
 363 {
 364   QTreeWidgetItem *item = new QTreeWidgetItem();
 365   item->setData(0,Qt::UserRole,"filename.vtk");
 366   item->setData(1,Qt::UserRole,tr("contour"));
 367   QBrush brush;
 368   brush.setColor(QColor(contour->r*255,contour->g*255,contour->b*255));
 369   brush.setStyle(Qt::SolidPattern);
 370   item->setData(COLUMN_IMAGE_NAME,Qt::BackgroundRole,brush);
 371   item->setData(COLUMN_IMAGE_NAME,Qt::DisplayRole,contour->structure_name.c_str());
 372
 373   for (int j = 1; j <= 4; j++)
 374     item->setData(j,Qt::CheckStateRole,DataTree->topLevelItem(image_index)->data(j,Qt::CheckStateRole));
 375
 376   QTreePushButton* cButton = new QTreePushButton;
 377   cButton->setItem(item);
 378   cButton->setColumn(COLUMN_CLOSE_IMAGE);
 379   cButton->setToolTip(tr("close image"));
 380   cButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/exit.png")));
 381   connect(cButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
 382           this,SLOT(CloseImage(QTreeWidgetItem*, int)));
 383
 384   QTreePushButton* rButton = new QTreePushButton;
 385   rButton->setItem(item);
 386   rButton->setColumn(COLUMN_RELOAD_IMAGE);
 387   rButton->setToolTip(tr("reload image"));
 388   rButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/rotateright.png")));
 389   rButton->setEnabled(false);
 390   //Not implemented
 391   //connect(rButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
 392   //this,SLOT(ReloadImage(QTreeWidgetItem*, int)));
 393
 394   DataTree->topLevelItem(image_index)->setExpanded(1);
 395   DataTree->topLevelItem(image_index)->addChild(item);
 396   DataTree->setItemWidget(item, COLUMN_CLOSE_IMAGE, cButton);
 397   DataTree->setItemWidget(item, COLUMN_RELOAD_IMAGE, rButton);
 398   QString id = DataTree->topLevelItem(image_index)->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString();
 399   item->setData(COLUMN_IMAGE_NAME,Qt::UserRole,id.toStdString().c_str());
 400
 401   UpdateTree();
 402   mSlicerManagers[image_index]->AddContour(contour,propagation);
 403   mSlicerManagers[image_index]->Render();
 404 }
 405 //------------------------------------------------------------------------------
 406
 407
 408 //------------------------------------------------------------------------------
 409 void vvMainWindow::OpenVTKContour()
 410 {
 411   if (mSlicerManagers.size() > 0) {
 412     QString Extensions = "Images ( *.vtk *.obj)";
 413     Extensions += ";;All Files (*)";
 414     QString file = QFileDialog::getOpenFileName(this,tr("Open vtkPolyData"),mInputPathName,Extensions);
 415     if (file.isNull())
 416       return;
 417     QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
 418     int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
 419     vvMeshReader reader;
 420     reader.SetImage(mSlicerManagers[index]->GetImage());
 421     reader.SetModeToVTK();
 422     reader.SetFilename(file.toStdString());
 423     reader.Update();
 424     AddContour(index,reader.GetOutput()[0],false);
 425     QApplication::restoreOverrideCursor();
 426   }
 427 }
 428 //------------------------------------------------------------------------------
 429
 430
 431 //------------------------------------------------------------------------------
 432 void vvMainWindow::OpenDCStructContour()
 433 {
 434   if (mSlicerManagers.size() > 0) {
 435     QString Extensions = "Dicom Files ( *.dcm RS*)";
 436     Extensions += ";;All Files (*)";
 437     QString file = QFileDialog::getOpenFileName(this,tr("Merge Images"),mInputPathName,Extensions);
 438     if (file.isNull())
 439       return;
 440     int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
 441     vvMeshReader reader;
 442     reader.SetFilename(file.toStdString());
 443     vvStructSelector selector;
 444     selector.SetStructures(reader.GetROINames());
 445     if (!mSlicerManagers[index]->GetVF().IsNull())
 446       selector.EnablePropagationCheckBox();
 447     if (selector.exec()) {
 448       QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
 449       reader.SetSelectedItems(selector.getSelectedItems());
 450       reader.SetImage(mSlicerManagers[index]->GetImage());
 451       if (selector.PropagationEnabled())
 452         reader.SetPropagationVF(mSlicerManagers[index]->GetVF());
 453       reader.Update();
 454       std::vector<vvMesh::Pointer> contours=reader.GetOutput();
 455       for (std::vector<vvMesh::Pointer>::iterator i=contours.begin();
 456            i!=contours.end(); i++)
 457         AddContour(index,*i,selector.PropagationEnabled());
 458       QApplication::restoreOverrideCursor();
 459     }
 460   }
 461 }
 462 //------------------------------------------------------------------------------
 463
 464
 465 //------------------------------------------------------------------------------
 466 void vvMainWindow::ComputeDeformableRegistration()
 467 {
 468   if (mSlicerManagers.size() > 0) {
 469     int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
 470     vvDeformationDialog dialog(index,mSlicerManagers);
 471     if (dialog.exec()) {
 472       std::string base_name=itksys::SystemTools::GetFilenameWithoutExtension(mSlicerManagers[dialog.GetInputFileIndex()]->GetFileName());
 473       AddField(dialog.GetOutput(),dialog.getFieldFile(),dialog.GetInputFileIndex());
 474       WarpImage(dialog.GetSelectedSlicer(),dialog.GetReferenceFrameIndex());
 475     } else
 476       std::cout << "Error or user cancellation while computing deformation field..." << std::endl;
 477   } else QMessageBox::information(this, "Need to open image","You must open an image first.");
 478 }
 479 //------------------------------------------------------------------------------
 480
 481
 482 //------------------------------------------------------------------------------
 483 void vvMainWindow::WarpImage()
 484 {
 485   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
 486   if (!mSlicerManagers[index]->GetVF().IsNull()) {
 487     bool ok;
 488     int ref = QInputDialog::getInteger(this,"Chose reference phase","Reference phase",0,0,\
 489                                        mSlicerManagers[index]->GetImage()->GetVTKImages().size()-1,1,&ok);
 490     if (ok) {
 491       WarpImage(mSlicerManagers[index],ref);
 492     }
 493   } else
 494     QMessageBox::warning(this,tr("No vector field"),tr("Sorry, can't warp without a vector field"));
 495 }
 496 //------------------------------------------------------------------------------
 497
 498
 499 //------------------------------------------------------------------------------
 500 void vvMainWindow::WarpImage(vvSlicerManager* selected_slicer,int reference_phase)
 501 {
 502   if (!selected_slicer->GetVF().IsNull()) {
 503     QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
 504     QFileInfo info(selected_slicer->GetFileName().c_str());
 505     vvImageWarp warp(selected_slicer->GetImage(),selected_slicer->GetVF(),
 506                      reference_phase,this);
 507     if (warp.ComputeWarpedImage()) {
 508       AddImage(warp.GetWarpedImage(),info.path().toStdString()+"/"+info.completeBaseName().toStdString()+"_warped.mhd");
 509       AddImage(warp.GetDiffImage()  ,info.path().toStdString()+"/"+info.completeBaseName().toStdString()+"_diff.mhd");
 510       AddImage(warp.GetJacobianImage()  ,info.path().toStdString()+"/"+info.completeBaseName().toStdString()+"_jacobian.mhd");
 511       QApplication::restoreOverrideCursor();
 512     } else {
 513       QApplication::restoreOverrideCursor();
 514       QMessageBox::warning(this,tr("Different spacings"),tr("The vector field and image spacings must be the same in order to warp."));
 515     }
 516   } else
 517     QMessageBox::warning(this,tr("No vector field"),tr("Sorry, can't warp without a vector field."));
 518 }
 519 //------------------------------------------------------------------------------
 520
 521
 522 //------------------------------------------------------------------------------
 523 vvMainWindow::~vvMainWindow()
 524 {
 525   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
 526     if (mSlicerManagers[i] != NULL)
 527       delete mSlicerManagers[i];
 528   }
 529 }
 530 //------------------------------------------------------------------------------
 531
 532 //------------------------------------------------------------------------------
 533 QTabWidget * vvMainWindow::GetTab()
 534 {
 535   return tabWidget;
 536 }
 537 //------------------------------------------------------------------------------
 538
 539
 540 //------------------------------------------------------------------------------
 541 void vvMainWindow::MergeImages()
 542 {
 543   QString Extensions = EXTENSIONS;
 544   Extensions += ";;All Files (*)";
 545   QStringList files = QFileDialog::getOpenFileNames(this,tr("Merge Images"),mInputPathName,Extensions);
 546   if (files.isEmpty())
 547     return;
 548   mInputPathName = itksys::SystemTools::GetFilenamePath(files[0].toStdString()).c_str();
 549   std::vector<std::string> vector;
 550
 551   unsigned int currentDim = 0;
 552   std::vector<double> currentSpacing;
 553   std::vector<int> currentSize;
 554   std::vector<double> currentOrigin;
 555
 556   for (int i = 0; i < files.size(); i++) {
 557     itk::ImageIOBase::Pointer reader = itk::ImageIOFactory::CreateImageIO(
 558                                          files[i].toStdString().c_str(), itk::ImageIOFactory::ReadMode);
 559     reader->SetFileName(files[i].toStdString().c_str());
 560     reader->ReadImageInformation();
 561     if (reader)        {
 562       //NOViewWidget->hide();
 563       //NEViewWidget->hide();
 564       //SOViewWidget->hide();
 565       //SEViewWidget->hide();
 566       if (i == 0)
 567         currentDim = reader->GetNumberOfDimensions();
 568       bool IsOk = true;
 569       for (unsigned int j = 0; j < currentDim; j++) {
 570         if (i == 0) {
 571           if (j == 0) {
 572             currentSpacing.resize(currentDim);
 573             currentSize.resize(currentDim);
 574             currentOrigin.resize(currentDim);
 575           }
 576           currentOrigin[j] = reader->GetOrigin(j);
 577           currentSpacing[j] = reader->GetSpacing(j);
 578           currentSize[j] = reader->GetDimensions(j);
 579         } else if (currentDim != reader->GetNumberOfDimensions()
 580                    || currentSpacing[j] != reader->GetSpacing(j)
 581                    || currentSize[j] != (int)reader->GetDimensions(j)
 582                    || currentOrigin[j] != reader->GetOrigin(j)) {
 583           QString error = "Cannot read file (too different from others ";
 584           error += files[i].toStdString().c_str();
 585           QMessageBox::information(this,tr("Reading problem"),error);
 586           IsOk = false;
 587           break;
 588         }
 589       }
 590       if (IsOk)
 591         vector.push_back(files[i].toStdString());
 592     }
 593   }
 594   if (vector.size() > 0)
 595     LoadImages(vector, MERGED);
 596 }
 597 //------------------------------------------------------------------------------
 598
 599 //------------------------------------------------------------------------------
 600 void vvMainWindow::SliceImages()
 601 {
 602   QString Extensions = EXTENSIONS;
 603   Extensions += ";;All Files (*)";
 604
 605   QStringList files = QFileDialog::getOpenFileNames(this,tr("Slice Images"),mInputPathName,Extensions);
 606   if (files.isEmpty())
 607     return;
 608   mInputPathName = itksys::SystemTools::GetFilenamePath(files[0].toStdString()).c_str();
 609   std::vector<std::string> vector;
 610   for (int i = 0; i < files.size(); i++)
 611     vector.push_back(files[i].toStdString());
 612   LoadImages(vector, SLICED);
 613 }
 614 //------------------------------------------------------------------------------
 615
 616 //------------------------------------------------------------------------------
 617 void vvMainWindow::MergeImagesWithTime()
 618 {
 619   QString Extensions = EXTENSIONS;
 620   Extensions += ";;All Files (*)";
 621   QStringList files = QFileDialog::getOpenFileNames(this,tr("Merge Images With Time"),mInputPathName,Extensions);
 622   if (files.isEmpty())
 623     return;
 624   mInputPathName = itksys::SystemTools::GetFilenamePath(files[0].toStdString()).c_str();
 625   std::vector<std::string> vector;
 626
 627   unsigned int currentDim = 0;
 628   std::vector<double> currentSpacing;
 629   std::vector<int> currentSize;
 630   std::vector<double> currentOrigin;
 631
 632   for (int i = 0; i < files.size(); i++) {
 633     itk::ImageIOBase::Pointer reader = itk::ImageIOFactory::CreateImageIO(
 634                                          files[i].toStdString().c_str(), itk::ImageIOFactory::ReadMode);
 635     if (reader) {
 636       reader->SetFileName(files[i].toStdString().c_str());
 637       reader->ReadImageInformation();
 638       if (i == 0)
 639         currentDim = reader->GetNumberOfDimensions();
 640       bool IsOk = true;
 641       for (unsigned int j = 0; j < currentDim; j++) {
 642         if (i == 0) {
 643           if (j == 0) {
 644             currentSpacing.resize(currentDim);
 645             currentSize.resize(currentDim);
 646             currentOrigin.resize(currentDim);
