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   connect(applyWindowLevelToAllButton,SIGNAL(clicked()),this,SLOT(ApplyWindowLevelToAllImages()));
 272
 273
 274   connect(this,SIGNAL(customContextMenuRequested(QPoint)),this,SLOT(ShowContextMenu(QPoint)));
 275
 276   connect(linkPanel,SIGNAL(addLink(QString,QString)),this,SLOT(AddLink(QString,QString)));
 277   connect(linkPanel,SIGNAL(removeLink(QString,QString)),this,SLOT(RemoveLink(QString,QString)));
 278   connect(overlayPanel,SIGNAL(VFPropertyUpdated(int,int,int,int)),this,SLOT(SetVFProperty(int,int,int,int)));
 279   connect(overlayPanel,SIGNAL(OverlayPropertyUpdated(int)),this,SLOT(SetOverlayProperty(int)));
 280   connect(overlayPanel,SIGNAL(FusionPropertyUpdated(int,int,double,double)),
 281           this,SLOT(SetFusionProperty(int,int,double,double)));
 282   connect(landmarksPanel,SIGNAL(UpdateRenderWindows()),this,SLOT(UpdateRenderWindows()));
 283
 284   playMode = 0;//pause
 285   mFrameRate = 10;
 286   playButton->setEnabled(0);
 287   frameRateLabel->setEnabled(0);
 288   frameRateSpinBox->setEnabled(0);
 289   connect(playButton, SIGNAL(clicked()),this,SLOT(PlayPause()));
 290   connect(frameRateSpinBox, SIGNAL(valueChanged(int)),this,SLOT(ChangeFrameRate(int)));
 291
 292   goToCursorPushButton->setEnabled(0);
 293   connect(goToCursorPushButton, SIGNAL(clicked()),this,SLOT(GoToCursor()));
 294
 295   NOViewWidget->hide();
 296   NEViewWidget->hide();
 297   SOViewWidget->hide();
 298   SEViewWidget->hide();
 299
 300   //Recently opened files
 301   std::list<std::string> recent_files = GetRecentlyOpenedImages();
 302   if ( !recent_files.empty() ) {
 303     QMenu * rmenu = new QMenu("Recently opened files...");
 304     rmenu->setIcon(QIcon(QString::fromUtf8(":/common/icons/open.png")));
 305     menuFile->insertMenu(actionOpen_Image_With_Time,rmenu);
 306     menuFile->insertSeparator(actionOpen_Image_With_Time);
 307     for (std::list<std::string>::iterator i = recent_files.begin(); i!=recent_files.end(); i++) {
 308       QAction* current=new QAction(QIcon(QString::fromUtf8(":/common/icons/open.png")),
 309                                    (*i).c_str(),this);
 310       rmenu->addAction(current);
 311       connect(current,SIGNAL(triggered()),this,SLOT(OpenRecentImage()));
 312     }
 313   }
 314
 315   // Adding all new tools (insertion in the menu)
 316   vvToolManager::GetInstance()->InsertToolsInMenu(this);
 317
 318   if (!CLITK_EXPERIMENTAL)
 319     menuExperimental->menuAction()->setVisible(false);
 320 }
 321 //------------------------------------------------------------------------------
 322
 323
 324 //------------------------------------------------------------------------------
 325 void vvMainWindow::ComputeMIP()
 326 {
 327   vvMaximumIntensityProjection mip;
 328   vvSlicerManager* selected_slicer = mSlicerManagers[GetSlicerIndexFromItem(DataTree->selectedItems()[0])];
 329   QFileInfo info(selected_slicer->GetFileName().c_str());
 330   mip.Compute(selected_slicer);
 331   if (!mip.error)
 332     AddImage(mip.GetOutput(),info.path().toStdString()+"/"+info.completeBaseName().toStdString()+"_mip.mhd");
 333 }
 334 //------------------------------------------------------------------------------
 335
 336
 337 //------------------------------------------------------------------------------
 338 void vvMainWindow::ComputeMidPosition()
 339 {
 340   bool ok;
 341   int index=GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
 342   int ref = QInputDialog::getInteger(this,"Chose reference phase","Reference phase",0,0,\
 343                                      mSlicerManagers[index]->GetImage()->GetVTKImages().size()-1,1,&ok);
 344   if (ok) {
 345     vvMidPosition midp;
 346     midp.slicer_manager = mSlicerManagers[index];
 347     midp.reference_image_index = ref;
 348     QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
 349     midp.Update();
 350     if (midp.error)
 351       QMessageBox::warning(this, "Error computing midposition image",midp.error_message.c_str());
 352     else {
 353       QFileInfo info(midp.slicer_manager->GetFileName().c_str());
 354       AddImage(midp.output,info.path().toStdString()+"/"+info.completeBaseName().toStdString()+"_midposition.mhd");
 355     }
 356     QApplication::restoreOverrideCursor();
 357   }
 358 }
 359 //------------------------------------------------------------------------------
 360
 361
 362 //------------------------------------------------------------------------------
 363 void vvMainWindow::AddContour(int image_index, vvMesh::Pointer contour, bool propagation)
 364 {
 365   QTreeWidgetItem *item = new QTreeWidgetItem();
 366   item->setData(0,Qt::UserRole,"filename.vtk");
 367   item->setData(1,Qt::UserRole,tr("contour"));
 368   QBrush brush;
 369   brush.setColor(QColor(contour->r*255,contour->g*255,contour->b*255));
 370   brush.setStyle(Qt::SolidPattern);
 371   item->setData(COLUMN_IMAGE_NAME,Qt::BackgroundRole,brush);
 372   item->setData(COLUMN_IMAGE_NAME,Qt::DisplayRole,contour->structure_name.c_str());
 373
 374   for (int j = 1; j <= 4; j++)
 375     item->setData(j,Qt::CheckStateRole,DataTree->topLevelItem(image_index)->data(j,Qt::CheckStateRole));
 376
 377   QTreePushButton* cButton = new QTreePushButton;
 378   cButton->setItem(item);
 379   cButton->setColumn(COLUMN_CLOSE_IMAGE);
 380   cButton->setToolTip(tr("close image"));
 381   cButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/exit.png")));
 382   connect(cButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
 383           this,SLOT(CloseImage(QTreeWidgetItem*, int)));
 384
 385   QTreePushButton* rButton = new QTreePushButton;
 386   rButton->setItem(item);
 387   rButton->setColumn(COLUMN_RELOAD_IMAGE);
 388   rButton->setToolTip(tr("reload image"));
 389   rButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/rotateright.png")));
 390   rButton->setEnabled(false);
 391   //Not implemented
 392   //connect(rButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
 393   //this,SLOT(ReloadImage(QTreeWidgetItem*, int)));
 394
 395   DataTree->topLevelItem(image_index)->setExpanded(1);
 396   DataTree->topLevelItem(image_index)->addChild(item);
 397   DataTree->setItemWidget(item, COLUMN_CLOSE_IMAGE, cButton);
 398   DataTree->setItemWidget(item, COLUMN_RELOAD_IMAGE, rButton);
 399   QString id = DataTree->topLevelItem(image_index)->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString();
 400   item->setData(COLUMN_IMAGE_NAME,Qt::UserRole,id.toStdString().c_str());
 401
 402   UpdateTree();
 403   mSlicerManagers[image_index]->AddContour(contour,propagation);
 404   mSlicerManagers[image_index]->Render();
 405 }
 406 //------------------------------------------------------------------------------
 407
 408
 409 //------------------------------------------------------------------------------
 410 void vvMainWindow::OpenVTKContour()
 411 {
 412   if (mSlicerManagers.size() > 0) {
 413     QString Extensions = "Images ( *.vtk *.obj)";
 414     Extensions += ";;All Files (*)";
 415     QString file = QFileDialog::getOpenFileName(this,tr("Open vtkPolyData"),mInputPathName,Extensions);
 416     if (file.isNull())
 417       return;
 418     QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
 419     int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
 420     vvMeshReader reader;
 421     reader.SetImage(mSlicerManagers[index]->GetImage());
 422     reader.SetModeToVTK();
 423     reader.SetFilename(file.toStdString());
 424     reader.Update();
 425     AddContour(index,reader.GetOutput()[0],false);
 426     QApplication::restoreOverrideCursor();
 427   }
 428 }
 429 //------------------------------------------------------------------------------
 430
 431
 432 //------------------------------------------------------------------------------
 433 void vvMainWindow::OpenDCStructContour()
 434 {
 435   if (mSlicerManagers.size() > 0) {
 436     QString Extensions = "Dicom Files ( *.dcm RS*)";
 437     Extensions += ";;All Files (*)";
 438     QString file = QFileDialog::getOpenFileName(this,tr("Merge Images"),mInputPathName,Extensions);
 439     if (file.isNull())
 440       return;
 441     int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
 442     vvMeshReader reader;
 443     reader.SetFilename(file.toStdString());
 444     vvStructSelector selector;
 445     selector.SetStructures(reader.GetROINames());
 446     if (!mSlicerManagers[index]->GetVF().IsNull())
 447       selector.EnablePropagationCheckBox();
 448     if (selector.exec()) {
 449       QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
 450       reader.SetSelectedItems(selector.getSelectedItems());
 451       reader.SetImage(mSlicerManagers[index]->GetImage());
 452       if (selector.PropagationEnabled())
 453         reader.SetPropagationVF(mSlicerManagers[index]->GetVF());
 454       reader.Update();
 455       std::vector<vvMesh::Pointer> contours=reader.GetOutput();
 456       for (std::vector<vvMesh::Pointer>::iterator i=contours.begin();
 457            i!=contours.end(); i++)
 458         AddContour(index,*i,selector.PropagationEnabled());
 459       QApplication::restoreOverrideCursor();
 460     }
 461   }
 462 }
 463 //------------------------------------------------------------------------------
 464
 465
 466 //------------------------------------------------------------------------------
 467 void vvMainWindow::ComputeDeformableRegistration()
 468 {
 469   if (mSlicerManagers.size() > 0) {
 470     int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
 471     vvDeformationDialog dialog(index,mSlicerManagers);
 472     if (dialog.exec()) {
 473       std::string base_name=itksys::SystemTools::GetFilenameWithoutExtension(mSlicerManagers[dialog.GetInputFileIndex()]->GetFileName());
 474       AddField(dialog.GetOutput(),dialog.getFieldFile(),dialog.GetInputFileIndex());
 475       WarpImage(dialog.GetSelectedSlicer(),dialog.GetReferenceFrameIndex());
 476     } else
 477       std::cout << "Error or user cancellation while computing deformation field..." << std::endl;
 478   } else QMessageBox::information(this, "Need to open image","You must open an image first.");
 479 }
 480 //------------------------------------------------------------------------------
 481
 482
 483 //------------------------------------------------------------------------------
 484 void vvMainWindow::WarpImage()
 485 {
 486   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
 487   if (!mSlicerManagers[index]->GetVF().IsNull()) {
 488     bool ok;
 489     int ref = QInputDialog::getInteger(this,"Chose reference phase","Reference phase",0,0,\
 490                                        mSlicerManagers[index]->GetImage()->GetVTKImages().size()-1,1,&ok);
 491     if (ok) {
 492       WarpImage(mSlicerManagers[index],ref);
 493     }
 494   } else
 495     QMessageBox::warning(this,tr("No vector field"),tr("Sorry, can't warp without a vector field"));
 496 }
 497 //------------------------------------------------------------------------------
 498
 499
 500 //------------------------------------------------------------------------------
 501 void vvMainWindow::WarpImage(vvSlicerManager* selected_slicer,int reference_phase)
 502 {
 503   if (!selected_slicer->GetVF().IsNull()) {
 504     QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
 505     QFileInfo info(selected_slicer->GetFileName().c_str());
 506     vvImageWarp warp(selected_slicer->GetImage(),selected_slicer->GetVF(),
 507                      reference_phase,this);
 508     if (warp.ComputeWarpedImage()) {
 509       AddImage(warp.GetWarpedImage(),info.path().toStdString()+"/"+info.completeBaseName().toStdString()+"_warped.mhd");
 510       AddImage(warp.GetDiffImage()  ,info.path().toStdString()+"/"+info.completeBaseName().toStdString()+"_diff.mhd");
 511       AddImage(warp.GetJacobianImage()  ,info.path().toStdString()+"/"+info.completeBaseName().toStdString()+"_jacobian.mhd");
 512       QApplication::restoreOverrideCursor();
 513     } else {
 514       QApplication::restoreOverrideCursor();
 515       QMessageBox::warning(this,tr("Different spacings"),tr("The vector field and image spacings must be the same in order to warp."));
 516     }
 517   } else
 518     QMessageBox::warning(this,tr("No vector field"),tr("Sorry, can't warp without a vector field."));
 519 }
 520 //------------------------------------------------------------------------------
 521
 522
 523 //------------------------------------------------------------------------------
 524 vvMainWindow::~vvMainWindow()
 525 {
 526   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
 527     if (mSlicerManagers[i] != NULL)
 528       delete mSlicerManagers[i];
 529   }
 530 }
 531 //------------------------------------------------------------------------------
 532
 533 //------------------------------------------------------------------------------
 534 QTabWidget * vvMainWindow::GetTab()
 535 {
 536   return tabWidget;
 537 }
 538 //------------------------------------------------------------------------------
 539
 540
 541 //------------------------------------------------------------------------------
 542 void vvMainWindow::MergeImages()
 543 {
 544   QString Extensions = EXTENSIONS;
 545   Extensions += ";;All Files (*)";
 546   QStringList files = QFileDialog::getOpenFileNames(this,tr("Merge Images"),mInputPathName,Extensions);
 547   if (files.isEmpty())
 548     return;
 549   mInputPathName = itksys::SystemTools::GetFilenamePath(files[0].toStdString()).c_str();
 550   std::vector<std::string> vector;
 551
 552   unsigned int currentDim = 0;
 553   std::vector<double> currentSpacing;
 554   std::vector<int> currentSize;
 555   std::vector<double> currentOrigin;
 556
 557   for (int i = 0; i < files.size(); i++) {
 558     itk::ImageIOBase::Pointer reader = itk::ImageIOFactory::CreateImageIO(
 559                                          files[i].toStdString().c_str(), itk::ImageIOFactory::ReadMode);
