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         item->setToolTip(COLUMN_IMAGE_NAME,fileinfo.absoluteFilePath());
 825         qApp->processEvents();
 826
 827         //Create the buttons for reload and close
 828         qApp->processEvents();
 829         QTreePushButton* cButton = new QTreePushButton;
 830         cButton->setItem(item);
 831         cButton->setColumn(COLUMN_CLOSE_IMAGE);
 832         cButton->setToolTip(tr("close image"));
 833         cButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/exit.png")));
 834         connect(cButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
 835                 this,SLOT(CloseImage(QTreeWidgetItem*, int)));
 836
 837         QTreePushButton* rButton = new QTreePushButton;
 838         rButton->setItem(item);
 839         rButton->setColumn(COLUMN_RELOAD_IMAGE);
 840         rButton->setToolTip(tr("reload image"));
 841         rButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/rotateright.png")));
 842         connect(rButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
 843                 this,SLOT(ReloadImage(QTreeWidgetItem*, int)));
 844
 845         DataTree->addTopLevelItem(item);
 846         DataTree->setItemWidget(item, COLUMN_CLOSE_IMAGE, cButton);
 847         DataTree->setItemWidget(item, COLUMN_RELOAD_IMAGE, rButton);
 848
 849         //set the id of the image
 850         QString id = files[i].c_str() + QString::number(mSlicerManagers.size()-1);
 851         item->setData(COLUMN_IMAGE_NAME,Qt::UserRole,id.toStdString().c_str());
 852         mSlicerManagers.back()->SetId(id.toStdString());
 853
 854         linkPanel->addImage(imageManager->GetFileName(), id.toStdString());
 855
 856         connect(mSlicerManagers.back(), SIGNAL(currentImageChanged(std::string)),
 857                 this,SLOT(CurrentImageChanged(std::string)));
 858         connect(mSlicerManagers.back(), SIGNAL(UpdatePosition(int, double, double, double, double, double, double, double)),
 859                 this,SLOT(MousePositionChanged(int,double, double, double, double, double, double, double)));
 860         connect(mSlicerManagers.back(), SIGNAL(UpdateVector(int, double, double, double, double)),
 861                 this, SLOT(VectorChanged(int,double,double,double, double)));
 862         connect(mSlicerManagers.back(), SIGNAL(UpdateOverlay(int, double, double)),
 863                 this, SLOT(OverlayChanged(int,double,double)));
 864         connect(mSlicerManagers.back(), SIGNAL(UpdateFusion(int, double)),
 865                 this, SLOT(FusionChanged(int,double)));
 866         connect(mSlicerManagers.back(), SIGNAL(UpdateWindows(int, int, int)),
 867                 this,SLOT(WindowsChanged(int, int, int)));
 868         connect(mSlicerManagers.back(), SIGNAL(WindowLevelChanged(double, double,int, int)),
 869                 this,SLOT(WindowLevelChanged(double, double, int, int)));
 870         connect(mSlicerManagers.back(), SIGNAL(UpdateSlice(int,int)),
 871                 this,SLOT(UpdateSlice(int,int)));
 872         connect(mSlicerManagers.back(), SIGNAL(UpdateTSlice(int, int)),
 873                 this,SLOT(UpdateTSlice(int, int)));
 874         connect(mSlicerManagers.back(), SIGNAL(UpdateSliceRange(int,int,int,int,int)),
 875                 this,SLOT(UpdateSliceRange(int,int,int,int,int)));
 876         connect(mSlicerManagers.back(), SIGNAL(UpdateLinkManager(std::string,int,double,double,double,int)),
 877                 this,SLOT(UpdateLinkManager(std::string,int,double,double,double,int)));
 878         connect(mSlicerManagers.back(), SIGNAL(UpdateLinkedNavigation(std::string,vvSlicerManager*)),
 879                 this,SLOT(UpdateLinkedNavigation(std::string,vvSlicerManager*)));
 880         connect(mSlicerManagers.back(), SIGNAL(ChangeImageWithIndexOffset(vvSlicerManager*,int,int)),
 881                 this,SLOT(ChangeImageWithIndexOffset(vvSlicerManager*,int,int)));
 882         connect(mSlicerManagers.back(),SIGNAL(LandmarkAdded()),landmarksPanel,SLOT(AddPoint()));
 883         InitSlicers();
 884       }
 885       numberofsuccesulreads++;
 886     }
 887   }
 888   if (numberofsuccesulreads) {
 889     NOViewWidget->show();
 890     NEViewWidget->show();
 891     SOViewWidget->show();
 892     SEViewWidget->show();
 893     UpdateTree();
 894     InitDisplay();
 895     ShowLastImage();
 896
 897     // Try to guess default WindowLevel
 898     double range[2];
 899     mSlicerManagers.back()->GetImage()->GetFirstVTKImageData()->GetScalarRange(range);
 900     // DD(range[0]);
 901     //   DD(range[1]);
 902     if ((range[0] == 0) && (range[1] == 1)) {
 903       presetComboBox->setCurrentIndex(5);// binary
 904     } else {
 905       // TODO
 906     }
 907   }
 908   QApplication::restoreOverrideCursor();
 909 }
 910 //------------------------------------------------------------------------------
 911
 912 //------------------------------------------------------------------------------
 913 void vvMainWindow::UpdateTree()
 914 {
 915   DataTree->resizeColumnToContents(COLUMN_TREE);
 916   DataTree->resizeColumnToContents(COLUMN_UL_VIEW);
 917   DataTree->resizeColumnToContents(COLUMN_UR_VIEW);
 918   DataTree->resizeColumnToContents(COLUMN_DL_VIEW);
 919   DataTree->resizeColumnToContents(COLUMN_DR_VIEW);
 920   DataTree->resizeColumnToContents(COLUMN_IMAGE_NAME);
 921   DataTree->resizeColumnToContents(COLUMN_CLOSE_IMAGE);
 922   DataTree->resizeColumnToContents(COLUMN_RELOAD_IMAGE);
 923 }
 924 //------------------------------------------------------------------------------
 925
 926 //------------------------------------------------------------------------------
 927 void vvMainWindow::CurrentImageChanged(std::string id)
 928 {
 929   // DD("CurrentImageChanged");
 930 //   DD(id);
 931 //   DD(mCurrentSelectedImageId);
 932   if (id == mCurrentSelectedImageId) return; // Do nothing
 933   int selected = 0;
 934   for (int i = 0; i < DataTree->topLevelItemCount(); i++) {
 935     if (DataTree->topLevelItem(i)->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString().toStdString() == id) {
 936       selected = i;
 937     } else {
 938       DataTree->topLevelItem(i)->setSelected(0);
 939     }
 940     for (int child = 0; child < DataTree->topLevelItem(i)->childCount(); child++)
 941       DataTree->topLevelItem(i)->child(child)->setSelected(0);
 942
 943   }
 944   DataTree->topLevelItem(selected)->setSelected(1);
 945   // DD(mSlicerManagers[selected]->GetFileName());
 946   mCurrentSelectedImageId = id;
 947   emit SelectedImageHasChanged(mSlicerManagers[selected]);
 948 }
 949 //------------------------------------------------------------------------------
 950
 951 //------------------------------------------------------------------------------
 952 void vvMainWindow::ImageInfoChanged()
 953 {
 954   contextActions[6]->setEnabled(1);
 955   contextActions[5]->setEnabled(1);
 956   actionSave_As->setEnabled(1);
 957   actionAdd_VF_to_current_Image->setEnabled(1);
 958   actionAdd_fusion_image->setEnabled(1);
 959   actionNorth_East_Window->setEnabled(1);
 960   actionNorth_West_Window->setEnabled(1);
 961   actionSouth_East_Window->setEnabled(1);
 962   actionSouth_West_Window->setEnabled(1);
 963   inverseButton->setEnabled(1);
 964
 965   goToCursorPushButton->setEnabled(1);
 966
 967   if (DataTree->selectedItems().size()) {
 968     int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
 969
 970     colorMapComboBox->setEnabled(1);
 971     for (int i = 0; i < DataTree->topLevelItem(index)->childCount(); i++) {
 972       if (DataTree->topLevelItem(index)->child(i)->data(1,Qt::UserRole).toString() == "overlay" ||
 973           DataTree->topLevelItem(index)->child(i)->data(1,Qt::UserRole).toString() == "fusion") {
 974         colorMapComboBox->setEnabled(0);
 975         break;
 976       }
 977     }
 978
 979     std::vector<double> origin;
 980     std::vector<double> inputSpacing;
 981     std::vector<int> inputSize;
 982     std::vector<double> sizeMM;
 983     int dimension=0;
 984     QString pixelType;
 985     QString inputSizeInBytes;
 986     QString image = DataTree->selectedItems()[0]->data(COLUMN_IMAGE_NAME,Qt::DisplayRole).toString();
 987
 988     if (mSlicerManagers[index]->GetSlicer(0)->GetImage()->GetVTKImages().size() > 1 || playMode == 1) {
 989       playButton->setEnabled(1);
 990       frameRateLabel->setEnabled(1);
 991       frameRateSpinBox->setEnabled(1);
 992     } else {
 993       playButton->setEnabled(0);
 994       frameRateLabel->setEnabled(0);
 995       frameRateSpinBox->setEnabled(0);
 996     }
 997
 998     //read image header
 999     int NPixel = 1;
1000
1001     if (DataTree->topLevelItem(index) == DataTree->selectedItems()[0]) {
1002       vvImage::Pointer imageSelected = mSlicerManagers[index]->GetSlicer(0)->GetImage();
1003       dimension = imageSelected->GetNumberOfDimensions();
1004       origin.resize(dimension);
1005       inputSpacing.resize(dimension);
1006       inputSize.resize(dimension);
1007       sizeMM.resize(dimension);
1008       pixelType = mSlicerManagers[index]->GetImage()->GetScalarTypeAsITKString().c_str();
1009       for (int i = 0; i < dimension; i++) {
1010         origin[i] = imageSelected->GetOrigin()[i];
1011         inputSpacing[i] = imageSelected->GetSpacing()[i];
1012         inputSize[i] = imageSelected->GetSize()[i];
1013         sizeMM[i] = inputSize[i]*inputSpacing[i];
1014         NPixel *= inputSize[i];
1015       }
1016       inputSizeInBytes = GetSizeInBytes(imageSelected->GetActualMemorySize()*1000);
1017     } else if (DataTree->selectedItems()[0]->data(1,Qt::UserRole).toString() == "vector") {
1018       vvImage::Pointer imageSelected = mSlicerManagers[index]->GetSlicer(0)->GetVF();
1019       dimension = imageSelected->GetNumberOfDimensions();
1020       origin.resize(dimension);
1021       inputSpacing.resize(dimension);
1022       inputSize.resize(dimension);
1023       sizeMM.resize(dimension);
1024       pixelType = mSlicerManagers[index]->GetVF()->GetScalarTypeAsITKString().c_str();
1025       for (int i = 0; i < dimension; i++) {
1026         origin[i] = imageSelected->GetOrigin()[i];
1027         inputSpacing[i] = imageSelected->GetSpacing()[i];
1028         inputSize[i] = imageSelected->GetSize()[i];
1029         sizeMM[i] = inputSize[i]*inputSpacing[i];
1030         NPixel *= inputSize[i];
1031       }
1032       inputSizeInBytes = GetSizeInBytes(imageSelected->GetActualMemorySize()*1000);
1033     } else if (DataTree->selectedItems()[0]->data(1,Qt::UserRole).toString() == "overlay") {
1034       vvImage::Pointer imageSelected = mSlicerManagers[index]->GetSlicer(0)->GetOverlay();
1035       dimension = imageSelected->GetNumberOfDimensions();
1036       origin.resize(dimension);
1037       inputSpacing.resize(dimension);
1038       inputSize.resize(dimension);
1039       sizeMM.resize(dimension);
1040       pixelType = mSlicerManagers[index]->GetImage()->GetScalarTypeAsITKString().c_str();
1041       for (int i = 0; i < dimension; i++) {
1042         origin[i] = imageSelected->GetOrigin()[i];
1043         inputSpacing[i] = imageSelected->GetSpacing()[i];
1044         inputSize[i] = imageSelected->GetSize()[i];
1045         sizeMM[i] = inputSize[i]*inputSpacing[i];
1046         NPixel *= inputSize[i];
1047       }
1048       inputSizeInBytes = GetSizeInBytes(imageSelected->GetActualMemorySize()*1000);
1049     } else if (DataTree->selectedItems()[0]->data(1,Qt::UserRole).toString() == "fusion") {