 647           }
 648           currentOrigin[j] = reader->GetOrigin(j);
 649           currentSpacing[j] = reader->GetSpacing(j);
 650           currentSize[j] = reader->GetDimensions(j);
 651         } else if (currentDim != reader->GetNumberOfDimensions()
 652                    || currentSpacing[j] != reader->GetSpacing(j)
 653                    || currentSize[j] != (int)reader->GetDimensions(j)
 654                    || currentOrigin[j] != reader->GetOrigin(j)) {
 655           QString error = "Cannot read file (too different from others ";
 656           error += files[i].toStdString().c_str();
 657           QMessageBox::information(this,tr("Reading problem"),error);
 658           IsOk = false;
 659           break;
 660         }
 661       }
 662       if (IsOk)
 663         vector.push_back(files[i].toStdString());
 664     } else {
 665       QString error = "Cannot read file info for ";
 666       error += files[i].toStdString().c_str();
 667       error += "\n";
 668       error += "Maybe you're trying to open an image in an unsupported format?\n";
 669       QMessageBox::information(this,tr("Reading problem"),error);
 670     }
 671   }
 672   sort(vector.begin(),vector.end());
 673   if (vector.size() > 1)
 674     LoadImages(vector, MERGEDWITHTIME);
 675   else
 676     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.");
 677 }
 678 //------------------------------------------------------------------------------
 679
 680
 681 //------------------------------------------------------------------------------
 682 void vvMainWindow::OpenDicom()
 683 {
 684   std::vector<std::string> files;
 685
 686   std::cout << "dicomSeriesSelector " << std::endl;
 687   if (dicomSeriesSelector->exec() == QDialog::Accepted) {
 688     files = *(dicomSeriesSelector->GetFilenames());
 689     LoadImages(files,DICOM);
 690   }
 691 }
 692 //------------------------------------------------------------------------------
 693
 694 //------------------------------------------------------------------------------
 695 void vvMainWindow::OpenImages()
 696 {
 697   QString Extensions = EXTENSIONS;
 698   Extensions += ";;All Files (*)";
 699
 700   QStringList files = QFileDialog::getOpenFileNames(this,tr("Load Images"),mInputPathName,Extensions);
 701   if (files.isEmpty())
 702     return;
 703   mInputPathName = itksys::SystemTools::GetFilenamePath(files[0].toStdString()).c_str();
 704   std::vector<std::string> vector;
 705   for (int i = 0; i < files.size(); i++)
 706     vector.push_back(files[i].toStdString());
 707   LoadImages(vector, IMAGE);
 708 }
 709 //------------------------------------------------------------------------------
 710 void vvMainWindow::OpenRecentImage()
 711 {
 712   QAction * caller = qobject_cast<QAction*>(sender());
 713   std::vector<std::string> images;
 714   images.push_back(caller->text().toStdString());
 715   mInputPathName = itksys::SystemTools::GetFilenamePath(images[0]).c_str();
 716   LoadImages(images,IMAGE);
 717 }
 718 //------------------------------------------------------------------------------
 719
 720
 721 //------------------------------------------------------------------------------
 722 void vvMainWindow::OpenImageWithTime()
 723 {
 724   QString Extensions = EXTENSIONS;
 725   Extensions += ";;All Files (*)";
 726
 727   QStringList files = QFileDialog::getOpenFileNames(this,tr("Load Images With Time"),mInputPathName,Extensions);
 728   if (files.isEmpty())
 729     return;
 730   mInputPathName = itksys::SystemTools::GetFilenamePath(files[0].toStdString()).c_str();
 731   std::vector<std::string> vector;
 732   for (int i = 0; i < files.size(); i++) {
 733     vector.push_back(files[i].toStdString());
 734   }
 735   LoadImages(vector, IMAGEWITHTIME);
 736 }
 737 //------------------------------------------------------------------------------
 738
 739
 740 //------------------------------------------------------------------------------
 741 void vvMainWindow::LoadImages(std::vector<std::string> files, LoadedImageType filetype)
 742 {
 743   //Separate the way to open images and dicoms
 744   int fileSize;
 745   if (filetype == IMAGE || filetype == IMAGEWITHTIME)
 746     fileSize = files.size();
 747   else
 748     fileSize = 1;
 749
 750   // For SLICED, we need the number of slices (ndim and #slices)
 751   std::vector<unsigned int> nSlices;
 752   nSlices.resize(files.size());
 753   std::fill(nSlices.begin(), nSlices.end(), 1);
 754   if (filetype == SLICED) {
 755     for (int i = 0; i < fileSize; i++) {
 756       itk::ImageIOBase::Pointer header = clitk::readImageHeader(files[i]);
 757       QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
 758       if (!header) {
 759         nSlices[i] = 0;
 760         QString error = "Cannot open file \n";
 761         error += files[i].c_str();
 762         QMessageBox::information(this,tr("Reading problem"),error);
 763         return;
 764       }
 765       if (header->GetNumberOfDimensions() < 3) {
 766         nSlices[i] = 0;
 767         QString error = "Dimension problem. Cannot slice \n";
 768         error += files[i].c_str();
 769         QMessageBox::information(this,tr("Reading problem"),error);
 770         return;
 771       }
 772       nSlices[i] = header->GetDimensions( header->GetNumberOfDimensions()-1 );
 773     }
 774   }
 775
 776   //Only add to the list of recently opened files when a single file is opened,
 777   //to avoid polluting the list of recently opened files
 778   if (files.size() == 1) {
 779     QFileInfo finfo=tr(files[0].c_str());
 780     AddToRecentlyOpenedImages(finfo.absoluteFilePath().toStdString());
 781   }
 782   //init the progress events
 783   QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
 784   vvProgressDialog progress("Opening " + files[0],fileSize>1);
 785   qApp->processEvents();
 786
 787   int numberofsuccesulreads=0;
 788   //open images as 1 or multiples
 789   for (int i = 0; i < fileSize; i++) {
 790
 791     progress.SetText("Opening " + files[i]);
 792     progress.SetProgress(i,fileSize);
 793     qApp->processEvents();
 794
 795     for (unsigned int j = 0; j < nSlices[i]; j++) {
 796       //read the image and put it in mSlicerManagers
 797       vvSlicerManager* imageManager = new vvSlicerManager(4);
 798       qApp->processEvents();
 799
 800       bool SetImageSucceed=false;
 801
 802       // Change filename if an image with the same already exist
 803       int number = GetImageDuplicateFilenameNumber(files[i] + std::string("_slice"));
 804
 805       if (filetype == IMAGE || filetype == IMAGEWITHTIME || filetype == SLICED)
 806         SetImageSucceed = imageManager->SetImage(files[i],filetype, number, j);
 807       else {
 808         SetImageSucceed = imageManager->SetImages(files,filetype, number);
 809       }
 810       if (SetImageSucceed == false) {
 811         QApplication::restoreOverrideCursor();
 812         QString error = "Cannot open file \n";
 813         error += imageManager->GetLastError().c_str();
 814         QMessageBox::information(this,tr("Reading problem"),error);
 815         delete imageManager;
 816       } else {
 817         mSlicerManagers.push_back(imageManager);
 818
 819         //create an item in the tree with good settings
 820         QTreeWidgetItem *item = new QTreeWidgetItem();
 821         item->setData(0,Qt::UserRole,files[i].c_str());
 822         QFileInfo fileinfo(imageManager->GetFileName().c_str()); //Do not show the path
 823         item->setData(COLUMN_IMAGE_NAME,Qt::DisplayRole,fileinfo.fileName());
 824         qApp->processEvents();
 825
 826         //Create the buttons for reload and close
 827         qApp->processEvents();
 828         QTreePushButton* cButton = new QTreePushButton;
 829         cButton->setItem(item);
 830         cButton->setColumn(COLUMN_CLOSE_IMAGE);
 831         cButton->setToolTip(tr("close image"));
 832         cButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/exit.png")));
 833         connect(cButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
 834                 this,SLOT(CloseImage(QTreeWidgetItem*, int)));
 835
 836         QTreePushButton* rButton = new QTreePushButton;
 837         rButton->setItem(item);
 838         rButton->setColumn(COLUMN_RELOAD_IMAGE);
 839         rButton->setToolTip(tr("reload image"));
 840         rButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/rotateright.png")));
 841         connect(rButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
 842                 this,SLOT(ReloadImage(QTreeWidgetItem*, int)));
 843
 844         DataTree->addTopLevelItem(item);
 845         DataTree->setItemWidget(item, COLUMN_CLOSE_IMAGE, cButton);
 846         DataTree->setItemWidget(item, COLUMN_RELOAD_IMAGE, rButton);
 847
 848         //set the id of the image
 849         QString id = files[i].c_str() + QString::number(mSlicerManagers.size()-1);
 850         item->setData(COLUMN_IMAGE_NAME,Qt::UserRole,id.toStdString().c_str());
 851         mSlicerManagers.back()->SetId(id.toStdString());
 852
 853         linkPanel->addImage(imageManager->GetFileName(), id.toStdString());
 854
 855         connect(mSlicerManagers.back(), SIGNAL(currentImageChanged(std::string)),
 856                 this,SLOT(CurrentImageChanged(std::string)));
 857         connect(mSlicerManagers.back(), SIGNAL(UpdatePosition(int, double, double, double, double, double, double, double)),
 858                 this,SLOT(MousePositionChanged(int,double, double, double, double, double, double, double)));
 859         connect(mSlicerManagers.back(), SIGNAL(UpdateVector(int, double, double, double, double)),
 860                 this, SLOT(VectorChanged(int,double,double,double, double)));
 861         connect(mSlicerManagers.back(), SIGNAL(UpdateOverlay(int, double, double)),
 862                 this, SLOT(OverlayChanged(int,double,double)));
 863         connect(mSlicerManagers.back(), SIGNAL(UpdateFusion(int, double)),
 864                 this, SLOT(FusionChanged(int,double)));
 865         connect(mSlicerManagers.back(), SIGNAL(UpdateWindows(int, int, int)),
 866                 this,SLOT(WindowsChanged(int, int, int)));
 867         connect(mSlicerManagers.back(), SIGNAL(WindowLevelChanged(double, double,int, int)),
 868                 this,SLOT(WindowLevelChanged(double, double, int, int)));
 869         connect(mSlicerManagers.back(), SIGNAL(UpdateSlice(int,int)),
 870                 this,SLOT(UpdateSlice(int,int)));
 871         connect(mSlicerManagers.back(), SIGNAL(UpdateTSlice(int, int)),
 872                 this,SLOT(UpdateTSlice(int, int)));
 873         connect(mSlicerManagers.back(), SIGNAL(UpdateSliceRange(int,int,int,int,int)),
 874                 this,SLOT(UpdateSliceRange(int,int,int,int,int)));
 875         connect(mSlicerManagers.back(), SIGNAL(UpdateLinkManager(std::string,int,double,double,double,int)),
 876                 this,SLOT(UpdateLinkManager(std::string,int,double,double,double,int)));
 877         connect(mSlicerManagers.back(), SIGNAL(UpdateLinkedNavigation(std::string,vvSlicerManager*)),
 878                 this,SLOT(UpdateLinkedNavigation(std::string,vvSlicerManager*)));
 879         connect(mSlicerManagers.back(), SIGNAL(ChangeImageWithIndexOffset(vvSlicerManager*,int,int)),
 880                 this,SLOT(ChangeImageWithIndexOffset(vvSlicerManager*,int,int)));
 881         connect(mSlicerManagers.back(),SIGNAL(LandmarkAdded()),landmarksPanel,SLOT(AddPoint()));
 882         InitSlicers();
 883       }
 884       numberofsuccesulreads++;
 885     }
 886   }
 887   if (numberofsuccesulreads) {
 888     NOViewWidget->show();
 889     NEViewWidget->show();
 890     SOViewWidget->show();
 891     SEViewWidget->show();
 892     UpdateTree();
 893     InitDisplay();
 894     ShowLastImage();
 895
 896     // Try to guess default WindowLevel
 897     double range[2];
 898     mSlicerManagers.back()->GetImage()->GetFirstVTKImageData()->GetScalarRange(range);
 899     // DD(range[0]);
 900     //   DD(range[1]);
 901     if ((range[0] == 0) && (range[1] == 1)) {
 902       presetComboBox->setCurrentIndex(5);// binary
 903     } else {
 904       // TODO
 905     }
 906   }
 907   QApplication::restoreOverrideCursor();
 908 }
 909 //------------------------------------------------------------------------------
 910
 911 //------------------------------------------------------------------------------
 912 void vvMainWindow::UpdateTree()
 913 {
 914   DataTree->resizeColumnToContents(COLUMN_TREE);
 915   DataTree->resizeColumnToContents(COLUMN_UL_VIEW);
 916   DataTree->resizeColumnToContents(COLUMN_UR_VIEW);
 917   DataTree->resizeColumnToContents(COLUMN_DL_VIEW);
 918   DataTree->resizeColumnToContents(COLUMN_DR_VIEW);
 919   DataTree->resizeColumnToContents(COLUMN_IMAGE_NAME);
 920   DataTree->resizeColumnToContents(COLUMN_CLOSE_IMAGE);
 921   DataTree->resizeColumnToContents(COLUMN_RELOAD_IMAGE);
 922 }
 923 //------------------------------------------------------------------------------
 924
 925 //------------------------------------------------------------------------------
 926 void vvMainWindow::CurrentImageChanged(std::string id)
 927 {
 928   // DD("CurrentImageChanged");
