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