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 "vvResamplerDialog.h"
  37 #include "vvSegmentationDialog.h"
  38 #include "vvSurfaceViewerDialog.h"
  39 #include "vvDeformationDialog.h"
  40 #include "vvImageWarp.h"
  41 #include "vvUtils.h"
  42 #include "vvMaximumIntensityProjection.h"
  43 #include "vvMidPosition.h"
  44 #include "vvMesh.h"
  45 #include "vvStructSelector.h"
  46 #include "vvMeshReader.h"
  47 #include "vvConstants.h"
  48
  49 #ifdef CLITK_VV_USE_BDCM
  50 #include <bdcmDicomFilesSelectorDialog.h>
  51 #endif
  52
  53 // ITK include
  54 #include "itkImage.h"
  55 #include "itkImageFileReader.h"
  56 #include "itkByteSwapper.h"
  57 #include "itkCommand.h"
  58 #include "itkNumericSeriesFileNames.h"
  59
  60 // VTK include
  61 #include "vtkImageData.h"
  62 #include "vtkImageActor.h"
  63 #include "vtkCornerAnnotation.h"
  64 #include "vtkRenderWindow.h"
  65 #include "vtkRenderWindowInteractor.h"
  66 #include "vtkRenderer.h"
  67 #include "vtkRendererCollection.h"
  68 #include "vtkWindowToImageFilter.h"
  69 #include "vtkBMPWriter.h"
  70 #include "vtkTIFFWriter.h"
  71 #include "vtkPNMWriter.h"
  72 #include "vtkPNGWriter.h"
  73 #include "vtkJPEGWriter.h"
  74
  75 // Standard includes
  76 #include <iostream>
  77
  78 #define COLUMN_TREE 0
  79 #define COLUMN_UL_VIEW 1
  80 #define COLUMN_UR_VIEW 2
  81 #define COLUMN_DL_VIEW 3
  82 #define COLUMN_DR_VIEW 4
  83 #define COLUMN_CLOSE_IMAGE 5
  84 #define COLUMN_RELOAD_IMAGE 6
  85 #define COLUMN_IMAGE_NAME 7
  86
  87 #define EXTENSIONS "Images ( *.bmp *.png *.jpeg *.jpg *.tif *.mhd *.hdr *.vox *.his *.xdr)"
  88
  89 /*Data Tree values
  90   0,Qt::UserRole full filename
  91   1,Qt::CheckStateRole checkbutton UL View
  92   1,Qt::UserRole overlay, fusion or vector
  93   2,Qt::CheckStateRole checkbutton UR View
  94   3,Qt::CheckStateRole checkbutton DL View
  95   4,Qt::CheckStateRole checkbutton DR View
  96   5,0  short filename
  97   5,Qt::UserRole mSlicerManager id*/
  98
  99 //------------------------------------------------------------------------------
 100 vvMainWindow::vvMainWindow():vvMainWindowBase() {
 101   setupUi(this); // this sets up the GUI
 102
 103   mInputPathName = "";
 104   mMenuTools = menuTools;
 105   mContextMenu = &contextMenu;
 106   mMenuExperimentalTools = menuExperimental;
 107   mMainWidget = this;
 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   // QAction* actionCrop_image = contextMenu.addAction(QIcon(QString::fromUtf8(":/common/icons/crop.png")),
 137   //                                                   tr("Crop Current Image"));
 138   // connect(actionCrop_image,SIGNAL(triggered()),this,SLOT(CropImage()));
 139   // contextActions.push_back(actionCrop_image);
 140
 141   QAction* actionSplit_image = contextMenu.addAction(QIcon(QString::fromUtf8(":/common/icons/cut.png")),
 142                                                      tr("Split Current Image"));
 143   connect(actionSplit_image,SIGNAL(triggered()),this,SLOT(SplitImage()));
 144   contextActions.push_back(actionSplit_image);
 145
 146   contextMenu.addSeparator();
 147
 148   contextMenu.addAction(actionAdd_VF_to_current_Image);
 149   contextActions.push_back(actionAdd_VF_to_current_Image);
 150
 151   QAction* actionAdd_Overlay_to_current_Image = menuOverlay->addAction(QIcon(QString::fromUtf8(":/common/icons/GPSup.png")),
 152                                                                        tr("Add overlay image to current image"));
 153   contextMenu.addAction(actionAdd_Overlay_to_current_Image);
 154   contextActions.push_back(actionAdd_Overlay_to_current_Image);
 155
 156   connect(actionAdd_Overlay_to_current_Image,SIGNAL(triggered()), this,SLOT(SelectOverlayImage()));
 157
 158   contextMenu.addAction(actionAdd_fusion_image);
 159   connect(actionAdd_fusion_image,SIGNAL(triggered()),this,SLOT(AddFusionImage()));
 160   contextActions.push_back(actionAdd_fusion_image);
 161
 162   // TRIAL DS
 163   /*
 164   QMenu * m = new QMenu(menubar);
 165   m->setTitle("TOTO");
 166   //  m->setObjectName(QString::fromUtf8("TOTOTO"));
 167   contextMenu.addMenu(m);
 168   QAction * a = m->addAction(QIcon(QString::fromUtf8(":/common/icons/GPSup.png")),
 169                      tr("BIDON"));
 170   QAction * b = m->addAction(QIcon(QString::fromUtf8(":/common/icons/GPSup.png")),
 171                      tr("BIDON2"));
 172   m->addAction(a);
 173   m->addAction(b);
 174   connect(a,SIGNAL(triggered()),this,SLOT(AddFusionImage()));
 175   */
 176
 177   //init the DataTree
 178   mSlicerManagers.resize(0);
 179
 180   QStringList header;
 181   header.append("");
 182   header.append("TL");
 183   header.append("TR");
 184   header.append("BL");
 185   header.append("BR");
 186   header.append("");
 187   header.append("");
 188   header.append("Name");
 189
 190   DataTree->setHeaderLabels(header);
 191   DataTree->resizeColumnToContents(COLUMN_TREE);
 192   DataTree->resizeColumnToContents(COLUMN_UL_VIEW);
 193   DataTree->resizeColumnToContents(COLUMN_UR_VIEW);
 194   DataTree->resizeColumnToContents(COLUMN_DL_VIEW);
 195   DataTree->resizeColumnToContents(COLUMN_DR_VIEW);
 196   DataTree->resizeColumnToContents(COLUMN_CLOSE_IMAGE);
 197   DataTree->resizeColumnToContents(COLUMN_RELOAD_IMAGE);
 198   DataTree->resizeColumnToContents(COLUMN_IMAGE_NAME);
 199
 200   viewMode = 1;
 201   documentation = new vvDocumentation();
 202   help_dialog = new vvHelpDialog();
 203   dicomSeriesSelector = new vvDicomSeriesSelector();
 204
 205   inverseButton->setEnabled(0);
 206   actionAdd_Overlay_to_current_Image->setEnabled(0);
 207   actionSave_As->setEnabled(0);
 208   actionAdd_VF_to_current_Image->setEnabled(0);
 209   actionAdd_fusion_image->setEnabled(0);
 210
 211   //init the sliders
 212   verticalSliders.push_back(NOVerticalSlider);
 213   verticalSliders.push_back(NEVerticalSlider);
 214   verticalSliders.push_back(SOVerticalSlider);
 215   verticalSliders.push_back(SEVerticalSlider);
 216
 217   for (int i =0; i < 4; i++)
 218     verticalSliders[i]->hide();
 219
 220   horizontalSliders.push_back(NOHorizontalSlider);
 221   horizontalSliders.push_back(NEHorizontalSlider);
 222   horizontalSliders.push_back(SOHorizontalSlider);
 223   horizontalSliders.push_back(SEHorizontalSlider);
 224
 225   for (int i =0; i < 4; i++)
 226     horizontalSliders[i]->hide();
 227
 228
 229   connect(NOVerticalSlider,SIGNAL(valueChanged(int)),this,SLOT(NOVerticalSliderChanged()));
 230   connect(NEVerticalSlider,SIGNAL(valueChanged(int)),this,SLOT(NEVerticalSliderChanged()));
 231   connect(SOVerticalSlider,SIGNAL(valueChanged(int)),this,SLOT(SOVerticalSliderChanged()));
 232   connect(SEVerticalSlider,SIGNAL(valueChanged(int)),this,SLOT(SEVerticalSliderChanged()));
 233
 234   connect(NOHorizontalSlider,SIGNAL(valueChanged(int)),this,SLOT(NOHorizontalSliderMoved()));
 235   connect(NEHorizontalSlider,SIGNAL(valueChanged(int)),this,SLOT(NEHorizontalSliderMoved()));
 236   connect(SOHorizontalSlider,SIGNAL(valueChanged(int)),this,SLOT(SOHorizontalSliderMoved()));
 237   connect(SEHorizontalSlider,SIGNAL(valueChanged(int)),this,SLOT(SEHorizontalSliderMoved()));
 238
 239   //connect everything
 240   connect(actionMaximum_Intensity_Projection,SIGNAL(triggered()),this,SLOT(ComputeMIP()));
 241   connect(actionCompute_mid_position_image,SIGNAL(triggered()),this,SLOT(ComputeMidPosition()));
 242   connect(actionDeformable_Registration,SIGNAL(triggered()),this,SLOT(ComputeDeformableRegistration()));
 243   connect(actionWarp_image_with_vector_field,SIGNAL(triggered()),this,SLOT(WarpImage()));
 244   connect(actionLoad_images,SIGNAL(triggered()),this,SLOT(OpenImages()));
 245   connect(actionOpen_Dicom,SIGNAL(triggered()),this,SLOT(OpenDicom()));
 246   connect(actionOpen_Dicom_Struct,SIGNAL(triggered()),this,SLOT(OpenDCStructContour()));
 247   connect(actionOpen_VTK_contour,SIGNAL(triggered()),this,SLOT(OpenVTKContour()));
 248   connect(actionOpen_Multiple_Images_As_One,SIGNAL(triggered()),this,SLOT(MergeImages()));
 249   connect(actionOpen_Image_With_Time,SIGNAL(triggered()),this,SLOT(OpenImageWithTime()));
 250   connect(actionMerge_images_as_n_dim_t, SIGNAL(triggered()), this, SLOT(MergeImagesWithTime()));
 251   connect(actionSave_As,SIGNAL(triggered()),this,SLOT(SaveAs()));
 252   connect(actionExit,SIGNAL(triggered()),this,SLOT(close()));
 253   connect(actionAdd_VF_to_current_Image,SIGNAL(triggered()),this,SLOT(OpenField()));
 254   connect(actionNavigation_Help,SIGNAL(triggered()),this,SLOT(ShowHelpDialog()));
 255   connect(actionDocumentation,SIGNAL(triggered()),this,SLOT(ShowDocumentation()));
 256
 257   ///////////////////////////////////////////////
 258   contextMenu.addAction(actionResampler);
 259   connect(actionResampler,SIGNAL(triggered()),this,SLOT(ResampleCurrentImage()));
 260   connect(actionSegmentation,SIGNAL(triggered()),this,SLOT(SegmentationOnCurrentImage()));
 261   connect(actionSurface_Viewer,SIGNAL(triggered()),this,SLOT(SurfaceViewerLaunch()));
 262   ///////////////////////////////////////////////
 263
 264   actionNorth_East_Window->setEnabled(0);
 265   actionNorth_West_Window->setEnabled(0);
 266   actionSouth_East_Window->setEnabled(0);
 267   actionSouth_West_Window->setEnabled(0);
 268
 269   connect(actionNorth_East_Window,SIGNAL(triggered()),this,SLOT(SaveNEScreenshot()));
 270   connect(actionNorth_West_Window,SIGNAL(triggered()),this,SLOT(SaveNOScreenshot()));
 271   connect(actionSouth_East_Window,SIGNAL(triggered()),this,SLOT(SaveSEScreenshot()));
 272   connect(actionSouth_West_Window,SIGNAL(triggered()),this,SLOT(SaveSOScreenshot()));
 273
 274   connect(DataTree,SIGNAL(itemSelectionChanged()),this,SLOT(ImageInfoChanged()));
 275   connect(DataTree,SIGNAL(itemClicked(QTreeWidgetItem*, int)),this,
 276           SLOT(DisplayChanged(QTreeWidgetItem*, int)));
 277
 278   connect(viewButton,SIGNAL(clicked()),this, SLOT(ChangeViewMode()) );
 279   connect(windowSpinBox,SIGNAL(editingFinished()),this,SLOT(WindowLevelEdited()));
 280   connect(levelSpinBox,SIGNAL(editingFinished()),this,SLOT(WindowLevelEdited()));
 281   connect(colorMapComboBox,SIGNAL(currentIndexChanged(int)),this,SLOT(UpdateColorMap()));
 282   connect(presetComboBox,SIGNAL(currentIndexChanged(int)),this,SLOT(UpdateWindowLevel()));
 283   connect(inverseButton,SIGNAL(clicked()),this,SLOT(SwitchWindowLevel()));
 284
 285
 286   connect(this,SIGNAL(customContextMenuRequested(QPoint)),this,SLOT(ShowContextMenu(QPoint)));
 287
 288   connect(linkPanel,SIGNAL(addLink(QString,QString)),this,SLOT(AddLink(QString,QString)));
 289   connect(linkPanel,SIGNAL(removeLink(QString,QString)),this,SLOT(RemoveLink(QString,QString)));
 290   connect(overlayPanel,SIGNAL(VFPropertyUpdated(int,int,int)),this,SLOT(SetVFProperty(int,int,int)));
 291   connect(overlayPanel,SIGNAL(OverlayPropertyUpdated(int)),this,SLOT(SetOverlayProperty(int)));
 292   connect(overlayPanel,SIGNAL(FusionPropertyUpdated(int,int,double,double)),
 293           this,SLOT(SetFusionProperty(int,int,double,double)));
 294   connect(landmarksPanel,SIGNAL(UpdateRenderWindows()),this,SLOT(UpdateRenderWindows()));
 295
 296   playMode = 0;//pause
 297   mFrameRate = 10;
 298   playButton->setEnabled(0);
 299   frameRateLabel->setEnabled(0);
 300   frameRateSpinBox->setEnabled(0);
 301   connect(playButton, SIGNAL(clicked()),this,SLOT(PlayPause()));
 302   connect(frameRateSpinBox, SIGNAL(valueChanged(int)),this,SLOT(ChangeFrameRate(int)));
 303
 304   goToCursorPushButton->setEnabled(0);
 305   connect(goToCursorPushButton, SIGNAL(clicked()),this,SLOT(GoToCursor()));
 306
 307   NOViewWidget->hide();
 308   NEViewWidget->hide();
 309   SOViewWidget->hide();
 310   SEViewWidget->hide();
 311
 312   //Recently opened files
 313   std::list<std::string> recent_files = GetRecentlyOpenedImages();
 314   if ( !recent_files.empty() )
 315     {
 316       QMenu * rmenu = new QMenu("Recently opened files...");
 317       rmenu->setIcon(QIcon(QString::fromUtf8(":/common/icons/open.png")));
 318       menuFile->insertMenu(actionOpen_Image_With_Time,rmenu);
 319       for (std::list<std::string>::iterator i = recent_files.begin();i!=recent_files.end();i++)
 320         {
 321           QAction* current=new QAction(QIcon(QString::fromUtf8(":/common/icons/open.png")),
 322                                        (*i).c_str(),this);
 323           rmenu->addAction(current);
 324           connect(current,SIGNAL(triggered()),this,SLOT(OpenRecentImage()));
 325         }
 326     }
 327
 328   // Adding all new tools (insertion in the menu)
 329   vvToolManager::GetInstance()->InsertToolsInMenu(this);
 330
 331   if (!CLITK_EXPERIMENTAL)
 332       menuExperimental->menuAction()->setVisible(false);
 333 }
 334 //------------------------------------------------------------------------------
 335
 336
 337 //------------------------------------------------------------------------------
 338 void vvMainWindow::ComputeMIP()
 339 {
 340   vvMaximumIntensityProjection mip;
 341   vvSlicerManager* selected_slicer = mSlicerManagers[GetSlicerIndexFromItem(DataTree->selectedItems()[0])];
 342   QFileInfo info(selected_slicer->GetFileName().c_str());
 343   mip.Compute(selected_slicer);
 344   if (!mip.error)
 345       AddImage(mip.GetOutput(),info.path().toStdString()+"/"+info.completeBaseName().toStdString()+"_mip.mhd");
 346 }
 347 //------------------------------------------------------------------------------
 348
 349
 350 //------------------------------------------------------------------------------
 351 void vvMainWindow::ComputeMidPosition()
 352 {
 353   bool ok;
 354   int index=GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
 355   int ref = QInputDialog::getInteger(this,"Chose reference phase","Reference phase",0,0,\
 356                                      mSlicerManagers[index]->GetImage()->GetVTKImages().size()-1,1,&ok);
 357   if (ok)
 358     {
 359       vvMidPosition midp;
 360       midp.slicer_manager = mSlicerManagers[index];
 361       midp.reference_image_index = ref;
 362       QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
 363       midp.Update();
 364       if (midp.error)
 365         QMessageBox::warning(this, "Error computing midposition image",midp.error_message.c_str());
 366       else
 367         {
 368           QFileInfo info(midp.slicer_manager->GetFileName().c_str());
 369           AddImage(midp.output,info.path().toStdString()+"/"+info.completeBaseName().toStdString()+"_midposition.mhd");
 370         }
 371       QApplication::restoreOverrideCursor();
 372     }
 373 }
 374 //------------------------------------------------------------------------------
 375
 376
 377 //------------------------------------------------------------------------------
 378 void vvMainWindow::AddContour(int image_index, vvMesh::Pointer contour, bool propagation)
 379 {
 380   QTreeWidgetItem *item = new QTreeWidgetItem();
 381   item->setData(0,Qt::UserRole,"filename.vtk");
 382   item->setData(1,Qt::UserRole,tr("contour"));
 383   QBrush brush;
 384   brush.setColor(QColor(contour->r*255,contour->g*255,contour->b*255));
 385   brush.setStyle(Qt::SolidPattern);
 386   item->setData(COLUMN_IMAGE_NAME,Qt::BackgroundRole,brush);
 387   item->setData(COLUMN_IMAGE_NAME,Qt::DisplayRole,contour->structure_name.c_str());
 388
 389   for (int j = 1; j <= 4; j++)
 390     item->setData(j,Qt::CheckStateRole,DataTree->topLevelItem(image_index)->data(j,Qt::CheckStateRole));
 391
 392   QTreePushButton* cButton = new QTreePushButton;
 393   cButton->setItem(item);
 394   cButton->setColumn(COLUMN_CLOSE_IMAGE);
 395   cButton->setToolTip(tr("close image"));
 396   cButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/exit.png")));
 397   connect(cButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
 398           this,SLOT(CloseImage(QTreeWidgetItem*, int)));
 399