 929 //   DD(id);
 930 //   DD(mCurrentSelectedImageId);
 931   if (id == mCurrentSelectedImageId) return; // Do nothing
 932   int selected = 0;
 933   for (int i = 0; i < DataTree->topLevelItemCount(); i++) {
 934     if (DataTree->topLevelItem(i)->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString().toStdString() == id) {
 935       selected = i;
 936     } else {
 937       DataTree->topLevelItem(i)->setSelected(0);
 938     }
 939     for (int child = 0; child < DataTree->topLevelItem(i)->childCount(); child++)
 940       DataTree->topLevelItem(i)->child(child)->setSelected(0);
 941
 942   }
 943   DataTree->topLevelItem(selected)->setSelected(1);
 944   // DD(mSlicerManagers[selected]->GetFileName());
 945   mCurrentSelectedImageId = id;
 946   emit SelectedImageHasChanged(mSlicerManagers[selected]);
 947 }
 948 //------------------------------------------------------------------------------
 949
 950 //------------------------------------------------------------------------------
 951 void vvMainWindow::ImageInfoChanged()
 952 {
 953   contextActions[6]->setEnabled(1);
 954   contextActions[5]->setEnabled(1);
 955   actionSave_As->setEnabled(1);
 956   actionAdd_VF_to_current_Image->setEnabled(1);
 957   actionAdd_fusion_image->setEnabled(1);
 958   actionNorth_East_Window->setEnabled(1);
 959   actionNorth_West_Window->setEnabled(1);
 960   actionSouth_East_Window->setEnabled(1);
 961   actionSouth_West_Window->setEnabled(1);
 962   inverseButton->setEnabled(1);
 963
 964   goToCursorPushButton->setEnabled(1);
 965
 966   if (DataTree->selectedItems().size()) {
 967     int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
 968
 969     colorMapComboBox->setEnabled(1);
 970     for (int i = 0; i < DataTree->topLevelItem(index)->childCount(); i++) {
 971       if (DataTree->topLevelItem(index)->child(i)->data(1,Qt::UserRole).toString() == "overlay" ||
 972           DataTree->topLevelItem(index)->child(i)->data(1,Qt::UserRole).toString() == "fusion") {
 973         colorMapComboBox->setEnabled(0);
 974         break;
 975       }
 976     }
 977
 978     std::vector<double> origin;
 979     std::vector<double> inputSpacing;
 980     std::vector<int> inputSize;
 981     std::vector<double> sizeMM;
 982     int dimension=0;
 983     QString pixelType;
 984     QString inputSizeInBytes;
 985     QString image = DataTree->selectedItems()[0]->data(COLUMN_IMAGE_NAME,Qt::DisplayRole).toString();
 986
 987     if (mSlicerManagers[index]->GetSlicer(0)->GetImage()->GetVTKImages().size() > 1 || playMode == 1) {
 988       playButton->setEnabled(1);
 989       frameRateLabel->setEnabled(1);
 990       frameRateSpinBox->setEnabled(1);
 991     } else {
 992       playButton->setEnabled(0);
 993       frameRateLabel->setEnabled(0);
 994       frameRateSpinBox->setEnabled(0);
 995     }
 996
 997     //read image header
 998     int NPixel = 1;
 999
1000     if (DataTree->topLevelItem(index) == DataTree->selectedItems()[0]) {
1001       vvImage::Pointer imageSelected = mSlicerManagers[index]->GetSlicer(0)->GetImage();
1002       dimension = imageSelected->GetNumberOfDimensions();
1003       origin.resize(dimension);
1004       inputSpacing.resize(dimension);
1005       inputSize.resize(dimension);
1006       sizeMM.resize(dimension);
1007       pixelType = mSlicerManagers[index]->GetImage()->GetScalarTypeAsITKString().c_str();
1008       for (int i = 0; i < dimension; i++) {
1009         origin[i] = imageSelected->GetOrigin()[i];
1010         inputSpacing[i] = imageSelected->GetSpacing()[i];
1011         inputSize[i] = imageSelected->GetSize()[i];
1012         sizeMM[i] = inputSize[i]*inputSpacing[i];
1013         NPixel *= inputSize[i];
1014       }
1015       inputSizeInBytes = GetSizeInBytes(imageSelected->GetActualMemorySize()*1000);
1016     } else if (DataTree->selectedItems()[0]->data(1,Qt::UserRole).toString() == "vector") {
1017       vvImage::Pointer imageSelected = mSlicerManagers[index]->GetSlicer(0)->GetVF();
1018       dimension = imageSelected->GetNumberOfDimensions();
1019       origin.resize(dimension);
1020       inputSpacing.resize(dimension);
1021       inputSize.resize(dimension);
1022       sizeMM.resize(dimension);
1023       pixelType = mSlicerManagers[index]->GetVF()->GetScalarTypeAsITKString().c_str();
1024       for (int i = 0; i < dimension; i++) {
1025         origin[i] = imageSelected->GetOrigin()[i];
1026         inputSpacing[i] = imageSelected->GetSpacing()[i];
1027         inputSize[i] = imageSelected->GetSize()[i];
1028         sizeMM[i] = inputSize[i]*inputSpacing[i];
1029         NPixel *= inputSize[i];
1030       }
1031       inputSizeInBytes = GetSizeInBytes(imageSelected->GetActualMemorySize()*1000);
1032     } else if (DataTree->selectedItems()[0]->data(1,Qt::UserRole).toString() == "overlay") {
1033       vvImage::Pointer imageSelected = mSlicerManagers[index]->GetSlicer(0)->GetOverlay();
1034       dimension = imageSelected->GetNumberOfDimensions();
1035       origin.resize(dimension);
1036       inputSpacing.resize(dimension);
1037       inputSize.resize(dimension);
1038       sizeMM.resize(dimension);
1039       pixelType = mSlicerManagers[index]->GetImage()->GetScalarTypeAsITKString().c_str();
1040       for (int i = 0; i < dimension; i++) {
1041         origin[i] = imageSelected->GetOrigin()[i];
1042         inputSpacing[i] = imageSelected->GetSpacing()[i];
1043         inputSize[i] = imageSelected->GetSize()[i];
1044         sizeMM[i] = inputSize[i]*inputSpacing[i];
1045         NPixel *= inputSize[i];
1046       }
1047       inputSizeInBytes = GetSizeInBytes(imageSelected->GetActualMemorySize()*1000);
1048     } else if (DataTree->selectedItems()[0]->data(1,Qt::UserRole).toString() == "fusion") {
1049       vvImage::Pointer imageSelected = mSlicerManagers[index]->GetSlicer(0)->GetFusion();
1050       dimension = imageSelected->GetNumberOfDimensions();
1051       origin.resize(dimension);
1052       inputSpacing.resize(dimension);
1053       inputSize.resize(dimension);
1054       sizeMM.resize(dimension);
1055       pixelType = mSlicerManagers[index]->GetImage()->GetScalarTypeAsITKString().c_str();
1056       for (int i = 0; i < dimension; i++) {
1057         origin[i] = imageSelected->GetOrigin()[i];
1058         inputSpacing[i] = imageSelected->GetSpacing()[i];
1059         inputSize[i] = imageSelected->GetSize()[i];
1060         sizeMM[i] = inputSize[i]*inputSpacing[i];
1061         NPixel *= inputSize[i];
1062       }
1063       inputSizeInBytes = GetSizeInBytes(imageSelected->GetActualMemorySize()*1000);
1064     }
1065
1066     QString dim = QString::number(dimension) + " (";
1067     dim += pixelType + ")";
1068
1069     infoPanel->setFileName(image);
1070     infoPanel->setDimension(dim);
1071     infoPanel->setSizePixel(GetVectorIntAsString(inputSize));
1072     infoPanel->setSizeMM(GetVectorDoubleAsString(sizeMM));
1073     infoPanel->setOrigin(GetVectorDoubleAsString(origin));
1074     infoPanel->setSpacing(GetVectorDoubleAsString(inputSpacing));
1075     infoPanel->setNPixel(QString::number(NPixel)+" ("+inputSizeInBytes+")");
1076
1077     landmarksPanel->SetCurrentLandmarks(mSlicerManagers[index]->GetLandmarks(),
1078                                         mSlicerManagers[index]->GetSlicer(0)->GetImage()->GetVTKImages().size());
1079     landmarksPanel->SetCurrentPath(mInputPathName.toStdString());
1080     landmarksPanel->SetCurrentImage(mSlicerManagers[index]->GetFileName().c_str());
1081
1082     overlayPanel->getCurrentImageName(mSlicerManagers[index]->GetFileName().c_str());
1083     for (int i = 0; i < 4; i++) {
1084       if (DataTree->selectedItems()[0]->data(i+1,Qt::CheckStateRole).toInt() > 0 || i == 3) {
1085         mSlicerManagers[index]->UpdateInfoOnCursorPosition(i);
1086         break;
1087       }
1088     }
1089     windowSpinBox->setValue(mSlicerManagers[index]->GetColorWindow());
1090     levelSpinBox->setValue(mSlicerManagers[index]->GetColorLevel());
1091     // DD(mSlicerManagers[index]->GetColorMap());
1092     // DD(mSlicerManagers[index]->GetPreset());
1093     presetComboBox->setCurrentIndex(mSlicerManagers[index]->GetPreset());
1094     colorMapComboBox->setCurrentIndex(mSlicerManagers[index]->GetColorMap());
1095
1096     infoPanel->setFileName(image);
1097     infoPanel->setDimension(dim);
1098     infoPanel->setSizePixel(GetVectorIntAsString(inputSize));
1099     infoPanel->setSizeMM(GetVectorDoubleAsString(sizeMM));
1100     infoPanel->setOrigin(GetVectorDoubleAsString(origin));
1101     infoPanel->setSpacing(GetVectorDoubleAsString(inputSpacing));
1102     infoPanel->setNPixel(QString::number(NPixel)+" ("+inputSizeInBytes+")");
1103
1104     landmarksPanel->SetCurrentLandmarks(mSlicerManagers[index]->GetLandmarks(),
1105                                         mSlicerManagers[index]->GetSlicer(0)->GetImage()->GetVTKImages().size());
1106     landmarksPanel->SetCurrentPath(mInputPathName.toStdString());
1107     landmarksPanel->SetCurrentImage(mSlicerManagers[index]->GetFileName().c_str());
1108
1109     overlayPanel->getCurrentImageName(mSlicerManagers[index]->GetFileName().c_str());
1110     for (int i = 0; i < 4; i++) {
1111       if (DataTree->selectedItems()[0]->data(i+1,Qt::CheckStateRole).toInt() > 0 || i == 3) {
1112         mSlicerManagers[index]->UpdateInfoOnCursorPosition(i);
1113         break;
1114       }
1115     }
1116     windowSpinBox->setValue(mSlicerManagers[index]->GetColorWindow());
1117     levelSpinBox->setValue(mSlicerManagers[index]->GetColorLevel());
1118     presetComboBox->setCurrentIndex(mSlicerManagers[index]->GetPreset());
1119     colorMapComboBox->setCurrentIndex(mSlicerManagers[index]->GetColorMap());
1120
1121     if (mSlicerManagers[index]->GetSlicer(0)->GetVF()) {
1122       overlayPanel->getVFName(mSlicerManagers[index]->GetVFName().c_str());
1123       overlayPanel->getVFProperty(mSlicerManagers[index]->GetSlicer(0)->GetVFSubSampling(),
1124                                   mSlicerManagers[index]->GetSlicer(0)->GetVFScale(),
1125                                   mSlicerManagers[index]->GetSlicer(0)->GetVFLog());
1126     } else {
1127       overlayPanel->getVFName(mSlicerManagers[index]->GetVFName().c_str());
1128       overlayPanel->getVFProperty(-1,-1,-1);
1129     }
1130     if (mSlicerManagers[index]->GetSlicer(0)->GetOverlay()) {
1131       overlayPanel->getOverlayName(mSlicerManagers[index]->GetOverlayName().c_str());
1132       overlayPanel->getOverlayProperty(mSlicerManagers[index]->GetOverlayColor());
1133     } else {
1134       overlayPanel->getOverlayName(mSlicerManagers[index]->GetOverlayName().c_str());
1135       overlayPanel->getOverlayProperty(-1);
1136     }
1137     if (mSlicerManagers[index]->GetSlicer(0)->GetFusion()) {
1138       overlayPanel->getFusionName(mSlicerManagers[index]->GetFusionName().c_str());
1139       overlayPanel->getFusionProperty(mSlicerManagers[index]->GetFusionOpacity(),
1140                                       mSlicerManagers[index]->GetFusionColorMap(),
1141                                       mSlicerManagers[index]->GetFusionWindow(),
1142                                       mSlicerManagers[index]->GetFusionLevel());
1143     } else {
1144       overlayPanel->getFusionName(mSlicerManagers[index]->GetFusionName().c_str());
1145       overlayPanel->getFusionProperty(-1, -1,-1,-1);
1146     }
1147   }
1148 }
1149 //------------------------------------------------------------------------------
1150
1151 //------------------------------------------------------------------------------
1152 void vvMainWindow::ShowDocumentation()
1153 {
1154   documentation->show();
1155 }
1156 //------------------------------------------------------------------------------
1157 void vvMainWindow::ShowHelpDialog()
1158 {
1159   help_dialog->show();
1160 }
1161 //------------------------------------------------------------------------------
1162
1163 //------------------------------------------------------------------------------
1164 void vvMainWindow::ChangeViewMode()
1165 {
1166   QListIterator<int> it0(splitter_3->sizes());
1167   QListIterator<int> it1(splitter_3->sizes());
1168   int max0 = 0;
1169   int max1 = 1;
1170   while (it0.hasNext()) {
1171     max0 += it0.next();
1172   }
1173   while (it1.hasNext()) {
1174     max1 += it1.next();
1175   }
1176   QList<int> size0;
1177   QList<int> size1;
1178   if (viewMode == 1) {
1179     viewMode = 0;
1180     size0.push_back(max0);
1181     size0.push_back(0);
1182     size1.push_back(max1);
1183     size1.push_back(0);
1184     splitter_3->setSizes(size0);
1185     OSplitter->setSizes(size1);
1186     DataTree->setColumnHidden(2,1);
1187     DataTree->setColumnHidden(3,1);
1188     DataTree->setColumnHidden(4,1);
1189   } else {
1190     viewMode = 1;
1191     size0.push_back(int(max0/2));
1192     size0.push_back(int(max0/2));
1193     size1.push_back(int(max1/2));
1194     size1.push_back(int(max1/2));
1195     splitter_3->setSizes(size0);
1196     OSplitter->setSizes(size1);
1197     DataTree->setColumnHidden(2,0);
1198     DataTree->setColumnHidden(3,0);
1199     DataTree->setColumnHidden(4,0);
1200   }
1201 }
1202 //------------------------------------------------------------------------------