1050       vvImage::Pointer imageSelected = mSlicerManagers[index]->GetSlicer(0)->GetFusion();
1051       dimension = imageSelected->GetNumberOfDimensions();
1052       origin.resize(dimension);
1053       inputSpacing.resize(dimension);
1054       inputSize.resize(dimension);
1055       sizeMM.resize(dimension);
1056       pixelType = mSlicerManagers[index]->GetImage()->GetScalarTypeAsITKString().c_str();
1057       for (int i = 0; i < dimension; i++) {
1058         origin[i] = imageSelected->GetOrigin()[i];
1059         inputSpacing[i] = imageSelected->GetSpacing()[i];
1060         inputSize[i] = imageSelected->GetSize()[i];
1061         sizeMM[i] = inputSize[i]*inputSpacing[i];
1062         NPixel *= inputSize[i];
1063       }
1064       inputSizeInBytes = GetSizeInBytes(imageSelected->GetActualMemorySize()*1000);
1065     }
1066
1067     QString dim = QString::number(dimension) + " (";
1068     dim += pixelType + ")";
1069
1070     infoPanel->setFileName(image);
1071     infoPanel->setDimension(dim);
1072     infoPanel->setSizePixel(GetVectorIntAsString(inputSize));
1073     infoPanel->setSizeMM(GetVectorDoubleAsString(sizeMM));
1074     infoPanel->setOrigin(GetVectorDoubleAsString(origin));
1075     infoPanel->setSpacing(GetVectorDoubleAsString(inputSpacing));
1076     infoPanel->setNPixel(QString::number(NPixel)+" ("+inputSizeInBytes+")");
1077
1078     landmarksPanel->SetCurrentLandmarks(mSlicerManagers[index]->GetLandmarks(),
1079                                         mSlicerManagers[index]->GetSlicer(0)->GetImage()->GetVTKImages().size());
1080     landmarksPanel->SetCurrentPath(mInputPathName.toStdString());
1081     landmarksPanel->SetCurrentImage(mSlicerManagers[index]->GetFileName().c_str());
1082
1083     overlayPanel->getCurrentImageName(mSlicerManagers[index]->GetFileName().c_str());
1084     for (int i = 0; i < 4; i++) {
1085       if (DataTree->selectedItems()[0]->data(i+1,Qt::CheckStateRole).toInt() > 0 || i == 3) {
1086         mSlicerManagers[index]->UpdateInfoOnCursorPosition(i);
1087         break;
1088       }
1089     }
1090     windowSpinBox->setValue(mSlicerManagers[index]->GetColorWindow());
1091     levelSpinBox->setValue(mSlicerManagers[index]->GetColorLevel());
1092     // DD(mSlicerManagers[index]->GetColorMap());
1093     // DD(mSlicerManagers[index]->GetPreset());
1094     presetComboBox->setCurrentIndex(mSlicerManagers[index]->GetPreset());
1095     colorMapComboBox->setCurrentIndex(mSlicerManagers[index]->GetColorMap());
1096
1097     infoPanel->setFileName(image);
1098     infoPanel->setDimension(dim);
1099     infoPanel->setSizePixel(GetVectorIntAsString(inputSize));
1100     infoPanel->setSizeMM(GetVectorDoubleAsString(sizeMM));
1101     infoPanel->setOrigin(GetVectorDoubleAsString(origin));
1102     infoPanel->setSpacing(GetVectorDoubleAsString(inputSpacing));
1103     infoPanel->setNPixel(QString::number(NPixel)+" ("+inputSizeInBytes+")");
1104
1105     landmarksPanel->SetCurrentLandmarks(mSlicerManagers[index]->GetLandmarks(),
1106                                         mSlicerManagers[index]->GetSlicer(0)->GetImage()->GetVTKImages().size());
1107     landmarksPanel->SetCurrentPath(mInputPathName.toStdString());
1108     landmarksPanel->SetCurrentImage(mSlicerManagers[index]->GetFileName().c_str());
1109
1110     overlayPanel->getCurrentImageName(mSlicerManagers[index]->GetFileName().c_str());
1111     for (int i = 0; i < 4; i++) {
1112       if (DataTree->selectedItems()[0]->data(i+1,Qt::CheckStateRole).toInt() > 0 || i == 3) {
1113         mSlicerManagers[index]->UpdateInfoOnCursorPosition(i);
1114         break;
1115       }
1116     }
1117     windowSpinBox->setValue(mSlicerManagers[index]->GetColorWindow());
1118     levelSpinBox->setValue(mSlicerManagers[index]->GetColorLevel());
1119     presetComboBox->setCurrentIndex(mSlicerManagers[index]->GetPreset());
1120     colorMapComboBox->setCurrentIndex(mSlicerManagers[index]->GetColorMap());
1121
1122     if (mSlicerManagers[index]->GetSlicer(0)->GetVF()) {
1123       overlayPanel->getVFName(mSlicerManagers[index]->GetVFName().c_str());
1124       overlayPanel->getVFProperty(mSlicerManagers[index]->GetSlicer(0)->GetVFSubSampling(),
1125                                   mSlicerManagers[index]->GetSlicer(0)->GetVFScale(),
1126                                   mSlicerManagers[index]->GetSlicer(0)->GetVFLog());
1127     } else {
1128       overlayPanel->getVFName(mSlicerManagers[index]->GetVFName().c_str());
1129       overlayPanel->getVFProperty(-1,-1,-1);
1130     }
1131     if (mSlicerManagers[index]->GetSlicer(0)->GetOverlay()) {
1132       overlayPanel->getOverlayName(mSlicerManagers[index]->GetOverlayName().c_str());
1133       overlayPanel->getOverlayProperty(mSlicerManagers[index]->GetOverlayColor());
1134     } else {
1135       overlayPanel->getOverlayName(mSlicerManagers[index]->GetOverlayName().c_str());
1136       overlayPanel->getOverlayProperty(-1);
1137     }
1138     if (mSlicerManagers[index]->GetSlicer(0)->GetFusion()) {
1139       overlayPanel->getFusionName(mSlicerManagers[index]->GetFusionName().c_str());
1140       overlayPanel->getFusionProperty(mSlicerManagers[index]->GetFusionOpacity(),
1141                                       mSlicerManagers[index]->GetFusionColorMap(),
1142                                       mSlicerManagers[index]->GetFusionWindow(),
1143                                       mSlicerManagers[index]->GetFusionLevel());
1144     } else {
1145       overlayPanel->getFusionName(mSlicerManagers[index]->GetFusionName().c_str());
1146       overlayPanel->getFusionProperty(-1, -1,-1,-1);
1147     }
1148   }
1149 }
1150 //------------------------------------------------------------------------------
1151
1152 //------------------------------------------------------------------------------
1153 void vvMainWindow::ShowDocumentation()
1154 {
1155   documentation->show();
1156 }
1157 //------------------------------------------------------------------------------
1158 void vvMainWindow::ShowHelpDialog()
1159 {
1160   help_dialog->show();
1161 }
1162 //------------------------------------------------------------------------------
1163
1164 //------------------------------------------------------------------------------
1165 void vvMainWindow::ChangeViewMode()
1166 {
1167   QListIterator<int> it0(splitter_3->sizes());
1168   QListIterator<int> it1(splitter_3->sizes());
1169   int max0 = 0;
1170   int max1 = 1;
1171   while (it0.hasNext()) {
1172     max0 += it0.next();
1173   }
1174   while (it1.hasNext()) {
1175     max1 += it1.next();
1176   }
1177   QList<int> size0;
1178   QList<int> size1;
1179   if (viewMode == 1) {
1180     viewMode = 0;
1181     size0.push_back(max0);
1182     size0.push_back(0);
1183     size1.push_back(max1);
1184     size1.push_back(0);
1185     splitter_3->setSizes(size0);
1186     OSplitter->setSizes(size1);
1187     DataTree->setColumnHidden(2,1);
1188     DataTree->setColumnHidden(3,1);
1189     DataTree->setColumnHidden(4,1);
1190   } else {
1191     viewMode = 1;
1192     size0.push_back(int(max0/2));
1193     size0.push_back(int(max0/2));
1194     size1.push_back(int(max1/2));
1195     size1.push_back(int(max1/2));
1196     splitter_3->setSizes(size0);
1197     OSplitter->setSizes(size1);
1198     DataTree->setColumnHidden(2,0);
1199     DataTree->setColumnHidden(3,0);
1200     DataTree->setColumnHidden(4,0);
1201   }
1202 }
1203 //------------------------------------------------------------------------------
1204
1205 //------------------------------------------------------------------------------
1206 QString vvMainWindow::GetSizeInBytes(unsigned long size)
1207 {
1208   QString result = "";// QString::number(size);
1209   //result += " bytes (";
1210   if (size > 1000000000) {
1211     size /= 1000000000;
1212     result += QString::number(size);
1213     result += "Gb";//)";
1214   } else if (size > 1000000) {
1215     size /= 1000000;
1216     result += QString::number(size);
1217     result += "Mb";//)";
1218   } else if (size > 1000) {
1219     size /= 1000;
1220     result += QString::number(size);
1221     result += "kb";//)";
1222   }
1223   return result;
1224 }
1225 //------------------------------------------------------------------------------
1226
1227 //------------------------------------------------------------------------------
1228 QString vvMainWindow::GetVectorDoubleAsString(std::vector<double> vectorDouble)
1229 {
1230   QString result;
1231   for (unsigned int i= 0; i < vectorDouble.size(); i++) {
1232     if (i != 0)
1233       result += " ";
1234     result += QString::number(vectorDouble[i]);
1235   }
1236   return result;
1237 }
1238 //------------------------------------------------------------------------------
1239
1240 //------------------------------------------------------------------------------
1241 QString vvMainWindow::GetVectorIntAsString(std::vector<int> vectorInt)
1242 {
1243   QString result;
1244   for (unsigned int i= 0; i < vectorInt.size(); i++) {
1245     if (i != 0)
1246       result += " ";
1247     result += QString::number(vectorInt[i]);
1248   }
1249   return result;
1250 }
1251 //------------------------------------------------------------------------------
1252
1253 //------------------------------------------------------------------------------
1254 int vvMainWindow::GetSlicerIndexFromItem(QTreeWidgetItem* item)
1255 {
1256   QString id = item->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString();
1257   for (int i = 0; i < DataTree->topLevelItemCount(); i++) {
1258     if (DataTree->topLevelItem(i)->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString() == id)
1259       return i;
1260   }
1261   return -1;
1262 }
1263 //------------------------------------------------------------------------------
1264
1265 //------------------------------------------------------------------------------
1266 QTreeWidgetItem* vvMainWindow::GetItemFromSlicerManager(vvSlicerManager* sm)
1267 {
1268   QString id = sm->GetId().c_str();
1269   for (int i = 0; i < DataTree->topLevelItemCount(); i++) {
1270     if (DataTree->topLevelItem(i)->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString() == id)
1271       return DataTree->topLevelItem(i);
1272   }
1273   return NULL;
1274 }
1275 //------------------------------------------------------------------------------
1276
1277 //------------------------------------------------------------------------------
1278 void vvMainWindow::DisplayChanged(QTreeWidgetItem *clicked_item, int column)
1279 {
1280   int index = GetSlicerIndexFromItem(clicked_item);
1281   if ( column >= COLUMN_CLOSE_IMAGE || column <= 0)
1282     return;
1283   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
1284     //Trick to avoid redoing twice the job for a key (sr)
1285     mSlicerManagers[i]->GetSlicer(column-1)->GetRenderWindow()-> GetInteractor()->SetKeySym("Crap");
1286
1287     QTreeWidgetItem* current_row=DataTree->topLevelItem(i);
1288     if (DataTree->topLevelItem(index) == current_row) {
1289       vvSlicer* clicked_slicer=mSlicerManagers[i]->GetSlicer(column-1);
1290       if (current_row == clicked_item) {
1291         //If we just activated a slicer
1292         if (current_row->data(column,Qt::CheckStateRole).toInt() > 0) {
1293           mSlicerManagers[i]->UpdateSlicer(column-1,clicked_item->data(column,Qt::CheckStateRole).toInt());
1294           mSlicerManagers[i]->UpdateInfoOnCursorPosition(column-1);