 400   QTreePushButton* rButton = new QTreePushButton;
 401   rButton->setItem(item);
 402   rButton->setColumn(COLUMN_RELOAD_IMAGE);
 403   rButton->setToolTip(tr("reload image"));
 404   rButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/rotateright.png")));
 405   rButton->setEnabled(false);
 406   //Not implemented
 407   //connect(rButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
 408   //this,SLOT(ReloadImage(QTreeWidgetItem*, int)));
 409
 410   DataTree->topLevelItem(image_index)->setExpanded(1);
 411   DataTree->topLevelItem(image_index)->addChild(item);
 412   DataTree->setItemWidget(item, COLUMN_CLOSE_IMAGE, cButton);
 413   DataTree->setItemWidget(item, COLUMN_RELOAD_IMAGE, rButton);
 414   QString id = DataTree->topLevelItem(image_index)->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString();
 415   item->setData(COLUMN_IMAGE_NAME,Qt::UserRole,id.toStdString().c_str());
 416
 417   UpdateTree();
 418   mSlicerManagers[image_index]->AddContour(contour,propagation);
 419   mSlicerManagers[image_index]->Render();
 420 }
 421 //------------------------------------------------------------------------------
 422
 423
 424 //------------------------------------------------------------------------------
 425 void vvMainWindow::OpenVTKContour()
 426 {
 427   if (mSlicerManagers.size() > 0)
 428     {
 429       QString Extensions = "Images ( *.vtk; *.obj)";
 430       Extensions += ";;All Files (*)";
 431       QString file = QFileDialog::getOpenFileName(this,tr("Open vtkPolyData"),mInputPathName,Extensions);
 432       if (file.isNull())
 433         return;
 434       QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
 435       int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
 436       vvMeshReader reader;
 437       reader.SetImage(mSlicerManagers[index]->GetImage());
 438       reader.SetModeToVTK();
 439       reader.SetFilename(file.toStdString());
 440       reader.Update();
 441       AddContour(index,reader.GetOutput()[0],false);
 442       QApplication::restoreOverrideCursor();
 443     }
 444 }
 445 //------------------------------------------------------------------------------
 446
 447
 448 //------------------------------------------------------------------------------
 449 void vvMainWindow::OpenDCStructContour()
 450 {
 451   if (mSlicerManagers.size() > 0)
 452     {
 453       QString Extensions = "Dicom Files ( *.dcm; RS*)";
 454       Extensions += ";;All Files (*)";
 455       QString file = QFileDialog::getOpenFileName(this,tr("Merge Images"),mInputPathName,Extensions);
 456       if (file.isNull())
 457         return;
 458       int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
 459       vvMeshReader reader;
 460       reader.SetFilename(file.toStdString());
 461       vvStructSelector selector;
 462       selector.SetStructures(reader.GetROINames());
 463       if (!mSlicerManagers[index]->GetVF().IsNull())
 464         selector.EnablePropagationCheckBox();
 465       if (selector.exec())
 466         {
 467           QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
 468           reader.SetSelectedItems(selector.getSelectedItems());
 469           reader.SetImage(mSlicerManagers[index]->GetImage());
 470           if (selector.PropagationEnabled())
 471             reader.SetPropagationVF(mSlicerManagers[index]->GetVF());
 472           reader.Update();
 473           std::vector<vvMesh::Pointer> contours=reader.GetOutput();
 474           for (std::vector<vvMesh::Pointer>::iterator i=contours.begin();
 475                i!=contours.end();i++)
 476             AddContour(index,*i,selector.PropagationEnabled());
 477           QApplication::restoreOverrideCursor();
 478         }
 479     }
 480 }
 481 //------------------------------------------------------------------------------
 482
 483
 484 //------------------------------------------------------------------------------
 485 void vvMainWindow::ComputeDeformableRegistration()
 486 {
 487   if (mSlicerManagers.size() > 0)
 488     {
 489       int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
 490       vvDeformationDialog dialog(index,mSlicerManagers);
 491       if (dialog.exec())
 492         {
 493           std::string base_name=itksys::SystemTools::GetFilenameWithoutExtension(mSlicerManagers[dialog.GetInputFileIndex()]->GetFileName());
 494           AddField(dialog.GetOutput(),dialog.getFieldFile(),dialog.GetInputFileIndex());
 495           WarpImage(dialog.GetSelectedSlicer(),dialog.GetReferenceFrameIndex());
 496         }
 497       else
 498         std::cout << "Error or user cancellation while computing deformation field..." << std::endl;
 499     }
 500   else QMessageBox::information(this, "Need to open image","You must open an image first.");
 501 }
 502 //------------------------------------------------------------------------------
 503
 504
 505 //------------------------------------------------------------------------------
 506 void vvMainWindow::WarpImage()
 507 {
 508   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
 509   if (!mSlicerManagers[index]->GetVF().IsNull())
 510     {
 511       bool ok;
 512       int ref = QInputDialog::getInteger(this,"Chose reference phase","Reference phase",0,0,\
 513                                          mSlicerManagers[index]->GetImage()->GetVTKImages().size()-1,1,&ok);
 514       if (ok)
 515         {
 516           WarpImage(mSlicerManagers[index],ref);
 517         }
 518     }
 519   else
 520     QMessageBox::warning(this,tr("No vector field"),tr("Sorry, can't warp without a vector field"));
 521 }
 522 //------------------------------------------------------------------------------
 523
 524
 525 //------------------------------------------------------------------------------
 526 void vvMainWindow::WarpImage(vvSlicerManager* selected_slicer,int reference_phase)
 527 {
 528   if (!selected_slicer->GetVF().IsNull())
 529     {
 530       QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
 531       QFileInfo info(selected_slicer->GetFileName().c_str());
 532       vvImageWarp warp(selected_slicer->GetImage(),selected_slicer->GetVF(),
 533                        reference_phase,this);
 534       if (warp.ComputeWarpedImage())
 535         {
 536           AddImage(warp.GetWarpedImage(),info.path().toStdString()+"/"+info.completeBaseName().toStdString()+"_warped.mhd");
 537           AddImage(warp.GetDiffImage()  ,info.path().toStdString()+"/"+info.completeBaseName().toStdString()+"_diff.mhd");
 538           AddImage(warp.GetJacobianImage()  ,info.path().toStdString()+"/"+info.completeBaseName().toStdString()+"_jacobian.mhd");
 539           QApplication::restoreOverrideCursor();
 540         }
 541       else
 542         {
 543           QApplication::restoreOverrideCursor();
 544           QMessageBox::warning(this,tr("Different spacings"),tr("The vector field and image spacings must be the same in order to warp."));
 545         }
 546     }
 547   else
 548     QMessageBox::warning(this,tr("No vector field"),tr("Sorry, can't warp without a vector field."));
 549 }
 550 //------------------------------------------------------------------------------
 551
 552
 553 //------------------------------------------------------------------------------
 554 vvMainWindow::~vvMainWindow() {
 555   for (unsigned int i = 0; i < mSlicerManagers.size(); i++)
 556     {
 557       if (mSlicerManagers[i] != NULL)
 558         delete mSlicerManagers[i];
 559     }
 560 }
 561 //------------------------------------------------------------------------------
 562
 563
 564 //------------------------------------------------------------------------------
 565 void vvMainWindow::MergeImages() {
 566   QString Extensions = EXTENSIONS;
 567   Extensions += ";;All Files (*)";
 568   QStringList files = QFileDialog::getOpenFileNames(this,tr("Merge Images"),mInputPathName,Extensions);
 569   if (files.isEmpty())
 570     return;
 571   mInputPathName = itksys::SystemTools::GetFilenamePath(files[0].toStdString()).c_str();
 572   std::vector<std::string> vector;
 573
 574   unsigned int currentDim = 0;
 575   std::vector<double> currentSpacing;
 576   std::vector<int> currentSize;
 577   std::vector<double> currentOrigin;
 578
 579   for (int i = 0; i < files.size(); i++)
 580     {
 581       itk::ImageIOBase::Pointer reader = itk::ImageIOFactory::CreateImageIO(
 582               files[i].toStdString().c_str(), itk::ImageIOFactory::ReadMode);
 583       reader->SetFileName(files[i].toStdString().c_str());
 584       reader->ReadImageInformation();
 585       if (reader)        {
 586           //NOViewWidget->hide();
 587           //NEViewWidget->hide();
 588           //SOViewWidget->hide();
 589           //SEViewWidget->hide();
 590           if (i == 0)
 591               currentDim = reader->GetNumberOfDimensions();
 592           bool IsOk = true;
 593           for (unsigned int j = 0;j < currentDim; j++)
 594           {
 595               if (i == 0)
 596               {
 597                   if (j == 0)
 598                   {
 599                       currentSpacing.resize(currentDim);
 600                       currentSize.resize(currentDim);
 601                       currentOrigin.resize(currentDim);
 602                   }
 603                   currentOrigin[j] = reader->GetOrigin(j);
 604                   currentSpacing[j] = reader->GetSpacing(j);
 605                   currentSize[j] = reader->GetDimensions(j);
 606               }
 607               else if (currentDim != reader->GetNumberOfDimensions()
 608                       || currentSpacing[j] != reader->GetSpacing(j)
 609                       || currentSize[j] != (int)reader->GetDimensions(j)
 610                       || currentOrigin[j] != reader->GetOrigin(j))
 611               {
 612                   QString error = "Cannot read file (too different from others ";
 613                   error += files[i].toStdString().c_str();
 614                   QMessageBox::information(this,tr("Reading problem"),error);
 615                   IsOk = false;
 616                   break;
 617               }
 618           }
 619           if (IsOk)
 620               vector.push_back(files[i].toStdString());
 621       }
 622     }
 623   if (vector.size() > 0)
 624     LoadImages(vector, MERGED);
 625 }
 626 //------------------------------------------------------------------------------
 627
 628
 629 //------------------------------------------------------------------------------
 630 void vvMainWindow::MergeImagesWithTime() {
 631   QString Extensions = EXTENSIONS;
 632   Extensions += ";;All Files (*)";
 633   QStringList files = QFileDialog::getOpenFileNames(this,tr("Merge Images With Time"),mInputPathName,Extensions);
 634   if (files.isEmpty())
 635     return;
 636   mInputPathName = itksys::SystemTools::GetFilenamePath(files[0].toStdString()).c_str();
 637   std::vector<std::string> vector;
 638
 639   unsigned int currentDim = 0;
 640   std::vector<double> currentSpacing;
 641   std::vector<int> currentSize;
 642   std::vector<double> currentOrigin;
 643
 644   for (int i = 0; i < files.size(); i++)
 645     {
 646       itk::ImageIOBase::Pointer reader = itk::ImageIOFactory::CreateImageIO(
 647                                                                             files[i].toStdString().c_str(), itk::ImageIOFactory::ReadMode);
 648       if (reader)
 649         {
 650           reader->SetFileName(files[i].toStdString().c_str());
 651           reader->ReadImageInformation();
 652           if (i == 0)
 653             currentDim = reader->GetNumberOfDimensions();
 654           bool IsOk = true;
 655           for (unsigned int j = 0;j < currentDim; j++)
 656             {
 657               if (i == 0)
 658                 {
 659                   if (j == 0)
 660                     {
 661                       currentSpacing.resize(currentDim);
 662                       currentSize.resize(currentDim);
 663                       currentOrigin.resize(currentDim);
 664                     }
 665                   currentOrigin[j] = reader->GetOrigin(j);
 666                   currentSpacing[j] = reader->GetSpacing(j);
 667                   currentSize[j] = reader->GetDimensions(j);
 668                 }
 669               else if (currentDim != reader->GetNumberOfDimensions()
 670                        || currentSpacing[j] != reader->GetSpacing(j)
 671                        || currentSize[j] != (int)reader->GetDimensions(j)
 672                        || currentOrigin[j] != reader->GetOrigin(j))
 673                 {
 674                   QString error = "Cannot read file (too different from others ";
 675                   error += files[i].toStdString().c_str();
 676                   QMessageBox::information(this,tr("Reading problem"),error);
 677                   IsOk = false;
 678                   break;
 679                 }
 680             }
 681           if (IsOk)
 682             vector.push_back(files[i].toStdString());
 683         }
 684       else
 685         {
 686           QString error = "Cannot read file info for ";
 687           error += files[i].toStdString().c_str();
 688           error += "\n";
 689           error += "Maybe you're trying to open an image in an unsupported format?\n";
 690           QMessageBox::information(this,tr("Reading problem"),error);
 691         }
 692     }
 693   sort(vector.begin(),vector.end());
 694   if (vector.size() > 1)
 695     LoadImages(vector, MERGEDWITHTIME);
 696   else
 697     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.");
 698 }
 699 //------------------------------------------------------------------------------
 700
 701
 702 //------------------------------------------------------------------------------
 703 void vvMainWindow::OpenDicom() {
 704   std::vector<std::string> files;
 705
 706 #ifdef CLITK_VV_USE_BDCM
 707   bool r = bdcm::OpenDicomFilesSelectorDialog(files,
 708                                               "DicomFilesSelectorDialog test",
 709                                               0,0,800,800,1);
 710
 711   if (r) {
 712     std::cout << "$$$$ main : user clicked 'OK' $$$$"<<std::endl;
 713     std::cout << "$$$$ selected files : "<<std::endl;
 714     std::vector<std::string>::iterator i;
 715     for (i=files.begin();i!=files.end();++i) {
 716       std::cout << *i << std::endl;
 717     }
 718     std::cout << "$$$$ "<<std::endl;
 719
 720     LoadImages(files,DICOM);
 721   }
 722   else {
 723     std::cout << "$$$$ main : user clicked 'CANCEL' $$$$"<<std::endl;
 724   }
 725 #else
 726   std::cout << "dicomSeriesSelector " << std::endl;
 727   if (dicomSeriesSelector->exec() == QDialog::Accepted) {
 728     files = *(dicomSeriesSelector->GetFilenames());
 729     LoadImages(files,DICOM);
 730   }
 731 #endif
 732
 733 }
 734 //------------------------------------------------------------------------------
 735
 736 //------------------------------------------------------------------------------
 737 void vvMainWindow::OpenImages() {
 738   QString Extensions = EXTENSIONS;
 739   Extensions += ";;All Files (*)";
 740
 741   QStringList files = QFileDialog::getOpenFileNames(this,tr("Load Images"),mInputPathName,Extensions);
 742   if (files.isEmpty())
 743     return;
 744   mInputPathName = itksys::SystemTools::GetFilenamePath(files[0].toStdString()).c_str();
 745   std::vector<std::string> vector;
 746   for (int i = 0; i < files.size(); i++)
 747     vector.push_back(files[i].toStdString());
 748   LoadImages(vector, IMAGE);
 749 }
 750 //------------------------------------------------------------------------------
 751 void vvMainWindow::OpenRecentImage()
 752 {
 753   QAction * caller = qobject_cast<QAction*>(sender());
 754   std::vector<std::string> images;
 755   images.push_back(caller->text().toStdString());
 756   mInputPathName = itksys::SystemTools::GetFilenamePath(images[0]).c_str();