 560     reader->SetFileName(files[i].toStdString().c_str());
 561     reader->ReadImageInformation();
 562     if (reader)        {
 563       //NOViewWidget->hide();
 564       //NEViewWidget->hide();
 565       //SOViewWidget->hide();
 566       //SEViewWidget->hide();
 567       if (i == 0)
 568         currentDim = reader->GetNumberOfDimensions();
 569       bool IsOk = true;
 570       for (unsigned int j = 0; j < currentDim; j++) {
 571         if (i == 0) {
 572           if (j == 0) {
 573             currentSpacing.resize(currentDim);
 574             currentSize.resize(currentDim);
 575             currentOrigin.resize(currentDim);
 576           }
 577           currentOrigin[j] = reader->GetOrigin(j);
 578           currentSpacing[j] = reader->GetSpacing(j);
 579           currentSize[j] = reader->GetDimensions(j);
 580         } else if (currentDim != reader->GetNumberOfDimensions()
 581                    || currentSpacing[j] != reader->GetSpacing(j)
 582                    || currentSize[j] != (int)reader->GetDimensions(j)
 583                    || currentOrigin[j] != reader->GetOrigin(j)) {
 584           QString error = "Cannot read file (too different from others ";
 585           error += files[i].toStdString().c_str();
 586           QMessageBox::information(this,tr("Reading problem"),error);
 587           IsOk = false;
 588           break;
 589         }
 590       }
 591       if (IsOk)
 592         vector.push_back(files[i].toStdString());
 593     }
 594   }
 595   if (vector.size() > 0)
 596     LoadImages(vector, MERGED);
 597 }
 598 //------------------------------------------------------------------------------
 599
 600 //------------------------------------------------------------------------------
 601 void vvMainWindow::SliceImages()
 602 {
 603   QString Extensions = EXTENSIONS;
 604   Extensions += ";;All Files (*)";
 605
 606   QStringList files = QFileDialog::getOpenFileNames(this,tr("Slice Images"),mInputPathName,Extensions);
 607   if (files.isEmpty())
 608     return;
 609   mInputPathName = itksys::SystemTools::GetFilenamePath(files[0].toStdString()).c_str();
 610   std::vector<std::string> vector;
 611   for (int i = 0; i < files.size(); i++)
 612     vector.push_back(files[i].toStdString());
 613   LoadImages(vector, SLICED);
 614 }
 615 //------------------------------------------------------------------------------
 616
 617 //------------------------------------------------------------------------------
 618 void vvMainWindow::MergeImagesWithTime()
 619 {
 620   QString Extensions = EXTENSIONS;
 621   Extensions += ";;All Files (*)";
 622   QStringList files = QFileDialog::getOpenFileNames(this,tr("Merge Images With Time"),mInputPathName,Extensions);
 623   if (files.isEmpty())
 624     return;
 625   mInputPathName = itksys::SystemTools::GetFilenamePath(files[0].toStdString()).c_str();
 626   std::vector<std::string> vector;
 627
 628   unsigned int currentDim = 0;
 629   std::vector<double> currentSpacing;
 630   std::vector<int> currentSize;
 631   std::vector<double> currentOrigin;
 632
 633   for (int i = 0; i < files.size(); i++) {
 634     itk::ImageIOBase::Pointer reader = itk::ImageIOFactory::CreateImageIO(
 635                                          files[i].toStdString().c_str(), itk::ImageIOFactory::ReadMode);
 636     if (reader) {
 637       reader->SetFileName(files[i].toStdString().c_str());
 638       reader->ReadImageInformation();
 639       if (i == 0)
 640         currentDim = reader->GetNumberOfDimensions();
 641       bool IsOk = true;
 642       for (unsigned int j = 0; j < currentDim; j++) {
 643         if (i == 0) {
 644           if (j == 0) {
 645             currentSpacing.resize(currentDim);
 646             currentSize.resize(currentDim);
 647             currentOrigin.resize(currentDim);
 648           }
 649           currentOrigin[j] = reader->GetOrigin(j);
 650           currentSpacing[j] = reader->GetSpacing(j);
 651           currentSize[j] = reader->GetDimensions(j);
 652         } else if (currentDim != reader->GetNumberOfDimensions()
 653                    || currentSpacing[j] != reader->GetSpacing(j)
 654                    || currentSize[j] != (int)reader->GetDimensions(j)
 655                    || currentOrigin[j] != reader->GetOrigin(j)) {
 656           QString error = "Cannot read file (too different from others ";
 657           error += files[i].toStdString().c_str();
 658           QMessageBox::information(this,tr("Reading problem"),error);
 659           IsOk = false;
 660           break;
 661         }
 662       }
 663       if (IsOk)
 664         vector.push_back(files[i].toStdString());
 665     } else {
 666       QString error = "Cannot read file info for ";
 667       error += files[i].toStdString().c_str();
 668       error += "\n";
 669       error += "Maybe you're trying to open an image in an unsupported format?\n";
 670       QMessageBox::information(this,tr("Reading problem"),error);
 671     }
 672   }
 673   sort(vector.begin(),vector.end());
 674   if (vector.size() > 1)
 675     LoadImages(vector, MERGEDWITHTIME);
 676   else
 677     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.");
 678 }
 679 //------------------------------------------------------------------------------
 680
 681
 682 //------------------------------------------------------------------------------
 683 void vvMainWindow::OpenDicom()
 684 {
 685   std::vector<std::string> files;
 686
 687   std::cout << "dicomSeriesSelector " << std::endl;
 688   if (dicomSeriesSelector->exec() == QDialog::Accepted) {
 689     files = *(dicomSeriesSelector->GetFilenames());
 690     LoadImages(files,DICOM);
 691   }
 692 }
 693 //------------------------------------------------------------------------------
 694
 695 //------------------------------------------------------------------------------
 696 void vvMainWindow::OpenImages()
 697 {
 698   QString Extensions = EXTENSIONS;
 699   Extensions += ";;All Files (*)";
 700
 701   QStringList files = QFileDialog::getOpenFileNames(this,tr("Load Images"),mInputPathName,Extensions);
 702   if (files.isEmpty())
 703     return;
 704   mInputPathName = itksys::SystemTools::GetFilenamePath(files[0].toStdString()).c_str();
 705   std::vector<std::string> vector;
 706   for (int i = 0; i < files.size(); i++)
 707     vector.push_back(files[i].toStdString());
 708   LoadImages(vector, IMAGE);
 709 }
 710 //------------------------------------------------------------------------------
 711 void vvMainWindow::OpenRecentImage()
 712 {
 713   QAction * caller = qobject_cast<QAction*>(sender());
 714   std::vector<std::string> images;
 715   images.push_back(caller->text().toStdString());
 716   mInputPathName = itksys::SystemTools::GetFilenamePath(images[0]).c_str();
 717   LoadImages(images,IMAGE);
 718 }
 719 //------------------------------------------------------------------------------
 720
 721
 722 //------------------------------------------------------------------------------
 723 void vvMainWindow::OpenImageWithTime()
 724 {
 725   QString Extensions = EXTENSIONS;
 726   Extensions += ";;All Files (*)";
 727
 728   QStringList files = QFileDialog::getOpenFileNames(this,tr("Load Images With Time"),mInputPathName,Extensions);
 729   if (files.isEmpty())
 730     return;
 731   mInputPathName = itksys::SystemTools::GetFilenamePath(files[0].toStdString()).c_str();
 732   std::vector<std::string> vector;
 733   for (int i = 0; i < files.size(); i++) {
 734     vector.push_back(files[i].toStdString());
 735   }
 736   LoadImages(vector, IMAGEWITHTIME);
 737 }
 738 //------------------------------------------------------------------------------
 739
 740
 741 //------------------------------------------------------------------------------
 742 void vvMainWindow::LoadImages(std::vector<std::string> files, LoadedImageType filetype)
 743 {
 744   //Separate the way to open images and dicoms
 745   int fileSize;
 746   if (filetype == IMAGE || filetype == IMAGEWITHTIME)
 747     fileSize = files.size();
 748   else
 749     fileSize = 1;
 750
 751   // For SLICED, we need the number of slices (ndim and #slices)
 752   std::vector<unsigned int> nSlices;
 753   nSlices.resize(files.size());
 754   std::fill(nSlices.begin(), nSlices.end(), 1);
 755   if (filetype == SLICED) {
 756     for (int i = 0; i < fileSize; i++) {
 757       itk::ImageIOBase::Pointer header = clitk::readImageHeader(files[i]);
 758       QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
 759       if (!header) {
 760         nSlices[i] = 0;
 761         QString error = "Cannot open file \n";
 762         error += files[i].c_str();
 763         QMessageBox::information(this,tr("Reading problem"),error);
 764         return;
 765       }
 766       if (header->GetNumberOfDimensions() < 3) {
 767         nSlices[i] = 0;
 768         QString error = "Dimension problem. Cannot slice \n";
 769         error += files[i].c_str();
 770         QMessageBox::information(this,tr("Reading problem"),error);
 771         return;
 772       }
 773       nSlices[i] = header->GetDimensions( header->GetNumberOfDimensions()-1 );
 774     }
 775   }
 776
 777   //Only add to the list of recently opened files when a single file is opened,
 778   //to avoid polluting the list of recently opened files
 779   if (files.size() == 1) {
 780     QFileInfo finfo=tr(files[0].c_str());
 781     AddToRecentlyOpenedImages(finfo.absoluteFilePath().toStdString());
 782   }
 783   //init the progress events
 784   QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
 785   vvProgressDialog progress("Opening " + files[0],fileSize>1);
 786   qApp->processEvents();
 787
 788   int numberofsuccesulreads=0;
 789   //open images as 1 or multiples
 790   for (int i = 0; i < fileSize; i++) {
 791
 792     progress.SetText("Opening " + files[i]);
 793     progress.SetProgress(i,fileSize);
 794     qApp->processEvents();
 795
 796     for (unsigned int j = 0; j < nSlices[i]; j++) {
 797       //read the image and put it in mSlicerManagers
 798       vvSlicerManager* imageManager = new vvSlicerManager(4);
 799       qApp->processEvents();
 800
 801       bool SetImageSucceed=false;
 802
 803       // Change filename if an image with the same already exist
 804       int number = GetImageDuplicateFilenameNumber(files[i] + std::string("_slice"));
 805
 806       if (filetype == IMAGE || filetype == IMAGEWITHTIME || filetype == SLICED)
 807         SetImageSucceed = imageManager->SetImage(files[i],filetype, number, j);
 808       else {
 809         SetImageSucceed = imageManager->SetImages(files,filetype, number);
 810       }
 811       if (SetImageSucceed == false) {
 812         QApplication::restoreOverrideCursor();
 813         QString error = "Cannot open file \n";
 814         error += imageManager->GetLastError().c_str();
 815         QMessageBox::information(this,tr("Reading problem"),error);
 816         delete imageManager;
 817       } else {
 818         mSlicerManagers.push_back(imageManager);
 819
 820         //create an item in the tree with good settings
 821         QTreeWidgetItem *item = new QTreeWidgetItem();
 822         item->setData(0,Qt::UserRole,files[i].c_str());
 823         QFileInfo fileinfo(imageManager->GetFileName().c_str()); //Do not show the path
 824         item->setData(COLUMN_IMAGE_NAME,Qt::DisplayRole,fileinfo.fileName());
 825         item->setToolTip(COLUMN_IMAGE_NAME,fileinfo.absoluteFilePath());
 826         qApp->processEvents();
 827
 828         //Create the buttons for reload and close
 829         qApp->processEvents();
 830         QTreePushButton* cButton = new QTreePushButton;
 831         cButton->setItem(item);
 832         cButton->setColumn(COLUMN_CLOSE_IMAGE);
 833         cButton->setToolTip(tr("close image"));
 834         cButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/exit.png")));
 835         connect(cButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
 836                 this,SLOT(CloseImage(QTreeWidgetItem*, int)));
 837
 838         QTreePushButton* rButton = new QTreePushButton;
 839         rButton->setItem(item);
 840         rButton->setColumn(COLUMN_RELOAD_IMAGE);
 841         rButton->setToolTip(tr("reload image"));
 842         rButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/rotateright.png")));
 843         connect(rButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
 844                 this,SLOT(ReloadImage(QTreeWidgetItem*, int)));
 845
 846         DataTree->addTopLevelItem(item);
 847         DataTree->setItemWidget(item, COLUMN_CLOSE_IMAGE, cButton);
 848         DataTree->setItemWidget(item, COLUMN_RELOAD_IMAGE, rButton);
 849
 850         //set the id of the image
 851         QString id = files[i].c_str() + QString::number(mSlicerManagers.size()-1);
 852         item->setData(COLUMN_IMAGE_NAME,Qt::UserRole,id.toStdString().c_str());
 853         mSlicerManagers.back()->SetId(id.toStdString());
 854
 855         linkPanel->addImage(imageManager->GetFileName(), id.toStdString());
 856
 857         connect(mSlicerManagers.back(), SIGNAL(currentImageChanged(std::string)),
 858                 this,SLOT(CurrentImageChanged(std::string)));
 859         connect(mSlicerManagers.back(), SIGNAL(UpdatePosition(int, double, double, double, double, double, double, double)),
 860                 this,SLOT(MousePositionChanged(int,double, double, double, double, double, double, double)));
 861         connect(mSlicerManagers.back(), SIGNAL(UpdateVector(int, double, double, double, double)),
 862                 this, SLOT(VectorChanged(int,double,double,double, double)));
 863         connect(mSlicerManagers.back(), SIGNAL(UpdateOverlay(int, double, double)),
 864                 this, SLOT(OverlayChanged(int,double,double)));
 865         connect(mSlicerManagers.back(), SIGNAL(UpdateFusion(int, double)),
 866                 this, SLOT(FusionChanged(int,double)));
 867         connect(mSlicerManagers.back(), SIGNAL(UpdateWindows(int, int, int)),
 868                 this,SLOT(WindowsChanged(int, int, int)));