1203
1204 //------------------------------------------------------------------------------
1205 QString vvMainWindow::GetSizeInBytes(unsigned long size)
1206 {
1207   QString result = "";// QString::number(size);
1208   //result += " bytes (";
1209   if (size > 1000000000) {
1210     size /= 1000000000;
1211     result += QString::number(size);
1212     result += "Gb";//)";
1213   } else if (size > 1000000) {
1214     size /= 1000000;
1215     result += QString::number(size);
1216     result += "Mb";//)";
1217   } else if (size > 1000) {
1218     size /= 1000;
1219     result += QString::number(size);
1220     result += "kb";//)";
1221   }
1222   return result;
1223 }
1224 //------------------------------------------------------------------------------
1225
1226 //------------------------------------------------------------------------------
1227 QString vvMainWindow::GetVectorDoubleAsString(std::vector<double> vectorDouble)
1228 {
1229   QString result;
1230   for (unsigned int i= 0; i < vectorDouble.size(); i++) {
1231     if (i != 0)
1232       result += " ";
1233     result += QString::number(vectorDouble[i]);
1234   }
1235   return result;
1236 }
1237 //------------------------------------------------------------------------------
1238
1239 //------------------------------------------------------------------------------
1240 QString vvMainWindow::GetVectorIntAsString(std::vector<int> vectorInt)
1241 {
1242   QString result;
1243   for (unsigned int i= 0; i < vectorInt.size(); i++) {
1244     if (i != 0)
1245       result += " ";
1246     result += QString::number(vectorInt[i]);
1247   }
1248   return result;
1249 }
1250 //------------------------------------------------------------------------------
1251
1252 //------------------------------------------------------------------------------
1253 int vvMainWindow::GetSlicerIndexFromItem(QTreeWidgetItem* item)
1254 {
1255   QString id = item->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString();
1256   for (int i = 0; i < DataTree->topLevelItemCount(); i++) {
1257     if (DataTree->topLevelItem(i)->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString() == id)
1258       return i;
1259   }
1260   return -1;
1261 }
1262 //------------------------------------------------------------------------------
1263
1264 //------------------------------------------------------------------------------
1265 QTreeWidgetItem* vvMainWindow::GetItemFromSlicerManager(vvSlicerManager* sm)
1266 {
1267   QString id = sm->GetId().c_str();
1268   for (int i = 0; i < DataTree->topLevelItemCount(); i++) {
1269     if (DataTree->topLevelItem(i)->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString() == id)
1270       return DataTree->topLevelItem(i);
1271   }
1272   return NULL;
1273 }
1274 //------------------------------------------------------------------------------
1275
1276 //------------------------------------------------------------------------------
1277 void vvMainWindow::DisplayChanged(QTreeWidgetItem *clicked_item, int column)
1278 {
1279   int index = GetSlicerIndexFromItem(clicked_item);
1280   if ( column >= COLUMN_CLOSE_IMAGE || column <= 0)
1281     return;
1282   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
1283     //Trick to avoid redoing twice the job for a key (sr)
1284     mSlicerManagers[i]->GetSlicer(column-1)->GetRenderWindow()-> GetInteractor()->SetKeySym("Crap");
1285
1286     QTreeWidgetItem* current_row=DataTree->topLevelItem(i);
1287     if (DataTree->topLevelItem(index) == current_row) {
1288       vvSlicer* clicked_slicer=mSlicerManagers[i]->GetSlicer(column-1);
1289       if (current_row == clicked_item) {
1290         //If we just activated a slicer
1291         if (current_row->data(column,Qt::CheckStateRole).toInt() > 0) {
1292           mSlicerManagers[i]->UpdateSlicer(column-1,clicked_item->data(column,Qt::CheckStateRole).toInt());
1293           mSlicerManagers[i]->UpdateInfoOnCursorPosition(column-1);
1294           DisplaySliders(i,column-1);
1295           std::map<std::string,int> overlay_counts;
1296           for (int child = 0; child < current_row->childCount(); child++) {
1297             std::string overlay_type =
1298               current_row->child(child)->data(1,Qt::UserRole).toString().toStdString();
1299             overlay_counts[overlay_type]++;
1300             current_row->child(child)->setData(column,Qt::CheckStateRole,
1301                                                current_row->data(column,Qt::CheckStateRole));
1302             clicked_slicer->SetActorVisibility(overlay_type,overlay_counts[overlay_type]-1,true);
1303           }
1304         } else { //We don't allow simply desactivating a slicer
1305           clicked_item->setData(column,Qt::CheckStateRole,2);
1306           return;
1307         }
1308       }
1309       //if we clicked on the vector(or overlay) and not the image
1310       else {
1311         if (clicked_item->data(column,Qt::CheckStateRole).toInt()) {
1312           current_row->setData(column,Qt::CheckStateRole,2);
1313           mSlicerManagers[i]->UpdateSlicer(column-1,2);
1314           mSlicerManagers[i]->UpdateInfoOnCursorPosition(column-1);
1315           DisplaySliders(i,column-1);
1316         }
1317         int vis = clicked_item->data(column,Qt::CheckStateRole).toInt();
1318         std::string overlay_type = clicked_item->data(1,Qt::UserRole).toString().toStdString();
1319         int overlay_index=0;
1320         for (int child = 0; child < current_row->childCount(); child++) {
1321           if (current_row->child(child)->data(1,Qt::UserRole).toString().toStdString() == overlay_type)
1322             overlay_index++;
1323           if (current_row->child(child) == clicked_item) break;
1324         }
1325         clicked_slicer->SetActorVisibility(
1326           clicked_item->data(1,Qt::UserRole).toString().toStdString(), overlay_index-1,vis);
1327       }
1328     } else if (current_row->data(column,Qt::CheckStateRole).toInt() > 0) {
1329       current_row->setData(column,Qt::CheckStateRole,0);
1330       mSlicerManagers[i]->UpdateSlicer(column-1,0);
1331       std::map<std::string,int> overlay_counts;
1332       for (int child = 0; child < current_row->childCount(); child++) {
1333         std::string overlay_type =
1334           current_row->child(child)->data(1,Qt::UserRole).toString().toStdString();
1335         overlay_counts[overlay_type]++;
1336         current_row->child(child)->setData(column,Qt::CheckStateRole,0);
1337         vvSlicer * current_slicer=mSlicerManagers[i]->GetSlicer(column-1);
1338         current_slicer->SetActorVisibility(overlay_type,overlay_counts[overlay_type]-1,false);
1339       }
1340     }
1341     //mSlicerManagers[i]->SetColorMap(-1);
1342     mSlicerManagers[i]->SetColorMap();
1343   }
1344   mSlicerManagers[index]->GetSlicer(column-1)->Render();
1345 }
1346 //------------------------------------------------------------------------------
1347
1348 void vvMainWindow::InitSlicers()
1349 {
1350   if (mSlicerManagers.size()) {
1351     mSlicerManagers.back()->GenerateDefaultLookupTable();
1352
1353     mSlicerManagers.back()->SetSlicerWindow(0,NOViewWidget->GetRenderWindow());
1354     mSlicerManagers.back()->SetSlicerWindow(1,NEViewWidget->GetRenderWindow());
1355     mSlicerManagers.back()->SetSlicerWindow(2,SOViewWidget->GetRenderWindow());
1356     mSlicerManagers.back()->SetSlicerWindow(3,SEViewWidget->GetRenderWindow());
1357   }
1358 }
1359
1360 //------------------------------------------------------------------------------
1361 void vvMainWindow::InitDisplay()
1362 {
1363   if (mSlicerManagers.size()) {
1364     //BE CAREFUL : this is absolutely necessary to set the interactor style
1365     //in order to have the same style instanciation for all SlicerManagers in
1366     // a same window
1367     for (int j = 0; j < 4; j++) {
1368       vvInteractorStyleNavigator* style = vvInteractorStyleNavigator::New();
1369       style->SetAutoAdjustCameraClippingRange(1);
1370       bool AlreadySelected = false;
1371       for (int i = 0; i < DataTree->topLevelItemCount(); i++) {
1372         mSlicerManagers[i]->SetInteractorStyleNavigator(j,style);
1373
1374         //select the image only if previous are not selected
1375         if (DataTree->topLevelItem(i)->data(j+1,Qt::CheckStateRole).toInt() > 1) {
1376           mSlicerManagers[i]->UpdateSlicer(j,1);
1377           AlreadySelected = true;
1378         } else if (i == DataTree->topLevelItemCount()-1 && !AlreadySelected) {
1379           if (DataTree->selectedItems().size() == 0)
1380             DataTree->topLevelItem(i)->setSelected(1);
1381           DataTree->topLevelItem(i)->setData(j+1,Qt::CheckStateRole,2);
1382           mSlicerManagers[i]->UpdateSlicer(j,1);
1383           DisplaySliders(i,j);
1384         } else {
1385           DataTree->topLevelItem(i)->setData(j+1,Qt::CheckStateRole,0);
1386           mSlicerManagers[i]->UpdateSlicer(j,0);
1387         }
1388       }
1389       style->Delete();
1390     }
1391   }
1392 }
1393 //------------------------------------------------------------------------------
1394
1395 //------------------------------------------------------------------------------
1396 void vvMainWindow::DisplaySliders(int slicer, int window)
1397 {
1398   int range[2];
1399   mSlicerManagers[slicer]->GetSlicer(window)->GetSliceRange(range);
1400   int position = mSlicerManagers[slicer]->GetSlicer(window)->GetSlice();
1401
1402   int tRange[2];
1403   tRange[0] = 0;
1404   tRange[1] = mSlicerManagers[slicer]->GetSlicer(window)->GetTMax();
1405   int tPosition = mSlicerManagers[slicer]->GetSlicer(window)->GetTSlice();
1406   bool showHorizontal = false;
1407   bool showVertical = false;
1408   if (mSlicerManagers[slicer]->GetSlicer(window)->GetImage()->GetNumberOfDimensions() > 3
1409       || (mSlicerManagers[slicer]->GetSlicer(window)->GetImage()->GetNumberOfDimensions() > 2
1410           && mSlicerManagers[slicer]->GetType() != IMAGEWITHTIME
1411           && mSlicerManagers[slicer]->GetType() != MERGEDWITHTIME))
1412     showVertical = true;
1413   if (mSlicerManagers[slicer]->GetSlicer(window)->GetImage()->GetNumberOfDimensions() > 3
1414       || mSlicerManagers[slicer]->GetType() == IMAGEWITHTIME
1415       || mSlicerManagers[slicer]->GetType() == MERGEDWITHTIME)
1416     showHorizontal = true;
1417
1418   if (showVertical)
1419     verticalSliders[window]->show();
1420   else
1421     verticalSliders[window]->hide();
1422   verticalSliders[window]->setRange(range[0],range[1]);
1423   verticalSliders[window]->setValue(position);
1424
1425   if (showHorizontal)
1426     horizontalSliders[window]->show();
1427   else
1428     horizontalSliders[window]->hide();
1429   horizontalSliders[window]->setRange(tRange[0],tRange[1]);
1430   horizontalSliders[window]->setValue(tPosition);
1431 }
1432 //------------------------------------------------------------------------------
1433
1434 //------------------------------------------------------------------------------
1435 void vvMainWindow::CloseImage(QTreeWidgetItem* item, int column)
1436 {
1437   int index = GetSlicerIndexFromItem(item);
1438
1439   if (DataTree->topLevelItem(index) != item) {
1440     QString warning = "Do you really want to close the overlay : ";
1441     warning += item->data(COLUMN_IMAGE_NAME,Qt::DisplayRole).toString();
1442     QMessageBox msgBox(QMessageBox::Warning, tr("Close Overlay"),
1443                        warning, 0, this);
1444     msgBox.addButton(tr("Close"), QMessageBox::AcceptRole);
1445     msgBox.addButton(tr("Cancel"), QMessageBox::RejectRole);
1446     if (msgBox.exec() == QMessageBox::AcceptRole) {
1447       std::string overlay_type=item->data(1,Qt::UserRole).toString().toStdString();
1448       int overlay_index=0;
1449       for (int child = 0; child < DataTree->topLevelItem(index)->childCount(); child++) {
1450         if (DataTree->topLevelItem(index)->\
1451             child(child)->data(1,Qt::UserRole).toString().toStdString() == overlay_type)
1452           overlay_index++;
1453         if (DataTree->topLevelItem(index)->child(child) == item) break;
1454       }
1455       mSlicerManagers[index]->RemoveActor(overlay_type, overlay_index-1);
1456       mSlicerManagers[index]->SetColorMap(0);
1457       DataTree->topLevelItem(index)->takeChild(DataTree->topLevelItem(index)->indexOfChild(item));
1458       mSlicerManagers[index]->Render();
1459     }
1460   } else if (DataTree->topLevelItemCount() <= 1) {
1461     QString warning = "Do you really want to close the image : ";
1462     warning += item->data(COLUMN_IMAGE_NAME,Qt::DisplayRole).toString();
1463     warning += "\nThis is the last image, you're about to close vv !!!";
1464     QMessageBox msgBox(QMessageBox::Warning, tr("Close Image"),
1465                        warning, 0, this);
1466     msgBox.addButton(tr("Close vv"), QMessageBox::AcceptRole);
1467     msgBox.addButton(tr("Cancel"), QMessageBox::RejectRole);
1468     if (msgBox.exec() == QMessageBox::AcceptRole) {
1469       this->close();
1470     }
1471   } else {
1472     QString warning = "Do you really want to close the image : ";
1473     warning += item->data(COLUMN_IMAGE_NAME,Qt::DisplayRole).toString();