 757   LoadImages(images,IMAGE);
 758 }
 759 //------------------------------------------------------------------------------
 760
 761
 762 //------------------------------------------------------------------------------
 763 void vvMainWindow::OpenImageWithTime() {
 764   QString Extensions = EXTENSIONS;
 765   Extensions += ";;All Files (*)";
 766
 767   QStringList files = QFileDialog::getOpenFileNames(this,tr("Load Images With Time"),mInputPathName,Extensions);
 768   if (files.isEmpty())
 769     return;
 770   mInputPathName = itksys::SystemTools::GetFilenamePath(files[0].toStdString()).c_str();
 771   std::vector<std::string> vector;
 772   for (int i = 0; i < files.size(); i++)
 773     {
 774       vector.push_back(files[i].toStdString());
 775     }
 776   LoadImages(vector, IMAGEWITHTIME);
 777 }
 778 //------------------------------------------------------------------------------
 779
 780
 781 //------------------------------------------------------------------------------
 782 void vvMainWindow::LoadImages(std::vector<std::string> files, LoadedImageType filetype) {
 783   //Separate the way to open images and dicoms
 784   int fileSize;
 785   if (filetype == IMAGE || filetype == IMAGEWITHTIME)
 786     fileSize = files.size();
 787   else
 788     fileSize = 1;
 789
 790   //Only add to the list of recently opened files when a single file is opened,
 791   //to avoid polluting the list of recently opened files
 792   if (files.size() == 1)
 793     {
 794       QFileInfo finfo=tr(files[0].c_str());
 795       AddToRecentlyOpenedImages(finfo.absoluteFilePath().toStdString());
 796     }
 797   //init the progress events
 798   QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
 799   vvProgressDialog progress("Opening " + files[0],fileSize>1);
 800   qApp->processEvents();
 801
 802   int numberofsuccesulreads=0;
 803   //open images as 1 or multiples
 804   for (int i = 0; i < fileSize; i++) {
 805
 806     progress.Update("Opening " + files[i]);
 807     progress.SetProgress(i,fileSize);
 808     qApp->processEvents();
 809
 810     //read the image and put it in mSlicerManagers
 811     vvSlicerManager* imageManager = new vvSlicerManager(4);
 812     qApp->processEvents();
 813
 814     bool SetImageSucceed=false;
 815
 816     // Change filename if an image with the same already exist
 817     //    DD(files[i]);
 818     int number=0;
 819     for(unsigned int l=0; l<mSlicerManagers.size(); l++) {
 820       vvSlicerManager * v = mSlicerManagers[l];
 821       //      DD(v->GetBaseFileName());
 822       // DD(v->GetFileName());
 823       if (v->GetBaseFileName() ==
 824           vtksys::SystemTools::GetFilenameName(vtksys::SystemTools::GetFilenameWithoutLastExtension(files[i]))) {
 825         number = std::max(number, v->GetBaseFileNameNumber()+1);
 826       }
 827     }
 828
 829
 830     if (filetype == IMAGE || filetype == IMAGEWITHTIME)
 831       SetImageSucceed = imageManager->SetImage(files[i],filetype, number);
 832     else
 833       {
 834         SetImageSucceed = imageManager->SetImages(files,filetype, number);
 835       }
 836     if (SetImageSucceed == false)
 837       {
 838         QApplication::restoreOverrideCursor();
 839         QString error = "Cannot open file \n";
 840         error += imageManager->GetLastError().c_str();
 841         QMessageBox::information(this,tr("Reading problem"),error);
 842         delete imageManager;
 843       }
 844     else
 845       {
 846         mSlicerManagers.push_back(imageManager);
 847
 848         //create an item in the tree with good settings
 849         QTreeWidgetItem *item = new QTreeWidgetItem();
 850         item->setData(0,Qt::UserRole,files[i].c_str());
 851         QFileInfo fileinfo(imageManager->GetFileName().c_str()); //Do not show the path
 852         item->setData(COLUMN_IMAGE_NAME,Qt::DisplayRole,fileinfo.fileName());
 853         qApp->processEvents();
 854
 855         //Create the buttons for reload and close
 856         qApp->processEvents();
 857         QTreePushButton* cButton = new QTreePushButton;
 858         cButton->setItem(item);
 859         cButton->setColumn(COLUMN_CLOSE_IMAGE);
 860         cButton->setToolTip(tr("close image"));
 861         cButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/exit.png")));
 862         connect(cButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
 863                 this,SLOT(CloseImage(QTreeWidgetItem*, int)));
 864
 865         QTreePushButton* rButton = new QTreePushButton;
 866         rButton->setItem(item);
 867         rButton->setColumn(COLUMN_RELOAD_IMAGE);
 868         rButton->setToolTip(tr("reload image"));
 869         rButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/rotateright.png")));
 870         connect(rButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
 871                 this,SLOT(ReloadImage(QTreeWidgetItem*, int)));
 872
 873         DataTree->addTopLevelItem(item);
 874         DataTree->setItemWidget(item, COLUMN_CLOSE_IMAGE, cButton);
 875         DataTree->setItemWidget(item, COLUMN_RELOAD_IMAGE, rButton);
 876
 877         //set the id of the image
 878         QString id = files[i].c_str() + QString::number(mSlicerManagers.size()-1);
 879         item->setData(COLUMN_IMAGE_NAME,Qt::UserRole,id.toStdString().c_str());
 880         mSlicerManagers.back()->SetId(id.toStdString());
 881
 882         linkPanel->addImage(imageManager->GetFileName(), id.toStdString());
 883
 884         connect(mSlicerManagers.back(), SIGNAL(currentImageChanged(std::string)),
 885                 this,SLOT(CurrentImageChanged(std::string)));
 886         connect(mSlicerManagers.back(), SIGNAL(UpdatePosition(int, double, double, double, double, double, double, double)),
 887              this,SLOT(MousePositionChanged(int,double, double, double, double, double, double, double)));
 888         connect(mSlicerManagers.back(), SIGNAL(UpdateVector(int, double, double, double, double)),
 889                 this, SLOT(VectorChanged(int,double,double,double, double)));
 890         connect(mSlicerManagers.back(), SIGNAL(UpdateOverlay(int, double, double)),
 891                 this, SLOT(OverlayChanged(int,double,double)));
 892         connect(mSlicerManagers.back(), SIGNAL(UpdateFusion(int, double)),
 893                 this, SLOT(FusionChanged(int,double)));
 894         connect(mSlicerManagers.back(), SIGNAL(UpdateWindows(int, int, int)),
 895                 this,SLOT(WindowsChanged(int, int, int)));
 896         connect(mSlicerManagers.back(), SIGNAL(WindowLevelChanged(double, double,int, int)),
 897                 this,SLOT(WindowLevelChanged(double, double, int, int)));
 898         connect(mSlicerManagers.back(), SIGNAL(UpdateSlice(int,int)),
 899                 this,SLOT(UpdateSlice(int,int)));
 900         connect(mSlicerManagers.back(), SIGNAL(UpdateTSlice(int, int)),
 901                 this,SLOT(UpdateTSlice(int, int)));
 902         connect(mSlicerManagers.back(), SIGNAL(UpdateSliceRange(int,int,int,int,int)),
 903                 this,SLOT(UpdateSliceRange(int,int,int,int,int)));
 904         connect(mSlicerManagers.back(), SIGNAL(UpdateLinkManager(std::string,int,double,double,double,int)),
 905                 this,SLOT(UpdateLinkManager(std::string,int,double,double,double,int)));
 906         connect(mSlicerManagers.back(), SIGNAL(ChangeImageWithIndexOffset(vvSlicerManager*,int,int)),
 907                 this,SLOT(ChangeImageWithIndexOffset(vvSlicerManager*,int,int)));
 908         connect(mSlicerManagers.back(),SIGNAL(LandmarkAdded()),landmarksPanel,SLOT(AddPoint()));
 909         InitSlicers();
 910         numberofsuccesulreads++;
 911       }
 912   }
 913   if (numberofsuccesulreads)
 914     {
 915       NOViewWidget->show();
 916       NEViewWidget->show();
 917       SOViewWidget->show();
 918       SEViewWidget->show();
 919       UpdateTree();
 920       InitDisplay();
 921       ShowLastImage();
 922     }
 923   QApplication::restoreOverrideCursor();
 924
 925 }
 926 //------------------------------------------------------------------------------
 927
 928 //------------------------------------------------------------------------------
 929 void vvMainWindow::UpdateTree() {
 930   DataTree->resizeColumnToContents(COLUMN_TREE);
 931   DataTree->resizeColumnToContents(COLUMN_UL_VIEW);
 932   DataTree->resizeColumnToContents(COLUMN_UR_VIEW);
 933   DataTree->resizeColumnToContents(COLUMN_DL_VIEW);
 934   DataTree->resizeColumnToContents(COLUMN_DR_VIEW);
 935   DataTree->resizeColumnToContents(COLUMN_IMAGE_NAME);
 936   DataTree->resizeColumnToContents(COLUMN_CLOSE_IMAGE);
 937   DataTree->resizeColumnToContents(COLUMN_RELOAD_IMAGE);
 938 }
 939 //------------------------------------------------------------------------------
 940
 941 //------------------------------------------------------------------------------
 942 void vvMainWindow::CurrentImageChanged(std::string id) {
 943   int selected = 0;
 944   for (int i = 0; i < DataTree->topLevelItemCount(); i++)
 945     {
 946       if (DataTree->topLevelItem(i)->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString().toStdString() == id)
 947         {
 948           selected = i;
 949         }
 950       else
 951         {
 952           DataTree->topLevelItem(i)->setSelected(0);
 953         }
 954       for (int child = 0; child < DataTree->topLevelItem(i)->childCount();child++)
 955         DataTree->topLevelItem(i)->child(child)->setSelected(0);
 956
 957     }
 958   DataTree->topLevelItem(selected)->setSelected(1);
 959 }
 960 //------------------------------------------------------------------------------
 961
 962 //------------------------------------------------------------------------------
 963 void vvMainWindow::ImageInfoChanged() {
 964   contextActions[7]->setEnabled(1);
 965   contextActions[6]->setEnabled(1);
 966   actionSave_As->setEnabled(1);
 967   actionAdd_VF_to_current_Image->setEnabled(1);
 968   actionAdd_fusion_image->setEnabled(1);
 969   actionNorth_East_Window->setEnabled(1);
 970   actionNorth_West_Window->setEnabled(1);
 971   actionSouth_East_Window->setEnabled(1);
 972   actionSouth_West_Window->setEnabled(1);
 973   inverseButton->setEnabled(1);
 974
 975   goToCursorPushButton->setEnabled(1);
 976
 977   if (DataTree->selectedItems().size()) {
 978     int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
 979
 980     colorMapComboBox->setEnabled(1);
 981     for (int i = 0; i < DataTree->topLevelItem(index)->childCount();i++)
 982       {
 983         if (DataTree->topLevelItem(index)->child(i)->data(1,Qt::UserRole).toString() == "overlay" ||
 984             DataTree->topLevelItem(index)->child(i)->data(1,Qt::UserRole).toString() == "fusion")
 985           {
 986             colorMapComboBox->setEnabled(0);
 987             break;
 988           }
 989       }
 990
 991     std::vector<double> origin;
 992     std::vector<double> inputSpacing;
 993     std::vector<int> inputSize;
 994     std::vector<double> sizeMM;
 995     int dimension=0;
 996     QString pixelType;
 997     QString inputSizeInBytes;
 998     QString image = DataTree->selectedItems()[0]->data(COLUMN_IMAGE_NAME,Qt::DisplayRole).toString();
 999
1000     if (mSlicerManagers[index]->GetSlicer(0)->GetImage()->GetVTKImages().size() > 1 || playMode == 1)
1001       {
1002         playButton->setEnabled(1);
1003         frameRateLabel->setEnabled(1);
1004         frameRateSpinBox->setEnabled(1);
1005       }
1006     else
1007       {
1008         playButton->setEnabled(0);
1009         frameRateLabel->setEnabled(0);
1010         frameRateSpinBox->setEnabled(0);
1011       }
1012
1013     //read image header
1014     int NPixel = 1;
1015
1016     if (DataTree->topLevelItem(index) == DataTree->selectedItems()[0])
1017       {
1018         vvImage::Pointer imageSelected = mSlicerManagers[index]->GetSlicer(0)->GetImage();
1019         dimension = imageSelected->GetNumberOfDimensions();
1020         origin.resize(dimension);
1021         inputSpacing.resize(dimension);
1022         inputSize.resize(dimension);
1023         sizeMM.resize(dimension);
1024         pixelType = mSlicerManagers[index]->GetImage()->GetScalarTypeAsString().c_str();
1025         for (int i = 0;i < dimension;i++)
1026           {
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       }
1035     else if (DataTree->selectedItems()[0]->data(1,Qt::UserRole).toString() == "vector")
1036       {
1037         vvImage::Pointer imageSelected = mSlicerManagers[index]->GetSlicer(0)->GetVF();
1038         dimension = imageSelected->GetNumberOfDimensions();
1039         origin.resize(dimension);
1040         inputSpacing.resize(dimension);
1041         inputSize.resize(dimension);
1042         sizeMM.resize(dimension);
1043         pixelType = mSlicerManagers[index]->GetVF()->GetScalarTypeAsString().c_str();
1044         for (int i = 0;i < dimension;i++)
1045           {
1046             origin[i] = imageSelected->GetOrigin()[i];
1047             inputSpacing[i] = imageSelected->GetSpacing()[i];
1048             inputSize[i] = imageSelected->GetSize()[i];
1049             sizeMM[i] = inputSize[i]*inputSpacing[i];
1050             NPixel *= inputSize[i];
1051           }
1052         inputSizeInBytes = GetSizeInBytes(imageSelected->GetActualMemorySize()*1000);
1053       }
1054     else if (DataTree->selectedItems()[0]->data(1,Qt::UserRole).toString() == "overlay")
1055       {
1056         vvImage::Pointer imageSelected = mSlicerManagers[index]->GetSlicer(0)->GetOverlay();
1057         dimension = imageSelected->GetNumberOfDimensions();
1058         origin.resize(dimension);
1059         inputSpacing.resize(dimension);
1060         inputSize.resize(dimension);
1061         sizeMM.resize(dimension);
1062         pixelType = mSlicerManagers[index]->GetImage()->GetScalarTypeAsString().c_str();
1063         for (int i = 0;i < dimension;i++)
1064           {
1065             origin[i] = imageSelected->GetOrigin()[i];
1066             inputSpacing[i] = imageSelected->GetSpacing()[i];
1067             inputSize[i] = imageSelected->GetSize()[i];
1068             sizeMM[i] = inputSize[i]*inputSpacing[i];
1069             NPixel *= inputSize[i];
1070           }
1071         inputSizeInBytes = GetSizeInBytes(imageSelected->GetActualMemorySize()*1000);
1072       }
1073     else if (DataTree->selectedItems()[0]->data(1,Qt::UserRole).toString() == "fusion")
1074       {
1075         vvImage::Pointer imageSelected = mSlicerManagers[index]->GetSlicer(0)->GetFusion();
1076         dimension = imageSelected->GetNumberOfDimensions();
1077         origin.resize(dimension);
1078         inputSpacing.resize(dimension);
1079         inputSize.resize(dimension);
1080         sizeMM.resize(dimension);
1081         pixelType = mSlicerManagers[index]->GetImage()->GetScalarTypeAsString().c_str();
1082         for (int i = 0;i < dimension;i++)
1083           {
1084             origin[i] = imageSelected->GetOrigin()[i];
1085             inputSpacing[i] = imageSelected->GetSpacing()[i];
1086             inputSize[i] = imageSelected->GetSize()[i];
1087             sizeMM[i] = inputSize[i]*inputSpacing[i];
1088             NPixel *= inputSize[i];
1089           }
1090         inputSizeInBytes = GetSizeInBytes(imageSelected->GetActualMemorySize()*1000);
1091       }
1092
1093     QString dim = QString::number(dimension) + " (";
1094     dim += pixelType + ")";
1095
1096     infoPanel->setFileName(image);
1097     infoPanel->setDimension(dim);
1098     infoPanel->setSizePixel(GetVectorIntAsString(inputSize));
1099     infoPanel->setSizeMM(GetVectorDoubleAsString(sizeMM));
1100     infoPanel->setOrigin(GetVectorDoubleAsString(origin));
1101     infoPanel->setSpacing(GetVectorDoubleAsString(inputSpacing));
1102     infoPanel->setNPixel(QString::number(NPixel)+" ("+inputSizeInBytes+")");