1295           DisplaySliders(i,column-1);
1296           std::map<std::string,int> overlay_counts;
1297           for (int child = 0; child < current_row->childCount(); child++) {
1298             std::string overlay_type =
1299               current_row->child(child)->data(1,Qt::UserRole).toString().toStdString();
1300             overlay_counts[overlay_type]++;
1301             current_row->child(child)->setData(column,Qt::CheckStateRole,
1302                                                current_row->data(column,Qt::CheckStateRole));
1303             clicked_slicer->SetActorVisibility(overlay_type,overlay_counts[overlay_type]-1,true);
1304           }
1305         } else { //We don't allow simply desactivating a slicer
1306           clicked_item->setData(column,Qt::CheckStateRole,2);
1307           return;
1308         }
1309       }
1310       //if we clicked on the vector(or overlay) and not the image
1311       else {
1312         if (clicked_item->data(column,Qt::CheckStateRole).toInt()) {
1313           current_row->setData(column,Qt::CheckStateRole,2);
1314           mSlicerManagers[i]->UpdateSlicer(column-1,2);
1315           mSlicerManagers[i]->UpdateInfoOnCursorPosition(column-1);
1316           DisplaySliders(i,column-1);
1317         }
1318         int vis = clicked_item->data(column,Qt::CheckStateRole).toInt();
1319         std::string overlay_type = clicked_item->data(1,Qt::UserRole).toString().toStdString();
1320         int overlay_index=0;
1321         for (int child = 0; child < current_row->childCount(); child++) {
1322           if (current_row->child(child)->data(1,Qt::UserRole).toString().toStdString() == overlay_type)
1323             overlay_index++;
1324           if (current_row->child(child) == clicked_item) break;
1325         }
1326         clicked_slicer->SetActorVisibility(
1327           clicked_item->data(1,Qt::UserRole).toString().toStdString(), overlay_index-1,vis);
1328       }
1329     } else if (current_row->data(column,Qt::CheckStateRole).toInt() > 0) {
1330       current_row->setData(column,Qt::CheckStateRole,0);
1331       mSlicerManagers[i]->UpdateSlicer(column-1,0);
1332       std::map<std::string,int> overlay_counts;
1333       for (int child = 0; child < current_row->childCount(); child++) {
1334         std::string overlay_type =
1335           current_row->child(child)->data(1,Qt::UserRole).toString().toStdString();
1336         overlay_counts[overlay_type]++;
1337         current_row->child(child)->setData(column,Qt::CheckStateRole,0);
1338         vvSlicer * current_slicer=mSlicerManagers[i]->GetSlicer(column-1);
1339         current_slicer->SetActorVisibility(overlay_type,overlay_counts[overlay_type]-1,false);
1340       }
1341     }
1342     //mSlicerManagers[i]->SetColorMap(-1);
1343     mSlicerManagers[i]->SetColorMap();
1344   }
1345   mSlicerManagers[index]->GetSlicer(column-1)->Render();
1346 }
1347 //------------------------------------------------------------------------------
1348
1349 void vvMainWindow::InitSlicers()
1350 {
1351   if (mSlicerManagers.size()) {
1352     mSlicerManagers.back()->GenerateDefaultLookupTable();
1353
1354     mSlicerManagers.back()->SetSlicerWindow(0,NOViewWidget->GetRenderWindow());
1355     mSlicerManagers.back()->SetSlicerWindow(1,NEViewWidget->GetRenderWindow());
1356     mSlicerManagers.back()->SetSlicerWindow(2,SOViewWidget->GetRenderWindow());
1357     mSlicerManagers.back()->SetSlicerWindow(3,SEViewWidget->GetRenderWindow());
1358   }
1359 }
1360
1361 //------------------------------------------------------------------------------
1362 void vvMainWindow::InitDisplay()
1363 {
1364   if (mSlicerManagers.size()) {
1365     //BE CAREFUL : this is absolutely necessary to set the interactor style
1366     //in order to have the same style instanciation for all SlicerManagers in
1367     // a same window
1368     for (int j = 0; j < 4; j++) {
1369       vvInteractorStyleNavigator* style = vvInteractorStyleNavigator::New();
1370       style->SetAutoAdjustCameraClippingRange(1);
1371       bool AlreadySelected = false;
1372       for (int i = 0; i < DataTree->topLevelItemCount(); i++) {
1373         mSlicerManagers[i]->SetInteractorStyleNavigator(j,style);
1374
1375         //select the image only if previous are not selected
1376         if (DataTree->topLevelItem(i)->data(j+1,Qt::CheckStateRole).toInt() > 1) {
1377           mSlicerManagers[i]->UpdateSlicer(j,1);
1378           AlreadySelected = true;
1379         } else if (i == DataTree->topLevelItemCount()-1 && !AlreadySelected) {
1380           if (DataTree->selectedItems().size() == 0)
1381             DataTree->topLevelItem(i)->setSelected(1);
1382           DataTree->topLevelItem(i)->setData(j+1,Qt::CheckStateRole,2);
1383           mSlicerManagers[i]->UpdateSlicer(j,1);
1384           DisplaySliders(i,j);
1385         } else {
1386           DataTree->topLevelItem(i)->setData(j+1,Qt::CheckStateRole,0);
1387           mSlicerManagers[i]->UpdateSlicer(j,0);
1388         }
1389       }
1390       style->Delete();
1391     }
1392   }
1393 }
1394 //------------------------------------------------------------------------------
1395
1396 //------------------------------------------------------------------------------
1397 void vvMainWindow::DisplaySliders(int slicer, int window)
1398 {
1399   int range[2];
1400   mSlicerManagers[slicer]->GetSlicer(window)->GetSliceRange(range);
1401   int position = mSlicerManagers[slicer]->GetSlicer(window)->GetSlice();
1402
1403   int tRange[2];
1404   tRange[0] = 0;
1405   tRange[1] = mSlicerManagers[slicer]->GetSlicer(window)->GetTMax();
1406   int tPosition = mSlicerManagers[slicer]->GetSlicer(window)->GetTSlice();
1407   bool showHorizontal = false;
1408   bool showVertical = false;
1409   if (mSlicerManagers[slicer]->GetSlicer(window)->GetImage()->GetNumberOfDimensions() > 3
1410       || (mSlicerManagers[slicer]->GetSlicer(window)->GetImage()->GetNumberOfDimensions() > 2
1411           && mSlicerManagers[slicer]->GetType() != IMAGEWITHTIME
1412           && mSlicerManagers[slicer]->GetType() != MERGEDWITHTIME))
1413     showVertical = true;
1414   if (mSlicerManagers[slicer]->GetSlicer(window)->GetImage()->GetNumberOfDimensions() > 3
1415       || mSlicerManagers[slicer]->GetType() == IMAGEWITHTIME
1416       || mSlicerManagers[slicer]->GetType() == MERGEDWITHTIME)
1417     showHorizontal = true;
1418
1419   if (showVertical)
1420     verticalSliders[window]->show();
1421   else
1422     verticalSliders[window]->hide();
1423   verticalSliders[window]->setRange(range[0],range[1]);
1424   verticalSliders[window]->setValue(position);
1425
1426   if (showHorizontal)
1427     horizontalSliders[window]->show();
1428   else
1429     horizontalSliders[window]->hide();
1430   horizontalSliders[window]->setRange(tRange[0],tRange[1]);
1431   horizontalSliders[window]->setValue(tPosition);
1432 }
1433 //------------------------------------------------------------------------------
1434
1435 //------------------------------------------------------------------------------
1436 void vvMainWindow::CloseImage(QTreeWidgetItem* item, int column)
1437 {
1438   int index = GetSlicerIndexFromItem(item);
1439
1440   if (DataTree->topLevelItem(index) != item) {
1441     QString warning = "Do you really want to close the overlay : ";
1442     warning += item->data(COLUMN_IMAGE_NAME,Qt::DisplayRole).toString();
1443     QMessageBox msgBox(QMessageBox::Warning, tr("Close Overlay"),
1444                        warning, 0, this);
1445     msgBox.addButton(tr("Close"), QMessageBox::AcceptRole);
1446     msgBox.addButton(tr("Cancel"), QMessageBox::RejectRole);
1447     if (msgBox.exec() == QMessageBox::AcceptRole) {
1448       std::string overlay_type=item->data(1,Qt::UserRole).toString().toStdString();
1449       int overlay_index=0;
1450       for (int child = 0; child < DataTree->topLevelItem(index)->childCount(); child++) {
1451         if (DataTree->topLevelItem(index)->\
1452             child(child)->data(1,Qt::UserRole).toString().toStdString() == overlay_type)
1453           overlay_index++;
1454         if (DataTree->topLevelItem(index)->child(child) == item) break;
1455       }
1456       mSlicerManagers[index]->RemoveActor(overlay_type, overlay_index-1);
1457       mSlicerManagers[index]->SetColorMap(0);
1458       DataTree->topLevelItem(index)->takeChild(DataTree->topLevelItem(index)->indexOfChild(item));
1459       mSlicerManagers[index]->Render();
1460     }
1461   } else if (DataTree->topLevelItemCount() <= 1) {
1462     QString warning = "Do you really want to close the image : ";
1463     warning += item->data(COLUMN_IMAGE_NAME,Qt::DisplayRole).toString();
1464     warning += "\nThis is the last image, you're about to close vv !!!";
1465     QMessageBox msgBox(QMessageBox::Warning, tr("Close Image"),
1466                        warning, 0, this);
1467     msgBox.addButton(tr("Close vv"), QMessageBox::AcceptRole);
1468     msgBox.addButton(tr("Cancel"), QMessageBox::RejectRole);
1469     if (msgBox.exec() == QMessageBox::AcceptRole) {
1470       this->close();
1471     }
1472   } else {
1473     QString warning = "Do you really want to close the image : ";
1474     warning += item->data(COLUMN_IMAGE_NAME,Qt::DisplayRole).toString();
1475     QMessageBox msgBox(QMessageBox::Warning, tr("Close Image"),
1476                        warning, 0, this);
1477     msgBox.addButton(tr("Close"), QMessageBox::AcceptRole);
1478     msgBox.addButton(tr("Cancel"), QMessageBox::RejectRole);
1479     if (msgBox.exec() == QMessageBox::AcceptRole) {
1480
1481       // Tell tools that we close an image
1482       emit AnImageIsBeingClosed(mSlicerManagers[index]);
1483
1484       std::vector<vvSlicerManager*>::iterator Manageriter = mSlicerManagers.begin();
1485       DataTree->takeTopLevelItem(index);
1486       for (int i = 0; i < index; i++) {
1487         Manageriter++;
1488       }
1489       linkPanel->removeImage(index);
1490       mSlicerManagers[index]->RemoveActors();
1491       delete mSlicerManagers[index];
1492       mSlicerManagers.erase(Manageriter);
1493
1494       //
1495       InitDisplay();
1496     }
1497   }
1498 }
1499 //------------------------------------------------------------------------------
1500
1501 //------------------------------------------------------------------------------
1502 void vvMainWindow::ReloadImage(QTreeWidgetItem* item, int column)
1503 {
1504   // int index = GetSlicerIndexFromItem(item);
1505   //   QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
1506   //   if (item->data(1,Qt::UserRole).toString() == "vector")
1507   //     mSlicerManagers[index]->ReloadVF();
1508   //   else
1509   //     mSlicerManagers[index]->Reload();
1510
1511   //   QApplication::restoreOverrideCursor();
1512   int index = GetSlicerIndexFromItem(item);
1513   QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
1514   QString role=item->data(1,Qt::UserRole).toString();
1515   if ( role == "vector")
1516     mSlicerManagers[index]->ReloadVF();
1517   else if (role == "overlay")
1518     mSlicerManagers[index]->ReloadOverlay();
1519   else if (role == "fusion")
1520     mSlicerManagers[index]->ReloadFusion();
1521   else
1522     mSlicerManagers[index]->Reload();
1523
1524   // Update view and info
1525   ImageInfoChanged();
1526   mSlicerManagers[index]->Render();
1527   QApplication::restoreOverrideCursor();
1528 }
1529 //------------------------------------------------------------------------------