 869         connect(mSlicerManagers.back(), SIGNAL(WindowLevelChanged(double, double,int, int)),
 870                 this,SLOT(WindowLevelChanged(double, double, int, int)));
 871         connect(mSlicerManagers.back(), SIGNAL(UpdateSlice(int,int)),
 872                 this,SLOT(UpdateSlice(int,int)));
 873         connect(mSlicerManagers.back(), SIGNAL(UpdateTSlice(int, int)),
 874                 this,SLOT(UpdateTSlice(int, int)));
 875         connect(mSlicerManagers.back(), SIGNAL(UpdateSliceRange(int,int,int,int,int)),
 876                 this,SLOT(UpdateSliceRange(int,int,int,int,int)));
 877         connect(mSlicerManagers.back(), SIGNAL(UpdateLinkManager(std::string,int,double,double,double,int)),
 878                 this,SLOT(UpdateLinkManager(std::string,int,double,double,double,int)));
 879         connect(mSlicerManagers.back(), SIGNAL(UpdateLinkedNavigation(std::string,vvSlicerManager*)),
 880                 this,SLOT(UpdateLinkedNavigation(std::string,vvSlicerManager*)));
 881         connect(mSlicerManagers.back(), SIGNAL(ChangeImageWithIndexOffset(vvSlicerManager*,int,int)),
 882                 this,SLOT(ChangeImageWithIndexOffset(vvSlicerManager*,int,int)));
 883         connect(mSlicerManagers.back(),SIGNAL(LandmarkAdded()),landmarksPanel,SLOT(AddPoint()));
 884         InitSlicers();
 885       }
 886       numberofsuccesulreads++;
 887     }
 888   }
 889   if (numberofsuccesulreads) {
 890     NOViewWidget->show();
 891     NEViewWidget->show();
 892     SOViewWidget->show();
 893     SEViewWidget->show();
 894     UpdateTree();
 895     InitDisplay();
 896     ShowLastImage();
 897
 898     // Try to guess default WindowLevel
 899     double range[2];
 900     mSlicerManagers.back()->GetImage()->GetFirstVTKImageData()->GetScalarRange(range);
 901     // DD(range[0]);
 902     //   DD(range[1]);
 903     if ((range[0] == 0) && (range[1] == 1)) {
 904       presetComboBox->setCurrentIndex(5);// binary
 905     } else {
 906       // TODO
 907     }
 908   }
 909   QApplication::restoreOverrideCursor();
 910 }
 911 //------------------------------------------------------------------------------
 912
 913 //------------------------------------------------------------------------------
 914 void vvMainWindow::UpdateTree()
 915 {
 916   DataTree->resizeColumnToContents(COLUMN_TREE);
 917   DataTree->resizeColumnToContents(COLUMN_UL_VIEW);
 918   DataTree->resizeColumnToContents(COLUMN_UR_VIEW);
 919   DataTree->resizeColumnToContents(COLUMN_DL_VIEW);
 920   DataTree->resizeColumnToContents(COLUMN_DR_VIEW);
 921   DataTree->resizeColumnToContents(COLUMN_IMAGE_NAME);
 922   DataTree->resizeColumnToContents(COLUMN_CLOSE_IMAGE);
 923   DataTree->resizeColumnToContents(COLUMN_RELOAD_IMAGE);
 924 }
 925 //------------------------------------------------------------------------------
 926
 927 //------------------------------------------------------------------------------
 928 void vvMainWindow::CurrentImageChanged(std::string id)
 929 {
 930   // DD("CurrentImageChanged");
 931 //   DD(id);
 932 //   DD(mCurrentSelectedImageId);
 933   if (id == mCurrentSelectedImageId) return; // Do nothing
 934   int selected = 0;
 935   for (int i = 0; i < DataTree->topLevelItemCount(); i++) {
 936     if (DataTree->topLevelItem(i)->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString().toStdString() == id) {
 937       selected = i;
 938     } else {
 939       DataTree->topLevelItem(i)->setSelected(0);
 940     }
 941     for (int child = 0; child < DataTree->topLevelItem(i)->childCount(); child++)
 942       DataTree->topLevelItem(i)->child(child)->setSelected(0);
 943
 944   }
 945   DataTree->topLevelItem(selected)->setSelected(1);
 946   // DD(mSlicerManagers[selected]->GetFileName());
 947   mCurrentSelectedImageId = id;
 948   emit SelectedImageHasChanged(mSlicerManagers[selected]);
 949 }
 950 //------------------------------------------------------------------------------
 951
 952 //------------------------------------------------------------------------------
 953 void vvMainWindow::ImageInfoChanged()
 954 {
 955   contextActions[6]->setEnabled(1);
 956   contextActions[5]->setEnabled(1);
 957   actionSave_As->setEnabled(1);
 958   actionAdd_VF_to_current_Image->setEnabled(1);
 959   actionAdd_fusion_image->setEnabled(1);
 960   actionNorth_East_Window->setEnabled(1);
 961   actionNorth_West_Window->setEnabled(1);
 962   actionSouth_East_Window->setEnabled(1);
 963   actionSouth_West_Window->setEnabled(1);
 964   inverseButton->setEnabled(1);
 965
 966   goToCursorPushButton->setEnabled(1);
 967
 968   if (DataTree->selectedItems().size()) {
 969     int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
 970
 971     colorMapComboBox->setEnabled(1);
 972     for (int i = 0; i < DataTree->topLevelItem(index)->childCount(); i++) {
 973       if (DataTree->topLevelItem(index)->child(i)->data(1,Qt::UserRole).toString() == "overlay" ||
 974           DataTree->topLevelItem(index)->child(i)->data(1,Qt::UserRole).toString() == "fusion") {
 975         colorMapComboBox->setEnabled(0);
 976         break;
 977       }
 978     }
 979
 980     std::vector<double> origin;
 981     std::vector<double> inputSpacing;
 982     std::vector<int> inputSize;
 983     std::vector<double> sizeMM;
 984     int dimension=0;
 985     QString pixelType;
 986     QString inputSizeInBytes;
 987     QString image = DataTree->selectedItems()[0]->data(COLUMN_IMAGE_NAME,Qt::DisplayRole).toString();
 988
 989     if (mSlicerManagers[index]->GetSlicer(0)->GetImage()->GetVTKImages().size() > 1 || playMode == 1) {
 990       playButton->setEnabled(1);
 991       frameRateLabel->setEnabled(1);
 992       frameRateSpinBox->setEnabled(1);
 993     } else {
 994       playButton->setEnabled(0);
 995       frameRateLabel->setEnabled(0);
 996       frameRateSpinBox->setEnabled(0);
 997     }
 998
 999     //read image header
1000     int NPixel = 1;
1001
1002     if (DataTree->topLevelItem(index) == DataTree->selectedItems()[0]) {
1003       vvImage::Pointer imageSelected = mSlicerManagers[index]->GetSlicer(0)->GetImage();
1004       dimension = imageSelected->GetNumberOfDimensions();
1005       origin.resize(dimension);
1006       inputSpacing.resize(dimension);
1007       inputSize.resize(dimension);
1008       sizeMM.resize(dimension);
1009       pixelType = mSlicerManagers[index]->GetImage()->GetScalarTypeAsITKString().c_str();
1010       for (int i = 0; i < dimension; i++) {
1011         origin[i] = imageSelected->GetOrigin()[i];
1012         inputSpacing[i] = imageSelected->GetSpacing()[i];
1013         inputSize[i] = imageSelected->GetSize()[i];
1014         sizeMM[i] = inputSize[i]*inputSpacing[i];
1015         NPixel *= inputSize[i];
1016       }
1017       inputSizeInBytes = GetSizeInBytes(imageSelected->GetActualMemorySize()*1000);
1018     } else if (DataTree->selectedItems()[0]->data(1,Qt::UserRole).toString() == "vector") {
1019       vvImage::Pointer imageSelected = mSlicerManagers[index]->GetSlicer(0)->GetVF();
1020       dimension = imageSelected->GetNumberOfDimensions();
1021       origin.resize(dimension);
1022       inputSpacing.resize(dimension);
1023       inputSize.resize(dimension);
1024       sizeMM.resize(dimension);
1025       pixelType = mSlicerManagers[index]->GetVF()->GetScalarTypeAsITKString().c_str();
1026       for (int i = 0; i < dimension; i++) {
1027         origin[i] = imageSelected->GetOrigin()[i];
1028         inputSpacing[i] = imageSelected->GetSpacing()[i];
1029         inputSize[i] = imageSelected->GetSize()[i];
1030         sizeMM[i] = inputSize[i]*inputSpacing[i];
1031         NPixel *= inputSize[i];
1032       }
1033       inputSizeInBytes = GetSizeInBytes(imageSelected->GetActualMemorySize()*1000);
1034     } else if (DataTree->selectedItems()[0]->data(1,Qt::UserRole).toString() == "overlay") {
1035       vvImage::Pointer imageSelected = mSlicerManagers[index]->GetSlicer(0)->GetOverlay();
1036       dimension = imageSelected->GetNumberOfDimensions();
1037       origin.resize(dimension);
1038       inputSpacing.resize(dimension);
1039       inputSize.resize(dimension);
1040       sizeMM.resize(dimension);
1041       pixelType = mSlicerManagers[index]->GetImage()->GetScalarTypeAsITKString().c_str();
1042       for (int i = 0; i < dimension; i++) {
1043         origin[i] = imageSelected->GetOrigin()[i];
1044         inputSpacing[i] = imageSelected->GetSpacing()[i];
1045         inputSize[i] = imageSelected->GetSize()[i];
1046         sizeMM[i] = inputSize[i]*inputSpacing[i];
1047         NPixel *= inputSize[i];
1048       }
1049       inputSizeInBytes = GetSizeInBytes(imageSelected->GetActualMemorySize()*1000);
1050     } else if (DataTree->selectedItems()[0]->data(1,Qt::UserRole).toString() == "fusion") {
1051       vvImage::Pointer imageSelected = mSlicerManagers[index]->GetSlicer(0)->GetFusion();
1052       dimension = imageSelected->GetNumberOfDimensions();
1053       origin.resize(dimension);
1054       inputSpacing.resize(dimension);
1055       inputSize.resize(dimension);
1056       sizeMM.resize(dimension);
1057       pixelType = mSlicerManagers[index]->GetImage()->GetScalarTypeAsITKString().c_str();
1058       for (int i = 0; i < dimension; i++) {
1059         origin[i] = imageSelected->GetOrigin()[i];
1060         inputSpacing[i] = imageSelected->GetSpacing()[i];
1061         inputSize[i] = imageSelected->GetSize()[i];
1062         sizeMM[i] = inputSize[i]*inputSpacing[i];
1063         NPixel *= inputSize[i];
1064       }
1065       inputSizeInBytes = GetSizeInBytes(imageSelected->GetActualMemorySize()*1000);
1066     }
1067
1068     QString dim = QString::number(dimension) + " (";
1069     dim += pixelType + ")";
1070
1071     infoPanel->setFileName(image);
1072     infoPanel->setDimension(dim);
1073     infoPanel->setSizePixel(GetVectorIntAsString(inputSize));
1074     infoPanel->setSizeMM(GetVectorDoubleAsString(sizeMM));
1075     infoPanel->setOrigin(GetVectorDoubleAsString(origin));
1076     infoPanel->setSpacing(GetVectorDoubleAsString(inputSpacing));
1077     infoPanel->setNPixel(QString::number(NPixel)+" ("+inputSizeInBytes+")");
1078
1079     landmarksPanel->SetCurrentLandmarks(mSlicerManagers[index]->GetLandmarks(),
1080                                         mSlicerManagers[index]->GetSlicer(0)->GetImage()->GetVTKImages().size());
1081     landmarksPanel->SetCurrentPath(mInputPathName.toStdString());
1082     landmarksPanel->SetCurrentImage(mSlicerManagers[index]->GetFileName().c_str());
1083
1084     overlayPanel->getCurrentImageName(mSlicerManagers[index]->GetFileName().c_str());
1085     for (int i = 0; i < 4; i++) {
1086       if (DataTree->selectedItems()[0]->data(i+1,Qt::CheckStateRole).toInt() > 0 || i == 3) {
1087         mSlicerManagers[index]->UpdateInfoOnCursorPosition(i);
1088         break;
1089       }
1090     }
1091     windowSpinBox->setValue(mSlicerManagers[index]->GetColorWindow());
1092     levelSpinBox->setValue(mSlicerManagers[index]->GetColorLevel());
1093     // DD(mSlicerManagers[index]->GetColorMap());
1094     // DD(mSlicerManagers[index]->GetPreset());
1095     presetComboBox->setCurrentIndex(mSlicerManagers[index]->GetPreset());
1096     colorMapComboBox->setCurrentIndex(mSlicerManagers[index]->GetColorMap());
1097
1098     infoPanel->setFileName(image);
1099     infoPanel->setDimension(dim);
1100     infoPanel->setSizePixel(GetVectorIntAsString(inputSize));
1101     infoPanel->setSizeMM(GetVectorDoubleAsString(sizeMM));
1102     infoPanel->setOrigin(GetVectorDoubleAsString(origin));
1103     infoPanel->setSpacing(GetVectorDoubleAsString(inputSpacing));
1104     infoPanel->setNPixel(QString::number(NPixel)+" ("+inputSizeInBytes+")");
1105
1106     landmarksPanel->SetCurrentLandmarks(mSlicerManagers[index]->GetLandmarks(),
1107                                         mSlicerManagers[index]->GetSlicer(0)->GetImage()->GetVTKImages().size());
1108     landmarksPanel->SetCurrentPath(mInputPathName.toStdString());
1109     landmarksPanel->SetCurrentImage(mSlicerManagers[index]->GetFileName().c_str());
1110
1111     overlayPanel->getCurrentImageName(mSlicerManagers[index]->GetFileName().c_str());
1112     for (int i = 0; i < 4; i++) {
1113       if (DataTree->selectedItems()[0]->data(i+1,Qt::CheckStateRole).toInt() > 0 || i == 3) {
1114         mSlicerManagers[index]->UpdateInfoOnCursorPosition(i);
1115         break;
1116       }
1117     }
1118     windowSpinBox->setValue(mSlicerManagers[index]->GetColorWindow());
1119     levelSpinBox->setValue(mSlicerManagers[index]->GetColorLevel());
1120     presetComboBox->setCurrentIndex(mSlicerManagers[index]->GetPreset());
1121     colorMapComboBox->setCurrentIndex(mSlicerManagers[index]->GetColorMap());
1122
1123     if (mSlicerManagers[index]->GetSlicer(0)->GetVF()) {
1124       overlayPanel->getVFName(mSlicerManagers[index]->GetVFName().c_str());
1125       overlayPanel->getVFProperty(mSlicerManagers[index]->GetSlicer(0)->GetVFSubSampling(),
1126                                   mSlicerManagers[index]->GetSlicer(0)->GetVFScale(),
1127                                   mSlicerManagers[index]->GetSlicer(0)->GetVFLog());
1128     } else {
1129       overlayPanel->getVFName(mSlicerManagers[index]->GetVFName().c_str());
1130       overlayPanel->getVFProperty(-1,-1,-1);
1131     }
1132     if (mSlicerManagers[index]->GetSlicer(0)->GetOverlay()) {
1133       overlayPanel->getOverlayName(mSlicerManagers[index]->GetOverlayName().c_str());
1134       overlayPanel->getOverlayProperty(mSlicerManagers[index]->GetOverlayColor());
1135     } else {
1136       overlayPanel->getOverlayName(mSlicerManagers[index]->GetOverlayName().c_str());
1137       overlayPanel->getOverlayProperty(-1);
1138     }
1139     if (mSlicerManagers[index]->GetSlicer(0)->GetFusion()) {
1140       overlayPanel->getFusionName(mSlicerManagers[index]->GetFusionName().c_str());
1141       overlayPanel->getFusionProperty(mSlicerManagers[index]->GetFusionOpacity(),