1103
1104     landmarksPanel->SetCurrentLandmarks(mSlicerManagers[index]->GetLandmarks(),
1105                                         mSlicerManagers[index]->GetSlicer(0)->GetImage()->GetVTKImages().size());
1106     landmarksPanel->SetCurrentPath(mInputPathName.toStdString());
1107     landmarksPanel->SetCurrentImage(mSlicerManagers[index]->GetFileName().c_str());
1108
1109     overlayPanel->getCurrentImageName(mSlicerManagers[index]->GetFileName().c_str());
1110     for (int i = 0; i < 4;i++)
1111       {
1112         if (DataTree->selectedItems()[0]->data(i+1,Qt::CheckStateRole).toInt() > 0 || i == 3)
1113           {
1114             mSlicerManagers[index]->UpdateInfoOnCursorPosition(i);
1115             break;
1116           }
1117       }
1118     windowSpinBox->setValue(mSlicerManagers[index]->GetColorWindow());
1119     levelSpinBox->setValue(mSlicerManagers[index]->GetColorLevel());
1120     // DD(mSlicerManagers[index]->GetColorMap());
1121     // DD(mSlicerManagers[index]->GetPreset());
1122     presetComboBox->setCurrentIndex(mSlicerManagers[index]->GetPreset());
1123     colorMapComboBox->setCurrentIndex(mSlicerManagers[index]->GetColorMap());
1124
1125     infoPanel->setFileName(image);
1126     infoPanel->setDimension(dim);
1127     infoPanel->setSizePixel(GetVectorIntAsString(inputSize));
1128     infoPanel->setSizeMM(GetVectorDoubleAsString(sizeMM));
1129     infoPanel->setOrigin(GetVectorDoubleAsString(origin));
1130     infoPanel->setSpacing(GetVectorDoubleAsString(inputSpacing));
1131     infoPanel->setNPixel(QString::number(NPixel)+" ("+inputSizeInBytes+")");
1132
1133     landmarksPanel->SetCurrentLandmarks(mSlicerManagers[index]->GetLandmarks(),
1134                                         mSlicerManagers[index]->GetSlicer(0)->GetImage()->GetVTKImages().size());
1135     landmarksPanel->SetCurrentPath(mInputPathName.toStdString());
1136     landmarksPanel->SetCurrentImage(mSlicerManagers[index]->GetFileName().c_str());
1137
1138     overlayPanel->getCurrentImageName(mSlicerManagers[index]->GetFileName().c_str());
1139     for (int i = 0; i < 4;i++)
1140       {
1141         if (DataTree->selectedItems()[0]->data(i+1,Qt::CheckStateRole).toInt() > 0 || i == 3)
1142           {
1143             mSlicerManagers[index]->UpdateInfoOnCursorPosition(i);
1144             break;
1145           }
1146       }
1147     windowSpinBox->setValue(mSlicerManagers[index]->GetColorWindow());
1148     levelSpinBox->setValue(mSlicerManagers[index]->GetColorLevel());
1149     presetComboBox->setCurrentIndex(mSlicerManagers[index]->GetPreset());
1150     colorMapComboBox->setCurrentIndex(mSlicerManagers[index]->GetColorMap());
1151
1152     if (mSlicerManagers[index]->GetSlicer(0)->GetVF())
1153       {
1154         overlayPanel->getVFName(mSlicerManagers[index]->GetVFName().c_str());
1155         overlayPanel->getVFProperty(mSlicerManagers[index]->GetSlicer(0)->GetVFSubSampling(),
1156                                     mSlicerManagers[index]->GetSlicer(0)->GetVFScale(),
1157                                     mSlicerManagers[index]->GetSlicer(0)->GetVFLog());
1158       }
1159     else
1160       {
1161         overlayPanel->getVFName(mSlicerManagers[index]->GetVFName().c_str());
1162         overlayPanel->getVFProperty(-1,-1,-1);
1163       }
1164     if (mSlicerManagers[index]->GetSlicer(0)->GetOverlay())
1165       {
1166         overlayPanel->getOverlayName(mSlicerManagers[index]->GetOverlayName().c_str());
1167         overlayPanel->getOverlayProperty(mSlicerManagers[index]->GetOverlayColor());
1168       }
1169     else
1170       {
1171         overlayPanel->getOverlayName(mSlicerManagers[index]->GetOverlayName().c_str());
1172         overlayPanel->getOverlayProperty(-1);
1173       }
1174     if (mSlicerManagers[index]->GetSlicer(0)->GetFusion())
1175       {
1176         overlayPanel->getFusionName(mSlicerManagers[index]->GetFusionName().c_str());
1177         overlayPanel->getFusionProperty(mSlicerManagers[index]->GetFusionOpacity(),
1178                                         mSlicerManagers[index]->GetFusionColorMap(),
1179                                         mSlicerManagers[index]->GetFusionWindow(),
1180                                         mSlicerManagers[index]->GetFusionLevel());
1181       }
1182     else
1183       {
1184         overlayPanel->getFusionName(mSlicerManagers[index]->GetFusionName().c_str());
1185         overlayPanel->getFusionProperty(-1, -1,-1,-1);
1186       }
1187   }
1188 }
1189 //------------------------------------------------------------------------------
1190
1191 //------------------------------------------------------------------------------
1192 void vvMainWindow::ShowDocumentation() {
1193   documentation->show();
1194 }
1195 //------------------------------------------------------------------------------
1196 void vvMainWindow::ShowHelpDialog() {
1197   help_dialog->show();
1198 }
1199 //------------------------------------------------------------------------------
1200
1201 //------------------------------------------------------------------------------
1202 void vvMainWindow::ChangeViewMode() {
1203   QListIterator<int> it0(splitter_3->sizes());
1204   QListIterator<int> it1(splitter_3->sizes());
1205   int max0 = 0;
1206   int max1 = 1;
1207   while (it0.hasNext())
1208     {
1209       max0 += it0.next();
1210     }
1211   while (it1.hasNext())
1212     {
1213       max1 += it1.next();
1214     }
1215   QList<int> size0;
1216   QList<int> size1;
1217   if (viewMode == 1)
1218     {
1219       viewMode = 0;
1220       size0.push_back(max0);
1221       size0.push_back(0);
1222       size1.push_back(max1);
1223       size1.push_back(0);
1224       splitter_3->setSizes(size0);
1225       OSplitter->setSizes(size1);
1226       DataTree->setColumnHidden(2,1);
1227       DataTree->setColumnHidden(3,1);
1228       DataTree->setColumnHidden(4,1);
1229     }
1230   else
1231     {
1232       viewMode = 1;
1233       size0.push_back(int(max0/2));
1234       size0.push_back(int(max0/2));
1235       size1.push_back(int(max1/2));
1236       size1.push_back(int(max1/2));
1237       splitter_3->setSizes(size0);
1238       OSplitter->setSizes(size1);
1239       DataTree->setColumnHidden(2,0);
1240       DataTree->setColumnHidden(3,0);
1241       DataTree->setColumnHidden(4,0);
1242     }
1243 }
1244 //------------------------------------------------------------------------------
1245
1246 //------------------------------------------------------------------------------
1247 QString vvMainWindow::GetSizeInBytes(unsigned long size) {
1248   QString result = "";// QString::number(size);
1249   //result += " bytes (";
1250   if (size > 1000000000)
1251     {
1252       size /= 1000000000;
1253       result += QString::number(size);
1254       result += "Gb";//)";
1255     }
1256   else if (size > 1000000)
1257     {
1258       size /= 1000000;
1259       result += QString::number(size);
1260       result += "Mb";//)";
1261     }
1262   else if (size > 1000)
1263     {
1264       size /= 1000;
1265       result += QString::number(size);
1266       result += "kb";//)";
1267     }
1268   return result;
1269 }
1270 //------------------------------------------------------------------------------
1271
1272 //------------------------------------------------------------------------------
1273 QString vvMainWindow::GetVectorDoubleAsString(std::vector<double> vectorDouble) {
1274   QString result;
1275   for (unsigned int i= 0; i < vectorDouble.size(); i++)
1276     {
1277       if (i != 0)
1278         result += " ";
1279       result += QString::number(vectorDouble[i]);
1280     }
1281   return result;
1282 }
1283 //------------------------------------------------------------------------------
1284
1285 //------------------------------------------------------------------------------
1286 QString vvMainWindow::GetVectorIntAsString(std::vector<int> vectorInt) {
1287   QString result;
1288   for (unsigned int i= 0; i < vectorInt.size(); i++)
1289     {
1290       if (i != 0)
1291         result += " ";
1292       result += QString::number(vectorInt[i]);
1293     }
1294   return result;
1295 }
1296 //------------------------------------------------------------------------------
1297
1298 //------------------------------------------------------------------------------
1299 int vvMainWindow::GetSlicerIndexFromItem(QTreeWidgetItem* item) {
1300   QString id = item->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString();
1301   for (int i = 0; i < DataTree->topLevelItemCount(); i++)
1302     {
1303       if (DataTree->topLevelItem(i)->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString() == id)
1304         return i;
1305     }
1306   return -1;
1307 }
1308 //------------------------------------------------------------------------------
1309
1310 //------------------------------------------------------------------------------
1311 QTreeWidgetItem* vvMainWindow::GetItemFromSlicerManager(vvSlicerManager* sm) {
1312     QString id = sm->GetId().c_str();
1313     for (int i = 0; i < DataTree->topLevelItemCount(); i++)
1314     {
1315         if (DataTree->topLevelItem(i)->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString() == id)
1316             return DataTree->topLevelItem(i);
1317     }
1318     return NULL;
1319 }
1320 //------------------------------------------------------------------------------
1321
1322 //------------------------------------------------------------------------------
1323 void vvMainWindow::DisplayChanged(QTreeWidgetItem *clicked_item, int column) {
1324   int index = GetSlicerIndexFromItem(clicked_item);
1325   if ( column >= COLUMN_CLOSE_IMAGE || column <= 0)
1326     return;
1327   for (unsigned int i = 0; i < mSlicerManagers.size(); i++)
1328     {
1329      //Trick to avoid redoing twice the job for a key (sr)
1330       mSlicerManagers[i]->GetSlicer(column-1)->GetRenderWindow()-> GetInteractor()->SetKeySym("Crap");
1331
1332       QTreeWidgetItem* current_row=DataTree->topLevelItem(i);
1333       if (DataTree->topLevelItem(index) == current_row)
1334         {
1335           vvSlicer* clicked_slicer=mSlicerManagers[i]->GetSlicer(column-1);
1336           if (current_row == clicked_item)
1337             {
1338               //If we just activated a slicer
1339               if (current_row->data(column,Qt::CheckStateRole).toInt() > 0)
1340                 {
1341                   mSlicerManagers[i]->UpdateSlicer(column-1,clicked_item->data(column,Qt::CheckStateRole).toInt());
1342                   mSlicerManagers[i]->UpdateInfoOnCursorPosition(column-1);
1343                   DisplaySliders(i,column-1);
1344                   std::map<std::string,int> overlay_counts;
1345                   for (int child = 0; child < current_row->childCount(); child++)
1346                     {
1347                       std::string overlay_type =
1348                         current_row->child(child)->data(1,Qt::UserRole).toString().toStdString();
1349                       overlay_counts[overlay_type]++;
1350                       current_row->child(child)->setData(column,Qt::CheckStateRole,
1351                                                          current_row->data(column,Qt::CheckStateRole));
1352                       clicked_slicer->SetActorVisibility(overlay_type,overlay_counts[overlay_type]-1,true);
1353                     }
1354                 }
1355               else //We don't allow simply desactivating a slicer
1356                 {
1357                   clicked_item->setData(column,Qt::CheckStateRole,2);
1358                   return;
1359                 }
1360             }
1361           //if we clicked on the vector(or overlay) and not the image
1362           else
1363             {
1364               if (clicked_item->data(column,Qt::CheckStateRole).toInt())
1365                 {
1366                   current_row->setData(column,Qt::CheckStateRole,2);
1367                   mSlicerManagers[i]->UpdateSlicer(column-1,2);
1368                   mSlicerManagers[i]->UpdateInfoOnCursorPosition(column-1);
1369                   DisplaySliders(i,column-1);
1370                 }
1371               int vis = clicked_item->data(column,Qt::CheckStateRole).toInt();
1372               std::string overlay_type = clicked_item->data(1,Qt::UserRole).toString().toStdString();
1373               int overlay_index=0;
1374               for (int child = 0; child < current_row->childCount(); child++)
1375                 {
1376                   if (current_row->child(child)->data(1,Qt::UserRole).toString().toStdString() == overlay_type)
1377                     overlay_index++;
1378                   if (current_row->child(child) == clicked_item) break;
1379                 }
1380               clicked_slicer->SetActorVisibility(
1381                                                  clicked_item->data(1,Qt::UserRole).toString().toStdString(), overlay_index-1,vis);
1382             }
1383         }
1384       else if (current_row->data(column,Qt::CheckStateRole).toInt() > 0)
1385         {
1386           current_row->setData(column,Qt::CheckStateRole,0);
1387           mSlicerManagers[i]->UpdateSlicer(column-1,0);
1388           std::map<std::string,int> overlay_counts;
1389           for (int child = 0; child < current_row->childCount(); child++)
1390             {
1391               std::string overlay_type =
1392                 current_row->child(child)->data(1,Qt::UserRole).toString().toStdString();
1393               overlay_counts[overlay_type]++;
1394               current_row->child(child)->setData(column,Qt::CheckStateRole,0);
1395               vvSlicer * current_slicer=mSlicerManagers[i]->GetSlicer(column-1);
1396               current_slicer->SetActorVisibility(overlay_type,overlay_counts[overlay_type]-1,false);
1397             }
1398         }
1399       //mSlicerManagers[i]->SetColorMap(-1);
1400       mSlicerManagers[i]->SetColorMap();
1401     }
1402   mSlicerManagers[index]->GetSlicer(column-1)->Render();
1403 }
1404 //------------------------------------------------------------------------------
1405
1406 void vvMainWindow::InitSlicers()
1407 {
1408   if (mSlicerManagers.size())
1409     {
1410       mSlicerManagers.back()->GenerateDefaultLookupTable();
1411
1412       mSlicerManagers.back()->SetSlicerWindow(0,NOViewWidget->GetRenderWindow());
1413       mSlicerManagers.back()->SetSlicerWindow(1,NEViewWidget->GetRenderWindow());
1414       mSlicerManagers.back()->SetSlicerWindow(2,SOViewWidget->GetRenderWindow());
1415       mSlicerManagers.back()->SetSlicerWindow(3,SEViewWidget->GetRenderWindow());
1416     }
1417 }
1418
1419 //------------------------------------------------------------------------------
1420 void vvMainWindow::InitDisplay() {
1421   if (mSlicerManagers.size())
1422     {
1423       //BE CAREFUL : this is absolutely necessary to set the interactor style
1424       //in order to have the same style instanciation for all SlicerManagers in
1425       // a same window
1426       for (int j = 0; j < 4; j++)
1427         {
1428           vvInteractorStyleNavigator* style = vvInteractorStyleNavigator::New();
1429           style->SetAutoAdjustCameraClippingRange(1);
1430           bool AlreadySelected = false;
1431           for (int i = 0; i < DataTree->topLevelItemCount(); i++)
1432             {
1433               mSlicerManagers[i]->SetInteractorStyleNavigator(j,style);
1434
1435               //select the image only if previous are not selected
1436               if (DataTree->topLevelItem(i)->data(j+1,Qt::CheckStateRole).toInt() > 1)
1437                 {
1438                   mSlicerManagers[i]->UpdateSlicer(j,1);
1439                   AlreadySelected = true;
1440                 }
1441               else if (i == DataTree->topLevelItemCount()-1 && !AlreadySelected)
1442                 {
1443                   if (DataTree->selectedItems().size() == 0)