1530
1531 //------------------------------------------------------------------------------
1532 void vvMainWindow::MousePositionChanged(int visibility,double x, double y, double z, double X, double Y, double Z , double value)
1533 {
1534   infoPanel->setCurrentInfo(visibility,x,y,z,X,Y,Z,value);
1535 }
1536 //------------------------------------------------------------------------------
1537
1538 //------------------------------------------------------------------------------
1539 void vvMainWindow::VectorChanged(int visibility,double x, double y, double z, double value)
1540 {
1541   overlayPanel->getCurrentVectorInfo(visibility,x,y,z,value);
1542 }
1543 //------------------------------------------------------------------------------
1544
1545 //------------------------------------------------------------------------------
1546 void vvMainWindow::OverlayChanged(int visibility, double valueOver, double valueRef)
1547 {
1548   overlayPanel->getCurrentOverlayInfo(visibility,valueOver, valueRef);
1549 }
1550 //------------------------------------------------------------------------------
1551
1552 //------------------------------------------------------------------------------
1553 void vvMainWindow::FusionChanged(int visibility, double value)
1554 {
1555   overlayPanel->getCurrentFusionInfo(visibility,value);
1556 }
1557 //------------------------------------------------------------------------------
1558
1559 //------------------------------------------------------------------------------
1560 void vvMainWindow::WindowsChanged(int window, int view, int slice)
1561 {
1562   infoPanel->setViews(window, view, slice);
1563 }
1564 //------------------------------------------------------------------------------
1565
1566 //------------------------------------------------------------------------------
1567 void vvMainWindow::WindowLevelChanged(double window, double level,int preset,int colormap)
1568 {
1569   windowSpinBox->setValue(window);
1570   levelSpinBox->setValue(level);
1571   colorMapComboBox->setCurrentIndex(colormap);
1572   presetComboBox->setCurrentIndex(preset);
1573 }
1574 //------------------------------------------------------------------------------
1575
1576 //------------------------------------------------------------------------------
1577 void vvMainWindow::WindowLevelEdited()
1578 {
1579   presetComboBox->setCurrentIndex(6);
1580   UpdateWindowLevel();
1581 }
1582 //------------------------------------------------------------------------------
1583
1584 //------------------------------------------------------------------------------
1585 void vvMainWindow::UpdateWindowLevel()
1586 {
1587   if (DataTree->selectedItems().size()) {
1588     if (presetComboBox->currentIndex() == 7) //For ventilation
1589       colorMapComboBox->setCurrentIndex(5);
1590     int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1591     mSlicerManagers[index]->SetColorWindow(windowSpinBox->value());
1592     mSlicerManagers[index]->SetColorLevel(levelSpinBox->value());
1593     mSlicerManagers[index]->SetPreset(presetComboBox->currentIndex());
1594     mSlicerManagers[index]->Render();
1595   }
1596 }
1597 //------------------------------------------------------------------------------
1598
1599 //------------------------------------------------------------------------------
1600 void vvMainWindow::UpdateColorMap()
1601 {
1602   if (DataTree->selectedItems().size()) {
1603     int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1604     mSlicerManagers[index]->SetColorMap(colorMapComboBox->currentIndex());
1605     mSlicerManagers[index]->Render();
1606   }
1607 }
1608 //------------------------------------------------------------------------------
1609 void vvMainWindow::SwitchWindowLevel()
1610 {
1611   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1612   int window = mSlicerManagers[index]->GetColorWindow();
1613   presetComboBox->setCurrentIndex(6);
1614   windowSpinBox->setValue(-window);
1615   UpdateWindowLevel();
1616 }
1617 //------------------------------------------------------------------------------
1618
1619 //------------------------------------------------------------------------------
1620 void vvMainWindow::UpdateLinkManager(std::string id, int slicer, double x, double y, double z, int temps)
1621 {
1622   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
1623     if (mSlicerManagers[i]->GetId() == id) {
1624       //mSlicerManagers[i]->SetTSlice(temps);
1625       mSlicerManagers[i]->GetSlicer(slicer)->SetCurrentPosition(x,y,z,temps);
1626       mSlicerManagers[i]->UpdateViews(0,slicer);
1627       break;
1628     }
1629   }
1630 }
1631 //------------------------------------------------------------------------------
1632
1633 //------------------------------------------------------------------------------
1634 void vvMainWindow::UpdateLinkedNavigation(std::string id, vvSlicerManager * sm)
1635 {
1636   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
1637     if (id == mSlicerManagers[i]->GetId()) {
1638       mSlicerManagers[i]->UpdateLinkedNavigation(sm->GetSlicer(0));
1639     }
1640   }
1641 }
1642 //------------------------------------------------------------------------------
1643
1644 //------------------------------------------------------------------------------
1645 void vvMainWindow::ShowContextMenu(QPoint point)
1646 {
1647   if (!DataTree->selectedItems().size()) {
1648     contextActions[1]->setEnabled(0);
1649     contextActions[2]->setEnabled(0);
1650     contextActions[3]->setEnabled(0);
1651     contextActions[4]->setEnabled(0);
1652     contextActions[5]->setEnabled(0);
1653     contextActions[6]->setEnabled(0);
1654   } else {
1655     int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1656     contextActions[1]->setEnabled(1);
1657     contextActions[2]->setEnabled(
1658       DataTree->itemWidget(DataTree->selectedItems()[0],
1659                            COLUMN_RELOAD_IMAGE)->isEnabled());
1660     contextActions[3]->setEnabled(1);
1661     contextActions[5]->setEnabled(1);
1662     contextActions[6]->setEnabled(1);
1663
1664     if (mSlicerManagers[index]->GetDimension() < 3)
1665       contextActions[4]->setEnabled(0);
1666     else
1667       contextActions[4]->setEnabled(1);
1668   }
1669   contextMenu.exec(QCursor::pos());
1670 }
1671 //------------------------------------------------------------------------------
1672
1673 //------------------------------------------------------------------------------
1674 void vvMainWindow::CloseImage()
1675 {
1676   CloseImage(DataTree->selectedItems()[0],0);
1677 }
1678 //------------------------------------------------------------------------------
1679
1680 //------------------------------------------------------------------------------
1681 void vvMainWindow::ReloadImage()
1682 {
1683   ReloadImage(DataTree->selectedItems()[0],0);
1684 }
1685 //------------------------------------------------------------------------------
1686
1687 //------------------------------------------------------------------------------
1688 void vvMainWindow::SelectOverlayImage()
1689 {
1690   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1691
1692   //check if one overlay image is added
1693   for (int child = 0; child < DataTree->topLevelItem(index)->childCount(); child++)
1694     if (DataTree->topLevelItem(index)->child(child)->data(1,Qt::UserRole).toString() == "overlay") {
1695       QString error = "Cannot add more than one compared image\n";
1696       error += "Please remove first ";
1697       error += DataTree->topLevelItem(index)->child(child)->data(COLUMN_IMAGE_NAME,Qt::DisplayRole).toString();
1698       QMessageBox::information(this,tr("Problem adding compared image !"),error);
1699       return;
1700     }
1701
1702   QString Extensions = EXTENSIONS;
1703   Extensions += ";;All Files (*)";
1704   QString file = QFileDialog::getOpenFileName(this,tr("Load Overlay image"),mInputPathName,Extensions);
1705   if (!file.isEmpty())
1706     AddOverlayImage(index,file);
1707 }
1708 //------------------------------------------------------------------------------
1709
1710 //------------------------------------------------------------------------------
1711 void vvMainWindow::AddOverlayImage(int index, QString file)
1712 {
1713
1714   mInputPathName = itksys::SystemTools::GetFilenamePath(file.toStdString()).c_str();
1715   itk::ImageIOBase::Pointer reader = itk::ImageIOFactory::CreateImageIO(
1716                                        file.toStdString().c_str(), itk::ImageIOFactory::ReadMode);
1717   reader->SetFileName(file.toStdString().c_str());
1718   reader->ReadImageInformation();
1719   std::string component = reader->GetComponentTypeAsString(reader->GetComponentType());
1720   int dimension = reader->GetNumberOfDimensions();
1721   QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
1722   vvProgressDialog progress("Opening " + file.toStdString());
1723   qApp->processEvents();
1724
1725   std::string filename = itksys::SystemTools::GetFilenameWithoutExtension(file.toStdString()).c_str();
1726   if (mSlicerManagers[index]->SetOverlay(file.toStdString(),dimension, component)) {
1727     //create an item in the tree with good settings
1728     QTreeWidgetItem *item = new QTreeWidgetItem();
1729     item->setData(0,Qt::UserRole,file.toStdString().c_str());
1730     item->setData(1,Qt::UserRole,tr("overlay"));
1731     QFileInfo fileinfo(file); //Do not show the path
1732     item->setData(COLUMN_IMAGE_NAME,Qt::DisplayRole,fileinfo.fileName());
1733     item->setToolTip(COLUMN_IMAGE_NAME,fileinfo.absoluteFilePath());
1734     qApp->processEvents();
1735
1736     for (int j = 1; j <= 4; j++) {
1737       item->setData(j,Qt::CheckStateRole,DataTree->topLevelItem(index)->data(j,Qt::CheckStateRole));
1738       mSlicerManagers[index]->GetSlicer(j-1)->SetActorVisibility("overlay",0,
1739           DataTree->topLevelItem(index)->data(j,Qt::CheckStateRole).toInt());
1740     }
1741
1742     //Create the buttons for reload and close
1743     qApp->processEvents();
1744     QTreePushButton* cButton = new QTreePushButton;
1745     cButton->setItem(item);
1746     cButton->setColumn(COLUMN_CLOSE_IMAGE);
1747     cButton->setToolTip(tr("close image"));
1748     cButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/exit.png")));
1749     connect(cButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
1750             this,SLOT(CloseImage(QTreeWidgetItem*, int)));
1751
1752     QTreePushButton* rButton = new QTreePushButton;
1753     rButton->setItem(item);
1754     rButton->setColumn(COLUMN_RELOAD_IMAGE);
1755     rButton->setToolTip(tr("reload image"));
1756     rButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/rotateright.png")));
1757     connect(rButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
1758             this,SLOT(ReloadImage(QTreeWidgetItem*, int)));
1759
1760     DataTree->topLevelItem(index)->setExpanded(1);
1761     DataTree->topLevelItem(index)->addChild(item);
1762     DataTree->setItemWidget(item, COLUMN_CLOSE_IMAGE, cButton);
1763     DataTree->setItemWidget(item, COLUMN_RELOAD_IMAGE, rButton);
1764
1765     //set the id of the image
1766     QString id = DataTree->topLevelItem(index)->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString();
1767     item->setData(COLUMN_IMAGE_NAME,Qt::UserRole,id.toStdString().c_str());
1768     UpdateTree();
1769     qApp->processEvents();
1770     ImageInfoChanged();
1771     QApplication::restoreOverrideCursor();