1142                                       mSlicerManagers[index]->GetFusionColorMap(),
1143                                       mSlicerManagers[index]->GetFusionWindow(),
1144                                       mSlicerManagers[index]->GetFusionLevel());
1145     } else {
1146       overlayPanel->getFusionName(mSlicerManagers[index]->GetFusionName().c_str());
1147       overlayPanel->getFusionProperty(-1, -1,-1,-1);
1148     }
1149   }
1150 }
1151 //------------------------------------------------------------------------------
1152
1153 //------------------------------------------------------------------------------
1154 void vvMainWindow::ShowDocumentation()
1155 {
1156   documentation->show();
1157 }
1158 //------------------------------------------------------------------------------
1159 void vvMainWindow::ShowHelpDialog()
1160 {
1161   help_dialog->show();
1162 }
1163 //------------------------------------------------------------------------------
1164
1165 //------------------------------------------------------------------------------
1166 void vvMainWindow::ChangeViewMode()
1167 {
1168   QListIterator<int> it0(splitter_3->sizes());
1169   QListIterator<int> it1(splitter_3->sizes());
1170   int max0 = 0;
1171   int max1 = 1;
1172   while (it0.hasNext()) {
1173     max0 += it0.next();
1174   }
1175   while (it1.hasNext()) {
1176     max1 += it1.next();
1177   }
1178   QList<int> size0;
1179   QList<int> size1;
1180   if (viewMode == 1) {
1181     viewMode = 0;
1182     size0.push_back(max0);
1183     size0.push_back(0);
1184     size1.push_back(max1);
1185     size1.push_back(0);
1186     splitter_3->setSizes(size0);
1187     OSplitter->setSizes(size1);
1188     DataTree->setColumnHidden(2,1);
1189     DataTree->setColumnHidden(3,1);
1190     DataTree->setColumnHidden(4,1);
1191   } else {
1192     viewMode = 1;
1193     size0.push_back(int(max0/2));
1194     size0.push_back(int(max0/2));
1195     size1.push_back(int(max1/2));
1196     size1.push_back(int(max1/2));
1197     splitter_3->setSizes(size0);
1198     OSplitter->setSizes(size1);
1199     DataTree->setColumnHidden(2,0);
1200     DataTree->setColumnHidden(3,0);
1201     DataTree->setColumnHidden(4,0);
1202   }
1203 }
1204 //------------------------------------------------------------------------------
1205
1206 //------------------------------------------------------------------------------
1207 QString vvMainWindow::GetSizeInBytes(unsigned long size)
1208 {
1209   QString result = "";// QString::number(size);
1210   //result += " bytes (";
1211   if (size > 1000000000) {
1212     size /= 1000000000;
1213     result += QString::number(size);
1214     result += "Gb";//)";
1215   } else if (size > 1000000) {
1216     size /= 1000000;
1217     result += QString::number(size);
1218     result += "Mb";//)";
1219   } else if (size > 1000) {
1220     size /= 1000;
1221     result += QString::number(size);
1222     result += "kb";//)";
1223   }
1224   return result;
1225 }
1226 //------------------------------------------------------------------------------
1227
1228 //------------------------------------------------------------------------------
1229 QString vvMainWindow::GetVectorDoubleAsString(std::vector<double> vectorDouble)
1230 {
1231   QString result;
1232   for (unsigned int i= 0; i < vectorDouble.size(); i++) {
1233     if (i != 0)
1234       result += " ";
1235     result += QString::number(vectorDouble[i]);
1236   }
1237   return result;
1238 }
1239 //------------------------------------------------------------------------------
1240
1241 //------------------------------------------------------------------------------
1242 QString vvMainWindow::GetVectorIntAsString(std::vector<int> vectorInt)
1243 {
1244   QString result;
1245   for (unsigned int i= 0; i < vectorInt.size(); i++) {
1246     if (i != 0)
1247       result += " ";
1248     result += QString::number(vectorInt[i]);
1249   }
1250   return result;
1251 }
1252 //------------------------------------------------------------------------------
1253
1254 //------------------------------------------------------------------------------
1255 int vvMainWindow::GetSlicerIndexFromItem(QTreeWidgetItem* item)
1256 {
1257   QString id = item->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString();
1258   for (int i = 0; i < DataTree->topLevelItemCount(); i++) {
1259     if (DataTree->topLevelItem(i)->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString() == id)
1260       return i;
1261   }
1262   return -1;
1263 }
1264 //------------------------------------------------------------------------------
1265
1266 //------------------------------------------------------------------------------
1267 QTreeWidgetItem* vvMainWindow::GetItemFromSlicerManager(vvSlicerManager* sm)
1268 {
1269   QString id = sm->GetId().c_str();
1270   for (int i = 0; i < DataTree->topLevelItemCount(); i++) {
1271     if (DataTree->topLevelItem(i)->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString() == id)
1272       return DataTree->topLevelItem(i);
1273   }
1274   return NULL;
1275 }
1276 //------------------------------------------------------------------------------
1277
1278 //------------------------------------------------------------------------------
1279 void vvMainWindow::DisplayChanged(QTreeWidgetItem *clicked_item, int column)
1280 {
1281   int index = GetSlicerIndexFromItem(clicked_item);
1282   if ( column >= COLUMN_CLOSE_IMAGE || column <= 0)
1283     return;
1284   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
1285     //Trick to avoid redoing twice the job for a key (sr)
1286     mSlicerManagers[i]->GetSlicer(column-1)->GetRenderWindow()-> GetInteractor()->SetKeySym("Crap");
1287
1288     QTreeWidgetItem* current_row=DataTree->topLevelItem(i);
1289     if (DataTree->topLevelItem(index) == current_row) {
1290       vvSlicer* clicked_slicer=mSlicerManagers[i]->GetSlicer(column-1);
1291       if (current_row == clicked_item) {
1292         //If we just activated a slicer
1293         if (current_row->data(column,Qt::CheckStateRole).toInt() > 0) {
1294           mSlicerManagers[i]->UpdateSlicer(column-1,clicked_item->data(column,Qt::CheckStateRole).toInt());
1295           mSlicerManagers[i]->UpdateInfoOnCursorPosition(column-1);
1296           DisplaySliders(i,column-1);
1297           std::map<std::string,int> overlay_counts;
1298           for (int child = 0; child < current_row->childCount(); child++) {
1299             std::string overlay_type =
1300               current_row->child(child)->data(1,Qt::UserRole).toString().toStdString();
1301             overlay_counts[overlay_type]++;
1302             current_row->child(child)->setData(column,Qt::CheckStateRole,
1303                                                current_row->data(column,Qt::CheckStateRole));
1304             clicked_slicer->SetActorVisibility(overlay_type,overlay_counts[overlay_type]-1,true);
1305           }
1306         } else { //We don't allow simply desactivating a slicer
1307           clicked_item->setData(column,Qt::CheckStateRole,2);
1308           return;
1309         }
1310       }
1311       //if we clicked on the vector(or overlay) and not the image
1312       else {
1313         if (clicked_item->data(column,Qt::CheckStateRole).toInt()) {
1314           current_row->setData(column,Qt::CheckStateRole,2);
1315           mSlicerManagers[i]->UpdateSlicer(column-1,2);
1316           mSlicerManagers[i]->UpdateInfoOnCursorPosition(column-1);
1317           DisplaySliders(i,column-1);
1318         }
1319         int vis = clicked_item->data(column,Qt::CheckStateRole).toInt();
1320         std::string overlay_type = clicked_item->data(1,Qt::UserRole).toString().toStdString();
1321         int overlay_index=0;
1322         for (int child = 0; child < current_row->childCount(); child++) {
1323           if (current_row->child(child)->data(1,Qt::UserRole).toString().toStdString() == overlay_type)
1324             overlay_index++;
1325           if (current_row->child(child) == clicked_item) break;
1326         }
1327         clicked_slicer->SetActorVisibility(
1328           clicked_item->data(1,Qt::UserRole).toString().toStdString(), overlay_index-1,vis);
1329       }
1330     } else if (current_row->data(column,Qt::CheckStateRole).toInt() > 0) {
1331       current_row->setData(column,Qt::CheckStateRole,0);
1332       mSlicerManagers[i]->UpdateSlicer(column-1,0);
1333       std::map<std::string,int> overlay_counts;
1334       for (int child = 0; child < current_row->childCount(); child++) {
1335         std::string overlay_type =
1336           current_row->child(child)->data(1,Qt::UserRole).toString().toStdString();
1337         overlay_counts[overlay_type]++;
1338         current_row->child(child)->setData(column,Qt::CheckStateRole,0);
1339         vvSlicer * current_slicer=mSlicerManagers[i]->GetSlicer(column-1);
1340         current_slicer->SetActorVisibility(overlay_type,overlay_counts[overlay_type]-1,false);
1341       }
1342     }
1343     //mSlicerManagers[i]->SetColorMap(-1);
1344     mSlicerManagers[i]->SetColorMap();
1345   }
1346   mSlicerManagers[index]->GetSlicer(column-1)->Render();
1347 }
1348 //------------------------------------------------------------------------------
1349
1350 void vvMainWindow::InitSlicers()
1351 {
1352   if (mSlicerManagers.size()) {
1353     mSlicerManagers.back()->GenerateDefaultLookupTable();
1354
1355     mSlicerManagers.back()->SetSlicerWindow(0,NOViewWidget->GetRenderWindow());
1356     mSlicerManagers.back()->SetSlicerWindow(1,NEViewWidget->GetRenderWindow());
1357     mSlicerManagers.back()->SetSlicerWindow(2,SOViewWidget->GetRenderWindow());
1358     mSlicerManagers.back()->SetSlicerWindow(3,SEViewWidget->GetRenderWindow());
1359   }
1360 }
1361
1362 //------------------------------------------------------------------------------
1363 void vvMainWindow::InitDisplay()
1364 {
1365   if (mSlicerManagers.size()) {
1366     //BE CAREFUL : this is absolutely necessary to set the interactor style
1367     //in order to have the same style instanciation for all SlicerManagers in
1368     // a same window
1369     for (int j = 0; j < 4; j++) {
1370       vvInteractorStyleNavigator* style = vvInteractorStyleNavigator::New();
1371       style->SetAutoAdjustCameraClippingRange(1);
1372       bool AlreadySelected = false;
1373       for (int i = 0; i < DataTree->topLevelItemCount(); i++) {
1374         mSlicerManagers[i]->SetInteractorStyleNavigator(j,style);
1375
1376         //select the image only if previous are not selected
1377         if (DataTree->topLevelItem(i)->data(j+1,Qt::CheckStateRole).toInt() > 1) {
1378           mSlicerManagers[i]->UpdateSlicer(j,1);
1379           AlreadySelected = true;
1380         } else if (i == DataTree->topLevelItemCount()-1 && !AlreadySelected) {
1381           if (DataTree->selectedItems().size() == 0)
1382             DataTree->topLevelItem(i)->setSelected(1);
1383           DataTree->topLevelItem(i)->setData(j+1,Qt::CheckStateRole,2);
1384           mSlicerManagers[i]->UpdateSlicer(j,1);
1385           DisplaySliders(i,j);
1386         } else {
1387           DataTree->topLevelItem(i)->setData(j+1,Qt::CheckStateRole,0);
1388           mSlicerManagers[i]->UpdateSlicer(j,0);
1389         }
1390       }
1391       style->Delete();
1392     }
1393   }
1394 }
1395 //------------------------------------------------------------------------------
1396
1397 //------------------------------------------------------------------------------
1398 void vvMainWindow::DisplaySliders(int slicer, int window)
1399 {
1400   int range[2];
1401   mSlicerManagers[slicer]->GetSlicer(window)->GetSliceRange(range);
1402   int position = mSlicerManagers[slicer]->GetSlicer(window)->GetSlice();
1403
1404   int tRange[2];
1405   tRange[0] = 0;
1406   tRange[1] = mSlicerManagers[slicer]->GetSlicer(window)->GetTMax();
1407   int tPosition = mSlicerManagers[slicer]->GetSlicer(window)->GetTSlice();
1408   bool showHorizontal = false;
1409   bool showVertical = false;
1410   if (mSlicerManagers[slicer]->GetSlicer(window)->GetImage()->GetNumberOfDimensions() > 3
1411       || (mSlicerManagers[slicer]->GetSlicer(window)->GetImage()->GetNumberOfDimensions() > 2
1412           && mSlicerManagers[slicer]->GetType() != IMAGEWITHTIME
1413           && mSlicerManagers[slicer]->GetType() != MERGEDWITHTIME))
1414     showVertical = true;
1415   if (mSlicerManagers[slicer]->GetSlicer(window)->GetImage()->GetNumberOfDimensions() > 3
1416       || mSlicerManagers[slicer]->GetType() == IMAGEWITHTIME
1417       || mSlicerManagers[slicer]->GetType() == MERGEDWITHTIME)
1418     showHorizontal = true;
1419
1420   if (showVertical)
1421     verticalSliders[window]->show();
1422   else
1423     verticalSliders[window]->hide();
1424   verticalSliders[window]->setRange(range[0],range[1]);
1425   verticalSliders[window]->setValue(position);
1426
1427   if (showHorizontal)
1428     horizontalSliders[window]->show();
1429   else
1430     horizontalSliders[window]->hide();
1431   horizontalSliders[window]->setRange(tRange[0],tRange[1]);
1432   horizontalSliders[window]->setValue(tPosition);
1433 }
1434 //------------------------------------------------------------------------------
1435
1436 //------------------------------------------------------------------------------
1437 void vvMainWindow::CloseImage(QTreeWidgetItem* item, int column)
1438 {
1439   int index = GetSlicerIndexFromItem(item);
1440
1441   if (DataTree->topLevelItem(index) != item) {
1442     QString warning = "Do you really want to close the overlay : ";
1443     warning += item->data(COLUMN_IMAGE_NAME,Qt::DisplayRole).toString();
1444     QMessageBox msgBox(QMessageBox::Warning, tr("Close Overlay"),
1445                        warning, 0, this);
1446     msgBox.addButton(tr("Close"), QMessageBox::AcceptRole);
1447     msgBox.addButton(tr("Cancel"), QMessageBox::RejectRole);
1448     if (msgBox.exec() == QMessageBox::AcceptRole) {
1449       std::string overlay_type=item->data(1,Qt::UserRole).toString().toStdString();
1450       int overlay_index=0;