1474     QMessageBox msgBox(QMessageBox::Warning, tr("Close Image"),
1475                        warning, 0, this);
1476     msgBox.addButton(tr("Close"), QMessageBox::AcceptRole);
1477     msgBox.addButton(tr("Cancel"), QMessageBox::RejectRole);
1478     if (msgBox.exec() == QMessageBox::AcceptRole) {
1479
1480       // Tell tools that we close an image
1481       emit AnImageIsBeingClosed(mSlicerManagers[index]);
1482
1483       std::vector<vvSlicerManager*>::iterator Manageriter = mSlicerManagers.begin();
1484       DataTree->takeTopLevelItem(index);
1485       for (int i = 0; i < index; i++) {
1486         Manageriter++;
1487       }
1488       linkPanel->removeImage(index);
1489       mSlicerManagers[index]->RemoveActors();
1490       delete mSlicerManagers[index];
1491       mSlicerManagers.erase(Manageriter);
1492
1493       //
1494       InitDisplay();
1495     }
1496   }
1497 }
1498 //------------------------------------------------------------------------------
1499
1500 //------------------------------------------------------------------------------
1501 void vvMainWindow::ReloadImage(QTreeWidgetItem* item, int column)
1502 {
1503   // int index = GetSlicerIndexFromItem(item);
1504   //   QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
1505   //   if (item->data(1,Qt::UserRole).toString() == "vector")
1506   //     mSlicerManagers[index]->ReloadVF();
1507   //   else
1508   //     mSlicerManagers[index]->Reload();
1509
1510   //   QApplication::restoreOverrideCursor();
1511   int index = GetSlicerIndexFromItem(item);
1512   QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
1513   QString role=item->data(1,Qt::UserRole).toString();
1514   if ( role == "vector")
1515     mSlicerManagers[index]->ReloadVF();
1516   else if (role == "overlay")
1517     mSlicerManagers[index]->ReloadOverlay();
1518   else if (role == "fusion")
1519     mSlicerManagers[index]->ReloadFusion();
1520   else
1521     mSlicerManagers[index]->Reload();
1522
1523   // Update view and info
1524   ImageInfoChanged();
1525   mSlicerManagers[index]->Render();
1526   QApplication::restoreOverrideCursor();
1527 }
1528 //------------------------------------------------------------------------------
1529
1530 //------------------------------------------------------------------------------
1531 void vvMainWindow::MousePositionChanged(int visibility,double x, double y, double z, double X, double Y, double Z , double value)
1532 {
1533   infoPanel->setCurrentInfo(visibility,x,y,z,X,Y,Z,value);
1534 }
1535 //------------------------------------------------------------------------------
1536
1537 //------------------------------------------------------------------------------
1538 void vvMainWindow::VectorChanged(int visibility,double x, double y, double z, double value)
1539 {
1540   overlayPanel->getCurrentVectorInfo(visibility,x,y,z,value);
1541 }
1542 //------------------------------------------------------------------------------
1543
1544 //------------------------------------------------------------------------------
1545 void vvMainWindow::OverlayChanged(int visibility, double valueOver, double valueRef)
1546 {
1547   overlayPanel->getCurrentOverlayInfo(visibility,valueOver, valueRef);
1548 }
1549 //------------------------------------------------------------------------------
1550
1551 //------------------------------------------------------------------------------
1552 void vvMainWindow::FusionChanged(int visibility, double value)
1553 {
1554   overlayPanel->getCurrentFusionInfo(visibility,value);
1555 }
1556 //------------------------------------------------------------------------------
1557
1558 //------------------------------------------------------------------------------
1559 void vvMainWindow::WindowsChanged(int window, int view, int slice)
1560 {
1561   infoPanel->setViews(window, view, slice);
1562 }
1563 //------------------------------------------------------------------------------
1564
1565 //------------------------------------------------------------------------------
1566 void vvMainWindow::WindowLevelChanged(double window, double level,int preset,int colormap)
1567 {
1568   windowSpinBox->setValue(window);
1569   levelSpinBox->setValue(level);
1570   colorMapComboBox->setCurrentIndex(colormap);
1571   presetComboBox->setCurrentIndex(preset);
1572 }
1573 //------------------------------------------------------------------------------
1574
1575 //------------------------------------------------------------------------------
1576 void vvMainWindow::WindowLevelEdited()
1577 {
1578   presetComboBox->setCurrentIndex(6);
1579   UpdateWindowLevel();
1580 }
1581 //------------------------------------------------------------------------------
1582
1583 //------------------------------------------------------------------------------
1584 void vvMainWindow::UpdateWindowLevel()
1585 {
1586   if (DataTree->selectedItems().size()) {
1587     if (presetComboBox->currentIndex() == 7) //For ventilation
1588       colorMapComboBox->setCurrentIndex(5);
1589     int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1590     mSlicerManagers[index]->SetColorWindow(windowSpinBox->value());
1591     mSlicerManagers[index]->SetColorLevel(levelSpinBox->value());
1592     mSlicerManagers[index]->SetPreset(presetComboBox->currentIndex());
1593     mSlicerManagers[index]->Render();
1594   }
1595 }
1596 //------------------------------------------------------------------------------
1597
1598 //------------------------------------------------------------------------------
1599 void vvMainWindow::UpdateColorMap()
1600 {
1601   if (DataTree->selectedItems().size()) {
1602     int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1603     mSlicerManagers[index]->SetColorMap(colorMapComboBox->currentIndex());
1604     mSlicerManagers[index]->Render();
1605   }
1606 }
1607 //------------------------------------------------------------------------------
1608 void vvMainWindow::SwitchWindowLevel()
1609 {
1610   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1611   int window = mSlicerManagers[index]->GetColorWindow();
1612   presetComboBox->setCurrentIndex(6);
1613   windowSpinBox->setValue(-window);
1614   UpdateWindowLevel();
1615 }
1616 //------------------------------------------------------------------------------
1617
1618 //------------------------------------------------------------------------------
1619 void vvMainWindow::UpdateLinkManager(std::string id, int slicer, double x, double y, double z, int temps)
1620 {
1621   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
1622     if (mSlicerManagers[i]->GetId() == id) {
1623       //mSlicerManagers[i]->SetTSlice(temps);
1624       mSlicerManagers[i]->GetSlicer(slicer)->SetCurrentPosition(x,y,z,temps);
1625       mSlicerManagers[i]->UpdateViews(0,slicer);
1626       break;
1627     }
1628   }
1629 }
1630 //------------------------------------------------------------------------------
1631
1632 //------------------------------------------------------------------------------
1633 void vvMainWindow::UpdateLinkedNavigation(std::string id, vvSlicerManager * sm)
1634 {
1635   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
1636     if (id == mSlicerManagers[i]->GetId()) {
1637       mSlicerManagers[i]->UpdateLinkedNavigation(sm->GetSlicer(0));
1638     }
1639   }
1640 }
1641 //------------------------------------------------------------------------------
1642
1643 //------------------------------------------------------------------------------
1644 void vvMainWindow::ShowContextMenu(QPoint point)
1645 {
1646   if (!DataTree->selectedItems().size()) {
1647     contextActions[1]->setEnabled(0);
1648     contextActions[2]->setEnabled(0);
1649     contextActions[3]->setEnabled(0);
1650     contextActions[4]->setEnabled(0);
1651     contextActions[5]->setEnabled(0);
1652     contextActions[6]->setEnabled(0);
1653   } else {
1654     int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1655     contextActions[1]->setEnabled(1);
1656     contextActions[2]->setEnabled(
1657       DataTree->itemWidget(DataTree->selectedItems()[0],
1658                            COLUMN_RELOAD_IMAGE)->isEnabled());
1659     contextActions[3]->setEnabled(1);
1660     contextActions[5]->setEnabled(1);
1661     contextActions[6]->setEnabled(1);
1662
1663     if (mSlicerManagers[index]->GetDimension() < 3)
1664       contextActions[4]->setEnabled(0);
1665     else
1666       contextActions[4]->setEnabled(1);
1667   }
1668   contextMenu.exec(QCursor::pos());
1669 }
1670 //------------------------------------------------------------------------------
1671
1672 //------------------------------------------------------------------------------
1673 void vvMainWindow::CloseImage()
1674 {
1675   CloseImage(DataTree->selectedItems()[0],0);
1676 }
1677 //------------------------------------------------------------------------------
1678
1679 //------------------------------------------------------------------------------
1680 void vvMainWindow::ReloadImage()
1681 {
1682   ReloadImage(DataTree->selectedItems()[0],0);
1683 }
1684 //------------------------------------------------------------------------------
1685
1686 //------------------------------------------------------------------------------
1687 void vvMainWindow::SelectOverlayImage()
1688 {
1689   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1690
1691   //check if one overlay image is added
1692   for (int child = 0; child < DataTree->topLevelItem(index)->childCount(); child++)
1693     if (DataTree->topLevelItem(index)->child(child)->data(1,Qt::UserRole).toString() == "overlay") {
1694       QString error = "Cannot add more than one compared image\n";
1695       error += "Please remove first ";
1696       error += DataTree->topLevelItem(index)->child(child)->data(COLUMN_IMAGE_NAME,Qt::DisplayRole).toString();
1697       QMessageBox::information(this,tr("Problem adding compared image !"),error);
1698       return;
1699     }
1700
1701   QString Extensions = EXTENSIONS;
1702   Extensions += ";;All Files (*)";
1703   QString file = QFileDialog::getOpenFileName(this,tr("Load Overlay image"),mInputPathName,Extensions);
1704   if (!file.isEmpty())
1705     AddOverlayImage(index,file);
1706 }
1707 //------------------------------------------------------------------------------
1708
1709 //------------------------------------------------------------------------------
1710 void vvMainWindow::AddOverlayImage(int index, QString file)
1711 {
1712
1713   mInputPathName = itksys::SystemTools::GetFilenamePath(file.toStdString()).c_str();
1714   itk::ImageIOBase::Pointer reader = itk::ImageIOFactory::CreateImageIO(
1715                                        file.toStdString().c_str(), itk::ImageIOFactory::ReadMode);
1716   reader->SetFileName(file.toStdString().c_str());
1717   reader->ReadImageInformation();
1718   std::string component = reader->GetComponentTypeAsString(reader->GetComponentType());
1719   int dimension = reader->GetNumberOfDimensions();
1720   QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
1721   vvProgressDialog progress("Opening " + file.toStdString());
1722   qApp->processEvents();
1723
1724   std::string filename = itksys::SystemTools::GetFilenameWithoutExtension(file.toStdString()).c_str();
1725   if (mSlicerManagers[index]->SetOverlay(file.toStdString(),dimension, component)) {
1726     //create an item in the tree with good settings
1727     QTreeWidgetItem *item = new QTreeWidgetItem();
1728     item->setData(0,Qt::UserRole,file.toStdString().c_str());
1729     item->setData(1,Qt::UserRole,tr("overlay"));
1730     item->setData(COLUMN_IMAGE_NAME,Qt::DisplayRole,filename.c_str());
1731     qApp->processEvents();
1732
1733     for (int j = 1; j <= 4; j++) {
1734       item->setData(j,Qt::CheckStateRole,DataTree->topLevelItem(index)->data(j,Qt::CheckStateRole));
1735       mSlicerManagers[index]->GetSlicer(j-1)->SetActorVisibility("overlay",0,
1736           DataTree->topLevelItem(index)->data(j,Qt::CheckStateRole).toInt());
1737     }
1738
1739     //Create the buttons for reload and close
1740     qApp->processEvents();
1741     QTreePushButton* cButton = new QTreePushButton;
1742     cButton->setItem(item);
1743     cButton->setColumn(COLUMN_CLOSE_IMAGE);
1744     cButton->setToolTip(tr("close image"));
1745     cButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/exit.png")));
1746     connect(cButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
1747             this,SLOT(CloseImage(QTreeWidgetItem*, int)));
1748
1749     QTreePushButton* rButton = new QTreePushButton;
1750     rButton->setItem(item);
1751     rButton->setColumn(COLUMN_RELOAD_IMAGE);
1752     rButton->setToolTip(tr("reload image"));
1753     rButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/rotateright.png")));
1754     connect(rButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
1755             this,SLOT(ReloadImage(QTreeWidgetItem*, int)));
1756
1757     DataTree->topLevelItem(index)->setExpanded(1);
1758     DataTree->topLevelItem(index)->addChild(item);
1759     DataTree->setItemWidget(item, COLUMN_CLOSE_IMAGE, cButton);
1760     DataTree->setItemWidget(item, COLUMN_RELOAD_IMAGE, rButton);