1772   } else {
1773     QApplication::restoreOverrideCursor();
1774     QString error = "Cannot import the new image.\n";
1775     error += mSlicerManagers[index]->GetLastError().c_str();
1776     QMessageBox::information(this,tr("Problem reading image !"),error);
1777   }
1778 }
1779 //------------------------------------------------------------------------------
1780
1781
1782 //------------------------------------------------------------------------------
1783 void vvMainWindow::AddROI(int index, QString file)
1784 {
1785   DD("AddImageAndROI");
1786   /*
1787   // Get slice manager
1788
1789   // Load image
1790
1791   vvImageReader * mReader = new vvImageReader;
1792   mReader->SetInputFilename(filename.toStdString());
1793   mReader->Update(IMAGE);
1794   if (mReader->GetLastError().size() != 0) {
1795     std::cerr << "Error while reading " << filename.toStdString() << std::endl;
1796     QString error = "Cannot open file \n";
1797     error += mReader->GetLastError().c_str();
1798     QMessageBox::information(this,tr("Reading problem"),error);
1799     delete mReader;
1800     return;
1801   }
1802   vvImage::Pointer roi = mReader->GetOutput();
1803
1804   // Create roi in new tool
1805   vvToolStructureSetManager::AddImage(mCurrentSlicerManager, roi);
1806 */
1807 }
1808 //------------------------------------------------------------------------------
1809
1810 //------------------------------------------------------------------------------
1811 void vvMainWindow::SelectFusionImage()
1812 {
1813   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1814
1815   //check if one fusion image is added
1816   for (int child = 0; child < DataTree->topLevelItem(index)->childCount(); child++)
1817     if (DataTree->topLevelItem(index)->child(child)->data(1,Qt::UserRole).toString() == "fusion") {
1818       QString error = "Cannot add more than one fusion image\n";
1819       error += "Please remove first ";
1820       error += DataTree->topLevelItem(index)->child(child)->data(COLUMN_IMAGE_NAME,Qt::DisplayRole).toString();
1821       QMessageBox::information(this,tr("Problem adding fusion image !"),error);
1822       return;
1823     }
1824
1825   QString Extensions = EXTENSIONS;
1826   Extensions += ";;All Files (*)";
1827   QString file = QFileDialog::getOpenFileName(this,tr("Load Fusion image"),mInputPathName,Extensions);
1828   if (!file.isEmpty())
1829     AddFusionImage(index,file);
1830 }
1831 //------------------------------------------------------------------------------
1832
1833 //------------------------------------------------------------------------------
1834 void vvMainWindow::AddFusionImage(int index, QString file)
1835 {
1836   mInputPathName = itksys::SystemTools::GetFilenamePath(file.toStdString()).c_str();
1837   itk::ImageIOBase::Pointer reader = itk::ImageIOFactory::CreateImageIO(
1838                                        file.toStdString().c_str(), itk::ImageIOFactory::ReadMode);
1839   reader->SetFileName(file.toStdString().c_str());
1840   reader->ReadImageInformation();
1841   std::string component = reader->GetComponentTypeAsString(reader->GetComponentType());
1842   if (reader) {
1843     QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
1844     vvProgressDialog progress("Opening fusion");
1845     qApp->processEvents();
1846
1847     std::string filename = itksys::SystemTools::GetFilenameWithoutExtension(file.toStdString()).c_str();
1848     if (mSlicerManagers[index]->SetFusion(file.toStdString(),
1849                                           reader->GetNumberOfDimensions(), component)) {
1850       //create an item in the tree with good settings
1851       QTreeWidgetItem *item = new QTreeWidgetItem();
1852       item->setData(0,Qt::UserRole,file.toStdString().c_str());
1853       item->setData(1,Qt::UserRole,tr("fusion"));
1854       QFileInfo fileinfo(filename.c_str()); //Do not show the path
1855       item->setData(COLUMN_IMAGE_NAME,Qt::DisplayRole,fileinfo.fileName());
1856       item->setToolTip(COLUMN_IMAGE_NAME,fileinfo.absoluteFilePath());
1857       qApp->processEvents();
1858
1859       for (int j = 1; j <= 4; j++) {
1860         item->setData(j,Qt::CheckStateRole,DataTree->topLevelItem(index)->data(j,Qt::CheckStateRole));
1861         mSlicerManagers[index]->GetSlicer(j-1)->SetActorVisibility("fusion",0,
1862             DataTree->topLevelItem(index)->data(j,Qt::CheckStateRole).toInt());
1863       }
1864
1865       //Create the buttons for reload and close
1866       qApp->processEvents();
1867       QTreePushButton* cButton = new QTreePushButton;
1868       cButton->setItem(item);
1869       cButton->setColumn(COLUMN_CLOSE_IMAGE);
1870       cButton->setToolTip(tr("close image"));
1871       cButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/exit.png")));
1872       connect(cButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
1873               this,SLOT(CloseImage(QTreeWidgetItem*, int)));
1874
1875       QTreePushButton* rButton = new QTreePushButton;
1876       rButton->setItem(item);
1877       rButton->setColumn(COLUMN_RELOAD_IMAGE);
1878       rButton->setToolTip(tr("reload image"));
1879       rButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/rotateright.png")));
1880       connect(rButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
1881               this,SLOT(ReloadImage(QTreeWidgetItem*, int)));
1882
1883       DataTree->topLevelItem(index)->setExpanded(1);
1884       DataTree->topLevelItem(index)->addChild(item);
1885       DataTree->setItemWidget(item, COLUMN_CLOSE_IMAGE, cButton);
1886       DataTree->setItemWidget(item, COLUMN_RELOAD_IMAGE, rButton);
1887
1888       //set the id of the image
1889       QString id = DataTree->topLevelItem(index)->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString();
1890       item->setData(COLUMN_IMAGE_NAME,Qt::UserRole,id.toStdString().c_str());
1891       UpdateTree();
1892       qApp->processEvents();
1893       ImageInfoChanged();
1894       QApplication::restoreOverrideCursor();
1895     } else {
1896       QApplication::restoreOverrideCursor();
1897       QString error = "Cannot import the new image.\n";
1898       error += mSlicerManagers[index]->GetLastError().c_str();
1899       QMessageBox::information(this,tr("Problem reading image !"),error);
1900     }
1901   } else {
1902     QString error = "Cannot import the new image.\n";
1903     QMessageBox::information(this,tr("Problem reading image !"),error);
1904   }
1905 }
1906 //------------------------------------------------------------------------------
1907
1908
1909 //------------------------------------------------------------------------------
1910 void vvMainWindow::OpenField()
1911 {
1912   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1913   //check if a vector field has already been added
1914   for (int child = 0; child < DataTree->topLevelItem(index)->childCount(); child++)
1915     if (DataTree->topLevelItem(index)->child(child)->data(1,Qt::UserRole).toString() == "vector") {
1916       QString error = "Cannot add more than one vector field\n";
1917       error += "Please remove first ";
1918       error += DataTree->topLevelItem(index)->child(child)->data(COLUMN_IMAGE_NAME,Qt::DisplayRole).toString();
1919       QMessageBox::information(this,tr("Problem adding vector field!"),error);
1920       return;
1921     }
1922
1923   QString Extensions = "Images ( *.mhd)";
1924   Extensions += ";;Images ( *.vf)";
1925   QString file = QFileDialog::getOpenFileName(this,tr("Load deformation field"),mInputPathName,Extensions);
1926   if (!file.isEmpty())
1927     AddField(file,index);
1928 }
1929 //------------------------------------------------------------------------------
1930
1931
1932 //------------------------------------------------------------------------------
1933 void vvMainWindow::AddFieldEntry(QString filename,int index,bool from_disk)
1934 {
1935   //create an item in the tree with good settings
1936   QTreeWidgetItem *item = new QTreeWidgetItem();
1937   item->setData(0,Qt::UserRole,filename.toStdString().c_str());
1938   item->setData(1,Qt::UserRole,tr("vector"));
1939   QFileInfo fileinfo(filename); //Do not show the path
1940   item->setData(COLUMN_IMAGE_NAME,Qt::DisplayRole,fileinfo.fileName());
1941   item->setToolTip(COLUMN_IMAGE_NAME,fileinfo.absoluteFilePath());
1942   qApp->processEvents();
1943
1944   for (int j = 1; j <= 4; j++) {
1945     item->setData(j,Qt::CheckStateRole,DataTree->topLevelItem(index)->data(j,Qt::CheckStateRole));
1946     mSlicerManagers[index]->GetSlicer(j-1)->SetActorVisibility("vector",0,
1947         DataTree->topLevelItem(index)->data(j,Qt::CheckStateRole).toInt());
1948   }
1949
1950   //Create the buttons for reload and close
1951   qApp->processEvents();
1952   QTreePushButton* cButton = new QTreePushButton;
1953   cButton->setItem(item);
1954   cButton->setColumn(COLUMN_CLOSE_IMAGE);
1955   cButton->setToolTip(tr("close vector field"));
1956   cButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/exit.png")));
1957   connect(cButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
1958           this,SLOT(CloseImage(QTreeWidgetItem*, int)));
1959
1960   QTreePushButton* rButton = new QTreePushButton;
1961   rButton->setItem(item);
1962   rButton->setColumn(COLUMN_RELOAD_IMAGE);
1963   rButton->setToolTip(tr("reload vector field"));
1964   rButton->setEnabled(from_disk);
1965   rButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/rotateright.png")));
1966   connect(rButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
1967           this,SLOT(ReloadImage(QTreeWidgetItem*, int)));
1968
1969   DataTree->topLevelItem(index)->setExpanded(1);
1970   DataTree->topLevelItem(index)->addChild(item);
1971   DataTree->setItemWidget(item, COLUMN_RELOAD_IMAGE, rButton);
1972   DataTree->setItemWidget(item, COLUMN_CLOSE_IMAGE, cButton);
1973
1974   //set the id of the image
1975   QString id = DataTree->topLevelItem(index)->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString();
1976   item->setData(COLUMN_IMAGE_NAME,Qt::UserRole,id.toStdString().c_str());
1977   UpdateTree();
1978   qApp->processEvents();
1979   ImageInfoChanged();
1980   QApplication::restoreOverrideCursor();
1981 }
1982 //------------------------------------------------------------------------------
1983
1984
1985 //------------------------------------------------------------------------------
1986 void vvMainWindow::AddField(vvImage::Pointer vf,QString file,int index)
1987 {
1988   QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
1989   vvSlicerManager* imageManager = mSlicerManagers[index];
1990   if (imageManager->SetVF(vf,file.toStdString())) {
1991     AddFieldEntry(file,index,false);
1992   } else {
1993     QString error = "Cannot import the vector field for this image.\n";
1994     error += imageManager->GetLastError().c_str();
1995     QMessageBox::information(this,tr("Problem reading VF !"),error);
1996   }
1997   QApplication::restoreOverrideCursor();
1998 }
1999 //------------------------------------------------------------------------------
2000
2001
2002 //------------------------------------------------------------------------------
2003 void vvMainWindow::AddField(QString file,int index)
2004 {
2005   if (QFile::exists(file)) {
2006     mInputPathName = itksys::SystemTools::GetFilenamePath(file.toStdString()).c_str();
2007
2008     //init the progress events
2009     QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