1451       for (int child = 0; child < DataTree->topLevelItem(index)->childCount(); child++) {
1452         if (DataTree->topLevelItem(index)->\
1453             child(child)->data(1,Qt::UserRole).toString().toStdString() == overlay_type)
1454           overlay_index++;
1455         if (DataTree->topLevelItem(index)->child(child) == item) break;
1456       }
1457       mSlicerManagers[index]->RemoveActor(overlay_type, overlay_index-1);
1458       mSlicerManagers[index]->SetColorMap(0);
1459       DataTree->topLevelItem(index)->takeChild(DataTree->topLevelItem(index)->indexOfChild(item));
1460       mSlicerManagers[index]->Render();
1461     }
1462   } else if (DataTree->topLevelItemCount() <= 1) {
1463     QString warning = "Do you really want to close the image : ";
1464     warning += item->data(COLUMN_IMAGE_NAME,Qt::DisplayRole).toString();
1465     warning += "\nThis is the last image, you're about to close vv !!!";
1466     QMessageBox msgBox(QMessageBox::Warning, tr("Close Image"),
1467                        warning, 0, this);
1468     msgBox.addButton(tr("Close vv"), QMessageBox::AcceptRole);
1469     msgBox.addButton(tr("Cancel"), QMessageBox::RejectRole);
1470     if (msgBox.exec() == QMessageBox::AcceptRole) {
1471       this->close();
1472     }
1473   } else {
1474     QString warning = "Do you really want to close the image : ";
1475     warning += item->data(COLUMN_IMAGE_NAME,Qt::DisplayRole).toString();
1476     QMessageBox msgBox(QMessageBox::Warning, tr("Close Image"),
1477                        warning, 0, this);
1478     msgBox.addButton(tr("Close"), QMessageBox::AcceptRole);
1479     msgBox.addButton(tr("Cancel"), QMessageBox::RejectRole);
1480     if (msgBox.exec() == QMessageBox::AcceptRole) {
1481
1482       // Tell tools that we close an image
1483       emit AnImageIsBeingClosed(mSlicerManagers[index]);
1484
1485       std::vector<vvSlicerManager*>::iterator Manageriter = mSlicerManagers.begin();
1486       DataTree->takeTopLevelItem(index);
1487       for (int i = 0; i < index; i++) {
1488         Manageriter++;
1489       }
1490       linkPanel->removeImage(index);
1491       mSlicerManagers[index]->RemoveActors();
1492       delete mSlicerManagers[index];
1493       mSlicerManagers.erase(Manageriter);
1494
1495       //
1496       InitDisplay();
1497     }
1498   }
1499 }
1500 //------------------------------------------------------------------------------
1501
1502 //------------------------------------------------------------------------------
1503 void vvMainWindow::ReloadImage(QTreeWidgetItem* item, int column)
1504 {
1505   // int index = GetSlicerIndexFromItem(item);
1506   //   QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
1507   //   if (item->data(1,Qt::UserRole).toString() == "vector")
1508   //     mSlicerManagers[index]->ReloadVF();
1509   //   else
1510   //     mSlicerManagers[index]->Reload();
1511
1512   //   QApplication::restoreOverrideCursor();
1513   int index = GetSlicerIndexFromItem(item);
1514   QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
1515   QString role=item->data(1,Qt::UserRole).toString();
1516   if ( role == "vector")
1517     mSlicerManagers[index]->ReloadVF();
1518   else if (role == "overlay")
1519     mSlicerManagers[index]->ReloadOverlay();
1520   else if (role == "fusion")
1521     mSlicerManagers[index]->ReloadFusion();
1522   else
1523     mSlicerManagers[index]->Reload();
1524
1525   // Update view and info
1526   ImageInfoChanged();
1527   mSlicerManagers[index]->Render();
1528   QApplication::restoreOverrideCursor();
1529 }
1530 //------------------------------------------------------------------------------
1531
1532 //------------------------------------------------------------------------------
1533 void vvMainWindow::MousePositionChanged(int visibility,double x, double y, double z, double X, double Y, double Z , double value)
1534 {
1535   infoPanel->setCurrentInfo(visibility,x,y,z,X,Y,Z,value);
1536 }
1537 //------------------------------------------------------------------------------
1538
1539 //------------------------------------------------------------------------------
1540 void vvMainWindow::VectorChanged(int visibility,double x, double y, double z, double value)
1541 {
1542   overlayPanel->getCurrentVectorInfo(visibility,x,y,z,value);
1543 }
1544 //------------------------------------------------------------------------------
1545
1546 //------------------------------------------------------------------------------
1547 void vvMainWindow::OverlayChanged(int visibility, double valueOver, double valueRef)
1548 {
1549   overlayPanel->getCurrentOverlayInfo(visibility,valueOver, valueRef);
1550 }
1551 //------------------------------------------------------------------------------
1552
1553 //------------------------------------------------------------------------------
1554 void vvMainWindow::FusionChanged(int visibility, double value)
1555 {
1556   overlayPanel->getCurrentFusionInfo(visibility,value);
1557 }
1558 //------------------------------------------------------------------------------
1559
1560 //------------------------------------------------------------------------------
1561 void vvMainWindow::WindowsChanged(int window, int view, int slice)
1562 {
1563   infoPanel->setViews(window, view, slice);
1564 }
1565 //------------------------------------------------------------------------------
1566
1567 //------------------------------------------------------------------------------
1568 void vvMainWindow::WindowLevelChanged(double window, double level,int preset,int colormap)
1569 {
1570   windowSpinBox->setValue(window);
1571   levelSpinBox->setValue(level);
1572   colorMapComboBox->setCurrentIndex(colormap);
1573   presetComboBox->setCurrentIndex(preset);
1574 }
1575 //------------------------------------------------------------------------------
1576
1577 //------------------------------------------------------------------------------
1578 void vvMainWindow::WindowLevelEdited()
1579 {
1580   presetComboBox->setCurrentIndex(6);
1581   UpdateWindowLevel();
1582 }
1583 //------------------------------------------------------------------------------
1584
1585 //------------------------------------------------------------------------------
1586 void vvMainWindow::UpdateWindowLevel()
1587 {
1588   if (DataTree->selectedItems().size()) {
1589     if (presetComboBox->currentIndex() == 7) //For ventilation
1590       colorMapComboBox->setCurrentIndex(5);
1591     int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1592     mSlicerManagers[index]->SetColorWindow(windowSpinBox->value());
1593     mSlicerManagers[index]->SetColorLevel(levelSpinBox->value());
1594     mSlicerManagers[index]->SetPreset(presetComboBox->currentIndex());
1595     mSlicerManagers[index]->Render();
1596   }
1597 }
1598 //------------------------------------------------------------------------------
1599
1600 //------------------------------------------------------------------------------
1601 void vvMainWindow::UpdateColorMap()
1602 {
1603   if (DataTree->selectedItems().size()) {
1604     int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1605     mSlicerManagers[index]->SetColorMap(colorMapComboBox->currentIndex());
1606     mSlicerManagers[index]->Render();
1607   }
1608 }
1609 //------------------------------------------------------------------------------
1610 void vvMainWindow::SwitchWindowLevel()
1611 {
1612   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1613   int window = mSlicerManagers[index]->GetColorWindow();
1614   presetComboBox->setCurrentIndex(6);
1615   windowSpinBox->setValue(-window);
1616   UpdateWindowLevel();
1617 }
1618 //------------------------------------------------------------------------------
1619
1620 //------------------------------------------------------------------------------
1621 void vvMainWindow::ApplyWindowLevelToAllImages()
1622 {
1623   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
1624     if (mSlicerManagers[i] == NULL)
1625       continue;
1626     mSlicerManagers[i]->SetColorWindow(windowSpinBox->value());
1627     mSlicerManagers[i]->SetColorLevel(levelSpinBox->value());
1628     mSlicerManagers[i]->SetPreset(6);
1629     mSlicerManagers[i]->Render();
1630   }
1631 }
1632 //------------------------------------------------------------------------------
1633
1634 //------------------------------------------------------------------------------
1635 void vvMainWindow::UpdateLinkManager(std::string id, int slicer, double x, double y, double z, int temps)
1636 {
1637   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
1638     if (mSlicerManagers[i]->GetId() == id) {
1639       //mSlicerManagers[i]->SetTSlice(temps);
1640       mSlicerManagers[i]->GetSlicer(slicer)->SetCurrentPosition(x,y,z,temps);
1641       mSlicerManagers[i]->UpdateViews(0,slicer);
1642       break;
1643     }
1644   }
1645 }
1646 //------------------------------------------------------------------------------
1647
1648 //------------------------------------------------------------------------------
1649 void vvMainWindow::UpdateLinkedNavigation(std::string id, vvSlicerManager * sm)
1650 {
1651   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
1652     if (id == mSlicerManagers[i]->GetId()) {
1653       mSlicerManagers[i]->UpdateLinkedNavigation(sm->GetSlicer(0));
1654     }
1655   }
1656 }
1657 //------------------------------------------------------------------------------
1658
1659 //------------------------------------------------------------------------------
1660 void vvMainWindow::ShowContextMenu(QPoint point)
1661 {
1662   if (!DataTree->selectedItems().size()) {
1663     contextActions[1]->setEnabled(0);
1664     contextActions[2]->setEnabled(0);
1665     contextActions[3]->setEnabled(0);
1666     contextActions[4]->setEnabled(0);
1667     contextActions[5]->setEnabled(0);
1668     contextActions[6]->setEnabled(0);
1669   } else {
1670     int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1671     contextActions[1]->setEnabled(1);
1672     contextActions[2]->setEnabled(
1673       DataTree->itemWidget(DataTree->selectedItems()[0],
1674                            COLUMN_RELOAD_IMAGE)->isEnabled());
1675     contextActions[3]->setEnabled(1);
1676     contextActions[5]->setEnabled(1);
1677     contextActions[6]->setEnabled(1);
1678
1679     if (mSlicerManagers[index]->GetDimension() < 3)
1680       contextActions[4]->setEnabled(0);
1681     else
1682       contextActions[4]->setEnabled(1);
1683   }
1684   contextMenu.exec(QCursor::pos());
1685 }
1686 //------------------------------------------------------------------------------
1687
1688 //------------------------------------------------------------------------------
1689 void vvMainWindow::CloseImage()
1690 {
1691   CloseImage(DataTree->selectedItems()[0],0);
1692 }
1693 //------------------------------------------------------------------------------
1694
1695 //------------------------------------------------------------------------------
1696 void vvMainWindow::ReloadImage()
1697 {
1698   ReloadImage(DataTree->selectedItems()[0],0);
1699 }
1700 //------------------------------------------------------------------------------
1701
1702 //------------------------------------------------------------------------------
1703 void vvMainWindow::SelectOverlayImage()
1704 {
1705   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1706
1707   //check if one overlay image is added
1708   for (int child = 0; child < DataTree->topLevelItem(index)->childCount(); child++)
1709     if (DataTree->topLevelItem(index)->child(child)->data(1,Qt::UserRole).toString() == "overlay") {
1710       QString error = "Cannot add more than one compared image\n";
1711       error += "Please remove first ";
1712       error += DataTree->topLevelItem(index)->child(child)->data(COLUMN_IMAGE_NAME,Qt::DisplayRole).toString();
1713       QMessageBox::information(this,tr("Problem adding compared image !"),error);
1714       return;
1715     }
1716
1717   QString Extensions = EXTENSIONS;
1718   Extensions += ";;All Files (*)";
1719   QString file = QFileDialog::getOpenFileName(this,tr("Load Overlay image"),mInputPathName,Extensions);
1720   if (!file.isEmpty())
1721     AddOverlayImage(index,file);
1722 }
1723 //------------------------------------------------------------------------------
1724
1725 //------------------------------------------------------------------------------
1726 void vvMainWindow::AddOverlayImage(int index, QString file)
1727 {
1728
1729   mInputPathName = itksys::SystemTools::GetFilenamePath(file.toStdString()).c_str();
1730   itk::ImageIOBase::Pointer reader = itk::ImageIOFactory::CreateImageIO(
1731                                        file.toStdString().c_str(), itk::ImageIOFactory::ReadMode);
1732   reader->SetFileName(file.toStdString().c_str());
1733   reader->ReadImageInformation();
1734   std::string component = reader->GetComponentTypeAsString(reader->GetComponentType());
1735   int dimension = reader->GetNumberOfDimensions();
1736   QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
1737   vvProgressDialog progress("Opening " + file.toStdString());
1738   qApp->processEvents();
1739
1740   std::string filename = itksys::SystemTools::GetFilenameWithoutExtension(file.toStdString()).c_str();
1741   if (mSlicerManagers[index]->SetOverlay(file.toStdString(),dimension, component)) {
1742     //create an item in the tree with good settings
1743     QTreeWidgetItem *item = new QTreeWidgetItem();
1744     item->setData(0,Qt::UserRole,file.toStdString().c_str());
1745     item->setData(1,Qt::UserRole,tr("overlay"));
1746     QFileInfo fileinfo(file); //Do not show the path
1747     item->setData(COLUMN_IMAGE_NAME,Qt::DisplayRole,fileinfo.fileName());
1748     item->setToolTip(COLUMN_IMAGE_NAME,fileinfo.absoluteFilePath());
1749     qApp->processEvents();
1750
1751     for (int j = 1; j <= 4; j++) {
1752       item->setData(j,Qt::CheckStateRole,DataTree->topLevelItem(index)->data(j,Qt::CheckStateRole));