1444                     DataTree->topLevelItem(i)->setSelected(1);
1445                   DataTree->topLevelItem(i)->setData(j+1,Qt::CheckStateRole,2);
1446                   mSlicerManagers[i]->UpdateSlicer(j,1);
1447                   DisplaySliders(i,j);
1448                 }
1449               else
1450                 {
1451                   DataTree->topLevelItem(i)->setData(j+1,Qt::CheckStateRole,0);
1452                   mSlicerManagers[i]->UpdateSlicer(j,0);
1453                 }
1454             }
1455           style->Delete();
1456         }
1457     }
1458 }
1459 //------------------------------------------------------------------------------
1460
1461 //------------------------------------------------------------------------------
1462 void vvMainWindow::DisplaySliders(int slicer, int window) {
1463   int range[2];
1464   mSlicerManagers[slicer]->GetSlicer(window)->GetSliceRange(range);
1465   int position = mSlicerManagers[slicer]->GetSlicer(window)->GetSlice();
1466
1467   int tRange[2];
1468   tRange[0] = 0;
1469   tRange[1] = mSlicerManagers[slicer]->GetSlicer(window)->GetTMax();
1470   int tPosition = mSlicerManagers[slicer]->GetSlicer(window)->GetTSlice();
1471   bool showHorizontal = false;
1472   bool showVertical = false;
1473   if (mSlicerManagers[slicer]->GetSlicer(window)->GetImage()->GetNumberOfDimensions() > 3
1474       || (mSlicerManagers[slicer]->GetSlicer(window)->GetImage()->GetNumberOfDimensions() > 2
1475           && mSlicerManagers[slicer]->GetType() != IMAGEWITHTIME
1476           && mSlicerManagers[slicer]->GetType() != MERGEDWITHTIME))
1477     showVertical = true;
1478   if (mSlicerManagers[slicer]->GetSlicer(window)->GetImage()->GetNumberOfDimensions() > 3
1479       || mSlicerManagers[slicer]->GetType() == IMAGEWITHTIME
1480       || mSlicerManagers[slicer]->GetType() == MERGEDWITHTIME)
1481     showHorizontal = true;
1482
1483   if (showVertical)
1484     verticalSliders[window]->show();
1485   else
1486     verticalSliders[window]->hide();
1487   verticalSliders[window]->setRange(range[0],range[1]);
1488   verticalSliders[window]->setValue(position);
1489
1490   if (showHorizontal)
1491     horizontalSliders[window]->show();
1492   else
1493     horizontalSliders[window]->hide();
1494   horizontalSliders[window]->setRange(tRange[0],tRange[1]);
1495   horizontalSliders[window]->setValue(tPosition);
1496 }
1497 //------------------------------------------------------------------------------
1498
1499 //------------------------------------------------------------------------------
1500 void vvMainWindow::CloseImage(QTreeWidgetItem* item, int column) {
1501   int index = GetSlicerIndexFromItem(item);
1502
1503   if (DataTree->topLevelItem(index) != item)
1504     {
1505       QString warning = "Do you really want to close the overlay : ";
1506       warning += item->data(COLUMN_IMAGE_NAME,Qt::DisplayRole).toString();
1507       QMessageBox msgBox(QMessageBox::Warning, tr("Close Overlay"),
1508                          warning, 0, this);
1509       msgBox.addButton(tr("Close"), QMessageBox::AcceptRole);
1510       msgBox.addButton(tr("Cancel"), QMessageBox::RejectRole);
1511       if (msgBox.exec() == QMessageBox::AcceptRole)
1512         {
1513           std::string overlay_type=item->data(1,Qt::UserRole).toString().toStdString();
1514           int overlay_index=0;
1515           for (int child = 0; child < DataTree->topLevelItem(index)->childCount(); child++)
1516             {
1517               if (DataTree->topLevelItem(index)->\
1518                   child(child)->data(1,Qt::UserRole).toString().toStdString() == overlay_type)
1519                 overlay_index++;
1520               if (DataTree->topLevelItem(index)->child(child) == item) break;
1521             }
1522           mSlicerManagers[index]->RemoveActor(overlay_type, overlay_index-1);
1523           mSlicerManagers[index]->SetColorMap(0);
1524           DataTree->topLevelItem(index)->takeChild(DataTree->topLevelItem(index)->indexOfChild(item));
1525           mSlicerManagers[index]->Render();
1526         }
1527     }
1528   else if (DataTree->topLevelItemCount() <= 1)
1529     {
1530       QString warning = "Do you really want to close the image : ";
1531       warning += item->data(COLUMN_IMAGE_NAME,Qt::DisplayRole).toString();
1532       warning += "\nThis is the last image, you're about to close vv !!!";
1533       QMessageBox msgBox(QMessageBox::Warning, tr("Close Image"),
1534                          warning, 0, this);
1535       msgBox.addButton(tr("Close vv"), QMessageBox::AcceptRole);
1536       msgBox.addButton(tr("Cancel"), QMessageBox::RejectRole);
1537       if (msgBox.exec() == QMessageBox::AcceptRole)
1538         {
1539           this->close();
1540         }
1541     }
1542   else
1543     {
1544       QString warning = "Do you really want to close the image : ";
1545       warning += item->data(COLUMN_IMAGE_NAME,Qt::DisplayRole).toString();
1546       QMessageBox msgBox(QMessageBox::Warning, tr("Close Image"),
1547                          warning, 0, this);
1548       msgBox.addButton(tr("Close"), QMessageBox::AcceptRole);
1549       msgBox.addButton(tr("Cancel"), QMessageBox::RejectRole);
1550       if (msgBox.exec() == QMessageBox::AcceptRole)
1551         {
1552
1553           // Tell tools that we close an image
1554           emit AnImageIsBeingClosed(mSlicerManagers[index]);
1555
1556           std::vector<vvSlicerManager*>::iterator Manageriter = mSlicerManagers.begin();
1557           DataTree->takeTopLevelItem(index);
1558           for (int i = 0; i < index; i++)
1559             {
1560               Manageriter++;
1561             }
1562           linkPanel->removeImage(index);
1563           mSlicerManagers[index]->RemoveActors();
1564           delete mSlicerManagers[index];
1565           mSlicerManagers.erase(Manageriter);
1566
1567           //
1568           InitDisplay();
1569         }
1570     }
1571 }
1572 //------------------------------------------------------------------------------
1573
1574 //------------------------------------------------------------------------------
1575 void vvMainWindow::ReloadImage(QTreeWidgetItem* item, int column) {
1576   // int index = GetSlicerIndexFromItem(item);
1577   //   QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
1578   //   if (item->data(1,Qt::UserRole).toString() == "vector")
1579   //     mSlicerManagers[index]->ReloadVF();
1580   //   else
1581   //     mSlicerManagers[index]->Reload();
1582
1583   //   QApplication::restoreOverrideCursor();
1584   int index = GetSlicerIndexFromItem(item);
1585   QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
1586   QString role=item->data(1,Qt::UserRole).toString();
1587   if ( role == "vector")
1588     mSlicerManagers[index]->ReloadVF();
1589   else if (role == "overlay")
1590     mSlicerManagers[index]->ReloadOverlay();
1591   else if (role == "fusion")
1592     mSlicerManagers[index]->ReloadFusion();
1593   else
1594     mSlicerManagers[index]->Reload();
1595   QApplication::restoreOverrideCursor();
1596 }
1597 //------------------------------------------------------------------------------
1598
1599 // void vvMainWindow::CropImage()
1600 // {
1601 //   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1602 //   vvCropDialog crop(mSlicerManagers,index);
1603 //   if(crop.exec())
1604 //     AddImage(crop.GetOutput(),"cropped.mhd");
1605 // }
1606
1607 //------------------------------------------------------------------------------
1608 void vvMainWindow::SplitImage() {
1609   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1610   int dim = mSlicerManagers[index]->GetDimension();
1611   QString warning = "Do you really want to split the ";
1612   warning += QString::number(dim) + "D image ";
1613   warning += DataTree->selectedItems()[0]->data(COLUMN_IMAGE_NAME,Qt::DisplayRole).toString() + " into ";
1614   warning += QString::number(mSlicerManagers[index]->GetSlicer(0)->GetImage()->GetSize()[dim-1]) + " ";
1615   warning += QString::number(dim-1) + "D images.";
1616   QMessageBox msgBox(QMessageBox::Warning, tr("Split Image"),
1617                      warning, 0, this);
1618   msgBox.addButton(tr("Split"), QMessageBox::AcceptRole);
1619   msgBox.addButton(tr("Cancel"), QMessageBox::RejectRole);
1620   if (msgBox.exec() == QMessageBox::AcceptRole)
1621     {
1622       QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
1623       if (dim > 2)
1624         {
1625           std::string filename = DataTree->selectedItems()[0]->data(0,Qt::UserRole).toString().toStdString();
1626           int numberOfSlice = mSlicerManagers[index]->GetSlicer(0)->GetImage()->GetSize()[dim-1];
1627           std::string path = itksys::SystemTools::GetFilenamePath(
1628                                                                   filename);
1629           path += "/";
1630           path += DataTree->selectedItems()[0]->data(COLUMN_IMAGE_NAME,Qt::DisplayRole).toString().toStdString();
1631           path += "%03d";
1632           path += itksys::SystemTools::GetFilenameLastExtension(
1633                                                                 filename).c_str();
1634
1635           typedef itk::NumericSeriesFileNames NameGeneratorType;
1636           NameGeneratorType::Pointer nameGenerator = NameGeneratorType::New();
1637           nameGenerator->SetSeriesFormat(path.c_str());
1638           nameGenerator->SetStartIndex(0);
1639           nameGenerator->SetEndIndex(numberOfSlice-1);
1640           nameGenerator->SetIncrementIndex(1);
1641
1642           for (int i = 0; i < numberOfSlice; i++)
1643             {
1644               vvSlicerManager* imageManager = new vvSlicerManager(4);
1645               imageManager->SetExtractedImage(nameGenerator->GetFileNames()[i],
1646                                               mSlicerManagers[index]->GetSlicer(0)->GetImage(), i);
1647               mSlicerManagers.push_back(imageManager);
1648
1649               //create an item in the tree with good settings
1650               QTreeWidgetItem *item = new QTreeWidgetItem();
1651               item->setData(0,Qt::UserRole,nameGenerator->GetFileNames()[i].c_str());
1652               std::string fileI = itksys::SystemTools::GetFilenameWithoutLastExtension(
1653                                                                                        nameGenerator->GetFileNames()[i]).c_str();
1654               item->setData(COLUMN_IMAGE_NAME,Qt::DisplayRole,fileI.c_str());
1655               for (int j = 1; j <= 4; j++)
1656                 {
1657                   for (int i = 0; i < DataTree->topLevelItemCount(); i++)
1658                     {
1659                       DataTree->topLevelItem(i)->setData(j,Qt::CheckStateRole,0);
1660                     }
1661                   item->setData(j,Qt::CheckStateRole,2);
1662                 }
1663
1664               //Create the buttons for reload and close
1665               QTreePushButton* cButton = new QTreePushButton;
1666               cButton->setItem(item);
1667               cButton->setColumn(COLUMN_CLOSE_IMAGE);
1668               cButton->setToolTip(tr("close image"));
1669               cButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/exit.png")));
1670               connect(cButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
1671                       this,SLOT(CloseImage(QTreeWidgetItem*, int)));
1672
1673               QTreePushButton* rButton = new QTreePushButton;
1674               rButton->setItem(item);
1675               rButton->setColumn(COLUMN_RELOAD_IMAGE);
1676               rButton->setToolTip(tr("reload image"));
1677               rButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/rotateright.png")));
1678               rButton->setEnabled(false);
1679               connect(rButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
1680                       this,SLOT(ReloadImage(QTreeWidgetItem*, int)));
1681
1682               DataTree->addTopLevelItem(item);
1683               DataTree->setItemWidget(item, COLUMN_CLOSE_IMAGE, cButton);
1684               DataTree->setItemWidget(item, COLUMN_RELOAD_IMAGE, rButton);
1685
1686               //set the id of the image
1687               QString id = nameGenerator->GetFileNames()[i].c_str() + QString::number(mSlicerManagers.size()-1);
1688               item->setData(COLUMN_IMAGE_NAME,Qt::UserRole,id.toStdString().c_str());
1689               mSlicerManagers.back()->SetId(id.toStdString());
1690               linkPanel->addImage(fileI, id.toStdString());
1691               connect(mSlicerManagers.back(),SIGNAL(currentImageChanged(std::string)),
1692                       this,SLOT(CurrentImageChanged(std::string)));
1693               connect(mSlicerManagers.back(),SIGNAL(
1694                                                     UpdatePosition(int, double, double, double, double, double, double, double)),this,
1695                       SLOT(MousePositionChanged(int,double, double, double, double, double, double, double)));
1696               connect(mSlicerManagers.back(),SIGNAL(UpdateVector(int, double, double, double, double)),
1697                       this, SLOT(VectorChanged(int,double,double,double, double)));
1698               connect(mSlicerManagers.back(),SIGNAL(UpdateOverlay(int, double, double)),
1699                       this, SLOT(OverlayChanged(int,double,double)));
1700               connect(mSlicerManagers.back(),SIGNAL(UpdateFusion(int, double)),
1701                       this, SLOT(FusionChanged(int,double)));
1702               connect(mSlicerManagers.back(),SIGNAL(UpdateWindows(int, int, int)),
1703                       this,SLOT(WindowsChanged(int, int, int)));
1704               connect(mSlicerManagers.back(),SIGNAL(WindowLevelChanged(double, double,int, int)),
1705                       this,SLOT(WindowLevelChanged(double, double, int, int)));
1706               connect(mSlicerManagers.back(),SIGNAL(UpdateSlice(int,int)),
1707                       this,SLOT(UpdateSlice(int,int)));
1708               connect(mSlicerManagers.back(),SIGNAL(UpdateTSlice(int, int)),
1709                       this,SLOT(UpdateTSlice(int, int)));
1710               connect(mSlicerManagers.back(),SIGNAL(UpdateSliceRange(int,int,int,int,int)),
1711                       this,SLOT(UpdateSliceRange(int,int,int,int,int)));
1712               connect(mSlicerManagers.back(),SIGNAL(UpdateLinkManager(std::string,int,double,double,double,int)),
1713                       this,SLOT(UpdateLinkManager(std::string,int,double,double,double,int)));
1714               connect(mSlicerManagers.back(),SIGNAL(LandmarkAdded()),landmarksPanel,SLOT(AddPoint()));
1715               UpdateTree();
1716               qApp->processEvents();
1717               InitSlicers();
1718               InitDisplay();
1719               qApp->processEvents();
1720             }
1721           QApplication::restoreOverrideCursor();
1722         }
1723       else
1724         {
1725           QApplication::restoreOverrideCursor();
1726           QString error = "Cannot split file (dimensions must be greater than 2) ";
1727           QMessageBox::information(this,tr("Splitting problem"),error);
1728         }
1729     }
1730 }
1731 //------------------------------------------------------------------------------
1732
1733 //------------------------------------------------------------------------------
1734 void vvMainWindow::MousePositionChanged(int visibility,double x, double y, double z, double X, double Y, double Z , double value) {
1735   infoPanel->setCurrentInfo(visibility,x,y,z,X,Y,Z,value);
1736 }
1737 //------------------------------------------------------------------------------
1738
1739 //------------------------------------------------------------------------------
1740 void vvMainWindow::VectorChanged(int visibility,double x, double y, double z, double value) {