2010     vvProgressDialog progress("Opening " + file.toStdString());
2011     qApp->processEvents();
2012
2013     //read the vector and put it in the current mSlicerManager
2014     vvSlicerManager* imageManager = mSlicerManagers[index];
2015     qApp->processEvents();
2016
2017     std::string filename = itksys::SystemTools::GetFilenameWithoutExtension(file.toStdString()).c_str();
2018     if (imageManager->SetVF(file.toStdString())) {
2019       imageManager->Render();
2020       AddFieldEntry(file,index,true);
2021     } else {
2022       QApplication::restoreOverrideCursor();
2023       QString error = "Cannot import the vector field for this image.\n";
2024       error += imageManager->GetLastError().c_str();
2025       QMessageBox::information(this,tr("Problem reading VF !"),error);
2026     }
2027   } else
2028     QMessageBox::information(this,tr("Problem reading VF !"),"File doesn't exist!");
2029
2030 }
2031 //------------------------------------------------------------------------------
2032
2033
2034 //------------------------------------------------------------------------------
2035 void vvMainWindow::SetVFProperty(int subsampling, int scale, int log, int width)
2036 {
2037   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2038   if (mSlicerManagers[index]->GetSlicer(0)->GetVF()) {
2039     for (int i = 0; i < 4; i++) {
2040       mSlicerManagers[index]->GetSlicer(i)->SetVFSubSampling(subsampling);
2041       mSlicerManagers[index]->GetSlicer(i)->SetVFScale(scale);
2042       mSlicerManagers[index]->GetSlicer(i)->SetVFWidth(width);
2043       if (log > 0)
2044         mSlicerManagers[index]->GetSlicer(i)->SetVFLog(1);
2045       else
2046         mSlicerManagers[index]->GetSlicer(i)->SetVFLog(0);
2047     }
2048   }
2049 }
2050 //------------------------------------------------------------------------------
2051
2052
2053 //------------------------------------------------------------------------------
2054 void vvMainWindow::SetOverlayProperty(int color)
2055 {
2056   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2057   if (mSlicerManagers[index]->GetSlicer(0)->GetOverlay()) {
2058     mSlicerManagers[index]->SetOverlayColor(color);
2059     mSlicerManagers[index]->SetColorMap(0);
2060     mSlicerManagers[index]->Render();
2061   }
2062 }
2063 //------------------------------------------------------------------------------
2064
2065 //------------------------------------------------------------------------------
2066 void vvMainWindow::SetFusionProperty(int opacity, int colormap,double window, double level)
2067 {
2068   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2069   if (mSlicerManagers[index]->GetSlicer(0)->GetFusion()) {
2070     mSlicerManagers[index]->SetFusionOpacity(opacity);
2071     mSlicerManagers[index]->SetFusionColorMap(colormap);
2072     mSlicerManagers[index]->SetFusionWindow(window);
2073     mSlicerManagers[index]->SetFusionLevel(level);
2074     mSlicerManagers[index]->SetColorMap(0);
2075     mSlicerManagers[index]->Render();
2076   }
2077 }
2078 //------------------------------------------------------------------------------
2079
2080 //------------------------------------------------------------------------------
2081 void vvMainWindow::SaveAs()
2082 {
2083   if (DataTree->selectedItems()[0]->data(1,Qt::UserRole).toString() == "vector") {
2084     QMessageBox::warning(this,tr("Unsupported type"),tr("Sorry, saving a vector field is unsupported for the moment"));
2085     return;
2086   }
2087
2088   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2089   int dimension = mSlicerManagers[index]->GetDimension();
2090   QStringList OutputListeFormat;
2091   OutputListeFormat.clear();
2092   if (dimension == 1) {
2093     OutputListeFormat.push_back(".mhd");
2094   }
2095   if (dimension == 2) {
2096     OutputListeFormat.push_back(".bmp");
2097     OutputListeFormat.push_back(".png");
2098     OutputListeFormat.push_back(".jpeg");
2099     OutputListeFormat.push_back(".tif");
2100     OutputListeFormat.push_back(".mhd");
2101     OutputListeFormat.push_back(".hdr");
2102     OutputListeFormat.push_back(".vox");
2103   } else if (dimension == 3) {
2104     OutputListeFormat.push_back(".mhd");
2105     OutputListeFormat.push_back(".hdr");
2106     OutputListeFormat.push_back(".vox");
2107   } else if (dimension == 4) {
2108     OutputListeFormat.push_back(".mhd");
2109   }
2110   QString Extensions = "AllFiles(*.*)";
2111   for (int i = 0; i < OutputListeFormat.count(); i++) {
2112     Extensions += ";;Images ( *";
2113     Extensions += OutputListeFormat[i];
2114     Extensions += ")";
2115   }
2116   QString fileName = QFileDialog::getSaveFileName(this,
2117                      tr("Save As"),
2118                      mSlicerManagers[index]->GetFileName().c_str(),
2119                      Extensions);
2120   if (!fileName.isEmpty()) {
2121     std::string fileformat = itksys::SystemTools::GetFilenameLastExtension(fileName.toStdString());
2122     if (OutputListeFormat.contains(
2123           fileformat.c_str())) {
2124       QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
2125       std::string action = "Saving";
2126       vvProgressDialog progress("Saving "+fileName.toStdString());
2127       qApp->processEvents();
2128       vvImageWriter *writer = new vvImageWriter;
2129       writer->SetOutputFileName(fileName.toStdString());
2130       writer->SetInput(mSlicerManagers[index]->GetImage());
2131       writer->Update();
2132       QApplication::restoreOverrideCursor();
2133       if (writer->GetLastError().size()) {
2134         QString error = "Saving did not succeed\n";
2135         error += writer->GetLastError().c_str();
2136         QMessageBox::information(this,tr("Saving Problem"),error);
2137         SaveAs();
2138       }
2139     } else {
2140       QString error = fileformat.c_str();
2141       if (error.isEmpty())
2142         error += "no file format specified !";
2143       else
2144         error += " format unknown !!!\n";
2145       QMessageBox::information(this,tr("Saving Problem"),error);
2146       SaveAs();
2147     }
2148   }
2149 }
2150 //------------------------------------------------------------------------------
2151
2152
2153 //------------------------------------------------------------------------------
2154 void vvMainWindow::AddLink(QString image1,QString image2)
2155 {
2156   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
2157     if (image1.toStdString() == mSlicerManagers[i]->GetId()) {
2158       mSlicerManagers[i]->AddLink(image2.toStdString());
2159     }
2160     if (image2.toStdString() == mSlicerManagers[i]->GetId()) {
2161       mSlicerManagers[i]->AddLink(image1.toStdString());
2162     }
2163   }
2164 }
2165 //------------------------------------------------------------------------------
2166
2167
2168 //------------------------------------------------------------------------------
2169 void vvMainWindow::RemoveLink(QString image1,QString image2)
2170 {
2171   // DD("vvMainWindow:RemoveLink");
2172   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
2173     if (image1.toStdString() == mSlicerManagers[i]->GetId()) {
2174       mSlicerManagers[i]->RemoveLink(image2.toStdString());
2175     }
2176     if (image2.toStdString() == mSlicerManagers[i]->GetId()) {
2177       mSlicerManagers[i]->RemoveLink(image1.toStdString());
2178     }
2179   }
2180 }
2181 //------------------------------------------------------------------------------
2182
2183 //------------------------------------------------------------------------------
2184 void vvMainWindow::ChangeImageWithIndexOffset(vvSlicerManager *sm, int slicer, int offset)
2185 {
2186   int index = 0;
2187   while(sm != mSlicerManagers[index])
2188     index++;
2189   index = (index+offset) % mSlicerManagers.size();
2190
2191   QTreeWidgetItem* item = GetItemFromSlicerManager(mSlicerManagers[index]);
2192   //CurrentImageChanged(mSlicerManagers[index]->GetId()); //select new image
2193   item->setData(slicer+1,Qt::CheckStateRole,2);         //change checkbox
2194   DisplayChanged(item,slicer+1);
2195 }
2196 //------------------------------------------------------------------------------
2197
2198 void vvMainWindow::HorizontalSliderMoved(int value,int column, int slicer_index)
2199 {
2200   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
2201     if (DataTree->topLevelItem(i)->data(column,Qt::CheckStateRole).toInt() > 1) {
2202       for (int j = 0; j < 4; j++) {
2203         mSlicerManagers[i]->SetTSliceInSlicer(value,j);
2204         //if (mSlicerManagers[i]->GetSlicer(j)->GetImageActor()->GetVisibility())
2205         //UpdateTSlice(j,value);
2206       }
2207       mSlicerManagers[i]->GetSlicer(slicer_index)->Render();
2208       break;
2209     }
2210   }
2211 }
2212 //------------------------------------------------------------------------------
2213
2214
2215 //------------------------------------------------------------------------------
2216 void vvMainWindow::NOHorizontalSliderMoved()
2217 {
2218   // if (mCurrentTime == NOHorizontalSlider->value()) return;
2219   HorizontalSliderMoved(NOHorizontalSlider->value(),COLUMN_UL_VIEW,0);
2220 //  mCurrentTime = NOHorizontalSlider->value();
2221 }
2222 //------------------------------------------------------------------------------
2223
2224
2225 //------------------------------------------------------------------------------
2226 void vvMainWindow::NEHorizontalSliderMoved()
2227 {
2228   // if (mCurrentTime == NEHorizontalSlider->value()) return;
2229   HorizontalSliderMoved(NEHorizontalSlider->value(),COLUMN_UR_VIEW,1);
2230 //  mCurrentTime = NEHorizontalSlider->value();
2231 }
2232 //------------------------------------------------------------------------------
2233
2234
2235 //------------------------------------------------------------------------------
2236 void vvMainWindow::SOHorizontalSliderMoved()
2237 {
2238   // if (mCurrentTime == SOHorizontalSlider->value()) return;
2239   HorizontalSliderMoved(SOHorizontalSlider->value(),COLUMN_DL_VIEW,2);
2240   // mCurrentTime = SOHorizontalSlider->value();
2241 }
2242 //------------------------------------------------------------------------------
2243
2244
2245 //------------------------------------------------------------------------------
2246 void vvMainWindow::SEHorizontalSliderMoved()
2247 {
2248   // if (mCurrentTime == SEHorizontalSlider->value()) return;
2249   HorizontalSliderMoved(SEHorizontalSlider->value(),COLUMN_DR_VIEW,3);
2250   // mCurrentTime = SEHorizontalSlider->value();
2251 }
2252 //------------------------------------------------------------------------------
2253
2254 //------------------------------------------------------------------------------
2255 void vvMainWindow::NOVerticalSliderChanged()
2256 {
2257   static int value=-1;
2258   if (value == NOVerticalSlider->value()) return;
2259   else value = NOVerticalSlider->value();
2260   //  int value = NOVerticalSlider->value();
2261   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
2262     if (DataTree->topLevelItem(i)->data(COLUMN_UL_VIEW,Qt::CheckStateRole).toInt() > 1) {
2263       if (mSlicerManagers[i]->GetSlicer(0)->GetSlice() != value) {
2264         mSlicerManagers[i]->GetSlicer(0)->SetSlice(value);
2265         mSlicerManagers[i]->VerticalSliderHasChanged(0, value);
2266
2267         // If nor Update/Render -> slider not work
2268         // only render = ok navigation, but for contour Update needed but slower ?