1753       mSlicerManagers[index]->GetSlicer(j-1)->SetActorVisibility("overlay",0,
1754           DataTree->topLevelItem(index)->data(j,Qt::CheckStateRole).toInt());
1755     }
1756
1757     //Create the buttons for reload and close
1758     qApp->processEvents();
1759     QTreePushButton* cButton = new QTreePushButton;
1760     cButton->setItem(item);
1761     cButton->setColumn(COLUMN_CLOSE_IMAGE);
1762     cButton->setToolTip(tr("close image"));
1763     cButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/exit.png")));
1764     connect(cButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
1765             this,SLOT(CloseImage(QTreeWidgetItem*, int)));
1766
1767     QTreePushButton* rButton = new QTreePushButton;
1768     rButton->setItem(item);
1769     rButton->setColumn(COLUMN_RELOAD_IMAGE);
1770     rButton->setToolTip(tr("reload image"));
1771     rButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/rotateright.png")));
1772     connect(rButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
1773             this,SLOT(ReloadImage(QTreeWidgetItem*, int)));
1774
1775     DataTree->topLevelItem(index)->setExpanded(1);
1776     DataTree->topLevelItem(index)->addChild(item);
1777     DataTree->setItemWidget(item, COLUMN_CLOSE_IMAGE, cButton);
1778     DataTree->setItemWidget(item, COLUMN_RELOAD_IMAGE, rButton);
1779
1780     //set the id of the image
1781     QString id = DataTree->topLevelItem(index)->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString();
1782     item->setData(COLUMN_IMAGE_NAME,Qt::UserRole,id.toStdString().c_str());
1783     UpdateTree();
1784     qApp->processEvents();
1785     ImageInfoChanged();
1786     QApplication::restoreOverrideCursor();
1787   } else {
1788     QApplication::restoreOverrideCursor();
1789     QString error = "Cannot import the new image.\n";
1790     error += mSlicerManagers[index]->GetLastError().c_str();
1791     QMessageBox::information(this,tr("Problem reading image !"),error);
1792   }
1793 }
1794 //------------------------------------------------------------------------------
1795
1796
1797 //------------------------------------------------------------------------------
1798 void vvMainWindow::AddROI(int index, QString file)
1799 {
1800   DD("AddImageAndROI");
1801   /*
1802   // Get slice manager
1803
1804   // Load image
1805
1806   vvImageReader * mReader = new vvImageReader;
1807   mReader->SetInputFilename(filename.toStdString());
1808   mReader->Update(IMAGE);
1809   if (mReader->GetLastError().size() != 0) {
1810     std::cerr << "Error while reading " << filename.toStdString() << std::endl;
1811     QString error = "Cannot open file \n";
1812     error += mReader->GetLastError().c_str();
1813     QMessageBox::information(this,tr("Reading problem"),error);
1814     delete mReader;
1815     return;
1816   }
1817   vvImage::Pointer roi = mReader->GetOutput();
1818
1819   // Create roi in new tool
1820   vvToolStructureSetManager::AddImage(mCurrentSlicerManager, roi);
1821 */
1822 }
1823 //------------------------------------------------------------------------------
1824
1825 //------------------------------------------------------------------------------
1826 void vvMainWindow::SelectFusionImage()
1827 {
1828   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1829
1830   //check if one fusion image is added
1831   for (int child = 0; child < DataTree->topLevelItem(index)->childCount(); child++)
1832     if (DataTree->topLevelItem(index)->child(child)->data(1,Qt::UserRole).toString() == "fusion") {
1833       QString error = "Cannot add more than one fusion image\n";
1834       error += "Please remove first ";
1835       error += DataTree->topLevelItem(index)->child(child)->data(COLUMN_IMAGE_NAME,Qt::DisplayRole).toString();
1836       QMessageBox::information(this,tr("Problem adding fusion image !"),error);
1837       return;
1838     }
1839
1840   QString Extensions = EXTENSIONS;
1841   Extensions += ";;All Files (*)";
1842   QString file = QFileDialog::getOpenFileName(this,tr("Load Fusion image"),mInputPathName,Extensions);
1843   if (!file.isEmpty())
1844     AddFusionImage(index,file);
1845 }
1846 //------------------------------------------------------------------------------
1847
1848 //------------------------------------------------------------------------------
1849 void vvMainWindow::AddFusionImage(int index, QString file)
1850 {
1851   mInputPathName = itksys::SystemTools::GetFilenamePath(file.toStdString()).c_str();
1852   itk::ImageIOBase::Pointer reader = itk::ImageIOFactory::CreateImageIO(
1853                                        file.toStdString().c_str(), itk::ImageIOFactory::ReadMode);
1854   reader->SetFileName(file.toStdString().c_str());
1855   reader->ReadImageInformation();
1856   std::string component = reader->GetComponentTypeAsString(reader->GetComponentType());
1857   if (reader) {
1858     QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
1859     vvProgressDialog progress("Opening fusion");
1860     qApp->processEvents();
1861
1862     std::string filename = itksys::SystemTools::GetFilenameWithoutExtension(file.toStdString()).c_str();
1863     if (mSlicerManagers[index]->SetFusion(file.toStdString(),
1864                                           reader->GetNumberOfDimensions(), component)) {
1865       //create an item in the tree with good settings
1866       QTreeWidgetItem *item = new QTreeWidgetItem();
1867       item->setData(0,Qt::UserRole,file.toStdString().c_str());
1868       item->setData(1,Qt::UserRole,tr("fusion"));
1869       QFileInfo fileinfo(filename.c_str()); //Do not show the path
1870       item->setData(COLUMN_IMAGE_NAME,Qt::DisplayRole,fileinfo.fileName());
1871       item->setToolTip(COLUMN_IMAGE_NAME,fileinfo.absoluteFilePath());
1872       qApp->processEvents();
1873
1874       for (int j = 1; j <= 4; j++) {
1875         item->setData(j,Qt::CheckStateRole,DataTree->topLevelItem(index)->data(j,Qt::CheckStateRole));
1876         mSlicerManagers[index]->GetSlicer(j-1)->SetActorVisibility("fusion",0,
1877             DataTree->topLevelItem(index)->data(j,Qt::CheckStateRole).toInt());
1878       }
1879
1880       //Create the buttons for reload and close
1881       qApp->processEvents();
1882       QTreePushButton* cButton = new QTreePushButton;
1883       cButton->setItem(item);
1884       cButton->setColumn(COLUMN_CLOSE_IMAGE);
1885       cButton->setToolTip(tr("close image"));
1886       cButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/exit.png")));
1887       connect(cButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
1888               this,SLOT(CloseImage(QTreeWidgetItem*, int)));
1889
1890       QTreePushButton* rButton = new QTreePushButton;
1891       rButton->setItem(item);
1892       rButton->setColumn(COLUMN_RELOAD_IMAGE);
1893       rButton->setToolTip(tr("reload image"));
1894       rButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/rotateright.png")));
1895       connect(rButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
1896               this,SLOT(ReloadImage(QTreeWidgetItem*, int)));
1897
1898       DataTree->topLevelItem(index)->setExpanded(1);
1899       DataTree->topLevelItem(index)->addChild(item);
1900       DataTree->setItemWidget(item, COLUMN_CLOSE_IMAGE, cButton);
1901       DataTree->setItemWidget(item, COLUMN_RELOAD_IMAGE, rButton);
1902
1903       //set the id of the image
1904       QString id = DataTree->topLevelItem(index)->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString();
1905       item->setData(COLUMN_IMAGE_NAME,Qt::UserRole,id.toStdString().c_str());
1906       UpdateTree();
1907       qApp->processEvents();
1908       ImageInfoChanged();
1909       QApplication::restoreOverrideCursor();
1910     } else {
1911       QApplication::restoreOverrideCursor();
1912       QString error = "Cannot import the new image.\n";
1913       error += mSlicerManagers[index]->GetLastError().c_str();
1914       QMessageBox::information(this,tr("Problem reading image !"),error);
1915     }
1916   } else {
1917     QString error = "Cannot import the new image.\n";
1918     QMessageBox::information(this,tr("Problem reading image !"),error);
1919   }
1920 }
1921 //------------------------------------------------------------------------------
1922
1923
1924 //------------------------------------------------------------------------------
1925 void vvMainWindow::OpenField()
1926 {
1927   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1928   //check if a vector field has already been added
1929   for (int child = 0; child < DataTree->topLevelItem(index)->childCount(); child++)
1930     if (DataTree->topLevelItem(index)->child(child)->data(1,Qt::UserRole).toString() == "vector") {
1931       QString error = "Cannot add more than one vector field\n";
1932       error += "Please remove first ";
1933       error += DataTree->topLevelItem(index)->child(child)->data(COLUMN_IMAGE_NAME,Qt::DisplayRole).toString();
1934       QMessageBox::information(this,tr("Problem adding vector field!"),error);
1935       return;
1936     }
1937
1938   QString Extensions = "Images ( *.mhd)";
1939   Extensions += ";;Images ( *.vf)";
1940   QString file = QFileDialog::getOpenFileName(this,tr("Load deformation field"),mInputPathName,Extensions);
1941   if (!file.isEmpty())
1942     AddField(file,index);
1943 }
1944 //------------------------------------------------------------------------------
1945
1946
1947 //------------------------------------------------------------------------------
1948 void vvMainWindow::AddFieldEntry(QString filename,int index,bool from_disk)
1949 {
1950   //create an item in the tree with good settings
1951   QTreeWidgetItem *item = new QTreeWidgetItem();
1952   item->setData(0,Qt::UserRole,filename.toStdString().c_str());
1953   item->setData(1,Qt::UserRole,tr("vector"));
1954   QFileInfo fileinfo(filename); //Do not show the path
1955   item->setData(COLUMN_IMAGE_NAME,Qt::DisplayRole,fileinfo.fileName());
1956   item->setToolTip(COLUMN_IMAGE_NAME,fileinfo.absoluteFilePath());
1957   qApp->processEvents();
1958
1959   for (int j = 1; j <= 4; j++) {
1960     item->setData(j,Qt::CheckStateRole,DataTree->topLevelItem(index)->data(j,Qt::CheckStateRole));
1961     mSlicerManagers[index]->GetSlicer(j-1)->SetActorVisibility("vector",0,
1962         DataTree->topLevelItem(index)->data(j,Qt::CheckStateRole).toInt());
1963   }
1964
1965   //Create the buttons for reload and close
1966   qApp->processEvents();
1967   QTreePushButton* cButton = new QTreePushButton;
1968   cButton->setItem(item);
1969   cButton->setColumn(COLUMN_CLOSE_IMAGE);
1970   cButton->setToolTip(tr("close vector field"));
1971   cButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/exit.png")));
1972   connect(cButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
1973           this,SLOT(CloseImage(QTreeWidgetItem*, int)));
1974
1975   QTreePushButton* rButton = new QTreePushButton;
1976   rButton->setItem(item);
1977   rButton->setColumn(COLUMN_RELOAD_IMAGE);
1978   rButton->setToolTip(tr("reload vector field"));
1979   rButton->setEnabled(from_disk);
1980   rButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/rotateright.png")));
1981   connect(rButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
1982           this,SLOT(ReloadImage(QTreeWidgetItem*, int)));
1983
1984   DataTree->topLevelItem(index)->setExpanded(1);
1985   DataTree->topLevelItem(index)->addChild(item);
1986   DataTree->setItemWidget(item, COLUMN_RELOAD_IMAGE, rButton);
1987   DataTree->setItemWidget(item, COLUMN_CLOSE_IMAGE, cButton);
1988
1989   //set the id of the image
1990   QString id = DataTree->topLevelItem(index)->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString();
1991   item->setData(COLUMN_IMAGE_NAME,Qt::UserRole,id.toStdString().c_str());
1992   UpdateTree();
1993   qApp->processEvents();
1994   ImageInfoChanged();
1995   QApplication::restoreOverrideCursor();
1996 }
1997 //------------------------------------------------------------------------------
1998
1999
2000 //------------------------------------------------------------------------------
2001 void vvMainWindow::AddField(vvImage::Pointer vf,QString file,int index)
2002 {
2003   QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
2004   vvSlicerManager* imageManager = mSlicerManagers[index];
2005   if (imageManager->SetVF(vf,file.toStdString())) {
2006     AddFieldEntry(file,index,false);
2007   } else {
2008     QString error = "Cannot import the vector field for this image.\n";
2009     error += imageManager->GetLastError().c_str();
2010     QMessageBox::information(this,tr("Problem reading VF !"),error);
2011   }
2012   QApplication::restoreOverrideCursor();
2013 }
2014 //------------------------------------------------------------------------------
2015
2016
2017 //------------------------------------------------------------------------------
2018 void vvMainWindow::AddField(QString file,int index)
2019 {
2020   if (QFile::exists(file)) {
2021     mInputPathName = itksys::SystemTools::GetFilenamePath(file.toStdString()).c_str();
2022
2023     //init the progress events
2024     QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
2025     vvProgressDialog progress("Opening " + file.toStdString());
2026     qApp->processEvents();
2027
2028     //read the vector and put it in the current mSlicerManager
2029     vvSlicerManager* imageManager = mSlicerManagers[index];
2030     qApp->processEvents();
2031
2032     std::string filename = itksys::SystemTools::GetFilenameWithoutExtension(file.toStdString()).c_str();
2033     if (imageManager->SetVF(file.toStdString())) {
2034       imageManager->Render();
2035       AddFieldEntry(file,index,true);
2036     } else {
2037       QApplication::restoreOverrideCursor();
2038       QString error = "Cannot import the vector field for this image.\n";
2039       error += imageManager->GetLastError().c_str();
2040       QMessageBox::information(this,tr("Problem reading VF !"),error);
2041     }
2042   } else