1741   overlayPanel->getCurrentVectorInfo(visibility,x,y,z,value);
1742 }
1743 //------------------------------------------------------------------------------
1744
1745 //------------------------------------------------------------------------------
1746 void vvMainWindow::OverlayChanged(int visibility, double valueOver, double valueRef) {
1747   overlayPanel->getCurrentOverlayInfo(visibility,valueOver, valueRef);
1748 }
1749 //------------------------------------------------------------------------------
1750
1751 //------------------------------------------------------------------------------
1752 void vvMainWindow::FusionChanged(int visibility, double value) {
1753   overlayPanel->getCurrentFusionInfo(visibility,value);
1754 }
1755 //------------------------------------------------------------------------------
1756
1757 //------------------------------------------------------------------------------
1758 void vvMainWindow::WindowsChanged(int window, int view, int slice) {
1759   infoPanel->setViews(window, view, slice);
1760 }
1761 //------------------------------------------------------------------------------
1762
1763 //------------------------------------------------------------------------------
1764 void vvMainWindow::WindowLevelChanged(double window, double level,int preset,int colormap) {
1765   windowSpinBox->setValue(window);
1766   levelSpinBox->setValue(level);
1767   colorMapComboBox->setCurrentIndex(colormap);
1768   presetComboBox->setCurrentIndex(preset);
1769 }
1770 //------------------------------------------------------------------------------
1771
1772 //------------------------------------------------------------------------------
1773 void vvMainWindow::WindowLevelEdited() {
1774   presetComboBox->setCurrentIndex(6);
1775   UpdateWindowLevel();
1776 }
1777 //------------------------------------------------------------------------------
1778
1779 //------------------------------------------------------------------------------
1780 void vvMainWindow::UpdateWindowLevel() {
1781   if (DataTree->selectedItems().size())
1782     {
1783       if (presetComboBox->currentIndex() == 7) //For ventilation
1784         colorMapComboBox->setCurrentIndex(5);
1785       int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1786       mSlicerManagers[index]->SetColorWindow(windowSpinBox->value());
1787       mSlicerManagers[index]->SetColorLevel(levelSpinBox->value());
1788       mSlicerManagers[index]->SetPreset(presetComboBox->currentIndex());
1789       mSlicerManagers[index]->Render();
1790     }
1791 }
1792 //------------------------------------------------------------------------------
1793
1794 //------------------------------------------------------------------------------
1795 void vvMainWindow::UpdateColorMap() {
1796   if (DataTree->selectedItems().size())
1797     {
1798       int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1799       mSlicerManagers[index]->SetColorMap(colorMapComboBox->currentIndex());
1800       mSlicerManagers[index]->Render();
1801     }
1802 }
1803 //------------------------------------------------------------------------------
1804 void vvMainWindow::SwitchWindowLevel() {
1805   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1806   int window = mSlicerManagers[index]->GetColorWindow();
1807   presetComboBox->setCurrentIndex(6);
1808   windowSpinBox->setValue(-window);
1809   UpdateWindowLevel();
1810 }
1811 //------------------------------------------------------------------------------
1812
1813 //------------------------------------------------------------------------------
1814 void vvMainWindow::UpdateLinkManager(std::string id, int slicer, double x, double y, double z, int temps) {
1815   for (unsigned int i = 0; i < mSlicerManagers.size(); i++)
1816     {
1817       if (mSlicerManagers[i]->GetId() == id)
1818         {
1819           //mSlicerManagers[i]->SetTSlice(temps);
1820           mSlicerManagers[i]->GetSlicer(slicer)->SetCurrentPosition(x,y,z,temps);
1821           mSlicerManagers[i]->UpdateViews(0,slicer);
1822           break;
1823         }
1824     }
1825 }
1826 //------------------------------------------------------------------------------
1827
1828 //------------------------------------------------------------------------------
1829 void vvMainWindow::ShowContextMenu(QPoint point) {
1830   if (!DataTree->selectedItems().size())
1831     {
1832       contextActions[1]->setEnabled(0);
1833       contextActions[2]->setEnabled(0);
1834       contextActions[3]->setEnabled(0);
1835       contextActions[4]->setEnabled(0);
1836       contextActions[5]->setEnabled(0);
1837       contextActions[6]->setEnabled(0);
1838       contextActions[7]->setEnabled(0);
1839     }
1840   else
1841     {
1842       int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1843       contextActions[1]->setEnabled(1);
1844       contextActions[2]->setEnabled(
1845                                     DataTree->itemWidget(DataTree->selectedItems()[0],
1846                                                          COLUMN_RELOAD_IMAGE)->isEnabled());
1847       contextActions[3]->setEnabled(1);
1848       contextActions[5]->setEnabled(1);
1849       contextActions[6]->setEnabled(1);
1850       contextActions[7]->setEnabled(1);
1851
1852       if (mSlicerManagers[index]->GetDimension() < 3)
1853         contextActions[4]->setEnabled(0);
1854       else
1855         contextActions[4]->setEnabled(1);
1856     }
1857   contextMenu.exec(QCursor::pos());
1858 }
1859 //------------------------------------------------------------------------------
1860
1861 //------------------------------------------------------------------------------
1862 void vvMainWindow::CloseImage() {
1863   CloseImage(DataTree->selectedItems()[0],0);
1864 }
1865 //------------------------------------------------------------------------------
1866
1867 //------------------------------------------------------------------------------
1868 void vvMainWindow::ReloadImage() {
1869   ReloadImage(DataTree->selectedItems()[0],0);
1870 }
1871 //------------------------------------------------------------------------------
1872
1873 //------------------------------------------------------------------------------
1874 void vvMainWindow::SelectOverlayImage() {
1875   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1876
1877   //check if one overlay image is added
1878   for (int child = 0; child < DataTree->topLevelItem(index)->childCount(); child++)
1879     if (DataTree->topLevelItem(index)->child(child)->data(1,Qt::UserRole).toString() == "overlay")
1880       {
1881         QString error = "Cannot add more than one compared image\n";
1882         error += "Please remove first ";
1883         error += DataTree->topLevelItem(index)->child(child)->data(COLUMN_IMAGE_NAME,Qt::DisplayRole).toString();
1884         QMessageBox::information(this,tr("Problem adding compared image !"),error);
1885         return;
1886       }
1887
1888   QString Extensions = EXTENSIONS;
1889   Extensions += ";;All Files (*)";
1890   QString file = QFileDialog::getOpenFileName(this,tr("Load Overlay image"),mInputPathName,Extensions);
1891   if (!file.isEmpty())
1892     AddOverlayImage(index,file);
1893 }
1894 //------------------------------------------------------------------------------
1895
1896 //------------------------------------------------------------------------------
1897 void vvMainWindow::AddOverlayImage(int index, QString file) {
1898   mInputPathName = itksys::SystemTools::GetFilenamePath(file.toStdString()).c_str();
1899   itk::ImageIOBase::Pointer reader = itk::ImageIOFactory::CreateImageIO(
1900                                                                         file.toStdString().c_str(), itk::ImageIOFactory::ReadMode);
1901   reader->SetFileName(file.toStdString().c_str());
1902   reader->ReadImageInformation();
1903   std::string component = reader->GetComponentTypeAsString(reader->GetComponentType());
1904   int dimension = reader->GetNumberOfDimensions();
1905   QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
1906   vvProgressDialog progress("Opening " + file.toStdString());
1907   qApp->processEvents();
1908
1909   std::string filename = itksys::SystemTools::GetFilenameWithoutExtension(file.toStdString()).c_str();
1910   if (mSlicerManagers[index]->SetOverlay(file.toStdString(),dimension, component))
1911     {
1912       //create an item in the tree with good settings
1913       QTreeWidgetItem *item = new QTreeWidgetItem();
1914       item->setData(0,Qt::UserRole,file.toStdString().c_str());
1915       item->setData(1,Qt::UserRole,tr("overlay"));
1916       item->setData(COLUMN_IMAGE_NAME,Qt::DisplayRole,filename.c_str());
1917       qApp->processEvents();
1918
1919       for (int j = 1; j <= 4; j++)
1920         {
1921           item->setData(j,Qt::CheckStateRole,DataTree->topLevelItem(index)->data(j,Qt::CheckStateRole));
1922           mSlicerManagers[index]->GetSlicer(j-1)->SetActorVisibility("overlay",0,
1923                                                                      DataTree->topLevelItem(index)->data(j,Qt::CheckStateRole).toInt());
1924         }
1925
1926       //Create the buttons for reload and close
1927       qApp->processEvents();
1928       QTreePushButton* cButton = new QTreePushButton;
1929       cButton->setItem(item);
1930       cButton->setColumn(COLUMN_CLOSE_IMAGE);
1931       cButton->setToolTip(tr("close image"));
1932       cButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/exit.png")));
1933       connect(cButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
1934               this,SLOT(CloseImage(QTreeWidgetItem*, int)));
1935
1936       QTreePushButton* rButton = new QTreePushButton;
1937       rButton->setItem(item);
1938       rButton->setColumn(COLUMN_RELOAD_IMAGE);
1939       rButton->setToolTip(tr("reload image"));
1940       rButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/rotateright.png")));
1941       connect(rButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
1942               this,SLOT(ReloadImage(QTreeWidgetItem*, int)));
1943
1944       DataTree->topLevelItem(index)->setExpanded(1);
1945       DataTree->topLevelItem(index)->addChild(item);
1946       DataTree->setItemWidget(item, COLUMN_CLOSE_IMAGE, cButton);
1947       DataTree->setItemWidget(item, COLUMN_RELOAD_IMAGE, rButton);
1948
1949       //set the id of the image
1950       QString id = DataTree->topLevelItem(index)->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString();
1951       item->setData(COLUMN_IMAGE_NAME,Qt::UserRole,id.toStdString().c_str());
1952       UpdateTree();
1953       qApp->processEvents();
1954       ImageInfoChanged();
1955       QApplication::restoreOverrideCursor();
1956     }
1957   else
1958     {
1959       QApplication::restoreOverrideCursor();
1960       QString error = "Cannot import the new image.\n";
1961       error += mSlicerManagers[index]->GetLastError().c_str();
1962       QMessageBox::information(this,tr("Problem reading image !"),error);
1963     }
1964 }
1965
1966 void vvMainWindow::AddFusionImage()
1967 {
1968   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
1969
1970   //check if one fusion image is added
1971   for (int child = 0; child < DataTree->topLevelItem(index)->childCount(); child++)
1972     if (DataTree->topLevelItem(index)->child(child)->data(1,Qt::UserRole).toString() == "fusion")
1973       {
1974         QString error = "Cannot add more than one fusion image\n";
1975         error += "Please remove first ";
1976         error += DataTree->topLevelItem(index)->child(child)->data(COLUMN_IMAGE_NAME,Qt::DisplayRole).toString();
1977         QMessageBox::information(this,tr("Problem adding fusion image !"),error);
1978         return;
1979       }
1980
1981   QString Extensions = EXTENSIONS;
1982   Extensions += ";;All Files (*)";
1983   QString file = QFileDialog::getOpenFileName(this,tr("Load Fusion image"),mInputPathName,Extensions);
1984   if (!file.isEmpty())
1985     {
1986       mInputPathName = itksys::SystemTools::GetFilenamePath(file.toStdString()).c_str();
1987       itk::ImageIOBase::Pointer reader = itk::ImageIOFactory::CreateImageIO(
1988                                                                             file.toStdString().c_str(), itk::ImageIOFactory::ReadMode);
1989       reader->SetFileName(file.toStdString().c_str());
1990       reader->ReadImageInformation();
1991       std::string component = reader->GetComponentTypeAsString(reader->GetComponentType());
1992       if (reader)
1993         {
1994           QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
1995           vvProgressDialog progress("Opening fusion");
1996           qApp->processEvents();
1997
1998           std::string filename = itksys::SystemTools::GetFilenameWithoutExtension(file.toStdString()).c_str();
1999           if (mSlicerManagers[index]->SetFusion(file.toStdString(),
2000                                                 reader->GetNumberOfDimensions(), component))
2001             {
2002               //create an item in the tree with good settings
2003               QTreeWidgetItem *item = new QTreeWidgetItem();
2004               item->setData(0,Qt::UserRole,file.toStdString().c_str());
2005               item->setData(1,Qt::UserRole,tr("fusion"));
2006               item->setData(COLUMN_IMAGE_NAME,Qt::DisplayRole,filename.c_str());
2007               qApp->processEvents();
2008
2009               for (int j = 1; j <= 4; j++)
2010                 {
2011                   item->setData(j,Qt::CheckStateRole,DataTree->topLevelItem(index)->data(j,Qt::CheckStateRole));
2012                   mSlicerManagers[index]->GetSlicer(j-1)->SetActorVisibility("fusion",0,
2013                                                                              DataTree->topLevelItem(index)->data(j,Qt::CheckStateRole).toInt());
2014                 }
2015
2016               //Create the buttons for reload and close
2017               qApp->processEvents();
2018               QTreePushButton* cButton = new QTreePushButton;
2019               cButton->setItem(item);
2020               cButton->setColumn(COLUMN_CLOSE_IMAGE);
2021               cButton->setToolTip(tr("close image"));
2022               cButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/exit.png")));
2023               connect(cButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
2024                       this,SLOT(CloseImage(QTreeWidgetItem*, int)));
2025
2026               QTreePushButton* rButton = new QTreePushButton;
2027               rButton->setItem(item);
2028               rButton->setColumn(COLUMN_RELOAD_IMAGE);
2029               rButton->setToolTip(tr("reload image"));
2030               rButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/rotateright.png")));
2031               connect(rButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
2032                       this,SLOT(ReloadImage(QTreeWidgetItem*, int)));
2033
2034               DataTree->topLevelItem(index)->setExpanded(1);
2035               DataTree->topLevelItem(index)->addChild(item);
2036               DataTree->setItemWidget(item, COLUMN_CLOSE_IMAGE, cButton);
2037               DataTree->setItemWidget(item, COLUMN_RELOAD_IMAGE, rButton);
2038
2039               //set the id of the image
2040               QString id = DataTree->topLevelItem(index)->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString();
2041               item->setData(COLUMN_IMAGE_NAME,Qt::UserRole,id.toStdString().c_str());
2042               UpdateTree();
2043               qApp->processEvents();
2044               ImageInfoChanged();
2045               QApplication::restoreOverrideCursor();
2046             }
2047           else
2048             {
2049               QApplication::restoreOverrideCursor();
2050               QString error = "Cannot import the new image.\n";