1761
1762     //set the id of the image
1763     QString id = DataTree->topLevelItem(index)->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString();
1764     item->setData(COLUMN_IMAGE_NAME,Qt::UserRole,id.toStdString().c_str());
1765     UpdateTree();
1766     qApp->processEvents();
1767     ImageInfoChanged();
1768     QApplication::restoreOverrideCursor();
1769   } else {
1770     QApplication::restoreOverrideCursor();
1771     QString error = "Cannot import the new image.\n";
1772     error += mSlicerManagers[index]->GetLastError().c_str();
1773     QMessageBox::information(this,tr("Problem reading image !"),error);
1774   }
1775 }
1776 //------------------------------------------------------------------------------
1777
1778
1779 //------------------------------------------------------------------------------
1780 void vvMainWindow::AddROI(int index, QString file)
1781 {
1782   DD("AddImageAndROI");
1783   /*
1784   // Get slice manager
1785
1786   // Load image
1787
1788   vvImageReader * mReader = new vvImageReader;
1789   mReader->SetInputFilename(filename.toStdString());
1790   mReader->Update(IMAGE);
1791   if (mReader->GetLastError().size() != 0) {
1792     std::cerr << "Error while reading " << filename.toStdString() << std::endl;
1793     QString error = "Cannot open file \n";
1794     error += mReader->GetLastError().c_str();
1795     QMessageBox::information(this,tr("Reading problem"),error);
1796     delete mReader;
1797     return;
1798   }
1799   vvImage::Pointer roi = mReader->GetOutput();
1800
1801   // Create roi in new tool
1802   vvToolStructureSetManager::AddImage(mCurrentSlicerManager, roi);
1803 */
1804 }
1805 //------------------------------------------------------------------------------
1806
1807 //------------------------------------------------------------------------------
1808 void vvMainWindow::SelectFusionImage()
1809 {
1810   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1811
1812   //check if one fusion image is added
1813   for (int child = 0; child < DataTree->topLevelItem(index)->childCount(); child++)
1814     if (DataTree->topLevelItem(index)->child(child)->data(1,Qt::UserRole).toString() == "fusion") {
1815       QString error = "Cannot add more than one fusion image\n";
1816       error += "Please remove first ";
1817       error += DataTree->topLevelItem(index)->child(child)->data(COLUMN_IMAGE_NAME,Qt::DisplayRole).toString();
1818       QMessageBox::information(this,tr("Problem adding fusion image !"),error);
1819       return;
1820     }
1821
1822   QString Extensions = EXTENSIONS;
1823   Extensions += ";;All Files (*)";
1824   QString file = QFileDialog::getOpenFileName(this,tr("Load Fusion image"),mInputPathName,Extensions);
1825   if (!file.isEmpty())
1826     AddFusionImage(index,file);
1827 }
1828 //------------------------------------------------------------------------------
1829
1830 //------------------------------------------------------------------------------
1831 void vvMainWindow::AddFusionImage(int index, QString file)
1832 {
1833   mInputPathName = itksys::SystemTools::GetFilenamePath(file.toStdString()).c_str();
1834   itk::ImageIOBase::Pointer reader = itk::ImageIOFactory::CreateImageIO(
1835                                        file.toStdString().c_str(), itk::ImageIOFactory::ReadMode);
1836   reader->SetFileName(file.toStdString().c_str());
1837   reader->ReadImageInformation();
1838   std::string component = reader->GetComponentTypeAsString(reader->GetComponentType());
1839   if (reader) {
1840     QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
1841     vvProgressDialog progress("Opening fusion");
1842     qApp->processEvents();
1843
1844     std::string filename = itksys::SystemTools::GetFilenameWithoutExtension(file.toStdString()).c_str();
1845     if (mSlicerManagers[index]->SetFusion(file.toStdString(),
1846                                           reader->GetNumberOfDimensions(), component)) {
1847       //create an item in the tree with good settings
1848       QTreeWidgetItem *item = new QTreeWidgetItem();
1849       item->setData(0,Qt::UserRole,file.toStdString().c_str());
1850       item->setData(1,Qt::UserRole,tr("fusion"));
1851       item->setData(COLUMN_IMAGE_NAME,Qt::DisplayRole,filename.c_str());
1852       qApp->processEvents();
1853
1854       for (int j = 1; j <= 4; j++) {
1855         item->setData(j,Qt::CheckStateRole,DataTree->topLevelItem(index)->data(j,Qt::CheckStateRole));
1856         mSlicerManagers[index]->GetSlicer(j-1)->SetActorVisibility("fusion",0,
1857             DataTree->topLevelItem(index)->data(j,Qt::CheckStateRole).toInt());
1858       }
1859
1860       //Create the buttons for reload and close
1861       qApp->processEvents();
1862       QTreePushButton* cButton = new QTreePushButton;
1863       cButton->setItem(item);
1864       cButton->setColumn(COLUMN_CLOSE_IMAGE);
1865       cButton->setToolTip(tr("close image"));
1866       cButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/exit.png")));
1867       connect(cButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
1868               this,SLOT(CloseImage(QTreeWidgetItem*, int)));
1869
1870       QTreePushButton* rButton = new QTreePushButton;
1871       rButton->setItem(item);
1872       rButton->setColumn(COLUMN_RELOAD_IMAGE);
1873       rButton->setToolTip(tr("reload image"));
1874       rButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/rotateright.png")));
1875       connect(rButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
1876               this,SLOT(ReloadImage(QTreeWidgetItem*, int)));
1877
1878       DataTree->topLevelItem(index)->setExpanded(1);
1879       DataTree->topLevelItem(index)->addChild(item);
1880       DataTree->setItemWidget(item, COLUMN_CLOSE_IMAGE, cButton);
1881       DataTree->setItemWidget(item, COLUMN_RELOAD_IMAGE, rButton);
1882
1883       //set the id of the image
1884       QString id = DataTree->topLevelItem(index)->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString();
1885       item->setData(COLUMN_IMAGE_NAME,Qt::UserRole,id.toStdString().c_str());
1886       UpdateTree();
1887       qApp->processEvents();
1888       ImageInfoChanged();
1889       QApplication::restoreOverrideCursor();
1890     } else {
1891       QApplication::restoreOverrideCursor();
1892       QString error = "Cannot import the new image.\n";
1893       error += mSlicerManagers[index]->GetLastError().c_str();
1894       QMessageBox::information(this,tr("Problem reading image !"),error);
1895     }
1896   } else {
1897     QString error = "Cannot import the new image.\n";
1898     QMessageBox::information(this,tr("Problem reading image !"),error);
1899   }
1900 }
1901 //------------------------------------------------------------------------------
1902
1903
1904 //------------------------------------------------------------------------------
1905 void vvMainWindow::OpenField()
1906 {
1907   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1908   //check if a vector field has already been added
1909   for (int child = 0; child < DataTree->topLevelItem(index)->childCount(); child++)
1910     if (DataTree->topLevelItem(index)->child(child)->data(1,Qt::UserRole).toString() == "vector") {
1911       QString error = "Cannot add more than one vector field\n";
1912       error += "Please remove first ";
1913       error += DataTree->topLevelItem(index)->child(child)->data(COLUMN_IMAGE_NAME,Qt::DisplayRole).toString();
1914       QMessageBox::information(this,tr("Problem adding vector field!"),error);
1915       return;
1916     }
1917
1918   QString Extensions = "Images ( *.mhd)";
1919   Extensions += ";;Images ( *.vf)";
1920   QString file = QFileDialog::getOpenFileName(this,tr("Load deformation field"),mInputPathName,Extensions);
1921   if (!file.isEmpty())
1922     AddField(file,index);
1923 }
1924 //------------------------------------------------------------------------------
1925
1926
1927 //------------------------------------------------------------------------------
1928 void vvMainWindow::AddFieldEntry(QString filename,int index,bool from_disk)
1929 {
1930   //create an item in the tree with good settings
1931   QTreeWidgetItem *item = new QTreeWidgetItem();
1932   item->setData(0,Qt::UserRole,filename.toStdString().c_str());
1933   item->setData(1,Qt::UserRole,tr("vector"));
1934   item->setData(COLUMN_IMAGE_NAME,Qt::DisplayRole,filename);
1935   qApp->processEvents();
1936
1937   for (int j = 1; j <= 4; j++) {
1938     item->setData(j,Qt::CheckStateRole,DataTree->topLevelItem(index)->data(j,Qt::CheckStateRole));
1939     mSlicerManagers[index]->GetSlicer(j-1)->SetActorVisibility("vector",0,
1940         DataTree->topLevelItem(index)->data(j,Qt::CheckStateRole).toInt());
1941   }
1942
1943   //Create the buttons for reload and close
1944   qApp->processEvents();
1945   QTreePushButton* cButton = new QTreePushButton;
1946   cButton->setItem(item);
1947   cButton->setColumn(COLUMN_CLOSE_IMAGE);
1948   cButton->setToolTip(tr("close vector field"));
1949   cButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/exit.png")));
1950   connect(cButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
1951           this,SLOT(CloseImage(QTreeWidgetItem*, int)));
1952
1953   QTreePushButton* rButton = new QTreePushButton;
1954   rButton->setItem(item);
1955   rButton->setColumn(COLUMN_RELOAD_IMAGE);
1956   rButton->setToolTip(tr("reload vector field"));
1957   rButton->setEnabled(from_disk);
1958   rButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/rotateright.png")));
1959   connect(rButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
1960           this,SLOT(ReloadImage(QTreeWidgetItem*, int)));
1961
1962   DataTree->topLevelItem(index)->setExpanded(1);
1963   DataTree->topLevelItem(index)->addChild(item);
1964   DataTree->setItemWidget(item, COLUMN_RELOAD_IMAGE, rButton);
1965   DataTree->setItemWidget(item, COLUMN_CLOSE_IMAGE, cButton);
1966
1967   //set the id of the image
1968   QString id = DataTree->topLevelItem(index)->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString();
1969   item->setData(COLUMN_IMAGE_NAME,Qt::UserRole,id.toStdString().c_str());
1970   UpdateTree();
1971   qApp->processEvents();
1972   ImageInfoChanged();
1973   QApplication::restoreOverrideCursor();
1974 }
1975 //------------------------------------------------------------------------------
1976
1977
1978 //------------------------------------------------------------------------------
1979 void vvMainWindow::AddField(vvImage::Pointer vf,QString file,int index)
1980 {
1981   QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
1982   vvSlicerManager* imageManager = mSlicerManagers[index];
1983   if (imageManager->SetVF(vf,file.toStdString())) {
1984     AddFieldEntry(file,index,false);
1985   } else {
1986     QString error = "Cannot import the vector field for this image.\n";
1987     error += imageManager->GetLastError().c_str();
1988     QMessageBox::information(this,tr("Problem reading VF !"),error);
1989   }
1990   QApplication::restoreOverrideCursor();
1991 }
1992 //------------------------------------------------------------------------------
1993
1994
1995 //------------------------------------------------------------------------------
1996 void vvMainWindow::AddField(QString file,int index)
1997 {
1998   if (QFile::exists(file)) {
1999     mInputPathName = itksys::SystemTools::GetFilenamePath(file.toStdString()).c_str();
2000
2001     //init the progress events
2002     QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
2003     vvProgressDialog progress("Opening " + file.toStdString());
2004     qApp->processEvents();
2005
2006     //read the vector and put it in the current mSlicerManager
2007     vvSlicerManager* imageManager = mSlicerManagers[index];
2008     qApp->processEvents();
2009
2010     std::string filename = itksys::SystemTools::GetFilenameWithoutExtension(file.toStdString()).c_str();
2011     if (imageManager->SetVF(file.toStdString())) {
2012       imageManager->Render();
2013       AddFieldEntry(file,index,true);
2014     } else {
2015       QApplication::restoreOverrideCursor();
2016       QString error = "Cannot import the vector field for this image.\n";
2017       error += imageManager->GetLastError().c_str();
2018       QMessageBox::information(this,tr("Problem reading VF !"),error);
2019     }
2020   } else
2021     QMessageBox::information(this,tr("Problem reading VF !"),"File doesn't exist!");
2022
2023 }
2024 //------------------------------------------------------------------------------
2025
2026
2027 //------------------------------------------------------------------------------
2028 void vvMainWindow::SetVFProperty(int subsampling, int scale, int log, int width)
2029 {
2030   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2031   if (mSlicerManagers[index]->GetSlicer(0)->GetVF()) {
2032     for (int i = 0; i < 4; i++) {
2033       mSlicerManagers[index]->GetSlicer(i)->SetVFSubSampling(subsampling);
2034       mSlicerManagers[index]->GetSlicer(i)->SetVFScale(scale);
2035       mSlicerManagers[index]->GetSlicer(i)->SetVFWidth(width);
2036       if (log > 0)
2037         mSlicerManagers[index]->GetSlicer(i)->SetVFLog(1);