2043     QMessageBox::information(this,tr("Problem reading VF !"),"File doesn't exist!");
2044
2045 }
2046 //------------------------------------------------------------------------------
2047
2048
2049 //------------------------------------------------------------------------------
2050 void vvMainWindow::SetVFProperty(int subsampling, int scale, int log, int width)
2051 {
2052   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2053   if (mSlicerManagers[index]->GetSlicer(0)->GetVF()) {
2054     for (int i = 0; i < 4; i++) {
2055       mSlicerManagers[index]->GetSlicer(i)->SetVFSubSampling(subsampling);
2056       mSlicerManagers[index]->GetSlicer(i)->SetVFScale(scale);
2057       mSlicerManagers[index]->GetSlicer(i)->SetVFWidth(width);
2058       if (log > 0)
2059         mSlicerManagers[index]->GetSlicer(i)->SetVFLog(1);
2060       else
2061         mSlicerManagers[index]->GetSlicer(i)->SetVFLog(0);
2062     }
2063   }
2064 }
2065 //------------------------------------------------------------------------------
2066
2067
2068 //------------------------------------------------------------------------------
2069 void vvMainWindow::SetOverlayProperty(int color)
2070 {
2071   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2072   if (mSlicerManagers[index]->GetSlicer(0)->GetOverlay()) {
2073     mSlicerManagers[index]->SetOverlayColor(color);
2074     mSlicerManagers[index]->SetColorMap(0);
2075     mSlicerManagers[index]->Render();
2076   }
2077 }
2078 //------------------------------------------------------------------------------
2079
2080 //------------------------------------------------------------------------------
2081 void vvMainWindow::SetFusionProperty(int opacity, int colormap,double window, double level)
2082 {
2083   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2084   if (mSlicerManagers[index]->GetSlicer(0)->GetFusion()) {
2085     mSlicerManagers[index]->SetFusionOpacity(opacity);
2086     mSlicerManagers[index]->SetFusionColorMap(colormap);
2087     mSlicerManagers[index]->SetFusionWindow(window);
2088     mSlicerManagers[index]->SetFusionLevel(level);
2089     mSlicerManagers[index]->SetColorMap(0);
2090     mSlicerManagers[index]->Render();
2091   }
2092 }
2093 //------------------------------------------------------------------------------
2094
2095 //------------------------------------------------------------------------------
2096 void vvMainWindow::SaveAs()
2097 {
2098   if (DataTree->selectedItems()[0]->data(1,Qt::UserRole).toString() == "vector") {
2099     QMessageBox::warning(this,tr("Unsupported type"),tr("Sorry, saving a vector field is unsupported for the moment"));
2100     return;
2101   }
2102
2103   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2104   int dimension = mSlicerManagers[index]->GetDimension();
2105   QStringList OutputListeFormat;
2106   OutputListeFormat.clear();
2107   if (dimension == 1) {
2108     OutputListeFormat.push_back(".mhd");
2109   }
2110   if (dimension == 2) {
2111     OutputListeFormat.push_back(".bmp");
2112     OutputListeFormat.push_back(".png");
2113     OutputListeFormat.push_back(".jpeg");
2114     OutputListeFormat.push_back(".tif");
2115     OutputListeFormat.push_back(".mhd");
2116     OutputListeFormat.push_back(".hdr");
2117     OutputListeFormat.push_back(".vox");
2118   } else if (dimension == 3) {
2119     OutputListeFormat.push_back(".mhd");
2120     OutputListeFormat.push_back(".hdr");
2121     OutputListeFormat.push_back(".vox");
2122   } else if (dimension == 4) {
2123     OutputListeFormat.push_back(".mhd");
2124   }
2125   QString Extensions = "AllFiles(*.*)";
2126   for (int i = 0; i < OutputListeFormat.count(); i++) {
2127     Extensions += ";;Images ( *";
2128     Extensions += OutputListeFormat[i];
2129     Extensions += ")";
2130   }
2131   QString fileName = QFileDialog::getSaveFileName(this,
2132                      tr("Save As"),
2133                      mSlicerManagers[index]->GetFileName().c_str(),
2134                      Extensions);
2135   if (!fileName.isEmpty()) {
2136     std::string fileformat = itksys::SystemTools::GetFilenameLastExtension(fileName.toStdString());
2137     if (OutputListeFormat.contains(
2138           fileformat.c_str())) {
2139       QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
2140       std::string action = "Saving";
2141       vvProgressDialog progress("Saving "+fileName.toStdString());
2142       qApp->processEvents();
2143       vvImageWriter *writer = new vvImageWriter;
2144       writer->SetOutputFileName(fileName.toStdString());
2145       writer->SetInput(mSlicerManagers[index]->GetImage());
2146       writer->Update();
2147       QApplication::restoreOverrideCursor();
2148       if (writer->GetLastError().size()) {
2149         QString error = "Saving did not succeed\n";
2150         error += writer->GetLastError().c_str();
2151         QMessageBox::information(this,tr("Saving Problem"),error);
2152         SaveAs();
2153       }
2154     } else {
2155       QString error = fileformat.c_str();
2156       if (error.isEmpty())
2157         error += "no file format specified !";
2158       else
2159         error += " format unknown !!!\n";
2160       QMessageBox::information(this,tr("Saving Problem"),error);
2161       SaveAs();
2162     }
2163   }
2164 }
2165 //------------------------------------------------------------------------------
2166
2167
2168 //------------------------------------------------------------------------------
2169 void vvMainWindow::AddLink(QString image1,QString image2)
2170 {
2171   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
2172     if (image1.toStdString() == mSlicerManagers[i]->GetId()) {
2173       mSlicerManagers[i]->AddLink(image2.toStdString());
2174     }
2175     if (image2.toStdString() == mSlicerManagers[i]->GetId()) {
2176       mSlicerManagers[i]->AddLink(image1.toStdString());
2177     }
2178   }
2179 }
2180 //------------------------------------------------------------------------------
2181
2182
2183 //------------------------------------------------------------------------------
2184 void vvMainWindow::RemoveLink(QString image1,QString image2)
2185 {
2186   // DD("vvMainWindow:RemoveLink");
2187   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
2188     if (image1.toStdString() == mSlicerManagers[i]->GetId()) {
2189       mSlicerManagers[i]->RemoveLink(image2.toStdString());
2190     }
2191     if (image2.toStdString() == mSlicerManagers[i]->GetId()) {
2192       mSlicerManagers[i]->RemoveLink(image1.toStdString());
2193     }
2194   }
2195 }
2196 //------------------------------------------------------------------------------
2197
2198 //------------------------------------------------------------------------------
2199 void vvMainWindow::ChangeImageWithIndexOffset(vvSlicerManager *sm, int slicer, int offset)
2200 {
2201   int index = 0;
2202   while(sm != mSlicerManagers[index])
2203     index++;
2204   index = (index+offset) % mSlicerManagers.size();
2205
2206   QTreeWidgetItem* item = GetItemFromSlicerManager(mSlicerManagers[index]);
2207   //CurrentImageChanged(mSlicerManagers[index]->GetId()); //select new image
2208   item->setData(slicer+1,Qt::CheckStateRole,2);         //change checkbox
2209   DisplayChanged(item,slicer+1);
2210 }
2211 //------------------------------------------------------------------------------
2212
2213 void vvMainWindow::HorizontalSliderMoved(int value,int column, int slicer_index)
2214 {
2215   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
2216     if (DataTree->topLevelItem(i)->data(column,Qt::CheckStateRole).toInt() > 1) {
2217       for (int j = 0; j < 4; j++) {
2218         mSlicerManagers[i]->SetTSliceInSlicer(value,j);
2219         //if (mSlicerManagers[i]->GetSlicer(j)->GetImageActor()->GetVisibility())
2220         //UpdateTSlice(j,value);
2221       }
2222       mSlicerManagers[i]->GetSlicer(slicer_index)->Render();
2223       break;
2224     }
2225   }
2226 }
2227 //------------------------------------------------------------------------------
2228
2229
2230 //------------------------------------------------------------------------------
2231 void vvMainWindow::NOHorizontalSliderMoved()
2232 {
2233   // if (mCurrentTime == NOHorizontalSlider->value()) return;
2234   HorizontalSliderMoved(NOHorizontalSlider->value(),COLUMN_UL_VIEW,0);
2235 //  mCurrentTime = NOHorizontalSlider->value();
2236 }
2237 //------------------------------------------------------------------------------
2238
2239
2240 //------------------------------------------------------------------------------
2241 void vvMainWindow::NEHorizontalSliderMoved()
2242 {
2243   // if (mCurrentTime == NEHorizontalSlider->value()) return;
2244   HorizontalSliderMoved(NEHorizontalSlider->value(),COLUMN_UR_VIEW,1);
2245 //  mCurrentTime = NEHorizontalSlider->value();
2246 }
2247 //------------------------------------------------------------------------------
2248
2249
2250 //------------------------------------------------------------------------------
2251 void vvMainWindow::SOHorizontalSliderMoved()
2252 {
2253   // if (mCurrentTime == SOHorizontalSlider->value()) return;
2254   HorizontalSliderMoved(SOHorizontalSlider->value(),COLUMN_DL_VIEW,2);
2255   // mCurrentTime = SOHorizontalSlider->value();
2256 }
2257 //------------------------------------------------------------------------------
2258
2259
2260 //------------------------------------------------------------------------------
2261 void vvMainWindow::SEHorizontalSliderMoved()
2262 {
2263   // if (mCurrentTime == SEHorizontalSlider->value()) return;
2264   HorizontalSliderMoved(SEHorizontalSlider->value(),COLUMN_DR_VIEW,3);
2265   // mCurrentTime = SEHorizontalSlider->value();
2266 }
2267 //------------------------------------------------------------------------------
2268
2269 //------------------------------------------------------------------------------
2270 void vvMainWindow::NOVerticalSliderChanged()
2271 {
2272   static int value=-1;
2273   if (value == NOVerticalSlider->value()) return;
2274   else value = NOVerticalSlider->value();
2275   //  int value = NOVerticalSlider->value();
2276   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
2277     if (DataTree->topLevelItem(i)->data(COLUMN_UL_VIEW,Qt::CheckStateRole).toInt() > 1) {
2278       if (mSlicerManagers[i]->GetSlicer(0)->GetSlice() != value) {
2279         mSlicerManagers[i]->GetSlicer(0)->SetSlice(value);
2280         mSlicerManagers[i]->VerticalSliderHasChanged(0, value);
2281
2282         // If nor Update/Render -> slider not work
2283         // only render = ok navigation, but for contour Update needed but slower ?
2284
2285         mSlicerManagers[i]->UpdateSlice(0);  // <-- DS add this. Not too much update ? YES. but needed for ImageContour ...
2286         //mSlicerManagers[i]->GetSlicer(0)->Render(); // <-- DS add this, needed for contour, seems ok ? not too slow ?
2287       }
2288       break;
2289     }
2290   }
2291 }
2292 //------------------------------------------------------------------------------
2293
2294
2295 //------------------------------------------------------------------------------
2296 void vvMainWindow::NEVerticalSliderChanged()
2297 {
2298   static int value=-1;
2299   if (value == NEVerticalSlider->value()) return;
2300   else value = NEVerticalSlider->value();
2301   //  int value = NEVerticalSlider->value();
2302   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
2303     if (DataTree->topLevelItem(i)->data(COLUMN_UR_VIEW,Qt::CheckStateRole).toInt() > 1) {
2304       if (mSlicerManagers[i]->GetSlicer(1)->GetSlice() != value) {
2305         mSlicerManagers[i]->GetSlicer(1)->SetSlice(value);
2306         mSlicerManagers[i]->VerticalSliderHasChanged(1, value);
2307         mSlicerManagers[i]->UpdateSlice(1);
2308         //mSlicerManagers[i]->GetSlicer(1)->Render(); // <-- DS add this, needed for contour, seems ok ? not too slow ?
2309       }
2310       break;
2311     }
2312   }
2313 }
2314 //------------------------------------------------------------------------------
2315
2316
2317 //------------------------------------------------------------------------------
2318 void vvMainWindow::SOVerticalSliderChanged()
2319 {
2320   static int value=-1;
2321   // DD(value);
2322 //   DD(SOVerticalSlider->value());
2323   if (value == SOVerticalSlider->value()) return;
2324   else value = SOVerticalSlider->value();
2325   //int value = SOVerticalSlider->value();
2326   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
2327     if (DataTree->topLevelItem(i)->data(COLUMN_DL_VIEW,Qt::CheckStateRole).toInt() > 1) {
2328       if (mSlicerManagers[i]->GetSlicer(2)->GetSlice() != value) {
2329         mSlicerManagers[i]->GetSlicer(2)->SetSlice(value);
2330         mSlicerManagers[i]->VerticalSliderHasChanged(2, value);
2331         mSlicerManagers[i]->UpdateSlice(2);
2332         //mSlicerManagers[i]->GetSlicer(2)->Render(); // <-- DS add this, needed for contour, seems ok ? not too slow ?
2333       }
2334       // else { DD("avoid SOVerticalSlider slicer update"); }
2335       break;
2336     }
2337   }
2338 }
2339 //------------------------------------------------------------------------------
2340
2341
2342 //------------------------------------------------------------------------------
2343 void vvMainWindow::SEVerticalSliderChanged()
2344 {
2345   static int value=-1;
2346   if (value == SEVerticalSlider->value()) return;
2347   else value = SEVerticalSlider->value();
2348   // int value = SEVerticalSlider->value();
2349   for (unsigned int i = 0; i < mSlicerManagers.size(); i++) {
2350     if (DataTree->topLevelItem(i)->data(COLUMN_DR_VIEW,Qt::CheckStateRole).toInt() > 1) {
2351       if (mSlicerManagers[i]->GetSlicer(3)->GetSlice() != value) {
2352         mSlicerManagers[i]->GetSlicer(3)->SetSlice(value);
2353         mSlicerManagers[i]->VerticalSliderHasChanged(3, value);
2354         mSlicerManagers[i]->UpdateSlice(3);
2355         //mSlicerManagers[i]->GetSlicer(3)->Render(); // <-- DS add this, needed for contour, seems ok ? not too slow ?