2051               error += mSlicerManagers[index]->GetLastError().c_str();
2052               QMessageBox::information(this,tr("Problem reading image !"),error);
2053             }
2054         }
2055       else
2056         {
2057           QString error = "Cannot import the new image.\n";
2058           QMessageBox::information(this,tr("Problem reading image !"),error);
2059         }
2060     }
2061 }
2062
2063
2064 void vvMainWindow::OpenField()
2065 {
2066   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2067   //check if a vector field has already been added
2068   for (int child = 0; child < DataTree->topLevelItem(index)->childCount(); child++)
2069     if (DataTree->topLevelItem(index)->child(child)->data(1,Qt::UserRole).toString() == "vector")
2070       {
2071         QString error = "Cannot add more than one vector field\n";
2072         error += "Please remove first ";
2073         error += DataTree->topLevelItem(index)->child(child)->data(COLUMN_IMAGE_NAME,Qt::DisplayRole).toString();
2074         QMessageBox::information(this,tr("Problem adding vector field!"),error);
2075         return;
2076       }
2077
2078   QString Extensions = "Images ( *.mhd)";
2079   Extensions += ";;Images ( *.vf)";
2080   QString file = QFileDialog::getOpenFileName(this,tr("Load deformation field"),mInputPathName,Extensions);
2081   if (!file.isEmpty())
2082     AddField(file,index);
2083 }
2084
2085 void vvMainWindow::AddFieldEntry(QString filename,int index,bool from_disk)
2086 {
2087   //create an item in the tree with good settings
2088   QTreeWidgetItem *item = new QTreeWidgetItem();
2089   item->setData(0,Qt::UserRole,filename.toStdString().c_str());
2090   item->setData(1,Qt::UserRole,tr("vector"));
2091   item->setData(COLUMN_IMAGE_NAME,Qt::DisplayRole,filename);
2092   qApp->processEvents();
2093
2094   for (int j = 1; j <= 4; j++)
2095     {
2096       item->setData(j,Qt::CheckStateRole,DataTree->topLevelItem(index)->data(j,Qt::CheckStateRole));
2097       mSlicerManagers[index]->GetSlicer(j-1)->SetActorVisibility("vector",0,
2098                                                                  DataTree->topLevelItem(index)->data(j,Qt::CheckStateRole).toInt());
2099     }
2100
2101   //Create the buttons for reload and close
2102   qApp->processEvents();
2103   QTreePushButton* cButton = new QTreePushButton;
2104   cButton->setItem(item);
2105   cButton->setColumn(COLUMN_CLOSE_IMAGE);
2106   cButton->setToolTip(tr("close vector field"));
2107   cButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/exit.png")));
2108   connect(cButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
2109           this,SLOT(CloseImage(QTreeWidgetItem*, int)));
2110
2111   QTreePushButton* rButton = new QTreePushButton;
2112   rButton->setItem(item);
2113   rButton->setColumn(COLUMN_RELOAD_IMAGE);
2114   rButton->setToolTip(tr("reload vector field"));
2115   rButton->setEnabled(from_disk);
2116   rButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/rotateright.png")));
2117   connect(rButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
2118           this,SLOT(ReloadImage(QTreeWidgetItem*, int)));
2119
2120   DataTree->topLevelItem(index)->setExpanded(1);
2121   DataTree->topLevelItem(index)->addChild(item);
2122   DataTree->setItemWidget(item, COLUMN_RELOAD_IMAGE, rButton);
2123   DataTree->setItemWidget(item, COLUMN_CLOSE_IMAGE, cButton);
2124
2125   //set the id of the image
2126   QString id = DataTree->topLevelItem(index)->data(COLUMN_IMAGE_NAME,Qt::UserRole).toString();
2127   item->setData(COLUMN_IMAGE_NAME,Qt::UserRole,id.toStdString().c_str());
2128   UpdateTree();
2129   qApp->processEvents();
2130   ImageInfoChanged();
2131   QApplication::restoreOverrideCursor();
2132 }
2133
2134 void vvMainWindow::AddField(vvImage::Pointer vf,QString file,int index)
2135 {
2136   QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
2137   vvSlicerManager* imageManager = mSlicerManagers[index];
2138   if (imageManager->SetVF(vf,file.toStdString()))
2139     {
2140       AddFieldEntry(file,index,false);
2141     }
2142   else
2143     {
2144       QString error = "Cannot import the vector field for this image.\n";
2145       error += imageManager->GetLastError().c_str();
2146       QMessageBox::information(this,tr("Problem reading VF !"),error);
2147     }
2148   QApplication::restoreOverrideCursor();
2149 }
2150
2151 void vvMainWindow::AddField(QString file,int index)
2152 {
2153   if (QFile::exists(file))
2154     {
2155       mInputPathName = itksys::SystemTools::GetFilenamePath(file.toStdString()).c_str();
2156
2157       //init the progress events
2158       QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
2159       vvProgressDialog progress("Opening " + file.toStdString());
2160       qApp->processEvents();
2161
2162       //read the vector and put it in the current mSlicerManager
2163       vvSlicerManager* imageManager = mSlicerManagers[index];
2164       qApp->processEvents();
2165
2166       std::string filename = itksys::SystemTools::GetFilenameWithoutExtension(file.toStdString()).c_str();
2167       if (imageManager->SetVF(file.toStdString()))
2168         {
2169           imageManager->Render();
2170           AddFieldEntry(file,index,true);
2171         }
2172       else
2173         {
2174           QApplication::restoreOverrideCursor();
2175           QString error = "Cannot import the vector field for this image.\n";
2176           error += imageManager->GetLastError().c_str();
2177           QMessageBox::information(this,tr("Problem reading VF !"),error);
2178         }
2179     }
2180   else
2181     QMessageBox::information(this,tr("Problem reading VF !"),"File doesn't exist!");
2182
2183 }
2184 //------------------------------------------------------------------------------
2185
2186 //------------------------------------------------------------------------------
2187 void vvMainWindow::SetVFProperty(int subsampling, int scale, int log) {
2188   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2189   if (mSlicerManagers[index]->GetSlicer(0)->GetVF())
2190     {
2191       for (int i = 0; i < 4; i++)
2192         {
2193           mSlicerManagers[index]->GetSlicer(i)->SetVFSubSampling(subsampling);
2194           mSlicerManagers[index]->GetSlicer(i)->SetVFScale(scale);
2195           if (log > 0)
2196             mSlicerManagers[index]->GetSlicer(i)->SetVFLog(1);
2197           else
2198             mSlicerManagers[index]->GetSlicer(i)->SetVFLog(0);
2199         }
2200     }
2201 }
2202 //------------------------------------------------------------------------------
2203
2204 //------------------------------------------------------------------------------
2205 void vvMainWindow::SetOverlayProperty(int color) {
2206   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2207   if (mSlicerManagers[index]->GetSlicer(0)->GetOverlay())
2208     {
2209       mSlicerManagers[index]->SetOverlayColor(color);
2210       mSlicerManagers[index]->SetColorMap(0);
2211       mSlicerManagers[index]->Render();
2212     }
2213 }
2214 //------------------------------------------------------------------------------
2215
2216 //------------------------------------------------------------------------------
2217 void vvMainWindow::SetFusionProperty(int opacity, int colormap,double window, double level) {
2218   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2219   if (mSlicerManagers[index]->GetSlicer(0)->GetFusion())
2220     {
2221       mSlicerManagers[index]->SetFusionOpacity(opacity);
2222       mSlicerManagers[index]->SetFusionColorMap(colormap);
2223       mSlicerManagers[index]->SetFusionWindow(window);
2224       mSlicerManagers[index]->SetFusionLevel(level);
2225       mSlicerManagers[index]->SetColorMap(0);
2226       mSlicerManagers[index]->Render();
2227     }
2228 }
2229 //------------------------------------------------------------------------------
2230
2231 //------------------------------------------------------------------------------
2232 void vvMainWindow::SaveAs() {
2233   if (DataTree->selectedItems()[0]->data(1,Qt::UserRole).toString() == "vector")
2234     {
2235       QMessageBox::warning(this,tr("Unsupported type"),tr("Sorry, saving a vector field is unsupported for the moment"));
2236       return;
2237     }
2238
2239   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2240   int dimension = mSlicerManagers[index]->GetDimension();
2241   QStringList OutputListeFormat;
2242   OutputListeFormat.clear();
2243   if (dimension == 1)
2244     {
2245       OutputListeFormat.push_back(".mhd");
2246     }
2247   if (dimension == 2)
2248     {
2249       OutputListeFormat.push_back(".bmp");
2250       OutputListeFormat.push_back(".png");
2251       OutputListeFormat.push_back(".jpeg");
2252       OutputListeFormat.push_back(".tif");
2253       OutputListeFormat.push_back(".mhd");
2254       OutputListeFormat.push_back(".hdr");
2255       OutputListeFormat.push_back(".vox");
2256     }
2257   else if (dimension == 3)
2258     {
2259       OutputListeFormat.push_back(".mhd");
2260       OutputListeFormat.push_back(".hdr");
2261       OutputListeFormat.push_back(".vox");
2262     }
2263   else if (dimension == 4)
2264     {
2265       OutputListeFormat.push_back(".mhd");
2266     }
2267   QString Extensions = "AllFiles(*.*)";
2268   for (int i = 0; i < OutputListeFormat.count(); i++)
2269     {
2270       Extensions += ";;Images ( *";
2271       Extensions += OutputListeFormat[i];
2272       Extensions += ")";
2273     }
2274   QString fileName = QFileDialog::getSaveFileName(this,
2275                                                   tr("Save As"),
2276                                                   mSlicerManagers[index]->GetFileName().c_str(),
2277                                                   Extensions);
2278   if (!fileName.isEmpty())
2279     {
2280       std::string fileformat = itksys::SystemTools::GetFilenameLastExtension(fileName.toStdString());
2281       if (OutputListeFormat.contains(
2282                                      fileformat.c_str()))
2283         {
2284           QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
2285           std::string action = "Saving";
2286           vvProgressDialog progress("Saving "+fileName.toStdString());
2287           qApp->processEvents();
2288           vvImageWriter *writer = new vvImageWriter;
2289           writer->SetOutputFileName(fileName.toStdString());
2290           writer->SetInput(mSlicerManagers[index]->GetImage());
2291           writer->Update();
2292           QApplication::restoreOverrideCursor();
2293           if (writer->GetLastError().size())
2294             {
2295               QString error = "Saving did not succeed\n";
2296               error += writer->GetLastError().c_str();
2297               QMessageBox::information(this,tr("Saving Problem"),error);
2298               SaveAs();
2299             }
2300         }
2301       else
2302         {
2303           QString error = fileformat.c_str();
2304           if (error.isEmpty())
2305             error += "no file format specified !";
2306           else
2307             error += " format unknown !!!\n";
2308           QMessageBox::information(this,tr("Saving Problem"),error);
2309           SaveAs();
2310         }
2311     }
2312 }
2313 //------------------------------------------------------------------------------
2314
2315 //------------------------------------------------------------------------------
2316 void vvMainWindow::AddLink(QString image1,QString image2) {
2317   for (unsigned int i = 0; i < mSlicerManagers.size();i++)
2318     {
2319       if (image1.toStdString() == mSlicerManagers[i]->GetId())
2320         {
2321           mSlicerManagers[i]->AddLink(image2.toStdString());
2322         }
2323       if (image2.toStdString() == mSlicerManagers[i]->GetId())
2324         {
2325           mSlicerManagers[i]->AddLink(image1.toStdString());
2326         }
2327     }
2328 }
2329 //------------------------------------------------------------------------------
2330
2331 //------------------------------------------------------------------------------
2332 void vvMainWindow::RemoveLink(QString image1,QString image2) {
2333   for (unsigned int i = 0; i < mSlicerManagers.size();i++)
2334     {
2335       if (image1.toStdString() == mSlicerManagers[i]->GetId())
2336         {
2337           mSlicerManagers[i]->RemoveLink(image2.toStdString());
2338         }
2339       if (image2.toStdString() == mSlicerManagers[i]->GetId())
2340         {
2341           mSlicerManagers[i]->RemoveLink(image1.toStdString());
2342         }
2343     }
2344 }
2345 //------------------------------------------------------------------------------
2346
2347 //------------------------------------------------------------------------------
2348 void vvMainWindow::ChangeImageWithIndexOffset(vvSlicerManager *sm, int slicer, int offset)
2349 {
2350     int index = 0;
2351     while(sm != mSlicerManagers[index])
2352         index++;
2353     index = (index+offset) % mSlicerManagers.size();
2354
2355     QTreeWidgetItem* item = GetItemFromSlicerManager(mSlicerManagers[index]);
2356     //CurrentImageChanged(mSlicerManagers[index]->GetId()); //select new image
2357     item->setData(slicer+1,Qt::CheckStateRole,2);         //change checkbox
2358     DisplayChanged(item,slicer+1);
2359 }
2360 //------------------------------------------------------------------------------
2361
2362 void vvMainWindow::HorizontalSliderMoved(int value,int column, int slicer_index)
2363 {
2364   for (unsigned int i = 0; i < mSlicerManagers.size(); i++)
2365     {
2366       if (DataTree->topLevelItem(i)->data(column,Qt::CheckStateRole).toInt() > 1)
2367         {
2368           for (int j = 0; j < 4; j++)
2369             {
2370               mSlicerManagers[i]->SetTSliceInSlicer(value,j);
2371               //if (mSlicerManagers[i]->GetSlicer(j)->GetImageActor()->GetVisibility())
2372               //UpdateTSlice(j,value);
2373             }
2374           mSlicerManagers[i]->GetSlicer(slicer_index)->Render();
2375           break;
2376         }
2377     }
2378 }
2379
2380 //------------------------------------------------------------------------------
2381 void vvMainWindow::NOHorizontalSliderMoved() {
2382   HorizontalSliderMoved(NOHorizontalSlider->value(),COLUMN_UL_VIEW,0);
2383 }
2384 //------------------------------------------------------------------------------
2385
2386 //------------------------------------------------------------------------------
2387 void vvMainWindow::NEHorizontalSliderMoved() {
2388   HorizontalSliderMoved(NEHorizontalSlider->value(),COLUMN_UR_VIEW,1);
2389 }
2390 //------------------------------------------------------------------------------
2391
2392 //------------------------------------------------------------------------------
2393 void vvMainWindow::SOHorizontalSliderMoved() {
2394   HorizontalSliderMoved(SOHorizontalSlider->value(),COLUMN_DL_VIEW,2);
2395 }
2396 //------------------------------------------------------------------------------
2397
2398 //------------------------------------------------------------------------------
2399 void vvMainWindow::SEHorizontalSliderMoved() {
2400   HorizontalSliderMoved(SEHorizontalSlider->value(),COLUMN_DR_VIEW,3);
2401 }
2402 //------------------------------------------------------------------------------
2403
2404 //------------------------------------------------------------------------------
2405 void vvMainWindow::NOVerticalSliderChanged() {
2406   int value = NOVerticalSlider->value();
2407   for (unsigned int i = 0; i < mSlicerManagers.size(); i++)
2408     {
2409       if (DataTree->topLevelItem(i)->data(COLUMN_UL_VIEW,Qt::CheckStateRole).toInt() > 1)
2410         {
2411           mSlicerManagers[i]->GetSlicer(0)->SetSlice(value);
2412           // mSlicerManagers[i]->UpdateSlice(0);
2413           // <-- DS add this. Not too much update ? YES.