2038       else
2039         mSlicerManagers[index]->GetSlicer(i)->SetVFLog(0);
2040     }
2041   }
2042 }
2043 //------------------------------------------------------------------------------
2044
2045
2046 //------------------------------------------------------------------------------
2047 void vvMainWindow::SetOverlayProperty(int color)
2048 {
2049   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2050   if (mSlicerManagers[index]->GetSlicer(0)->GetOverlay()) {
2051     mSlicerManagers[index]->SetOverlayColor(color);
2052     mSlicerManagers[index]->SetColorMap(0);
2053     mSlicerManagers[index]->Render();
2054   }
2055 }
2056 //------------------------------------------------------------------------------
2057
2058 //------------------------------------------------------------------------------
2059 void vvMainWindow::SetFusionProperty(int opacity, int colormap,double window, double level)
2060 {
2061   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2062   if (mSlicerManagers[index]->GetSlicer(0)->GetFusion()) {
2063     mSlicerManagers[index]->SetFusionOpacity(opacity);
2064     mSlicerManagers[index]->SetFusionColorMap(colormap);
2065     mSlicerManagers[index]->SetFusionWindow(window);
2066     mSlicerManagers[index]->SetFusionLevel(level);
2067     mSlicerManagers[index]->SetColorMap(0);
2068     mSlicerManagers[index]->Render();
2069   }
2070 }
2071 //------------------------------------------------------------------------------
2072
2073 //------------------------------------------------------------------------------
2074 void vvMainWindow::SaveAs()
2075 {
2076   if (DataTree->selectedItems()[0]->data(1,Qt::UserRole).toString() == "vector") {
2077     QMessageBox::warning(this,tr("Unsupported type"),tr("Sorry, saving a vector field is unsupported for the moment"));
2078     return;
2079   }
2080
2081   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2082   int dimension = mSlicerManagers[index]->GetDimension();
2083   QStringList OutputListeFormat;
2084   OutputListeFormat.clear();
2085   if (dimension == 1) {
2086     OutputListeFormat.push_back(".mhd");
2087   }
2088   if (dimension == 2) {
2089     OutputListeFormat.push_back(".bmp");
2090     OutputListeFormat.push_back(".png");
2091     OutputListeFormat.push_back(".jpeg");
2092     OutputListeFormat.push_back(".tif");
2093     OutputListeFormat.push_back(".mhd");
2094     OutputListeFormat.push_back(".hdr");
2095     OutputListeFormat.push_back(".vox");
2096   } else if (dimension == 3) {
2097     OutputListeFormat.push_back(".mhd");
2098     OutputListeFormat.push_back(".hdr");
2099     OutputListeFormat.push_back(".vox");
2100   } else if (dimension == 4) {
2101     OutputListeFormat.push_back(".mhd");
2102   }
2103   QString Extensions = "AllFiles(*.*)";
2104   for (int i = 0; i < OutputListeFormat.count(); i++) {
2105     Extensions += ";;Images ( *";
2106     Extensions += OutputListeFormat[i];
2107     Extensions += ")";
2108   }
2109   QString fileName = QFileDialog::getSaveFileName(this,
2110                      tr("Save As"),
2111                      mSlicerManagers[index]->GetFileName().c_str(),
2112                      Extensions);
2113   if (!fileName.isEmpty()) {
2114     std::string fileformat = itksys::SystemTools::GetFilenameLastExtension(fileName.toStdString());
2115     if (OutputListeFormat.contains(
2116           fileformat.c_str())) {
2117       QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
2118       std::string action = "Saving";
2119       vvProgressDialog progress("Saving "+fileName.toStdString());
2120       qApp->processEvents();
2121       vvImageWriter *writer = new vvImageWriter;
2122       writer->SetOutputFileName(fileName.toStdString());
2123       writer->SetInput(mSlicerManagers[index]->GetImage());
2124       writer->Update();
2125       QApplication::restoreOverrideCursor();
2126       if (writer->GetLastError().size()) {
2127         QString error = "Saving did not succeed\n";
2128         error += writer->GetLastError().c_str();
2129         QMessageBox::information(this,tr("Saving Problem"),error);
2130         SaveAs();
2131       }
2132     } else {
2133       QString error = fileformat.c_str();
2134       if (error.isEmpty())
2135         error += "no file format specified !";
2136       else
2137         error += " format unknown !!!\n";
2138       QMessageBox::information(this,tr("Saving Problem"),error);
2139       SaveAs();
2140     }
2141   }
2142 }
2143 //------------------------------------------------------------------------------
2144
2145
2146 //------------------------------------------------------------------------------
2147 void vvMainWindow::AddLink(QString image1,QString image2)
2148 {
2149   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
2150     if (image1.toStdString() == mSlicerManagers[i]->GetId()) {
2151       mSlicerManagers[i]->AddLink(image2.toStdString());
2152     }
2153     if (image2.toStdString() == mSlicerManagers[i]->GetId()) {
2154       mSlicerManagers[i]->AddLink(image1.toStdString());
2155     }
2156   }
2157 }
2158 //------------------------------------------------------------------------------
2159
2160
2161 //------------------------------------------------------------------------------
2162 void vvMainWindow::RemoveLink(QString image1,QString image2)
2163 {
2164   // DD("vvMainWindow:RemoveLink");
2165   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
2166     if (image1.toStdString() == mSlicerManagers[i]->GetId()) {
2167       mSlicerManagers[i]->RemoveLink(image2.toStdString());
2168     }
2169     if (image2.toStdString() == mSlicerManagers[i]->GetId()) {
2170       mSlicerManagers[i]->RemoveLink(image1.toStdString());
2171     }
2172   }
2173 }
2174 //------------------------------------------------------------------------------
2175
2176 //------------------------------------------------------------------------------
2177 void vvMainWindow::ChangeImageWithIndexOffset(vvSlicerManager *sm, int slicer, int offset)
2178 {
2179   int index = 0;
2180   while(sm != mSlicerManagers[index])
2181     index++;
2182   index = (index+offset) % mSlicerManagers.size();
2183
2184   QTreeWidgetItem* item = GetItemFromSlicerManager(mSlicerManagers[index]);
2185   //CurrentImageChanged(mSlicerManagers[index]->GetId()); //select new image
2186   item->setData(slicer+1,Qt::CheckStateRole,2);         //change checkbox
2187   DisplayChanged(item,slicer+1);
2188 }
2189 //------------------------------------------------------------------------------
2190
2191 void vvMainWindow::HorizontalSliderMoved(int value,int column, int slicer_index)
2192 {
2193   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
2194     if (DataTree->topLevelItem(i)->data(column,Qt::CheckStateRole).toInt() > 1) {
2195       for (int j = 0; j < 4; j++) {
2196         mSlicerManagers[i]->SetTSliceInSlicer(value,j);
2197         //if (mSlicerManagers[i]->GetSlicer(j)->GetImageActor()->GetVisibility())
2198         //UpdateTSlice(j,value);
2199       }
2200       mSlicerManagers[i]->GetSlicer(slicer_index)->Render();
2201       break;
2202     }
2203   }
2204 }
2205 //------------------------------------------------------------------------------
2206
2207
2208 //------------------------------------------------------------------------------
2209 void vvMainWindow::NOHorizontalSliderMoved()
2210 {
2211   // if (mCurrentTime == NOHorizontalSlider->value()) return;
2212   HorizontalSliderMoved(NOHorizontalSlider->value(),COLUMN_UL_VIEW,0);
2213 //  mCurrentTime = NOHorizontalSlider->value();
2214 }
2215 //------------------------------------------------------------------------------
2216
2217
2218 //------------------------------------------------------------------------------
2219 void vvMainWindow::NEHorizontalSliderMoved()
2220 {
2221   // if (mCurrentTime == NEHorizontalSlider->value()) return;
2222   HorizontalSliderMoved(NEHorizontalSlider->value(),COLUMN_UR_VIEW,1);
2223 //  mCurrentTime = NEHorizontalSlider->value();
2224 }
2225 //------------------------------------------------------------------------------
2226
2227
2228 //------------------------------------------------------------------------------
2229 void vvMainWindow::SOHorizontalSliderMoved()
2230 {
2231   // if (mCurrentTime == SOHorizontalSlider->value()) return;
2232   HorizontalSliderMoved(SOHorizontalSlider->value(),COLUMN_DL_VIEW,2);
2233   // mCurrentTime = SOHorizontalSlider->value();
2234 }
2235 //------------------------------------------------------------------------------
2236
2237
2238 //------------------------------------------------------------------------------
2239 void vvMainWindow::SEHorizontalSliderMoved()
2240 {
2241   // if (mCurrentTime == SEHorizontalSlider->value()) return;
2242   HorizontalSliderMoved(SEHorizontalSlider->value(),COLUMN_DR_VIEW,3);
2243   // mCurrentTime = SEHorizontalSlider->value();
2244 }
2245 //------------------------------------------------------------------------------
2246
2247 //------------------------------------------------------------------------------
2248 void vvMainWindow::NOVerticalSliderChanged()
2249 {
2250   static int value=-1;
2251   if (value == NOVerticalSlider->value()) return;
2252   else value = NOVerticalSlider->value();
2253   //  int value = NOVerticalSlider->value();
2254   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
2255     if (DataTree->topLevelItem(i)->data(COLUMN_UL_VIEW,Qt::CheckStateRole).toInt() > 1) {
2256       if (mSlicerManagers[i]->GetSlicer(0)->GetSlice() != value) {
2257         mSlicerManagers[i]->GetSlicer(0)->SetSlice(value);
2258         mSlicerManagers[i]->VerticalSliderHasChanged(0, value);
2259
2260         // If nor Update/Render -> slider not work
2261         // only render = ok navigation, but for contour Update needed but slower ?
2262
2263         mSlicerManagers[i]->UpdateSlice(0);  // <-- DS add this. Not too much update ? YES. but needed for ImageContour ...
2264         //mSlicerManagers[i]->GetSlicer(0)->Render(); // <-- DS add this, needed for contour, seems ok ? not too slow ?
2265       }
2266       break;
2267     }
2268   }
2269 }
2270 //------------------------------------------------------------------------------
2271
2272
2273 //------------------------------------------------------------------------------
2274 void vvMainWindow::NEVerticalSliderChanged()
2275 {
2276   static int value=-1;
2277   if (value == NEVerticalSlider->value()) return;
2278   else value = NEVerticalSlider->value();
2279   //  int value = NEVerticalSlider->value();
2280   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
2281     if (DataTree->topLevelItem(i)->data(COLUMN_UR_VIEW,Qt::CheckStateRole).toInt() > 1) {
2282       if (mSlicerManagers[i]->GetSlicer(1)->GetSlice() != value) {
2283         mSlicerManagers[i]->GetSlicer(1)->SetSlice(value);
2284         mSlicerManagers[i]->VerticalSliderHasChanged(1, value);
2285         mSlicerManagers[i]->UpdateSlice(1);
2286         //mSlicerManagers[i]->GetSlicer(1)->Render(); // <-- DS add this, needed for contour, seems ok ? not too slow ?
2287       }
2288       break;
2289     }
2290   }
2291 }
2292 //------------------------------------------------------------------------------
2293
2294
2295 //------------------------------------------------------------------------------
2296 void vvMainWindow::SOVerticalSliderChanged()
2297 {
2298   static int value=-1;
2299   // DD(value);
2300 //   DD(SOVerticalSlider->value());
2301   if (value == SOVerticalSlider->value()) return;
2302   else value = SOVerticalSlider->value();
2303   //int value = SOVerticalSlider->value();
2304   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
2305     if (DataTree->topLevelItem(i)->data(COLUMN_DL_VIEW,Qt::CheckStateRole).toInt() > 1) {
2306       if (mSlicerManagers[i]->GetSlicer(2)->GetSlice() != value) {
2307         mSlicerManagers[i]->GetSlicer(2)->SetSlice(value);
2308         mSlicerManagers[i]->VerticalSliderHasChanged(2, value);
2309         mSlicerManagers[i]->UpdateSlice(2);
2310         //mSlicerManagers[i]->GetSlicer(2)->Render(); // <-- DS add this, needed for contour, seems ok ? not too slow ?
2311       }
2312       // else { DD("avoid SOVerticalSlider slicer update"); }
2313       break;
2314     }
2315   }
2316 }
2317 //------------------------------------------------------------------------------
2318
2319
2320 //------------------------------------------------------------------------------
2321 void vvMainWindow::SEVerticalSliderChanged()
2322 {
2323   static int value=-1;
2324   if (value == SEVerticalSlider->value()) return;
2325   else value = SEVerticalSlider->value();
2326   // int value = SEVerticalSlider->value();
2327   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
2328     if (DataTree->topLevelItem(i)->data(COLUMN_DR_VIEW,Qt::CheckStateRole).toInt() > 1) {
2329       if (mSlicerManagers[i]->GetSlicer(3)->GetSlice() != value) {
2330         mSlicerManagers[i]->GetSlicer(3)->SetSlice(value);
2331         mSlicerManagers[i]->VerticalSliderHasChanged(3, value);
2332         mSlicerManagers[i]->UpdateSlice(3);
2333         //mSlicerManagers[i]->GetSlicer(3)->Render(); // <-- DS add this, needed for contour, seems ok ? not too slow ?