2356       }
2357       break;
2358     }
2359   }
2360 }
2361 //------------------------------------------------------------------------------
2362
2363
2364 //------------------------------------------------------------------------------
2365 void vvMainWindow::UpdateSlice(int slicer, int slice)
2366 {
2367   // DD("vvMainWindow::UpdateSlice");
2368 //   DD(slicer);
2369 //   DD(slice);
2370   if (slicer == 0) {
2371     //    if (slice != NOVerticalSlider->value())
2372     NOVerticalSlider->setValue(slice);
2373   } else {
2374     if (slicer == 1)
2375       NEVerticalSlider->setValue(slice);
2376     else {
2377       if (slicer == 2)
2378         SOVerticalSlider->setValue(slice);
2379       else {
2380         if (slicer == 3)
2381           SEVerticalSlider->setValue(slice);
2382       }
2383     }
2384   }
2385   // DD("vvMainWindow:UpdateSlice END");
2386 }
2387 //------------------------------------------------------------------------------
2388
2389
2390 //------------------------------------------------------------------------------
2391 void vvMainWindow::UpdateTSlice(int slicer, int slice)
2392 {
2393   switch (slicer) {
2394   case 0:
2395     NOHorizontalSlider->setValue(slice);
2396     break;
2397   case 1:
2398     NEHorizontalSlider->setValue(slice);
2399     break;
2400   case 2:
2401     SOHorizontalSlider->setValue(slice);
2402     break;
2403   case 3:
2404     SEHorizontalSlider->setValue(slice);
2405     break;
2406   }
2407 }
2408 //------------------------------------------------------------------------------
2409
2410
2411 //------------------------------------------------------------------------------
2412 void vvMainWindow::UpdateSliceRange(int slicer, int min, int max, int tmin, int tmax)
2413 {
2414   int position = int((min+max)/2);
2415   int tPosition = int((tmin+tmax)/2);
2416   if (slicer == 0) {
2417     NOVerticalSlider->setValue(position);
2418     NOVerticalSlider->setRange(min,max);
2419     NOHorizontalSlider->setRange(tmin,tmax);
2420     NOHorizontalSlider->setValue(tPosition);
2421   } else if (slicer == 1) {
2422     NEVerticalSlider->setValue(position);
2423     NEVerticalSlider->setRange(min,max);
2424     NEHorizontalSlider->setRange(tmin,tmax);
2425     NEHorizontalSlider->setValue(tPosition);
2426   } else if (slicer == 2) {
2427     SOVerticalSlider->setValue(position);
2428     SOVerticalSlider->setRange(min,max);
2429     SOHorizontalSlider->setRange(tmin,tmax);
2430     SOHorizontalSlider->setValue(tPosition);
2431   } else if (slicer == 3) {
2432     SEVerticalSlider->setValue(position);
2433     SEVerticalSlider->setRange(min,max);
2434     SEHorizontalSlider->setRange(tmin,tmax);
2435     SEHorizontalSlider->setValue(tPosition);
2436   }
2437 }
2438 //------------------------------------------------------------------------------
2439
2440
2441 //------------------------------------------------------------------------------
2442 void vvMainWindow::SaveNOScreenshot()
2443 {
2444   vtkWindowToImageFilter *w2i = vtkWindowToImageFilter::New();
2445   w2i->SetInput(NOViewWidget->GetRenderWindow());
2446   w2i->Update();
2447   SaveScreenshot(w2i->GetOutput());
2448   w2i->Delete();
2449 }
2450 //------------------------------------------------------------------------------
2451
2452
2453 //------------------------------------------------------------------------------
2454 void vvMainWindow::SaveNEScreenshot()
2455 {
2456   vtkWindowToImageFilter *w2i = vtkWindowToImageFilter::New();
2457   w2i->SetInput(NEViewWidget->GetRenderWindow());
2458   w2i->Update();
2459   SaveScreenshot(w2i->GetOutput());
2460   w2i->Delete();
2461 }
2462 //------------------------------------------------------------------------------
2463
2464
2465 //------------------------------------------------------------------------------
2466 void vvMainWindow::SaveSOScreenshot()
2467 {
2468   vtkWindowToImageFilter *w2i = vtkWindowToImageFilter::New();
2469   w2i->SetInput(SOViewWidget->GetRenderWindow());
2470   w2i->Update();
2471   SaveScreenshot(w2i->GetOutput());
2472   w2i->Delete();
2473 }
2474 //------------------------------------------------------------------------------
2475
2476
2477 //------------------------------------------------------------------------------
2478 void vvMainWindow::SaveSEScreenshot()
2479 {
2480   vtkWindowToImageFilter *w2i = vtkWindowToImageFilter::New();
2481   w2i->SetInput(SEViewWidget->GetRenderWindow());
2482   w2i->Update();
2483   SaveScreenshot(w2i->GetOutput());
2484   w2i->Delete();
2485 }
2486 //------------------------------------------------------------------------------
2487
2488
2489 //------------------------------------------------------------------------------
2490 void vvMainWindow::SaveScreenshot(vtkImageData* image)
2491 {
2492   QString Extensions = "Images( *.png);;";
2493   Extensions += "Images( *.jpg);;";
2494   Extensions += "Images( *.bmp);;";
2495   Extensions += "Images( *.tif);;";
2496   Extensions += "Images( *.ppm)";
2497   QString fileName = QFileDialog::getSaveFileName(this,
2498                      tr("Save As"),
2499                      itksys::SystemTools::GetFilenamePath(
2500                        mSlicerManagers[0]->GetFileName()).c_str(),
2501                      Extensions);
2502   if (!fileName.isEmpty()) {
2503     const char *ext = fileName.toStdString().c_str() + strlen(fileName.toStdString().c_str()) - 4;
2504     if (!strcmp(ext, ".bmp")) {
2505       vtkBMPWriter *bmp = vtkBMPWriter::New();
2506       bmp->SetInput(image);
2507       bmp->SetFileName(fileName.toStdString().c_str());
2508       bmp->Write();
2509       bmp->Delete();
2510     } else if (!strcmp(ext, ".tif")) {
2511       vtkTIFFWriter *tif = vtkTIFFWriter::New();
2512       tif->SetInput(image);
2513       tif->SetFileName(fileName.toStdString().c_str());
2514       tif->Write();
2515       tif->Delete();
2516     } else if (!strcmp(ext, ".ppm")) {
2517       vtkPNMWriter *pnm = vtkPNMWriter::New();
2518       pnm->SetInput(image);
2519       pnm->SetFileName(fileName.toStdString().c_str());
2520       pnm->Write();
2521       pnm->Delete();
2522     } else if (!strcmp(ext, ".png")) {
2523       vtkPNGWriter *png = vtkPNGWriter::New();
2524       png->SetInput(image);
2525       png->SetFileName(fileName.toStdString().c_str());
2526       png->Write();
2527       png->Delete();
2528     } else if (!strcmp(ext, ".jpg")) {
2529       vtkJPEGWriter *jpg = vtkJPEGWriter::New();
2530       jpg->SetInput(image);
2531       jpg->SetFileName(fileName.toStdString().c_str());
2532       jpg->Write();
2533       jpg->Delete();
2534     } else {
2535       QMessageBox::information(this,tr("Problem saving screenshot !"),tr("Cannot save image.\nPlease set a file extension !!!"));
2536     }
2537   }
2538
2539 }
2540 //------------------------------------------------------------------------------
2541
2542
2543 //------------------------------------------------------------------------------
2544 void vvMainWindow::GoToCursor()
2545 {
2546   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2547   for (int column = 1; column < 5; column++) {
2548     if (DataTree->selectedItems()[0]->data(column,Qt::CheckStateRole).toInt() > 1) {
2549       double* cursorPos = mSlicerManagers[index]->GetSlicer(column-1)->GetCursorPosition();
2550       mSlicerManagers[index]->GetSlicer(column-1)->SetCurrentPosition(
2551         cursorPos[0],cursorPos[1],cursorPos[2],cursorPos[3]);
2552       mSlicerManagers[index]->UpdateViews(1,column-1);
2553       mSlicerManagers[index]->UpdateLinked(column-1);
2554       break;
2555     }
2556   }
2557 }
2558 //------------------------------------------------------------------------------
2559
2560 //------------------------------------------------------------------------------
2561 void vvMainWindow::PlayPause()
2562 {
2563   if (playMode) {
2564     playMode = 0;
2565     playButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/player_play.png")));
2566     ImageInfoChanged();
2567     return;
2568   } else {
2569     int image_number=DataTree->topLevelItemCount();
2570     bool has_temporal;
2571     for (int i=0; i<image_number; i++)
2572       if (mSlicerManagers[i]->GetImage()->GetVTKImages().size() > 1) {
2573         has_temporal=true;
2574         break;
2575       }
2576     if (has_temporal) {
2577       playMode = 1;
2578       playButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/player_pause.png")));
2579       QTimer::singleShot(1000/mFrameRate, this, SLOT(PlayNext()));
2580     }
2581   }
2582 }
2583 //------------------------------------------------------------------------------
2584
2585 //------------------------------------------------------------------------------
2586 void vvMainWindow::PlayNext()
2587 {
2588   if (playMode && !this->isHidden()) {
2589     int image_number=DataTree->topLevelItemCount();
2590     ///Only play one slicer per SM, and only if the SM is being displayed
2591     for (int i=0; i<image_number; i++)
2592       for (int j=0; j<4; j++)
2593         if (mSlicerManagers[i]->GetImage()->GetVTKImages().size() > 1 &&
2594             DataTree->topLevelItem(i)->data(j+1,Qt::CheckStateRole).toInt() > 0) {
2595           mSlicerManagers[i]->SetNextTSlice(j);
2596           break;
2597         }
2598     QTimer::singleShot(1000/mFrameRate, this, SLOT(PlayNext()));
2599   }
2600 }
2601 //------------------------------------------------------------------------------
2602
2603 void vvMainWindow::ShowLastImage()
2604 {
2605   if (mSlicerManagers.size() > 1) {
2606     QTreeWidgetItem * item=DataTree->topLevelItem(DataTree->topLevelItemCount()-1);
2607     CurrentImageChanged(mSlicerManagers.back()->GetId()); //select new image
2608     item->setData(1,Qt::CheckStateRole,2); //show the new image in the first panel
2609     DisplayChanged(item,1);
2610   }
2611 }
2612
2613 //------------------------------------------------------------------------------
2614 void vvMainWindow::UpdateRenderWindows()
2615 {
2616   if (NOViewWidget->GetRenderWindow()) NOViewWidget->GetRenderWindow()->Render();
2617   if (NEViewWidget->GetRenderWindow()) NEViewWidget->GetRenderWindow()->Render();
2618   if (SOViewWidget->GetRenderWindow()) SOViewWidget->GetRenderWindow()->Render();
2619   if (SEViewWidget->GetRenderWindow()) SEViewWidget->GetRenderWindow()->Render();
2620 }
2621 //------------------------------------------------------------------------------
2622
2623 //------------------------------------------------------------------------------
2624 void vvMainWindow::SegmentationOnCurrentImage()
2625 {
2626   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2627
2628   vvSegmentationDialog segmentation;
2629   segmentation.SetImage(mSlicerManagers[index]->GetSlicer(0)->GetImage());
2630   segmentation.exec();
2631 }
2632 //------------------------------------------------------------------------------
2633
2634 void vvMainWindow::SurfaceViewerLaunch()
2635 {
2636   vvSurfaceViewerDialog surfaceViewer;
2637   surfaceViewer.exec();
2638 }
2639 //------------------------------------------------------------------------------
2640
2641
2642 //------------------------------------------------------------------------------
2643 int vvMainWindow::GetImageDuplicateFilenameNumber(std::string filename)
2644 {
2645   int number=0;
2646   for(unsigned int l=0; l<mSlicerManagers.size(); l++) {
2647     vvSlicerManager * v = mSlicerManagers[l];
2648     if (v->GetBaseFileName() ==
2649         vtksys::SystemTools::GetFilenameName(vtksys::SystemTools::GetFilenameWithoutLastExtension(filename))) {
2650       number = std::max(number, v->GetBaseFileNameNumber()+1);
2651     }
2652   }
2653   return number;
2654 }
2655 //------------------------------------------------------------------------------
2656
2657
2658 //------------------------------------------------------------------------------
2659 vvSlicerManager* vvMainWindow::AddImage(vvImage::Pointer image,std::string filename)
2660 {
2661   // Change filename if another image exist with the same name
2662   int number = GetImageDuplicateFilenameNumber(filename);
2663
2664   // Create new SliceManager
2665   vvSlicerManager* slicer_manager = new vvSlicerManager(4);
2666   slicer_manager->SetImage(image);//, IMAGE, number);
2667   //  filename = filename+"_"+clitk::toString(number);
2668   slicer_manager->SetFilename(filename, number);
2669   mSlicerManagers.push_back(slicer_manager);
2670
2671   //create an item in the tree with good settings
2672   QTreeWidgetItem *item = new QTreeWidgetItem();
2673   item->setData(0,Qt::UserRole,slicer_manager->GetFileName().c_str());//files[i].c_str());
2674   item->setData(COLUMN_IMAGE_NAME,Qt::DisplayRole,filename.c_str());
2675   qApp->processEvents();
2676
2677   for (int j = 1; j <= 4; j++) item->setData(j,Qt::CheckStateRole,1);
2678
2679   //Create the buttons for reload and close
2680   qApp->processEvents();
2681   QTreePushButton* cButton = new QTreePushButton;
2682   cButton->setItem(item);
2683   cButton->setColumn(COLUMN_CLOSE_IMAGE);
2684   cButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/exit.png")));
2685   connect(cButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
2686           this,SLOT(CloseImage(QTreeWidgetItem*, int)));
2687
2688   QTreePushButton* rButton = new QTreePushButton;
2689   rButton->setItem(item);
2690   rButton->setColumn(COLUMN_RELOAD_IMAGE);
2691   rButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/rotateright.png")));
2692   rButton->setEnabled(0);
2693   connect(rButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
2694           this,SLOT(ReloadImage(QTreeWidgetItem*, int)));
2695
2696   DataTree->addTopLevelItem(item);
2697   DataTree->setItemWidget(item, COLUMN_CLOSE_IMAGE, cButton);
2698   DataTree->setItemWidget(item, COLUMN_RELOAD_IMAGE, rButton);
2699
2700   //set the id of the image
2701   QString id = slicer_manager->GetFileName().c_str() + QString::number(mSlicerManagers.size()-1);
2702   item->setData(COLUMN_IMAGE_NAME,Qt::UserRole,id.toStdString().c_str());
2703   mSlicerManagers.back()->SetId(id.toStdString());
2704
2705   linkPanel->addImage(filename, id.toStdString());
2706
2707   connect(mSlicerManagers.back(), SIGNAL(currentImageChanged(std::string)),
2708           this, SLOT(CurrentImageChanged(std::string)));
2709   connect(mSlicerManagers.back(), SIGNAL(UpdatePosition(int, double, double, double, double, double, double, double)),
2710           this, SLOT(MousePositionChanged(int,double, double, double, double, double, double, double)));
2711   connect(mSlicerManagers.back(), SIGNAL(UpdateVector(int, double, double, double, double)),
2712           this, SLOT(VectorChanged(int,double,double,double, double)));
2713   connect(mSlicerManagers.back(), SIGNAL(UpdateOverlay(int, double, double)),
2714           this, SLOT(OverlayChanged(int,double,double)));
2715   connect(mSlicerManagers.back(), SIGNAL(UpdateFusion(int, double)),
2716           this, SLOT(FusionChanged(int,double)));
2717   connect(mSlicerManagers.back(), SIGNAL(UpdateWindows(int, int, int)),
2718           this,SLOT(WindowsChanged(int, int, int)));
2719   connect(mSlicerManagers.back(), SIGNAL(WindowLevelChanged(double, double,int, int)),
2720           this,SLOT(WindowLevelChanged(double, double, int, int)));
2721   connect(mSlicerManagers.back(), SIGNAL(UpdateSlice(int,int)),
2722           this,SLOT(UpdateSlice(int,int)));
2723   connect(mSlicerManagers.back(), SIGNAL(UpdateTSlice(int, int)),
2724           this,SLOT(UpdateTSlice(int, int)));
2725   connect(mSlicerManagers.back(), SIGNAL(UpdateSliceRange(int,int,int,int,int)),
2726           this,SLOT(UpdateSliceRange(int,int,int,int,int)));
2727   connect(mSlicerManagers.back(), SIGNAL(UpdateLinkManager(std::string,int,double,double,double,int)),
2728           this,SLOT(UpdateLinkManager(std::string,int,double,double,double,int)));
2729   connect(mSlicerManagers.back(), SIGNAL(UpdateLinkedNavigation(std::string,vvSlicerManager*)),
2730           this,SLOT(UpdateLinkedNavigation(std::string,vvSlicerManager*)));
2731   connect(mSlicerManagers.back(), SIGNAL(ChangeImageWithIndexOffset(vvSlicerManager*,int,int)),
2732           this,SLOT(ChangeImageWithIndexOffset(vvSlicerManager*,int,int)));
2733   connect(mSlicerManagers.back(), SIGNAL(LandmarkAdded()),landmarksPanel,SLOT(AddPoint()));
2734   UpdateTree();
2735   qApp->processEvents();
2736   InitSlicers();
2737   ShowLastImage();
2738   InitDisplay();
2739   qApp->processEvents();
2740
2741   // End
2742   return slicer_manager;
2743 }
2744 //------------------------------------------------------------------------------
2745
2746
2747 //------------------------------------------------------------------------------
2748 void vvMainWindow::UpdateCurrentSlicer()
2749 {
2750   int index = -1;
2751   if (DataTree->selectedItems().size() > 0) {
2752     index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2753   }
2754   mSlicerManagerCurrentIndex = index;
2755 }
2756 //------------------------------------------------------------------------------
2757