2414           break;
2415         }
2416     }
2417 }
2418 //------------------------------------------------------------------------------
2419
2420 //------------------------------------------------------------------------------
2421 void vvMainWindow::NEVerticalSliderChanged() {
2422   int value = NEVerticalSlider->value();
2423   for (unsigned int i = 0; i < mSlicerManagers.size(); i++)
2424     {
2425       if (DataTree->topLevelItem(i)->data(COLUMN_UR_VIEW,Qt::CheckStateRole).toInt() > 1)
2426         {
2427           mSlicerManagers[i]->GetSlicer(1)->SetSlice(value);
2428           break;
2429         }
2430     }
2431 }
2432 //------------------------------------------------------------------------------
2433
2434 //------------------------------------------------------------------------------
2435 void vvMainWindow::SOVerticalSliderChanged() {
2436   int value = SOVerticalSlider->value();
2437   for (unsigned int i = 0; i < mSlicerManagers.size(); i++)
2438     {
2439       if (DataTree->topLevelItem(i)->data(COLUMN_DL_VIEW,Qt::CheckStateRole).toInt() > 1)
2440         {
2441           mSlicerManagers[i]->GetSlicer(2)->SetSlice(value);
2442           break;
2443         }
2444     }
2445 }
2446 //------------------------------------------------------------------------------
2447
2448 //------------------------------------------------------------------------------
2449 void vvMainWindow::SEVerticalSliderChanged() {
2450   int value = SEVerticalSlider->value();
2451   for (unsigned int i = 0; i < mSlicerManagers.size(); i++)
2452     {
2453       if (DataTree->topLevelItem(i)->data(COLUMN_DR_VIEW,Qt::CheckStateRole).toInt() > 1)
2454         {
2455           mSlicerManagers[i]->GetSlicer(3)->SetSlice(value);
2456           break;
2457         }
2458     }
2459 }
2460 //------------------------------------------------------------------------------
2461
2462 //------------------------------------------------------------------------------
2463 void vvMainWindow::UpdateSlice(int slicer, int slice) {
2464   if (slicer == 0) {
2465     if (slice != NOVerticalSlider->value())
2466       NOVerticalSlider->setValue(slice);
2467   }
2468   else if (slicer == 1)
2469     NEVerticalSlider->setValue(slice);
2470   else if (slicer == 2)
2471     SOVerticalSlider->setValue(slice);
2472   else if (slicer == 3)
2473     SEVerticalSlider->setValue(slice);
2474 }
2475 //------------------------------------------------------------------------------
2476
2477 //------------------------------------------------------------------------------
2478 void vvMainWindow::UpdateTSlice(int slicer, int slice) {
2479   switch (slicer)
2480     {
2481     case 0:
2482       NOHorizontalSlider->setValue(slice);
2483       break;
2484     case 1:
2485       NEHorizontalSlider->setValue(slice);
2486       break;
2487     case 2:
2488       SOHorizontalSlider->setValue(slice);
2489       break;
2490     case 3:
2491       SEHorizontalSlider->setValue(slice);
2492       break;
2493     }
2494 }
2495 //------------------------------------------------------------------------------
2496
2497 //------------------------------------------------------------------------------
2498 void vvMainWindow::UpdateSliceRange(int slicer, int min, int max, int tmin, int tmax) {
2499   int position = int((min+max)/2);
2500   int tPosition = int((tmin+tmax)/2);
2501   if (slicer == 0)
2502     {
2503       NOVerticalSlider->setValue(position);
2504       NOVerticalSlider->setRange(min,max);
2505       NOHorizontalSlider->setRange(tmin,tmax);
2506       NOHorizontalSlider->setValue(tPosition);
2507     }
2508   else if (slicer == 1)
2509     {
2510       NEVerticalSlider->setValue(position);
2511       NEVerticalSlider->setRange(min,max);
2512       NEHorizontalSlider->setRange(tmin,tmax);
2513       NEHorizontalSlider->setValue(tPosition);
2514     }
2515   else if (slicer == 2)
2516     {
2517       SOVerticalSlider->setValue(position);
2518       SOVerticalSlider->setRange(min,max);
2519       SOHorizontalSlider->setRange(tmin,tmax);
2520       SOHorizontalSlider->setValue(tPosition);
2521     }
2522   else if (slicer == 3)
2523     {
2524       SEVerticalSlider->setValue(position);
2525       SEVerticalSlider->setRange(min,max);
2526       SEHorizontalSlider->setRange(tmin,tmax);
2527       SEHorizontalSlider->setValue(tPosition);
2528     }
2529 }
2530 //------------------------------------------------------------------------------
2531
2532 //------------------------------------------------------------------------------
2533 void vvMainWindow::SaveNOScreenshot() {
2534   vtkWindowToImageFilter *w2i = vtkWindowToImageFilter::New();
2535   w2i->SetInput(NOViewWidget->GetRenderWindow());
2536   w2i->Update();
2537   SaveScreenshot(w2i->GetOutput());
2538   w2i->Delete();
2539 }
2540 //------------------------------------------------------------------------------
2541
2542 //------------------------------------------------------------------------------
2543 void vvMainWindow::SaveNEScreenshot() {
2544   vtkWindowToImageFilter *w2i = vtkWindowToImageFilter::New();
2545   w2i->SetInput(NEViewWidget->GetRenderWindow());
2546   w2i->Update();
2547   SaveScreenshot(w2i->GetOutput());
2548   w2i->Delete();
2549 }
2550 //------------------------------------------------------------------------------
2551
2552 //------------------------------------------------------------------------------
2553 void vvMainWindow::SaveSOScreenshot() {
2554   vtkWindowToImageFilter *w2i = vtkWindowToImageFilter::New();
2555   w2i->SetInput(SOViewWidget->GetRenderWindow());
2556   w2i->Update();
2557   SaveScreenshot(w2i->GetOutput());
2558   w2i->Delete();
2559 }
2560 //------------------------------------------------------------------------------
2561
2562 //------------------------------------------------------------------------------
2563 void vvMainWindow::SaveSEScreenshot() {
2564   vtkWindowToImageFilter *w2i = vtkWindowToImageFilter::New();
2565   w2i->SetInput(SEViewWidget->GetRenderWindow());
2566   w2i->Update();
2567   SaveScreenshot(w2i->GetOutput());
2568   w2i->Delete();
2569 }
2570 //------------------------------------------------------------------------------
2571
2572 //------------------------------------------------------------------------------
2573 void vvMainWindow::SaveScreenshot(vtkImageData* image) {
2574   QString Extensions = "Images( *.png);;";
2575   Extensions += "Images( *.jpg);;";
2576   Extensions += "Images( *.bmp);;";
2577   Extensions += "Images( *.tif);;";
2578   Extensions += "Images( *.ppm)";
2579   QString fileName = QFileDialog::getSaveFileName(this,
2580                                                   tr("Save As"),
2581                                                   itksys::SystemTools::GetFilenamePath(
2582                                                                                        mSlicerManagers[0]->GetFileName()).c_str(),
2583                                                   Extensions);
2584   if (!fileName.isEmpty())
2585     {
2586       const char *ext = fileName.toStdString().c_str() + strlen(fileName.toStdString().c_str()) - 4;
2587       if (!strcmp(ext, ".bmp"))
2588         {
2589           vtkBMPWriter *bmp = vtkBMPWriter::New();
2590           bmp->SetInput(image);
2591           bmp->SetFileName(fileName.toStdString().c_str());
2592           bmp->Write();
2593           bmp->Delete();
2594         }
2595       else if (!strcmp(ext, ".tif"))
2596         {
2597           vtkTIFFWriter *tif = vtkTIFFWriter::New();
2598           tif->SetInput(image);
2599           tif->SetFileName(fileName.toStdString().c_str());
2600           tif->Write();
2601           tif->Delete();
2602         }
2603       else if (!strcmp(ext, ".ppm"))
2604         {
2605           vtkPNMWriter *pnm = vtkPNMWriter::New();
2606           pnm->SetInput(image);
2607           pnm->SetFileName(fileName.toStdString().c_str());
2608           pnm->Write();
2609           pnm->Delete();
2610         }
2611       else if (!strcmp(ext, ".png"))
2612         {
2613           vtkPNGWriter *png = vtkPNGWriter::New();
2614           png->SetInput(image);
2615           png->SetFileName(fileName.toStdString().c_str());
2616           png->Write();
2617           png->Delete();
2618         }
2619       else if (!strcmp(ext, ".jpg"))
2620         {
2621           vtkJPEGWriter *jpg = vtkJPEGWriter::New();
2622           jpg->SetInput(image);
2623           jpg->SetFileName(fileName.toStdString().c_str());
2624           jpg->Write();
2625           jpg->Delete();
2626         }
2627       else
2628         {
2629           QMessageBox::information(this,tr("Problem saving screenshot !"),tr("Cannot save image.\nPlease set a file extension !!!"));
2630         }
2631     }
2632
2633 }
2634 //------------------------------------------------------------------------------
2635
2636 //------------------------------------------------------------------------------
2637 void vvMainWindow::GoToCursor() {
2638   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2639   for (int column = 1; column < 5; column++)
2640     {
2641       if (DataTree->selectedItems()[0]->data(column,Qt::CheckStateRole).toInt() > 1)
2642         {
2643           double* cursorPos = mSlicerManagers[index]->GetSlicer(column-1)->GetCursorPosition();
2644           mSlicerManagers[index]->GetSlicer(column-1)->SetCurrentPosition(
2645                                                                           cursorPos[0],cursorPos[1],cursorPos[2],cursorPos[3]);
2646           mSlicerManagers[index]->UpdateViews(1,column-1);
2647           mSlicerManagers[index]->UpdateLinked(column-1);
2648           break;
2649         }
2650     }
2651 }
2652 //------------------------------------------------------------------------------
2653
2654 //------------------------------------------------------------------------------
2655 void vvMainWindow::PlayPause() {
2656   if (playMode)
2657     {
2658       playMode = 0;
2659       playButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/player_play.png")));
2660       ImageInfoChanged();
2661       return;
2662     }
2663   else
2664     {
2665       int image_number=DataTree->topLevelItemCount();
2666       bool has_temporal;
2667       for (int i=0;i<image_number;i++)
2668         if (mSlicerManagers[i]->GetImage()->GetVTKImages().size() > 1)
2669           {
2670             has_temporal=true;
2671             break;
2672           }
2673       if (has_temporal)
2674         {
2675           playMode = 1;
2676           playButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/player_pause.png")));
2677           QTimer::singleShot(1000/mFrameRate, this, SLOT(PlayNext()));
2678         }
2679     }
2680 }
2681 //------------------------------------------------------------------------------
2682
2683 //------------------------------------------------------------------------------
2684 void vvMainWindow::PlayNext() {
2685   if (playMode && !this->isHidden())
2686     {
2687       int image_number=DataTree->topLevelItemCount();
2688       ///Only play one slicer per SM, and only if the SM is being displayed
2689       for (int i=0;i<image_number;i++)
2690         for (int j=0;j<4;j++)
2691           if (mSlicerManagers[i]->GetImage()->GetVTKImages().size() > 1 &&
2692               DataTree->topLevelItem(i)->data(j+1,Qt::CheckStateRole).toInt() > 0)
2693             {
2694               mSlicerManagers[i]->SetNextTSlice(j);
2695               break;
2696             }
2697       QTimer::singleShot(1000/mFrameRate, this, SLOT(PlayNext()));
2698     }
2699 }
2700 //------------------------------------------------------------------------------
2701
2702 void vvMainWindow::ShowLastImage()
2703 {
2704   if (mSlicerManagers.size() > 1)
2705     {
2706       QTreeWidgetItem * item=DataTree->topLevelItem(DataTree->topLevelItemCount()-1);
2707       CurrentImageChanged(mSlicerManagers.back()->GetId()); //select new image
2708       item->setData(1,Qt::CheckStateRole,2); //show the new image in the first panel
2709       DisplayChanged(item,1);
2710     }
2711 }
2712
2713 //------------------------------------------------------------------------------
2714 void vvMainWindow::UpdateRenderWindows() {
2715   if (NOViewWidget->GetRenderWindow()) NOViewWidget->GetRenderWindow()->Render();
2716   if (NEViewWidget->GetRenderWindow()) NEViewWidget->GetRenderWindow()->Render();
2717   if (SOViewWidget->GetRenderWindow()) SOViewWidget->GetRenderWindow()->Render();
2718   if (SEViewWidget->GetRenderWindow()) SEViewWidget->GetRenderWindow()->Render();
2719 }
2720 //------------------------------------------------------------------------------
2721
2722 //------------------------------------------------------------------------------
2723 void vvMainWindow::ResampleCurrentImage() {
2724   vvResamplerDialog resampler;
2725   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2726   resampler.SetSlicerManagers(mSlicerManagers,index);
2727   if (resampler.exec())
2728     AddImage(resampler.GetOutput(),resampler.GetOutputFileName());
2729 }
2730 //------------------------------------------------------------------------------
2731
2732 //------------------------------------------------------------------------------
2733 void vvMainWindow::SegmentationOnCurrentImage() {
2734   int index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2735
2736   vvSegmentationDialog segmentation;
2737   segmentation.SetImage(mSlicerManagers[index]->GetSlicer(0)->GetImage());
2738   segmentation.exec();
2739 }
2740 //------------------------------------------------------------------------------
2741
2742 void vvMainWindow::SurfaceViewerLaunch()
2743 {
2744   vvSurfaceViewerDialog surfaceViewer;
2745   surfaceViewer.exec();
2746 }
2747
2748 //------------------------------------------------------------------------------
2749 void vvMainWindow::AddImage(vvImage::Pointer image,std::string filename)
2750 {
2751   vvSlicerManager* slicer_manager = new vvSlicerManager(4);
2752   slicer_manager->SetImage(image);
2753   slicer_manager->SetFilename(filename);
2754   mSlicerManagers.push_back(slicer_manager);
2755
2756   //create an item in the tree with good settings
2757   QTreeWidgetItem *item = new QTreeWidgetItem();
2758   item->setData(0,Qt::UserRole,slicer_manager->GetFileName().c_str());//files[i].c_str());
2759   item->setData(COLUMN_IMAGE_NAME,Qt::DisplayRole,filename.c_str());
2760   qApp->processEvents();
2761
2762   for (int j = 1; j <= 4; j++) item->setData(j,Qt::CheckStateRole,1);
2763
2764   //Create the buttons for reload and close
2765   qApp->processEvents();
2766   QTreePushButton* cButton = new QTreePushButton;
2767   cButton->setItem(item);
2768   cButton->setColumn(COLUMN_CLOSE_IMAGE);
2769   cButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/exit.png")));
2770   connect(cButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
2771           this,SLOT(CloseImage(QTreeWidgetItem*, int)));
2772
2773   QTreePushButton* rButton = new QTreePushButton;
2774   rButton->setItem(item);
2775   rButton->setColumn(COLUMN_RELOAD_IMAGE);
2776   rButton->setIcon(QIcon(QString::fromUtf8(":/common/icons/rotateright.png")));
2777   rButton->setEnabled(0);
2778   connect(rButton,SIGNAL(clickedInto(QTreeWidgetItem*, int)),
2779           this,SLOT(ReloadImage(QTreeWidgetItem*, int)));
2780
2781   DataTree->addTopLevelItem(item);
2782   DataTree->setItemWidget(item, COLUMN_CLOSE_IMAGE, cButton);
2783   DataTree->setItemWidget(item, COLUMN_RELOAD_IMAGE, rButton);
2784
2785   //set the id of the image
2786   QString id = slicer_manager->GetFileName().c_str() + QString::number(mSlicerManagers.size()-1);
2787   item->setData(COLUMN_IMAGE_NAME,Qt::UserRole,id.toStdString().c_str());
2788   mSlicerManagers.back()->SetId(id.toStdString());
2789
2790   linkPanel->addImage(filename, id.toStdString());
2791
2792   connect(mSlicerManagers.back(), SIGNAL(currentImageChanged(std::string)),
2793           this, SLOT(CurrentImageChanged(std::string)));
2794   connect(mSlicerManagers.back(), SIGNAL(UpdatePosition(int, double, double, double, double, double, double, double)),
2795           this, SLOT(MousePositionChanged(int,double, double, double, double, double, double, double)));
2796   connect(mSlicerManagers.back(), SIGNAL(UpdateVector(int, double, double, double, double)),
2797           this, SLOT(VectorChanged(int,double,double,double, double)));
2798   connect(mSlicerManagers.back(), SIGNAL(UpdateOverlay(int, double, double)),
2799           this, SLOT(OverlayChanged(int,double,double)));
2800   connect(mSlicerManagers.back(), SIGNAL(UpdateFusion(int, double)),
2801           this, SLOT(FusionChanged(int,double)));
2802   connect(mSlicerManagers.back(), SIGNAL(UpdateWindows(int, int, int)),
2803           this,SLOT(WindowsChanged(int, int, int)));
2804   connect(mSlicerManagers.back(), SIGNAL(WindowLevelChanged(double, double,int, int)),
2805           this,SLOT(WindowLevelChanged(double, double, int, int)));
2806   connect(mSlicerManagers.back(), SIGNAL(UpdateSlice(int,int)),
2807           this,SLOT(UpdateSlice(int,int)));
2808   connect(mSlicerManagers.back(), SIGNAL(UpdateTSlice(int, int)),
2809           this,SLOT(UpdateTSlice(int, int)));
2810   connect(mSlicerManagers.back(), SIGNAL(UpdateSliceRange(int,int,int,int,int)),
2811           this,SLOT(UpdateSliceRange(int,int,int,int,int)));
2812   connect(mSlicerManagers.back(), SIGNAL(UpdateLinkManager(std::string,int,double,double,double,int)),
2813           this,SLOT(UpdateLinkManager(std::string,int,double,double,double,int)));
2814   connect(mSlicerManagers.back(), SIGNAL(ChangeImageWithIndexOffset(vvSlicerManager*,int,int)),
2815           this,SLOT(ChangeImageWithIndexOffset(vvSlicerManager*,int,int)));
2816   connect(mSlicerManagers.back(), SIGNAL(LandmarkAdded()),landmarksPanel,SLOT(AddPoint()));
2817   UpdateTree();
2818   qApp->processEvents();
2819   InitSlicers();
2820   ShowLastImage();
2821   InitDisplay();
2822   qApp->processEvents();
2823 }
2824 //------------------------------------------------------------------------------
2825
2826
2827 //------------------------------------------------------------------------------
2828 void vvMainWindow::UpdateCurrentSlicer() {
2829   int index = -1;
2830   if (DataTree->selectedItems().size() > 0) {
2831     index = GetSlicerIndexFromItem(DataTree->selectedItems()[0]);
2832   }
2833   mSlicerManagerCurrentIndex = index;
2834 }
2835 //------------------------------------------------------------------------------
2836