2334       }
2335       break;
2336     }
2337   }
2338 }
2339 //------------------------------------------------------------------------------
2340
2341
2342 //------------------------------------------------------------------------------
2343 void vvMainWindow::UpdateSlice(int slicer, int slice)
2344 {
2345   // DD("vvMainWindow::UpdateSlice");
2346 //   DD(slicer);
2347 //   DD(slice);
2348   if (slicer == 0) {
2349     //    if (slice != NOVerticalSlider->value())
2350     NOVerticalSlider->setValue(slice);
2351   } else {
2352     if (slicer == 1)
2353       NEVerticalSlider->setValue(slice);
2354     else {
2355       if (slicer == 2)
2356         SOVerticalSlider->setValue(slice);
2357       else {
2358         if (slicer == 3)
2359           SEVerticalSlider->setValue(slice);
2360       }
2361     }
2362   }
2363   // DD("vvMainWindow:UpdateSlice END");
2364 }
2365 //------------------------------------------------------------------------------
2366
2367
2368 //------------------------------------------------------------------------------
2369 void vvMainWindow::UpdateTSlice(int slicer, int slice)
2370 {
2371   switch (slicer) {
2372   case 0:
2373     NOHorizontalSlider->setValue(slice);
2374     break;
2375   case 1:
2376     NEHorizontalSlider->setValue(slice);
2377     break;
2378   case 2:
2379     SOHorizontalSlider->setValue(slice);
2380     break;
2381   case 3:
2382     SEHorizontalSlider->setValue(slice);
2383     break;
2384   }
2385 }
2386 //------------------------------------------------------------------------------
2387
2388
2389 //------------------------------------------------------------------------------
2390 void vvMainWindow::UpdateSliceRange(int slicer, int min, int max, int tmin, int tmax)
2391 {
2392   int position = int((min+max)/2);
2393   int tPosition = int((tmin+tmax)/2);
2394   if (slicer == 0) {
2395     NOVerticalSlider->setValue(position);
2396     NOVerticalSlider->setRange(min,max);
2397     NOHorizontalSlider->setRange(tmin,tmax);
2398     NOHorizontalSlider->setValue(tPosition);
2399   } else if (slicer == 1) {
2400     NEVerticalSlider->setValue(position);
2401     NEVerticalSlider->setRange(min,max);
2402     NEHorizontalSlider->setRange(tmin,tmax);
2403     NEHorizontalSlider->setValue(tPosition);
2404   } else if (slicer == 2) {
2405     SOVerticalSlider->setValue(position);
2406     SOVerticalSlider->setRange(min,max);
2407     SOHorizontalSlider->setRange(tmin,tmax);
2408     SOHorizontalSlider->setValue(tPosition);
2409   } else if (slicer == 3) {
2410     SEVerticalSlider->setValue(position);
2411     SEVerticalSlider->setRange(min,max);
2412     SEHorizontalSlider->setRange(tmin,tmax);
2413     SEHorizontalSlider->setValue(tPosition);
2414   }
2415 }
2416 //------------------------------------------------------------------------------
2417
2418
2419 //------------------------------------------------------------------------------
2420 void vvMainWindow::SaveNOScreenshot()
2421 {
2422   vtkWindowToImageFilter *w2i = vtkWindowToImageFilter::New();
2423   w2i->SetInput(NOViewWidget->GetRenderWindow());
2424   w2i->Update();
2425   SaveScreenshot(w2i->GetOutput());
2426   w2i->Delete();
2427 }
2428 //------------------------------------------------------------------------------
2429
2430
2431 //------------------------------------------------------------------------------
2432 void vvMainWindow::SaveNEScreenshot()
2433 {
2434   vtkWindowToImageFilter *w2i = vtkWindowToImageFilter::New();
2435   w2i->SetInput(NEViewWidget->GetRenderWindow());
2436   w2i->Update();
2437   SaveScreenshot(w2i->GetOutput());
2438   w2i->Delete();
2439 }
2440 //------------------------------------------------------------------------------
2441
2442
2443 //------------------------------------------------------------------------------
2444 void vvMainWindow::SaveSOScreenshot()
2445 {
2446   vtkWindowToImageFilter *w2i = vtkWindowToImageFilter::New();
2447   w2i->SetInput(SOViewWidget->GetRenderWindow());
2448   w2i->Update();
2449   SaveScreenshot(w2i->GetOutput());
2450   w2i->Delete();
2451 }
2452 //------------------------------------------------------------------------------
2453
2454
2455 //------------------------------------------------------------------------------
2456 void vvMainWindow::SaveSEScreenshot()
2457 {
2458   vtkWindowToImageFilter *w2i = vtkWindowToImageFilter::New();
2459   w2i->SetInput(SEViewWidget->GetRenderWindow());
2460   w2i->Update();
2461   SaveScreenshot(w2i->GetOutput());
2462   w2i->Delete();
2463 }
2464 //------------------------------------------------------------------------------
2465
2466
2467 //------------------------------------------------------------------------------
2468 void vvMainWindow::SaveScreenshot(vtkImageData* image)
2469 {
2470   QString Extensions = "Images( *.png);;";
2471   Extensions += "Images( *.jpg);;";
2472   Extensions += "Images( *.bmp);;";
2473   Extensions += "Images( *.tif);;";
2474   Extensions += "Images( *.ppm)";
2475   QString fileName = QFileDialog::getSaveFileName(this,
2476                      tr("Save As"),
2477                      itksys::SystemTools::GetFilenamePath(
2478                        mSlicerManagers[0]->GetFileName()).c_str(),
2479                      Extensions);
2480   if (!fileName.isEmpty()) {
2481     const char *ext = fileName.toStdString().c_str() + strlen(fileName.toStdString().c_str()) - 4;
2482     if (!strcmp(ext, ".bmp")) {
2483       vtkBMPWriter *bmp = vtkBMPWriter::New();
2484       bmp->SetInput(image);
2485       bmp->SetFileName(fileName.toStdString().c_str());
2486       bmp->Write();
2487       bmp->Delete();
2488     } else if (!strcmp(ext, ".tif")) {
2489       vtkTIFFWriter *tif = vtkTIFFWriter::New();
2490       tif->SetInput(image);
2491       tif->SetFileName(fileName.toStdString().c_str());
2492       tif->Write();
2493       tif->Delete();
2494     } else if (!strcmp(ext, ".ppm")) {
2495       vtkPNMWriter *pnm = vtkPNMWriter::New();
2496       pnm->SetInput(image);
2497       pnm->SetFileName(fileName.toStdString().c_str());
2498       pnm->Write();
2499       pnm->Delete();
2500     } else if (!strcmp(ext, ".png")) {
2501       vtkPNGWriter *png = vtkPNGWriter::New();
2502       png->SetInput(image);
2503       png->SetFileName(fileName.toStdString().c_str());
2504       png->Write();
2505       png->Delete();
2506     } else if (!strcmp(ext, ".jpg")) {
2507       vtkJPEGWriter *jpg = vtkJPEGWriter::New();
2508       jpg->SetInput(image);
2509       jpg->SetFileName(fileName.toStdString().c_str());
2510       jpg->Write();
2511       jpg->Delete();
2512     } else {
2513       QMessageBox::information(this,tr("Problem saving screenshot !"),tr("Cannot save image.\nPlease set a file extension !!!"));
2514     }
2515   }
2516
2517 }
2518 //------------------------------------------------------------------------------
2519
2520
2521 //------------------------------------------------------------------------------
2522 void vvMainWindow::GoToCursor()
2523 {
2524   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2525   for (int column = 1; column < 5; column++) {
2526     if (DataTree->selectedItems()[0]->data(column,Qt::CheckStateRole).toInt() > 1) {
2527       double* cursorPos = mSlicerManagers[index]->GetSlicer(column-1)->GetCursorPosition();
2528       mSlicerManagers[index]->GetSlicer(column-1)->SetCurrentPosition(
2529         cursorPos[0],cursorPos[1],cursorPos[2],cursorPos[3]);
2530       mSlicerManagers[index]->UpdateViews(1,column-1);
2531       mSlicerManagers[index]->UpdateLinked(column-1);
2532       break;
2533     }
2534   }
2535 }
2536 //------------------------------------------------------------------------------
2537
2538 //------------------------------------------------------------------------------
2539 void vvMainWindow::PlayPause()
2540 {
2541   if (playMode) {
2542     playMode = 0;
2543     playButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/player_play.png")));
2544     ImageInfoChanged();
2545     return;
2546   } else {
2547     int image_number=DataTree->topLevelItemCount();
2548     bool has_temporal;
2549     for (int i=0; i<image_number; i++)
2550       if (mSlicerManagers[i]->GetImage()->GetVTKImages().size() > 1) {
2551         has_temporal=true;
2552         break;
2553       }
2554     if (has_temporal) {
2555       playMode = 1;
2556       playButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/player_pause.png")));
2557       QTimer::singleShot(1000/mFrameRate, this, SLOT(PlayNext()));
2558     }
2559   }
2560 }
2561 //------------------------------------------------------------------------------
2562
2563 //------------------------------------------------------------------------------
2564 void vvMainWindow::PlayNext()
2565 {
2566   if (playMode && !this->isHidden()) {
2567     int image_number=DataTree->topLevelItemCount();
2568     ///Only play one slicer per SM, and only if the SM is being displayed
2569     for (int i=0; i<image_number; i++)
2570       for (int j=0; j<4; j++)
2571         if (mSlicerManagers[i]->GetImage()->GetVTKImages().size() > 1 &&
2572             DataTree->topLevelItem(i)->data(j+1,Qt::CheckStateRole).toInt() > 0) {
2573           mSlicerManagers[i]->SetNextTSlice(j);
2574           break;
2575         }
2576     QTimer::singleShot(1000/mFrameRate, this, SLOT(PlayNext()));
2577   }
2578 }
2579 //------------------------------------------------------------------------------
2580
2581 void vvMainWindow::ShowLastImage()
2582 {
2583   if (mSlicerManagers.size() > 1) {
2584     QTreeWidgetItem * item=DataTree->topLevelItem(DataTree->topLevelItemCount()-1);
2585     CurrentImageChanged(mSlicerManagers.back()->GetId()); //select new image
2586     item->setData(1,Qt::CheckStateRole,2); //show the new image in the first panel
2587     DisplayChanged(item,1);
2588   }
2589 }
2590
2591 //------------------------------------------------------------------------------
2592 void vvMainWindow::UpdateRenderWindows()
2593 {
2594   if (NOViewWidget->GetRenderWindow()) NOViewWidget->GetRenderWindow()->Render();
2595   if (NEViewWidget->GetRenderWindow()) NEViewWidget->GetRenderWindow()->Render();
2596   if (SOViewWidget->GetRenderWindow()) SOViewWidget->GetRenderWindow()->Render();
2597   if (SEViewWidget->GetRenderWindow()) SEViewWidget->GetRenderWindow()->Render();
2598 }
2599 //------------------------------------------------------------------------------
2600
2601 //------------------------------------------------------------------------------
2602 void vvMainWindow::SegmentationOnCurrentImage()
2603 {
2604   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2605
2606   vvSegmentationDialog segmentation;
2607   segmentation.SetImage(mSlicerManagers[index]->GetSlicer(0)->GetImage());
2608   segmentation.exec();
2609 }
2610 //------------------------------------------------------------------------------
2611
2612 void vvMainWindow::SurfaceViewerLaunch()
2613 {
2614   vvSurfaceViewerDialog surfaceViewer;
2615   surfaceViewer.exec();
2616 }
2617 //------------------------------------------------------------------------------
2618
2619
2620 //------------------------------------------------------------------------------
2621 int vvMainWindow::GetImageDuplicateFilenameNumber(std::string filename)
2622 {
2623   int number=0;
2624   for(unsigned int l=0; l<mSlicerManagers.size(); l++) {
2625     vvSlicerManager * v = mSlicerManagers[l];
2626     if (v->GetBaseFileName() ==
2627         vtksys::SystemTools::GetFilenameName(vtksys::SystemTools::GetFilenameWithoutLastExtension(filename))) {
2628       number = std::max(number, v->GetBaseFileNameNumber()+1);
2629     }
2630   }
2631   return number;
2632 }
2633 //------------------------------------------------------------------------------
2634
2635
2636 //------------------------------------------------------------------------------
2637 vvSlicerManager* vvMainWindow::AddImage(vvImage::Pointer image,std::string filename)
2638 {
2639   // Change filename if another image exist with the same name
2640   int number = GetImageDuplicateFilenameNumber(filename);
2641
2642   // Create new SliceManager
2643   vvSlicerManager* slicer_manager = new vvSlicerManager(4);
2644   slicer_manager->SetImage(image);//, IMAGE, number);
2645   //  filename = filename+"_"+clitk::toString(number);
2646   slicer_manager->SetFilename(filename, number);
2647   mSlicerManagers.push_back(slicer_manager);
2648
2649   //create an item in the tree with good settings
2650   QTreeWidgetItem *item = new QTreeWidgetItem();
2651   item->setData(0,Qt::UserRole,slicer_manager->GetFileName().c_str());//files[i].c_str());
2652   item->setData(COLUMN_IMAGE_NAME,Qt::DisplayRole,filename.c_str());
2653   qApp->processEvents();
2654
2655   for (int j = 1; j <= 4; j++) item->setData(j,Qt::CheckStateRole,1);
2656
2657   //Create the buttons for reload and close
2658   qApp->processEvents();
2659   QTreePushButton* cButton = new QTreePushButton;
2660   cButton->setItem(item);
2661   cButton->setColumn(COLUMN_CLOSE_IMAGE);
2662   cButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/exit.png")));
2663   connect(cButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
2664           this,SLOT(CloseImage(QTreeWidgetItem*, int)));
2665
2666   QTreePushButton* rButton = new QTreePushButton;
2667   rButton->setItem(item);
2668   rButton->setColumn(COLUMN_RELOAD_IMAGE);
2669   rButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/rotateright.png")));
2670   rButton->setEnabled(0);
2671   connect(rButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
2672           this,SLOT(ReloadImage(QTreeWidgetItem*, int)));
2673
2674   DataTree->addTopLevelItem(item);
2675   DataTree->setItemWidget(item, COLUMN_CLOSE_IMAGE, cButton);
2676   DataTree->setItemWidget(item, COLUMN_RELOAD_IMAGE, rButton);
2677
2678   //set the id of the image
2679   QString id = slicer_manager->GetFileName().c_str() + QString::number(mSlicerManagers.size()-1);
2680   item->setData(COLUMN_IMAGE_NAME,Qt::UserRole,id.toStdString().c_str());
2681   mSlicerManagers.back()->SetId(id.toStdString());
2682
2683   linkPanel->addImage(filename, id.toStdString());
2684
2685   connect(mSlicerManagers.back(), SIGNAL(currentImageChanged(std::string)),
2686           this, SLOT(CurrentImageChanged(std::string)));
2687   connect(mSlicerManagers.back(), SIGNAL(UpdatePosition(int, double, double, double, double, double, double, double)),
2688           this, SLOT(MousePositionChanged(int,double, double, double, double, double, double, double)));
2689   connect(mSlicerManagers.back(), SIGNAL(UpdateVector(int, double, double, double, double)),
2690           this, SLOT(VectorChanged(int,double,double,double, double)));
2691   connect(mSlicerManagers.back(), SIGNAL(UpdateOverlay(int, double, double)),
2692           this, SLOT(OverlayChanged(int,double,double)));
2693   connect(mSlicerManagers.back(), SIGNAL(UpdateFusion(int, double)),
2694           this, SLOT(FusionChanged(int,double)));
2695   connect(mSlicerManagers.back(), SIGNAL(UpdateWindows(int, int, int)),
2696           this,SLOT(WindowsChanged(int, int, int)));
2697   connect(mSlicerManagers.back(), SIGNAL(WindowLevelChanged(double, double,int, int)),
2698           this,SLOT(WindowLevelChanged(double, double, int, int)));
2699   connect(mSlicerManagers.back(), SIGNAL(UpdateSlice(int,int)),
2700           this,SLOT(UpdateSlice(int,int)));
2701   connect(mSlicerManagers.back(), SIGNAL(UpdateTSlice(int, int)),
2702           this,SLOT(UpdateTSlice(int, int)));
2703   connect(mSlicerManagers.back(), SIGNAL(UpdateSliceRange(int,int,int,int,int)),
2704           this,SLOT(UpdateSliceRange(int,int,int,int,int)));
2705   connect(mSlicerManagers.back(), SIGNAL(UpdateLinkManager(std::string,int,double,double,double,int)),
2706           this,SLOT(UpdateLinkManager(std::string,int,double,double,double,int)));
2707   connect(mSlicerManagers.back(), SIGNAL(UpdateLinkedNavigation(std::string,vvSlicerManager*)),
2708           this,SLOT(UpdateLinkedNavigation(std::string,vvSlicerManager*)));
2709   connect(mSlicerManagers.back(), SIGNAL(ChangeImageWithIndexOffset(vvSlicerManager*,int,int)),
2710           this,SLOT(ChangeImageWithIndexOffset(vvSlicerManager*,int,int)));
2711   connect(mSlicerManagers.back(), SIGNAL(LandmarkAdded()),landmarksPanel,SLOT(AddPoint()));
2712   UpdateTree();
2713   qApp->processEvents();
2714   InitSlicers();
2715   ShowLastImage();
2716   InitDisplay();
2717   qApp->processEvents();
2718
2719   // End
2720   return slicer_manager;
2721 }
2722 //------------------------------------------------------------------------------
2723
2724
2725 //------------------------------------------------------------------------------
2726 void vvMainWindow::UpdateCurrentSlicer()
2727 {
2728   int index = -1;
2729   if (DataTree->selectedItems().size() > 0) {
2730     index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2731   }
2732   mSlicerManagerCurrentIndex = index;
2733 }
2734 //------------------------------------------------------------------------------
2735