2269
2270         mSlicerManagers[i]->UpdateSlice(0);  // <-- DS add this. Not too much update ? YES. but needed for ImageContour ...
2271         //mSlicerManagers[i]->GetSlicer(0)->Render(); // <-- DS add this, needed for contour, seems ok ? not too slow ?
2272       }
2273       break;
2274     }
2275   }
2276 }
2277 //------------------------------------------------------------------------------
2278
2279
2280 //------------------------------------------------------------------------------
2281 void vvMainWindow::NEVerticalSliderChanged()
2282 {
2283   static int value=-1;
2284   if (value == NEVerticalSlider->value()) return;
2285   else value = NEVerticalSlider->value();
2286   //  int value = NEVerticalSlider->value();
2287   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
2288     if (DataTree->topLevelItem(i)->data(COLUMN_UR_VIEW,Qt::CheckStateRole).toInt() > 1) {
2289       if (mSlicerManagers[i]->GetSlicer(1)->GetSlice() != value) {
2290         mSlicerManagers[i]->GetSlicer(1)->SetSlice(value);
2291         mSlicerManagers[i]->VerticalSliderHasChanged(1, value);
2292         mSlicerManagers[i]->UpdateSlice(1);
2293         //mSlicerManagers[i]->GetSlicer(1)->Render(); // <-- DS add this, needed for contour, seems ok ? not too slow ?
2294       }
2295       break;
2296     }
2297   }
2298 }
2299 //------------------------------------------------------------------------------
2300
2301
2302 //------------------------------------------------------------------------------
2303 void vvMainWindow::SOVerticalSliderChanged()
2304 {
2305   static int value=-1;
2306   // DD(value);
2307 //   DD(SOVerticalSlider->value());
2308   if (value == SOVerticalSlider->value()) return;
2309   else value = SOVerticalSlider->value();
2310   //int value = SOVerticalSlider->value();
2311   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
2312     if (DataTree->topLevelItem(i)->data(COLUMN_DL_VIEW,Qt::CheckStateRole).toInt() > 1) {
2313       if (mSlicerManagers[i]->GetSlicer(2)->GetSlice() != value) {
2314         mSlicerManagers[i]->GetSlicer(2)->SetSlice(value);
2315         mSlicerManagers[i]->VerticalSliderHasChanged(2, value);
2316         mSlicerManagers[i]->UpdateSlice(2);
2317         //mSlicerManagers[i]->GetSlicer(2)->Render(); // <-- DS add this, needed for contour, seems ok ? not too slow ?
2318       }
2319       // else { DD("avoid SOVerticalSlider slicer update"); }
2320       break;
2321     }
2322   }
2323 }
2324 //------------------------------------------------------------------------------
2325
2326
2327 //------------------------------------------------------------------------------
2328 void vvMainWindow::SEVerticalSliderChanged()
2329 {
2330   static int value=-1;
2331   if (value == SEVerticalSlider->value()) return;
2332   else value = SEVerticalSlider->value();
2333   // int value = SEVerticalSlider->value();
2334   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
2335     if (DataTree->topLevelItem(i)->data(COLUMN_DR_VIEW,Qt::CheckStateRole).toInt() > 1) {
2336       if (mSlicerManagers[i]->GetSlicer(3)->GetSlice() != value) {
2337         mSlicerManagers[i]->GetSlicer(3)->SetSlice(value);
2338         mSlicerManagers[i]->VerticalSliderHasChanged(3, value);
2339         mSlicerManagers[i]->UpdateSlice(3);
2340         //mSlicerManagers[i]->GetSlicer(3)->Render(); // <-- DS add this, needed for contour, seems ok ? not too slow ?
2341       }
2342       break;
2343     }
2344   }
2345 }
2346 //------------------------------------------------------------------------------
2347
2348
2349 //------------------------------------------------------------------------------
2350 void vvMainWindow::UpdateSlice(int slicer, int slice)
2351 {
2352   // DD("vvMainWindow::UpdateSlice");
2353 //   DD(slicer);
2354 //   DD(slice);
2355   if (slicer == 0) {
2356     //    if (slice != NOVerticalSlider->value())
2357     NOVerticalSlider->setValue(slice);
2358   } else {
2359     if (slicer == 1)
2360       NEVerticalSlider->setValue(slice);
2361     else {
2362       if (slicer == 2)
2363         SOVerticalSlider->setValue(slice);
2364       else {
2365         if (slicer == 3)
2366           SEVerticalSlider->setValue(slice);
2367       }
2368     }
2369   }
2370   // DD("vvMainWindow:UpdateSlice END");
2371 }
2372 //------------------------------------------------------------------------------
2373
2374
2375 //------------------------------------------------------------------------------
2376 void vvMainWindow::UpdateTSlice(int slicer, int slice)
2377 {
2378   switch (slicer) {
2379   case 0:
2380     NOHorizontalSlider->setValue(slice);
2381     break;
2382   case 1:
2383     NEHorizontalSlider->setValue(slice);
2384     break;
2385   case 2:
2386     SOHorizontalSlider->setValue(slice);
2387     break;
2388   case 3:
2389     SEHorizontalSlider->setValue(slice);
2390     break;
2391   }
2392 }
2393 //------------------------------------------------------------------------------
2394
2395
2396 //------------------------------------------------------------------------------
2397 void vvMainWindow::UpdateSliceRange(int slicer, int min, int max, int tmin, int tmax)
2398 {
2399   int position = int((min+max)/2);
2400   int tPosition = int((tmin+tmax)/2);
2401   if (slicer == 0) {
2402     NOVerticalSlider->setValue(position);
2403     NOVerticalSlider->setRange(min,max);
2404     NOHorizontalSlider->setRange(tmin,tmax);
2405     NOHorizontalSlider->setValue(tPosition);
2406   } else if (slicer == 1) {
2407     NEVerticalSlider->setValue(position);
2408     NEVerticalSlider->setRange(min,max);
2409     NEHorizontalSlider->setRange(tmin,tmax);
2410     NEHorizontalSlider->setValue(tPosition);
2411   } else if (slicer == 2) {
2412     SOVerticalSlider->setValue(position);
2413     SOVerticalSlider->setRange(min,max);
2414     SOHorizontalSlider->setRange(tmin,tmax);
2415     SOHorizontalSlider->setValue(tPosition);
2416   } else if (slicer == 3) {
2417     SEVerticalSlider->setValue(position);
2418     SEVerticalSlider->setRange(min,max);
2419     SEHorizontalSlider->setRange(tmin,tmax);
2420     SEHorizontalSlider->setValue(tPosition);
2421   }
2422 }
2423 //------------------------------------------------------------------------------
2424
2425
2426 //------------------------------------------------------------------------------
2427 void vvMainWindow::SaveNOScreenshot()
2428 {
2429   vtkWindowToImageFilter *w2i = vtkWindowToImageFilter::New();
2430   w2i->SetInput(NOViewWidget->GetRenderWindow());
2431   w2i->Update();
2432   SaveScreenshot(w2i->GetOutput());
2433   w2i->Delete();
2434 }
2435 //------------------------------------------------------------------------------
2436
2437
2438 //------------------------------------------------------------------------------
2439 void vvMainWindow::SaveNEScreenshot()
2440 {
2441   vtkWindowToImageFilter *w2i = vtkWindowToImageFilter::New();
2442   w2i->SetInput(NEViewWidget->GetRenderWindow());
2443   w2i->Update();
2444   SaveScreenshot(w2i->GetOutput());
2445   w2i->Delete();
2446 }
2447 //------------------------------------------------------------------------------
2448
2449
2450 //------------------------------------------------------------------------------
2451 void vvMainWindow::SaveSOScreenshot()
2452 {
2453   vtkWindowToImageFilter *w2i = vtkWindowToImageFilter::New();
2454   w2i->SetInput(SOViewWidget->GetRenderWindow());
2455   w2i->Update();
2456   SaveScreenshot(w2i->GetOutput());
2457   w2i->Delete();
2458 }
2459 //------------------------------------------------------------------------------
2460
2461
2462 //------------------------------------------------------------------------------
2463 void vvMainWindow::SaveSEScreenshot()
2464 {
2465   vtkWindowToImageFilter *w2i = vtkWindowToImageFilter::New();
2466   w2i->SetInput(SEViewWidget->GetRenderWindow());
2467   w2i->Update();
2468   SaveScreenshot(w2i->GetOutput());
2469   w2i->Delete();
2470 }
2471 //------------------------------------------------------------------------------
2472
2473
2474 //------------------------------------------------------------------------------
2475 void vvMainWindow::SaveScreenshot(vtkImageData* image)
2476 {
2477   QString Extensions = "Images( *.png);;";
2478   Extensions += "Images( *.jpg);;";
2479   Extensions += "Images( *.bmp);;";
2480   Extensions += "Images( *.tif);;";
2481   Extensions += "Images( *.ppm)";
2482   QString fileName = QFileDialog::getSaveFileName(this,
2483                      tr("Save As"),
2484                      itksys::SystemTools::GetFilenamePath(
2485                        mSlicerManagers[0]->GetFileName()).c_str(),
2486                      Extensions);
2487   if (!fileName.isEmpty()) {
2488     const char *ext = fileName.toStdString().c_str() + strlen(fileName.toStdString().c_str()) - 4;
2489     if (!strcmp(ext, ".bmp")) {
2490       vtkBMPWriter *bmp = vtkBMPWriter::New();
2491       bmp->SetInput(image);
2492       bmp->SetFileName(fileName.toStdString().c_str());
2493       bmp->Write();
2494       bmp->Delete();
2495     } else if (!strcmp(ext, ".tif")) {
2496       vtkTIFFWriter *tif = vtkTIFFWriter::New();
2497       tif->SetInput(image);
2498       tif->SetFileName(fileName.toStdString().c_str());
2499       tif->Write();
2500       tif->Delete();
2501     } else if (!strcmp(ext, ".ppm")) {
2502       vtkPNMWriter *pnm = vtkPNMWriter::New();
2503       pnm->SetInput(image);
2504       pnm->SetFileName(fileName.toStdString().c_str());
2505       pnm->Write();
2506       pnm->Delete();
2507     } else if (!strcmp(ext, ".png")) {
2508       vtkPNGWriter *png = vtkPNGWriter::New();
2509       png->SetInput(image);
2510       png->SetFileName(fileName.toStdString().c_str());
2511       png->Write();
2512       png->Delete();
2513     } else if (!strcmp(ext, ".jpg")) {
2514       vtkJPEGWriter *jpg = vtkJPEGWriter::New();
2515       jpg->SetInput(image);
2516       jpg->SetFileName(fileName.toStdString().c_str());
2517       jpg->Write();
2518       jpg->Delete();
2519     } else {
2520       QMessageBox::information(this,tr("Problem saving screenshot !"),tr("Cannot save image.\nPlease set a file extension !!!"));
2521     }
2522   }
2523
2524 }
2525 //------------------------------------------------------------------------------
2526
2527
2528 //------------------------------------------------------------------------------
2529 void vvMainWindow::GoToCursor()
2530 {
2531   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2532   for (int column = 1; column < 5; column++) {
2533     if (DataTree->selectedItems()[0]->data(column,Qt::CheckStateRole).toInt() > 1) {
2534       double* cursorPos = mSlicerManagers[index]->GetSlicer(column-1)->GetCursorPosition();
2535       mSlicerManagers[index]->GetSlicer(column-1)->SetCurrentPosition(
2536         cursorPos[0],cursorPos[1],cursorPos[2],cursorPos[3]);
2537       mSlicerManagers[index]->UpdateViews(1,column-1);
2538       mSlicerManagers[index]->UpdateLinked(column-1);
2539       break;
2540     }
2541   }
2542 }
2543 //------------------------------------------------------------------------------
2544
2545 //------------------------------------------------------------------------------
2546 void vvMainWindow::PlayPause()
2547 {
2548   if (playMode) {
2549     playMode = 0;
2550     playButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/player_play.png")));
2551     ImageInfoChanged();
2552     return;
2553   } else {
2554     int image_number=DataTree->topLevelItemCount();
2555     bool has_temporal;
2556     for (int i=0; i<image_number; i++)
2557       if (mSlicerManagers[i]->GetImage()->GetVTKImages().size() > 1) {
2558         has_temporal=true;
2559         break;
2560       }
2561     if (has_temporal) {
2562       playMode = 1;
2563       playButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/player_pause.png")));
2564       QTimer::singleShot(1000/mFrameRate, this, SLOT(PlayNext()));
2565     }
2566   }
2567 }
2568 //------------------------------------------------------------------------------
2569
2570 //------------------------------------------------------------------------------
2571 void vvMainWindow::PlayNext()
2572 {
2573   if (playMode && !this->isHidden()) {
2574     int image_number=DataTree->topLevelItemCount();
2575     ///Only play one slicer per SM, and only if the SM is being displayed
2576     for (int i=0; i<image_number; i++)
2577       for (int j=0; j<4; j++)
2578         if (mSlicerManagers[i]->GetImage()->GetVTKImages().size() > 1 &&
2579             DataTree->topLevelItem(i)->data(j+1,Qt::CheckStateRole).toInt() > 0) {
2580           mSlicerManagers[i]->SetNextTSlice(j);
2581           break;
2582         }
2583     QTimer::singleShot(1000/mFrameRate, this, SLOT(PlayNext()));
2584   }
2585 }
2586 //------------------------------------------------------------------------------
2587
2588 void vvMainWindow::ShowLastImage()
2589 {
2590   if (mSlicerManagers.size() > 1) {
2591     QTreeWidgetItem * item=DataTree->topLevelItem(DataTree->topLevelItemCount()-1);
2592     CurrentImageChanged(mSlicerManagers.back()->GetId()); //select new image
2593     item->setData(1,Qt::CheckStateRole,2); //show the new image in the first panel
2594     DisplayChanged(item,1);
2595   }
2596 }
2597
2598 //------------------------------------------------------------------------------
2599 void vvMainWindow::UpdateRenderWindows()
2600 {
2601   if (NOViewWidget->GetRenderWindow()) NOViewWidget->GetRenderWindow()->Render();
2602   if (NEViewWidget->GetRenderWindow()) NEViewWidget->GetRenderWindow()->Render();
2603   if (SOViewWidget->GetRenderWindow()) SOViewWidget->GetRenderWindow()->Render();
2604   if (SEViewWidget->GetRenderWindow()) SEViewWidget->GetRenderWindow()->Render();
2605 }
2606 //------------------------------------------------------------------------------
2607
2608 //------------------------------------------------------------------------------
2609 void vvMainWindow::SegmentationOnCurrentImage()
2610 {
2611   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2612
2613   vvSegmentationDialog segmentation;
2614   segmentation.SetImage(mSlicerManagers[index]->GetSlicer(0)->GetImage());
2615   segmentation.exec();
2616 }
2617 //------------------------------------------------------------------------------
2618
2619 void vvMainWindow::SurfaceViewerLaunch()
2620 {
2621   vvSurfaceViewerDialog surfaceViewer;
2622   surfaceViewer.exec();
2623 }
2624 //------------------------------------------------------------------------------
2625
2626
2627 //------------------------------------------------------------------------------
2628 int vvMainWindow::GetImageDuplicateFilenameNumber(std::string filename)
2629 {
2630   int number=0;
2631   for(unsigned int l=0; l<mSlicerManagers.size(); l++) {
2632     vvSlicerManager * v = mSlicerManagers[l];
2633     if (v->GetBaseFileName() ==
2634         vtksys::SystemTools::GetFilenameName(vtksys::SystemTools::GetFilenameWithoutLastExtension(filename))) {
2635       number = std::max(number, v->GetBaseFileNameNumber()+1);
2636     }
2637   }
2638   return number;
2639 }
2640 //------------------------------------------------------------------------------
2641
2642
2643 //------------------------------------------------------------------------------
2644 vvSlicerManager* vvMainWindow::AddImage(vvImage::Pointer image,std::string filename)
2645 {
2646   // Change filename if another image exist with the same name
2647   int number = GetImageDuplicateFilenameNumber(filename);
2648
2649   // Create new SliceManager
2650   vvSlicerManager* slicer_manager = new vvSlicerManager(4);
2651   slicer_manager->SetImage(image);//, IMAGE, number);
2652   //  filename = filename+"_"+clitk::toString(number);
2653   slicer_manager->SetFilename(filename, number);
2654   mSlicerManagers.push_back(slicer_manager);
2655
2656   //create an item in the tree with good settings
2657   QTreeWidgetItem *item = new QTreeWidgetItem();
2658   item->setData(0,Qt::UserRole,slicer_manager->GetFileName().c_str());//files[i].c_str());
2659   item->setData(COLUMN_IMAGE_NAME,Qt::DisplayRole,filename.c_str());
2660   qApp->processEvents();
2661
2662   for (int j = 1; j <= 4; j++) item->setData(j,Qt::CheckStateRole,1);
2663
2664   //Create the buttons for reload and close
2665   qApp->processEvents();
2666   QTreePushButton* cButton = new QTreePushButton;
2667   cButton->setItem(item);
2668   cButton->setColumn(COLUMN_CLOSE_IMAGE);
2669   cButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/exit.png")));
2670   connect(cButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
2671           this,SLOT(CloseImage(QTreeWidgetItem*, int)));
2672
2673   QTreePushButton* rButton = new QTreePushButton;
2674   rButton->setItem(item);
2675   rButton->setColumn(COLUMN_RELOAD_IMAGE);
2676   rButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/rotateright.png")));
2677   rButton->setEnabled(0);
2678   connect(rButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
2679           this,SLOT(ReloadImage(QTreeWidgetItem*, int)));
2680
2681   DataTree->addTopLevelItem(item);
2682   DataTree->setItemWidget(item, COLUMN_CLOSE_IMAGE, cButton);
2683   DataTree->setItemWidget(item, COLUMN_RELOAD_IMAGE, rButton);
2684
2685   //set the id of the image
2686   QString id = slicer_manager->GetFileName().c_str() + QString::number(mSlicerManagers.size()-1);
2687   item->setData(COLUMN_IMAGE_NAME,Qt::UserRole,id.toStdString().c_str());
2688   mSlicerManagers.back()->SetId(id.toStdString());
2689
2690   linkPanel->addImage(filename, id.toStdString());
2691
2692   connect(mSlicerManagers.back(), SIGNAL(currentImageChanged(std::string)),
2693           this, SLOT(CurrentImageChanged(std::string)));
2694   connect(mSlicerManagers.back(), SIGNAL(UpdatePosition(int, double, double, double, double, double, double, double)),
2695           this, SLOT(MousePositionChanged(int,double, double, double, double, double, double, double)));
2696   connect(mSlicerManagers.back(), SIGNAL(UpdateVector(int, double, double, double, double)),
2697           this, SLOT(VectorChanged(int,double,double,double, double)));
2698   connect(mSlicerManagers.back(), SIGNAL(UpdateOverlay(int, double, double)),
2699           this, SLOT(OverlayChanged(int,double,double)));
2700   connect(mSlicerManagers.back(), SIGNAL(UpdateFusion(int, double)),
2701           this, SLOT(FusionChanged(int,double)));
2702   connect(mSlicerManagers.back(), SIGNAL(UpdateWindows(int, int, int)),
2703           this,SLOT(WindowsChanged(int, int, int)));
2704   connect(mSlicerManagers.back(), SIGNAL(WindowLevelChanged(double, double,int, int)),
2705           this,SLOT(WindowLevelChanged(double, double, int, int)));
2706   connect(mSlicerManagers.back(), SIGNAL(UpdateSlice(int,int)),
2707           this,SLOT(UpdateSlice(int,int)));
2708   connect(mSlicerManagers.back(), SIGNAL(UpdateTSlice(int, int)),
2709           this,SLOT(UpdateTSlice(int, int)));
2710   connect(mSlicerManagers.back(), SIGNAL(UpdateSliceRange(int,int,int,int,int)),
2711           this,SLOT(UpdateSliceRange(int,int,int,int,int)));
2712   connect(mSlicerManagers.back(), SIGNAL(UpdateLinkManager(std::string,int,double,double,double,int)),
2713           this,SLOT(UpdateLinkManager(std::string,int,double,double,double,int)));
2714   connect(mSlicerManagers.back(), SIGNAL(UpdateLinkedNavigation(std::string,vvSlicerManager*)),
2715           this,SLOT(UpdateLinkedNavigation(std::string,vvSlicerManager*)));
2716   connect(mSlicerManagers.back(), SIGNAL(ChangeImageWithIndexOffset(vvSlicerManager*,int,int)),
2717           this,SLOT(ChangeImageWithIndexOffset(vvSlicerManager*,int,int)));
2718   connect(mSlicerManagers.back(), SIGNAL(LandmarkAdded()),landmarksPanel,SLOT(AddPoint()));
2719   UpdateTree();
2720   qApp->processEvents();
2721   InitSlicers();
2722   ShowLastImage();
2723   InitDisplay();
2724   qApp->processEvents();
2725
2726   // End
2727   return slicer_manager;
2728 }
2729 //------------------------------------------------------------------------------
2730
2731
2732 //------------------------------------------------------------------------------
2733 void vvMainWindow::UpdateCurrentSlicer()
2734 {
2735   int index = -1;
2736   if (DataTree->selectedItems().size() > 0) {
2737     index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2738   }
2739   mSlicerManagerCurrentIndex = index;
2740 }
2741 //------------------------------------------------------------------------------
2742